From 5d618886570e98e6745593701246b877998a5367 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Mon, 23 Nov 2015 16:51:16 -0500
Subject: Correct Spack cc script

---
 lib/spack/env/cc | 34 +++++++++++++++++++++++++++++++++-
 1 file changed, 33 insertions(+), 1 deletion(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 75a63f6fac..f3fadfcf45 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -126,6 +126,11 @@ if [ -z "$mode" ]; then
         elif [ "$arg" = -c ]; then
             mode=cc
             break
+        elif [ "$arg" = -S ]; then
+            mode=as
+	    echo "spac cc mode as" "$@"
+	    exit 1
+            break
         fi
     done
 fi
@@ -155,6 +160,7 @@ libraries=()
 libs=()
 rpaths=()
 other_args=()
+all_args=("$@")
 
 while [ -n "$1" ]; do
     case "$1" in
@@ -178,6 +184,8 @@ while [ -n "$1" ]; do
             if [ -z "$arg" ]; then shift; arg="$1"; fi
             if [[ "$arg" = -rpath=* ]]; then
                 rpaths+=("${arg#-rpath=}")
+            elif [[ "$arg" = -rpath,* ]]; then
+                rpaths+=("${arg#-rpath,}")
             elif [[ "$arg" = -rpath ]]; then
                 shift; arg="$1"
                 if [[ "$arg" != -Wl,* ]]; then
@@ -193,6 +201,8 @@ while [ -n "$1" ]; do
             if [ -z "$arg" ]; then shift; arg="$1"; fi
             if [[ "$arg" = -rpath=* ]]; then
                 rpaths+=("${arg#-rpath=}")
+            elif [[ "$arg" = -rpath,* ]]; then
+                rpaths+=("${arg#-rpath,}")
             elif [[ "$arg" = -rpath ]]; then
                 shift; arg="$1"
                 if [[ "$arg" != -Xlinker,* ]]; then
@@ -247,25 +257,46 @@ IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
     if [ -d "$dep/include" ]; then
         includes+=("$dep/include")
+	all_args=("-I$dep/include" ${all_args[@]})
     fi
 
     if [ -d "$dep/lib" ]; then
         libraries+=("$dep/lib")
         rpaths+=("$dep/lib")
+	if [ "$mode" = ccld ]; then
+	    all_args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" ${all_args[@]})
+	elif [ "$mode" = ld ]; then
+	    all_args=("-L$dep/lib" "-rpath" "$dep/lib" ${all_args[@]})
+	fi
     fi
 
     if [ -d "$dep/lib64" ]; then
         libraries+=("$dep/lib64")
         rpaths+=("$dep/lib64")
+        if [ "$mode" = ccld ]; then
+	    all_args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" ${all_args[@]})
+        elif [ "$mode" = ld ]; then
+	    all_args=("-L$dep/lib" "-rpath" "$dep/lib" ${all_args[@]})
+	fi
     fi
 done
 
 # Include all -L's and prefix/whatever dirs in rpath
 for dir in "${libraries[@]}"; do
     [[ dir = $SPACK_INSTALL* ]] && rpaths+=("$dir")
+    if [ "$mode" = ccld ]; then
+	[[ dir = $SPACK_INSTALL* ]] && all_args=("-Wl,-rpath,$dir" ${all_args[@]})
+    elif [ "$mode" = ld ]; then
+	[[ dir = $SPACK_INSTALL* ]] && all_args=("-rpath" "$dir" ${all_args[@]})
+    fi
 done
 rpaths+=("$SPACK_PREFIX/lib")
 rpaths+=("$SPACK_PREFIX/lib64")
+if [ "$mode" = ccld ]; then
+    all_args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" ${all_args[@]})
+elif [ "$mode" = ld ]; then
+    all_args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" ${all_args[@]})
+fi
 
 # Put the arguments together
 args=()
@@ -317,7 +348,8 @@ done
 export PATH
 
 full_command=("$command")
-full_command+=("${args[@]}")
+# full_command+=("${args[@]}")
+full_command+=("${all_args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.
-- 
cgit v1.2.3-70-g09d2


From ba22fc8b78841728500966d471db7b5bfd26cf56 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Mon, 21 Dec 2015 10:21:33 -0500
Subject: Simplify Spack cc script

---
 lib/spack/env/cc | 283 +++++++++++++++++++++++++------------------------------
 1 file changed, 130 insertions(+), 153 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index f3fadfcf45..053295f42d 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -65,7 +65,7 @@ function die {
 }
 
 for param in $parameters; do
-    if [ -z "${!param}" ]; then
+    if [[ -z ${!param} ]]; then
         die "Spack compiler must be run from spack!  Input $param was missing!"
     fi
 done
@@ -114,114 +114,118 @@ case "$command" in
 esac
 
 # Finish setting up the mode.
-if [ -z "$mode" ]; then
+if [[ -z $mode ]]; then
     mode=ccld
     for arg in "$@"; do
-        if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then
-            mode=vcheck
-            break
-        elif [ "$arg" = -E ]; then
-            mode=cpp
-            break
-        elif [ "$arg" = -c ]; then
-            mode=cc
-            break
-        elif [ "$arg" = -S ]; then
-            mode=as
-	    echo "spac cc mode as" "$@"
-	    exit 1
-            break
-        fi
+        case "$arg" in
+            -v|-V|--version|-dumpversion)
+                mode=vcheck
+                break
+                ;;
+            -E)
+                mode=cpp
+                break
+                ;;
+            -c)
+                mode=cc
+                break
+                ;;
+            -S)
+                mode=as
+                break
+                ;;
+        esac
     done
 fi
 
 # Dump the version and exist if we're in testing mode.
-if [ "$SPACK_TEST_COMMAND" = "dump-mode" ]; then
+if [[ $SPACK_TEST_COMMAND = dump-mode ]]; then
     echo "$mode"
     exit
 fi
 
 # Check that at least one of the real commands was actually selected,
 # otherwise we don't know what to execute.
-if [ -z "$command" ]; then
+if [[ -z $command ]]; then
     die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
 fi
 
 # Save original command for debug logging
 input_command="$@"
+args=("$@")
 
-#
-# Now do real parsing of the command line args, trying hard to keep
-# non-rpath linker arguments in the proper order w.r.t. other command
-# line arguments.  This is important for things like groups.
-#
-includes=()
-libraries=()
-libs=()
-rpaths=()
-other_args=()
-all_args=("$@")
+# Dump parsed values for unit testing if asked for
+if [[ -n $SPACK_TEST_COMMAND ]]; then
 
-while [ -n "$1" ]; do
-    case "$1" in
-        -I*)
-            arg="${1#-I}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            includes+=("$arg")
-            ;;
-        -L*)
-            arg="${1#-L}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libraries+=("$arg")
-            ;;
-        -l*)
-            arg="${1#-l}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libs+=("$arg")
-            ;;
-        -Wl,*)
-            arg="${1#-Wl,}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            if [[ "$arg" = -rpath=* ]]; then
-                rpaths+=("${arg#-rpath=}")
-            elif [[ "$arg" = -rpath,* ]]; then
-                rpaths+=("${arg#-rpath,}")
-            elif [[ "$arg" = -rpath ]]; then
-                shift; arg="$1"
-                if [[ "$arg" != -Wl,* ]]; then
-                    die "-Wl,-rpath was not followed by -Wl,*"
+    #
+    # Now do real parsing of the command line args, trying hard to keep
+    # non-rpath linker arguments in the proper order w.r.t. other command line
+    # arguments.  This is important for things like groups.
+    #
+    includes=()
+    libraries=()
+    libs=()
+    rpaths=()
+    other_args=()
+
+    while [[ -n $1 ]]; do
+        case "$1" in
+            -I*)
+                arg="${1#-I}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                includes+=("$arg")
+                ;;
+            -L*)
+                arg="${1#-L}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                libraries+=("$arg")
+                ;;
+            -l*)
+                arg="${1#-l}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                libs+=("$arg")
+                ;;
+            -Wl,*)
+                arg="${1#-Wl,}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [[ $arg = -rpath=* ]]; then
+                    rpaths+=("${arg#-rpath=}")
+                elif [[ $arg = -rpath,* ]]; then
+                    rpaths+=("${arg#-rpath,}")
+                elif [[ $arg = -rpath ]]; then
+                    shift; arg="$1"
+                    if [[ $arg != -Wl,* ]]; then
+                        die "-Wl,-rpath was not followed by -Wl,*"
+                    fi
+                    rpaths+=("${arg#-Wl,}")
+                else
+                    other_args+=("-Wl,$arg")
                 fi
-                rpaths+=("${arg#-Wl,}")
-            else
-                other_args+=("-Wl,$arg")
-            fi
-            ;;
-        -Xlinker,*)
-            arg="${1#-Xlinker,}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            if [[ "$arg" = -rpath=* ]]; then
-                rpaths+=("${arg#-rpath=}")
-            elif [[ "$arg" = -rpath,* ]]; then
-                rpaths+=("${arg#-rpath,}")
-            elif [[ "$arg" = -rpath ]]; then
-                shift; arg="$1"
-                if [[ "$arg" != -Xlinker,* ]]; then
-                    die "-Xlinker,-rpath was not followed by -Xlinker,*"
+                ;;
+            -Xlinker,*)
+                arg="${1#-Xlinker,}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [[ $arg = -rpath=* ]]; then
+                    rpaths+=("${arg#-rpath=}")
+                elif [[ $arg = -rpath,* ]]; then
+                    rpaths+=("${arg#-rpath,}")
+                elif [[ $arg = -rpath ]]; then
+                    shift; arg="$1"
+                    if [[ $arg != -Xlinker,* ]]; then
+                        die "-Xlinker,-rpath was not followed by -Xlinker,*"
+                    fi
+                    rpaths+=("${arg#-Xlinker,}")
+                else
+                    other_args+=("-Xlinker,$arg")
                 fi
-                rpaths+=("${arg#-Xlinker,}")
-            else
-                other_args+=("-Xlinker,$arg")
-            fi
-            ;;
-        *)
-            other_args+=("$1")
-            ;;
-    esac
-    shift
-done
+                ;;
+            *)
+                other_args+=("$1")
+                ;;
+        esac
+        shift
+    done
 
-# Dump parsed values for unit testing if asked for
-if [ -n "$SPACK_TEST_COMMAND" ]; then
     IFS=$'\n'
     case "$SPACK_TEST_COMMAND" in
         dump-includes)   echo "${includes[*]}";;
@@ -246,8 +250,8 @@ if [ -n "$SPACK_TEST_COMMAND" ]; then
             echo "${other_args[*]}"
             ;;
         *)
-            echo "ERROR: Unknown test command"
-            exit 1 ;;
+            die "ERROR: Unknown test command"
+            ;;
     esac
     exit
 fi
@@ -255,66 +259,44 @@ fi
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
-    if [ -d "$dep/include" ]; then
-        includes+=("$dep/include")
-	all_args=("-I$dep/include" ${all_args[@]})
+    if [[ -d $dep/include ]]; then
+        args=("-I$dep/include" "${args[@]}")
     fi
 
-    if [ -d "$dep/lib" ]; then
-        libraries+=("$dep/lib")
-        rpaths+=("$dep/lib")
-	if [ "$mode" = ccld ]; then
-	    all_args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" ${all_args[@]})
-	elif [ "$mode" = ld ]; then
-	    all_args=("-L$dep/lib" "-rpath" "$dep/lib" ${all_args[@]})
-	fi
+    if [[ -d $dep/lib ]]; then
+        # libraries+=("$dep/lib")
+	    if [[ $mode = ccld ]]; then
+            args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
+        elif [[ $mode = ld ]]; then
+            args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
+        fi
     fi
 
-    if [ -d "$dep/lib64" ]; then
-        libraries+=("$dep/lib64")
-        rpaths+=("$dep/lib64")
-        if [ "$mode" = ccld ]; then
-	    all_args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" ${all_args[@]})
-        elif [ "$mode" = ld ]; then
-	    all_args=("-L$dep/lib" "-rpath" "$dep/lib" ${all_args[@]})
-	fi
+    if [[ -d $dep/lib64 ]]; then
+        # libraries+=("$dep/lib64")
+        if [[ $mode = ccld ]]; then
+            args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
+        elif [[ $mode = ld ]]; then
+            args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
+        fi
     fi
 done
 
 # Include all -L's and prefix/whatever dirs in rpath
-for dir in "${libraries[@]}"; do
-    [[ dir = $SPACK_INSTALL* ]] && rpaths+=("$dir")
-    if [ "$mode" = ccld ]; then
-	[[ dir = $SPACK_INSTALL* ]] && all_args=("-Wl,-rpath,$dir" ${all_args[@]})
-    elif [ "$mode" = ld ]; then
-	[[ dir = $SPACK_INSTALL* ]] && all_args=("-rpath" "$dir" ${all_args[@]})
-    fi
-done
-rpaths+=("$SPACK_PREFIX/lib")
-rpaths+=("$SPACK_PREFIX/lib64")
-if [ "$mode" = ccld ]; then
-    all_args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" ${all_args[@]})
-elif [ "$mode" = ld ]; then
-    all_args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" ${all_args[@]})
-fi
-
-# Put the arguments together
-args=()
-for dir in "${includes[@]}";  do args+=("-I$dir"); done
-args+=("${other_args[@]}")
-for dir in "${libraries[@]}"; do args+=("-L$dir"); done
-for lib in "${libs[@]}";      do args+=("-l$lib"); done
-
-if [ "$mode" = ccld ]; then
-    for dir in "${rpaths[@]}"; do
-        args+=("-Wl,-rpath")
-        args+=("-Wl,$dir");
-    done
-elif [ "$mode" = ld ]; then
-    for dir in "${rpaths[@]}"; do
-        args+=("-rpath")
-        args+=("$dir");
-    done
+if [[ $mode = ccld ]]; then
+    # for dir in "${libraries[@]}"; do
+    #     if [[ dir = $SPACK_INSTALL* ]]; then
+    #         args=("-Wl,-rpath,$dir" "${args[@]}")
+    #     fi
+    # done
+    args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" ${args[@]})
+elif [[ $mode = ld ]]; then
+    # for dir in "${libraries[@]}"; do
+    #     if [[ dir = $SPACK_INSTALL* ]]; then
+    #         args=("-rpath" "$dir" "${args[@]}")
+    #     fi
+    # done
+    args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" ${args[@]})
 fi
 
 #
@@ -330,34 +312,29 @@ unset DYLD_LIBRARY_PATH
 #
 IFS=':' read -ra env_path <<< "$PATH"
 IFS=':' read -ra spack_env_dirs <<< "$SPACK_ENV_PATH"
-spack_env_dirs+=(".")
+spack_env_dirs+=("" ".")
 PATH=""
 for dir in "${env_path[@]}"; do
     remove=""
     for rm_dir in "${spack_env_dirs[@]}"; do
-        if [ "$dir" = "$rm_dir" ]; then remove=True; fi
+        if [[ $dir = $rm_dir ]]; then remove=True; fi
     done
-    if [ -z "$remove" ]; then
-        if [ -z "$PATH" ]; then
-            PATH="$dir"
-        else
-            PATH="$PATH:$dir"
-        fi
+    if [[ -z $remove ]]; then
+        PATH="${PATH:+$PATH:}$dir"
     fi
 done
 export PATH
 
 full_command=("$command")
-# full_command+=("${args[@]}")
-full_command+=("${all_args[@]}")
+full_command+=("${args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
-if [ "$SPACK_DEBUG" = "TRUE" ]; then
+if [[ $SPACK_DEBUG = TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$input_command"     >> $input_log
+    echo "$input_command" >> $input_log
     echo "$mode       ${full_command[@]}" >> $output_log
 fi
 
-- 
cgit v1.2.3-70-g09d2


From 3427174eb065a6e74fc279076423c2c5c5e8e737 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 22 Dec 2015 15:49:14 -0500
Subject: Correct quoting

---
 lib/spack/env/cc | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 565f959ca4..4ac8f2e7f4 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -265,7 +265,7 @@ for dep in "${deps[@]}"; do
 
     if [[ -d $dep/lib ]]; then
         # libraries+=("$dep/lib")
-	    if [[ $mode = ccld ]]; then
+        if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
             args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
@@ -289,14 +289,14 @@ if [[ $mode = ccld ]]; then
     #         args=("-Wl,-rpath,$dir" "${args[@]}")
     #     fi
     # done
-    args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" ${args[@]})
+    args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
     # for dir in "${libraries[@]}"; do
     #     if [[ dir = $SPACK_INSTALL* ]]; then
     #         args=("-rpath" "$dir" "${args[@]}")
     #     fi
     # done
-    args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" ${args[@]})
+    args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
 #
@@ -325,8 +325,7 @@ for dir in "${env_path[@]}"; do
 done
 export PATH
 
-full_command=("$command")
-full_command+=("${args[@]}")
+full_command=("$command" "${args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.
-- 
cgit v1.2.3-70-g09d2


From ff81aff2540f9eadd8d0ce123ae3143ebcb68789 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Fri, 12 Feb 2016 13:05:42 -0500
Subject: Remove source-code optimization and cleanup

---
 lib/spack/env/cc | 106 +++++++++++++++++++++++--------------------------------
 1 file changed, 44 insertions(+), 62 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index b83731404b..ac8f717cc7 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -65,7 +65,7 @@ function die {
 }
 
 for param in $parameters; do
-    if [[ -z ${!param} ]]; then
+    if [ -z "${!param}" ]; then
         die "Spack compiler must be run from spack!  Input $param was missing!"
     fi
 done
@@ -114,39 +114,31 @@ case "$command" in
 esac
 
 # Finish setting up the mode.
-if [[ -z $mode ]]; then
+if [ -z "$mode" ]; then
     mode=ccld
     for arg in "$@"; do
-        case "$arg" in
-            -v|-V|--version|-dumpversion)
-                mode=vcheck
-                break
-                ;;
-            -E)
-                mode=cpp
-                break
-                ;;
-            -c)
-                mode=cc
-                break
-                ;;
-            -S)
-                mode=as
-                break
-                ;;
-        esac
+        if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then
+            mode=vcheck
+            break
+        elif [ "$arg" = -E ]; then
+            mode=cpp
+            break
+        elif [ "$arg" = -c ]; then
+            mode=cc
+            break
+        fi
     done
 fi
 
 # Dump the version and exist if we're in testing mode.
-if [[ $SPACK_TEST_COMMAND = dump-mode ]]; then
+if [ "$SPACK_TEST_COMMAND" = "dump-mode" ]; then
     echo "$mode"
     exit
 fi
 
 # Check that at least one of the real commands was actually selected,
 # otherwise we don't know what to execute.
-if [[ -z $command ]]; then
+if [ -z "$command" ]; then
     die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
 fi
 
@@ -159,8 +151,8 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
 
     #
     # Now do real parsing of the command line args, trying hard to keep
-    # non-rpath linker arguments in the proper order w.r.t. other command line
-    # arguments.  This is important for things like groups.
+    # non-rpath linker arguments in the proper order w.r.t. other command
+    # line arguments.  This is important for things like groups.
     #
     includes=()
     libraries=()
@@ -168,33 +160,31 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
     rpaths=()
     other_args=()
 
-    while [[ -n $1 ]]; do
+    while [ -n "$1" ]; do
         case "$1" in
             -I*)
                 arg="${1#-I}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
                 includes+=("$arg")
                 ;;
             -L*)
                 arg="${1#-L}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
                 libraries+=("$arg")
                 ;;
             -l*)
                 arg="${1#-l}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
                 libs+=("$arg")
                 ;;
             -Wl,*)
                 arg="${1#-Wl,}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
-                if [[ $arg = -rpath=* ]]; then
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
+                if [[ "$arg" = -rpath=* ]]; then
                     rpaths+=("${arg#-rpath=}")
-                elif [[ $arg = -rpath,* ]]; then
-                    rpaths+=("${arg#-rpath,}")
-                elif [[ $arg = -rpath ]]; then
+                elif [[ "$arg" = -rpath ]]; then
                     shift; arg="$1"
-                    if [[ $arg != -Wl,* ]]; then
+                    if [[ "$arg" != -Wl,* ]]; then
                         die "-Wl,-rpath was not followed by -Wl,*"
                     fi
                     rpaths+=("${arg#-Wl,}")
@@ -204,14 +194,12 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
                 ;;
             -Xlinker,*)
                 arg="${1#-Xlinker,}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
-                if [[ $arg = -rpath=* ]]; then
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
+                if [[ "$arg" = -rpath=* ]]; then
                     rpaths+=("${arg#-rpath=}")
-                elif [[ $arg = -rpath,* ]]; then
-                    rpaths+=("${arg#-rpath,}")
-                elif [[ $arg = -rpath ]]; then
+                elif [[ "$arg" = -rpath ]]; then
                     shift; arg="$1"
-                    if [[ $arg != -Xlinker,* ]]; then
+                    if [[ "$arg" != -Xlinker,* ]]; then
                         die "-Xlinker,-rpath was not followed by -Xlinker,*"
                     fi
                     rpaths+=("${arg#-Xlinker,}")
@@ -250,8 +238,8 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
             echo "${other_args[*]}"
             ;;
         *)
-            die "ERROR: Unknown test command"
-            ;;
+            echo "ERROR: Unknown test command"
+            exit 1 ;;
     esac
     exit
 fi
@@ -259,12 +247,11 @@ fi
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
-    if [[ -d $dep/include ]]; then
+    if [ -d "$dep/include" ]; then
         args=("-I$dep/include" "${args[@]}")
     fi
 
-    if [[ -d $dep/lib ]]; then
-        # libraries+=("$dep/lib")
+    if [ -d "$dep/lib" ]; then
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
@@ -272,7 +259,7 @@ for dep in "${deps[@]}"; do
         fi
     fi
 
-    if [[ -d $dep/lib64 ]]; then
+    if [ -d "$dep/lib64" ]; then
         # libraries+=("$dep/lib64")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
@@ -284,18 +271,8 @@ done
 
 # Include all -L's and prefix/whatever dirs in rpath
 if [[ $mode = ccld ]]; then
-    # for dir in "${libraries[@]}"; do
-    #     if [[ dir = $SPACK_INSTALL* ]]; then
-    #         args=("-Wl,-rpath,$dir" "${args[@]}")
-    #     fi
-    # done
     args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
-    # for dir in "${libraries[@]}"; do
-    #     if [[ dir = $SPACK_INSTALL* ]]; then
-    #         args=("-rpath" "$dir" "${args[@]}")
-    #     fi
-    # done
     args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
@@ -317,23 +294,28 @@ PATH=""
 for dir in "${env_path[@]}"; do
     remove=""
     for rm_dir in "${spack_env_dirs[@]}"; do
-        if [[ $dir = $rm_dir ]]; then remove=True; fi
+        if [ "$dir" = "$rm_dir" ]; then remove=True; fi
     done
-    if [[ -z $remove ]]; then
-        PATH="${PATH:+$PATH:}$dir"
+    if [ -z "$remove" ]; then
+        if [ -z "$PATH" ]; then
+            PATH="$dir"
+        else
+            PATH="$PATH:$dir"
+        fi
     fi
 done
 export PATH
 
-full_command=("$command" "${args[@]}")
+full_command=("$command")
+full_command+=("${args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
-if [[ $SPACK_DEBUG = TRUE ]]; then
+if [ "$SPACK_DEBUG" = "TRUE" ]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$input_command" >> $input_log
+    echo "$input_command"     >> $input_log
     echo "$mode       ${full_command[@]}" >> $output_log
 fi
 
-- 
cgit v1.2.3-70-g09d2


From f3ea0420f80f418a0f3e628479c782f197e6a43e Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Thu, 17 Mar 2016 21:53:13 -0400
Subject: Import recent changes

---
 lib/spack/env/cc | 185 +++++++++++++++++++------------------------------------
 1 file changed, 65 insertions(+), 120 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index df6795c264..c6a09724e9 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -65,7 +65,7 @@ function die {
 }
 
 for param in $parameters; do
-    if [ -z "${!param}" ]; then
+    if [[ -z ${!param} ]]; then
         die "Spack compiler must be run from spack!  Input $param was missing!"
     fi
 done
@@ -78,10 +78,11 @@ done
 # 'command' is set based on the input command to $SPACK_[CC|CXX|F77|F90]
 #
 # 'mode' is set to one of:
+#    cpp     preprocess
 #    cc      compile
+#    as      assemble
 #    ld      link
 #    ccld    compile & link
-#    cpp     preprocessor
 #    vcheck  version check
 #
 command=$(basename "$0")
@@ -131,6 +132,9 @@ if [ -z "$mode" ]; then
         if [ "$arg" = -E ]; then
             mode=cpp
             break
+        elif [ "$arg" = -S ]; then
+            mode=as
+            break
         elif [ "$arg" = -c ]; then
             mode=cc
             break
@@ -146,22 +150,25 @@ fi
 
 # Check that at least one of the real commands was actually selected,
 # otherwise we don't know what to execute.
-if [ -z "$command" ]; then
+if [[ -z $command ]]; then
     die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
 fi
 
+if [ "$mode" == vcheck ] ; then
+    exec ${command} "$@"
+fi
+
 # Save original command for debug logging
 input_command="$@"
 args=("$@")
 
-<<<<<<< HEAD
 # Dump parsed values for unit testing if asked for
 if [[ -n $SPACK_TEST_COMMAND ]]; then
 
     #
     # Now do real parsing of the command line args, trying hard to keep
-    # non-rpath linker arguments in the proper order w.r.t. other command
-    # line arguments.  This is important for things like groups.
+    # non-rpath linker arguments in the proper order w.r.t. other command line
+    # arguments.  This is important for things like groups.
     #
     includes=()
     libraries=()
@@ -188,32 +195,44 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
                 ;;
             -Wl,*)
                 arg="${1#-Wl,}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                if [[ "$arg" = -rpath=* ]]; then
-                    rpaths+=("${arg#-rpath=}")
-                elif [[ "$arg" = -rpath ]]; then
+                # TODO: Handle multiple -Wl, continuations of -Wl,-rpath
+                if [[ $arg == -rpath=* ]]; then
+                    arg="${arg#-rpath=}"
+                    for rpath in ${arg//,/ }; do
+                        rpaths+=("$rpath")
+                    done
+                elif [[ $arg == -rpath,* ]]; then
+                    arg="${arg#-rpath,}"
+                    for rpath in ${arg//,/ }; do
+                        rpaths+=("$rpath")
+                    done
+                elif [[ $arg == -rpath ]]; then
                     shift; arg="$1"
-                    if [[ "$arg" != -Wl,* ]]; then
+                    if [[ $arg != '-Wl,'* ]]; then
                         die "-Wl,-rpath was not followed by -Wl,*"
                     fi
-                    rpaths+=("${arg#-Wl,}")
+                    arg="${arg#-Wl,}"
+                    for rpath in ${arg//,/ }; do
+                        rpaths+=("$rpath")
+                    done
                 else
                     other_args+=("-Wl,$arg")
                 fi
                 ;;
-            -Xlinker,*)
-                arg="${1#-Xlinker,}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                if [[ "$arg" = -rpath=* ]]; then
+            -Xlinker)
+                shift; arg="$1";
+                if [[ $arg = -rpath=* ]]; then
                     rpaths+=("${arg#-rpath=}")
-                elif [[ "$arg" = -rpath ]]; then
+                elif [[ $arg = -rpath ]]; then
                     shift; arg="$1"
-                    if [[ "$arg" != -Xlinker,* ]]; then
-                        die "-Xlinker,-rpath was not followed by -Xlinker,*"
+                    if [[ $arg != -Xlinker ]]; then
+                        die "-Xlinker -rpath was not followed by -Xlinker <arg>"
                     fi
-                    rpaths+=("${arg#-Xlinker,}")
+                    shift; arg="$1"
+                    rpaths+=("$arg")
                 else
-                    other_args+=("-Xlinker,$arg")
+                    other_args+=("-Xlinker")
+                    other_args+=("$arg")
                 fi
                 ;;
             *)
@@ -222,88 +241,6 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
         esac
         shift
     done
-=======
-if [ "$mode" == vcheck ] ; then
-    exec ${command} "$@"
-fi
-
-#
-# Now do real parsing of the command line args, trying hard to keep
-# non-rpath linker arguments in the proper order w.r.t. other command
-# line arguments.  This is important for things like groups.
-#
-includes=()
-libraries=()
-libs=()
-rpaths=()
-other_args=()
-
-while [ -n "$1" ]; do
-    case "$1" in
-        -I*)
-            arg="${1#-I}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            includes+=("$arg")
-            ;;
-        -L*)
-            arg="${1#-L}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libraries+=("$arg")
-            ;;
-        -l*)
-            arg="${1#-l}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libs+=("$arg")
-            ;;
-        -Wl,*)
-            arg="${1#-Wl,}"
-            # TODO: Handle multiple -Wl, continuations of -Wl,-rpath
-            if [[ $arg == -rpath=* ]]; then
-                arg="${arg#-rpath=}"
-                for rpath in ${arg//,/ }; do
-                    rpaths+=("$rpath")
-                done
-            elif [[ $arg == -rpath,* ]]; then
-                arg="${arg#-rpath,}"
-                for rpath in ${arg//,/ }; do
-                    rpaths+=("$rpath")
-                done
-            elif [[ $arg == -rpath ]]; then
-                shift; arg="$1"
-                if [[ $arg != '-Wl,'* ]]; then
-                    die "-Wl,-rpath was not followed by -Wl,*"
-                fi
-                arg="${arg#-Wl,}"
-                for rpath in ${arg//,/ }; do
-                    rpaths+=("$rpath")
-                done
-            else
-                other_args+=("-Wl,$arg")
-            fi
-            ;;
-        -Xlinker)
-            shift; arg="$1";
-            if [[ $arg = -rpath=* ]]; then
-                rpaths+=("${arg#-rpath=}")
-            elif [[ $arg = -rpath ]]; then
-                shift; arg="$1"
-                if [[ $arg != -Xlinker ]]; then
-                    die "-Xlinker -rpath was not followed by -Xlinker <arg>"
-                fi
-                shift; arg="$1"
-                rpaths+=("$arg")
-            else
-                other_args+=("-Xlinker")
-                other_args+=("$arg")
-            fi
-            ;;
-        *)
-            other_args+=("$1")
-            ;;
-    esac
-    shift
-done
->>>>>>> develop
 
     IFS=$'\n'
     case "$SPACK_TEST_COMMAND" in
@@ -329,8 +266,8 @@ done
             echo "${other_args[*]}"
             ;;
         *)
-            echo "ERROR: Unknown test command"
-            exit 1 ;;
+            die "ERROR: Unknown test command"
+            ;;
     esac
     exit
 fi
@@ -338,11 +275,14 @@ fi
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
-    if [ -d "$dep/include" ]; then
-        args=("-I$dep/include" "${args[@]}")
+    if [[ -d $dep/include ]]; then
+        if [[ $mode = cpp || $mode = cc || $mode = as || $mode = ccld ]]; then
+            args=("-I$dep/include" "${args[@]}")
+        fi
     fi
 
-    if [ -d "$dep/lib" ]; then
+    if [[ -d $dep/lib ]]; then
+        # libraries+=("$dep/lib")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
@@ -350,7 +290,7 @@ for dep in "${deps[@]}"; do
         fi
     fi
 
-    if [ -d "$dep/lib64" ]; then
+    if [[ -d $dep/lib64 ]]; then
         # libraries+=("$dep/lib64")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
@@ -362,8 +302,18 @@ done
 
 # Include all -L's and prefix/whatever dirs in rpath
 if [[ $mode = ccld ]]; then
+    # for dir in "${libraries[@]}"; do
+    #     if [[ dir = $SPACK_INSTALL* ]]; then
+    #         args=("-Wl,-rpath,$dir" "${args[@]}")
+    #     fi
+    # done
     args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
+    # for dir in "${libraries[@]}"; do
+    #     if [[ dir = $SPACK_INSTALL* ]]; then
+    #         args=("-rpath" "$dir" "${args[@]}")
+    #     fi
+    # done
     args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
@@ -385,28 +335,23 @@ PATH=""
 for dir in "${env_path[@]}"; do
     remove=""
     for rm_dir in "${spack_env_dirs[@]}"; do
-        if [ "$dir" = "$rm_dir" ]; then remove=True; fi
+        if [[ $dir = $rm_dir ]]; then remove=True; fi
     done
-    if [ -z "$remove" ]; then
-        if [ -z "$PATH" ]; then
-            PATH="$dir"
-        else
-            PATH="$PATH:$dir"
-        fi
+    if [[ -z $remove ]]; then
+        PATH="${PATH:+$PATH:}$dir"
     fi
 done
 export PATH
 
-full_command=("$command")
-full_command+=("${args[@]}")
+full_command=("$command" "${args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
-if [ "$SPACK_DEBUG" = "TRUE" ]; then
+if [[ $SPACK_DEBUG = TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$input_command"     >> $input_log
+    echo "$input_command" >> $input_log
     echo "$mode       ${full_command[@]}" >> $output_log
 fi
 
-- 
cgit v1.2.3-70-g09d2


From c4134ee71e43a6a2a38822e25cc72ca73efdcfea Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 23 Mar 2016 00:36:32 -0700
Subject: Fix #608: broken numpy build.

- Failed to catch all instances of modify_module when it was renamed
  to setup_dependent_package.

- Refactored remaining modify_module calls.

- Also modified Python's setup_dependent_package slightly: only
  creates empty site-packages directory for Python extensions now, not
  for all dependents.
---
 lib/spack/spack/modules.py                         |  4 ++--
 lib/spack/spack/preferred_packages.py              |  4 +++-
 var/spack/repos/builtin/packages/python/package.py | 11 ++++++-----
 var/spack/repos/builtin/packages/ruby/package.py   |  6 +++---
 4 files changed, 14 insertions(+), 11 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 05c93cd3e6..8ed98e5d38 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -160,8 +160,8 @@ class EnvModule(object):
         # package-specific modifications
         for extendee in self.pkg.extendees:
             extendee_spec = self.spec[extendee]
-            extendee_spec.package.modify_module(
-                self.pkg.module, extendee_spec, self.spec)
+            extendee_spec.package.setup_dependent_package(
+                self.pkg.module, self.spec)
 
         # Package-specific environment modifications
         spack_env = EnvironmentModifications()
diff --git a/lib/spack/spack/preferred_packages.py b/lib/spack/spack/preferred_packages.py
index 4d8526c75f..f0a5382dc9 100644
--- a/lib/spack/spack/preferred_packages.py
+++ b/lib/spack/spack/preferred_packages.py
@@ -150,7 +150,9 @@ class PreferredPackages(object):
     def version_compare(self, pkgname, a, b):
         """Return less-than-0, 0, or greater than 0 if version a of pkgname is
            respecively less-than, equal-to, or greater-than version b of pkgname.
-           One version is less-than another if it is preferred over the other."""
+           Versions marked 'preferred=True' in package.py take precedence over any
+           versions not marked preferred.
+        """
         return self._spec_compare(pkgname, 'version', a, b, True, None)
 
 
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 4f55bc803e..6d9030805b 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -108,7 +108,7 @@ class Python(Package):
         run_env.set('PYTHONPATH', pythonpath)
 
 
-    def modify_module(self, module, spec, ext_spec):
+    def setup_dependent_package(self, module, ext_spec):
         """
         Called before python modules' install() methods.
 
@@ -118,17 +118,18 @@ class Python(Package):
         """
         # Python extension builds can have a global python executable function
         if self.version >= Version("3.0.0") and self.version < Version("4.0.0"):
-            module.python = Executable(join_path(spec.prefix.bin, 'python3'))
+            module.python = Executable(join_path(self.spec.prefix.bin, 'python3'))
         else:
-            module.python = Executable(join_path(spec.prefix.bin, 'python'))
+            module.python = Executable(join_path(self.spec.prefix.bin, 'python'))
 
         # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs.
         module.python_lib_dir     = os.path.join(ext_spec.prefix, self.python_lib_dir)
         module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir)
         module.site_packages_dir  = os.path.join(ext_spec.prefix, self.site_packages_dir)
 
-        # Make the site packages directory if it does not exist already.
-        mkdirp(module.site_packages_dir)
+        # Make the site packages directory for extensions, if it does not exist already.
+        if ext_spec.package.is_extension:
+            mkdirp(module.site_packages_dir)
 
     # ========================================================================
     # Handle specifics of activating and deactivating python modules.
diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py
index 7ff1898ce9..e13677e4d2 100644
--- a/var/spack/repos/builtin/packages/ruby/package.py
+++ b/var/spack/repos/builtin/packages/ruby/package.py
@@ -30,7 +30,7 @@ class Ruby(Package):
         # The actual installation path for this gem
         spack_env.set('GEM_HOME', extension_spec.prefix)
 
-    def modify_module(self, module, spec, ext_spec):
+    def setup_dependent_package(self, module, ext_spec):
         """Called before ruby modules' install() methods.  Sets GEM_HOME
         and GEM_PATH to values appropriate for the package being built.
 
@@ -39,5 +39,5 @@ class Ruby(Package):
             gem('install', '<gem-name>.gem')
         """
         # Ruby extension builds have global ruby and gem functions
-        module.ruby = Executable(join_path(spec.prefix.bin, 'ruby'))
-        module.gem = Executable(join_path(spec.prefix.bin, 'gem'))
+        module.ruby = Executable(join_path(self.spec.prefix.bin, 'ruby'))
+        module.gem = Executable(join_path(self.spec.prefix.bin, 'gem'))
-- 
cgit v1.2.3-70-g09d2


From 38350ae33d29e108803cebdf13b90b6898947328 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 23 Mar 2016 01:32:54 -0700
Subject: resurrect preferred=True option for packages lost in merge of
 externals support.

- Pyton 2.7.11 is preferred again.
---
 lib/spack/spack/concretize.py         | 4 ++++
 lib/spack/spack/preferred_packages.py | 4 +---
 lib/spack/spack/test/concretize.py    | 9 +++++++++
 3 files changed, 14 insertions(+), 3 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py
index 2e576743ec..ed9bf79868 100644
--- a/lib/spack/spack/concretize.py
+++ b/lib/spack/spack/concretize.py
@@ -159,6 +159,10 @@ class DefaultConcretizer(object):
              if any(v.satisfies(sv) for sv in spec.versions)],
             cmp=cmp_versions)
 
+        def prefer_key(v):
+            return pkg.versions.get(Version(v)).get('preferred', False)
+        valid_versions.sort(key=prefer_key, reverse=True)
+
         if valid_versions:
             spec.versions = ver([valid_versions[0]])
         else:
diff --git a/lib/spack/spack/preferred_packages.py b/lib/spack/spack/preferred_packages.py
index f0a5382dc9..4d8526c75f 100644
--- a/lib/spack/spack/preferred_packages.py
+++ b/lib/spack/spack/preferred_packages.py
@@ -150,9 +150,7 @@ class PreferredPackages(object):
     def version_compare(self, pkgname, a, b):
         """Return less-than-0, 0, or greater than 0 if version a of pkgname is
            respecively less-than, equal-to, or greater-than version b of pkgname.
-           Versions marked 'preferred=True' in package.py take precedence over any
-           versions not marked preferred.
-        """
+           One version is less-than another if it is preferred over the other."""
         return self._spec_compare(pkgname, 'version', a, b, True, None)
 
 
diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py
index 08cce09674..9cd8c969ae 100644
--- a/lib/spack/spack/test/concretize.py
+++ b/lib/spack/spack/test/concretize.py
@@ -24,6 +24,7 @@
 ##############################################################################
 import spack
 from spack.spec import Spec, CompilerSpec
+from spack.version import ver
 from spack.concretize import find_spec
 from spack.test.mock_packages_test import *
 
@@ -77,6 +78,14 @@ class ConcretizeTest(MockPackagesTest):
         self.check_concretize('mpich')
 
 
+    def test_concretize_preferred_version(self):
+        spec = self.check_concretize('python')
+        self.assertEqual(spec.versions, ver('2.7.11'))
+
+        spec = self.check_concretize('python@3.5.1')
+        self.assertEqual(spec.versions, ver('3.5.1'))
+
+
     def test_concretize_with_virtual(self):
         self.check_concretize('mpileaks ^mpi')
         self.check_concretize('mpileaks ^mpi@:1.1')
-- 
cgit v1.2.3-70-g09d2


From 0fbdb3f65d234d6ed8f77d3732c134962ad47b35 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 23 Mar 2016 15:43:16 +0100
Subject: modules : added configuration file with disable keyword

---
 lib/spack/spack/config.py  | 28 +++++++++++++++++++++++++---
 lib/spack/spack/modules.py | 12 ++++++++++--
 2 files changed, 35 insertions(+), 5 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 6afd69b3ac..6ef79c70b1 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -237,7 +237,29 @@ section_schemas = {
                                 'type' : 'object',
                                 'default' : {},
                             }
-                        },},},},},}
+                        },},},},},},
+    'modules': {
+        '$schema': 'http://json-schema.org/schema#',
+        'title': 'Spack module file configuration file schema',
+        'type': 'object',
+        'additionalProperties': False,
+        'patternProperties': {
+            r'modules:?': {
+                'type': 'object',
+                'default': {},
+                'additionalProperties': False,
+                'properties': {
+                    'disable': {
+                        'type': 'array',
+                        'default': [],
+                        'items': {
+                            'type': 'string'
+                        }
+                    }
+                }
+            },
+        },
+    },
 }
 
 """OrderedDict of config scopes keyed by name.
@@ -405,11 +427,11 @@ def _read_config_file(filename, schema):
             validate_section(data, schema)
         return data
 
-    except MarkedYAMLError, e:
+    except MarkedYAMLError as e:
         raise ConfigFileError(
             "Error parsing yaml%s: %s" % (str(e.context_mark), e.problem))
 
-    except IOError, e:
+    except IOError as e:
         raise ConfigFileError(
             "Error reading configuration file %s: %s" % (filename, str(e)))
 
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 8ed98e5d38..639f1101b8 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -48,6 +48,7 @@ import textwrap
 
 import llnl.util.tty as tty
 import spack
+import spack.config
 from llnl.util.filesystem import join_path, mkdirp
 from spack.environment import *
 
@@ -57,6 +58,13 @@ __all__ = ['EnvModule', 'Dotkit', 'TclModule']
 module_types = {}
 
 
+def read_configuration_file():
+    f = spack.config.get_config('modules')
+    f.setdefault('disable', [])  # Default : disable nothing
+    return f
+
+CONFIGURATION = read_configuration_file()
+
 def print_help():
     """For use by commands to tell user how to activate shell support."""
 
@@ -115,8 +123,8 @@ class EnvModule(object):
     class __metaclass__(type):
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
-            if cls.name != 'env_module':
-                module_types[cls.name] = cls
+            if cls.name != 'env_module' and cls.name not in CONFIGURATION['disable']:
+                    module_types[cls.name] = cls
 
     def __init__(self, spec=None):
         self.spec = spec
-- 
cgit v1.2.3-70-g09d2


From d93f2b335d5a5198b943cc6293a1d24d614c979b Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 23 Mar 2016 16:04:36 +0100
Subject: modules : fixed annoying indent

---
 lib/spack/spack/modules.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'lib')

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 639f1101b8..d354c8bb71 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -124,7 +124,7 @@ class EnvModule(object):
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
             if cls.name != 'env_module' and cls.name not in CONFIGURATION['disable']:
-                    module_types[cls.name] = cls
+                module_types[cls.name] = cls
 
     def __init__(self, spec=None):
         self.spec = spec
-- 
cgit v1.2.3-70-g09d2


From f095e619b985a9271ff96cd469086d4654edf489 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 24 Mar 2016 09:31:28 +0100
Subject: module files configuration : enable/disable logic is now positive

---
 lib/spack/spack/config.py  | 2 +-
 lib/spack/spack/modules.py | 9 ++-------
 2 files changed, 3 insertions(+), 8 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 6ef79c70b1..14e5aaf4fb 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -249,7 +249,7 @@ section_schemas = {
                 'default': {},
                 'additionalProperties': False,
                 'properties': {
-                    'disable': {
+                    'enable': {
                         'type': 'array',
                         'default': [],
                         'items': {
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index d354c8bb71..6c32937c3c 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -57,13 +57,8 @@ __all__ = ['EnvModule', 'Dotkit', 'TclModule']
 # Registry of all types of modules.  Entries created by EnvModule's metaclass
 module_types = {}
 
+CONFIGURATION = spack.config.get_config('modules')
 
-def read_configuration_file():
-    f = spack.config.get_config('modules')
-    f.setdefault('disable', [])  # Default : disable nothing
-    return f
-
-CONFIGURATION = read_configuration_file()
 
 def print_help():
     """For use by commands to tell user how to activate shell support."""
@@ -123,7 +118,7 @@ class EnvModule(object):
     class __metaclass__(type):
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
-            if cls.name != 'env_module' and cls.name not in CONFIGURATION['disable']:
+            if cls.name != 'env_module' and cls.name in CONFIGURATION['enable']:
                 module_types[cls.name] = cls
 
     def __init__(self, spec=None):
-- 
cgit v1.2.3-70-g09d2


From 758a9c9096bd6c306f2dba0e40b46544dcec1992 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 23 Mar 2016 11:18:11 +0100
Subject: python extensions : create PYTHONPATH in module files

---
 lib/spack/spack/modules.py                         | 10 +++++-----
 var/spack/repos/builtin/packages/python/package.py |  5 ++++-
 2 files changed, 9 insertions(+), 6 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 6c32937c3c..d45fdde703 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -161,13 +161,13 @@ class EnvModule(object):
 
         # Let the extendee modify their extensions before asking for
         # package-specific modifications
-        for extendee in self.pkg.extendees:
-            extendee_spec = self.spec[extendee]
-            extendee_spec.package.setup_dependent_package(
-                self.pkg.module, self.spec)
+        spack_env = EnvironmentModifications()
+        for item in self.pkg.extendees:
+            package = self.spec[item].package
+            package.setup_dependent_package(self.pkg.module, self.spec)
+            package.setup_dependent_environment(spack_env, env, self.spec)
 
         # Package-specific environment modifications
-        spack_env = EnvironmentModifications()
         self.spec.package.setup_environment(spack_env, env)
 
         # TODO : implement site-specific modifications and filters
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 6d9030805b..f5237c3b57 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -105,7 +105,10 @@ class Python(Package):
 
         pythonpath = ':'.join(python_paths)
         spack_env.set('PYTHONPATH', pythonpath)
-        run_env.set('PYTHONPATH', pythonpath)
+
+        # For run time environment set only the path for extension_spec and prepend it to PYTHONPATH
+        if extension_spec.package.extends(self.spec):
+            run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir))
 
 
     def setup_dependent_package(self, module, ext_spec):
-- 
cgit v1.2.3-70-g09d2


From 9985816642bad10008f45583a7d715761a6ae03d Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 24 Mar 2016 14:49:41 -0500
Subject: Fix spack info indentation

---
 lib/spack/spack/cmd/info.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/cmd/info.py b/lib/spack/spack/cmd/info.py
index e7abe7f4a5..c93db55c63 100644
--- a/lib/spack/spack/cmd/info.py
+++ b/lib/spack/spack/cmd/info.py
@@ -52,7 +52,7 @@ def print_text_info(pkg):
     print "Safe versions:  "
 
     if not pkg.versions:
-        print("None")
+        print("    None")
     else:
         pad = padder(pkg.versions, 4)
         for v in reversed(sorted(pkg.versions)):
@@ -62,7 +62,7 @@ def print_text_info(pkg):
     print
     print "Variants:"
     if not pkg.variants:
-        print "None"
+        print "    None"
     else:
         pad = padder(pkg.variants, 4)
 
-- 
cgit v1.2.3-70-g09d2


From b0b882cbb3d903a85413acb0439a02d6ac9e26fc Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sat, 26 Mar 2016 00:56:19 -0700
Subject: Speed up directives  by skipping debug info in stack traversal.

- `caller_locals()` doesn't need debug info, only frame locals.
- `get_calling_module()` doesn't either.

- Changed calls to `inspect.stack()` -> `inspect.stack(0)`
---
 lib/spack/llnl/util/lang.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/llnl/util/lang.py b/lib/spack/llnl/util/lang.py
index 13d301f84e..3b4e2c8352 100644
--- a/lib/spack/llnl/util/lang.py
+++ b/lib/spack/llnl/util/lang.py
@@ -117,7 +117,8 @@ def caller_locals():
        scope.  Yes, this is some black magic, and yes it's useful
        for implementing things like depends_on and provides.
     """
-    stack = inspect.stack()
+    # Passing zero here skips line context for speed.
+    stack = inspect.stack(0)
     try:
         return stack[2][0].f_locals
     finally:
@@ -128,7 +129,8 @@ def get_calling_module_name():
     """Make sure that the caller is a class definition, and return the
        enclosing module's name.
     """
-    stack = inspect.stack()
+    # Passing zero here skips line context for speed.
+    stack = inspect.stack(0)
     try:
         # Make sure locals contain __module__
         caller_locals = stack[2][0].f_locals
-- 
cgit v1.2.3-70-g09d2


From dce590fb21af844230727b283f6c8bf759ea805c Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sat, 26 Mar 2016 19:59:02 -0700
Subject: Add a dso_suffix variable to build_environment

- Consolidate this in one place so that we don't have to do it in every build.

- Will update further once better OS support is committed.  Shoudl
  really be an attribute of the forthcoming `Platform` class.
---
 lib/spack/spack/build_environment.py | 8 ++++++++
 1 file changed, 8 insertions(+)

(limited to 'lib')

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 119a255a34..640db0c1d1 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -59,6 +59,11 @@ SPACK_SHORT_SPEC       = 'SPACK_SHORT_SPEC'
 SPACK_DEBUG_LOG_DIR    = 'SPACK_DEBUG_LOG_DIR'
 
 
+# Platform-specific library suffix.
+dso_suffix = 'dylib' if sys.platform == 'darwin' else 'so'
+
+
+
 class MakeExecutable(Executable):
     """Special callable executable object for make so the user can
        specify parallel or not on a per-invocation basis.  Using
@@ -246,6 +251,9 @@ def set_module_variables_for_package(pkg, module):
     # a Prefix object.
     m.prefix  = pkg.prefix
 
+    # Platform-specific library suffix.
+    m.dso_suffix = dso_suffix
+
 
 def get_rpaths(pkg):
     """Get a list of all the rpaths for a package."""
-- 
cgit v1.2.3-70-g09d2


From cde33205827edbed988ec4548c983ff93e9445c6 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sat, 26 Mar 2016 20:00:28 -0700
Subject: Add a method to find the containing directory of a library.

---
 lib/spack/llnl/util/filesystem.py | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

(limited to 'lib')

diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index c4665c284c..92f9ca2983 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -27,7 +27,7 @@ __all__ = ['set_install_permissions', 'install', 'install_tree', 'traverse_tree'
            'force_remove', 'join_path', 'ancestor', 'can_access', 'filter_file',
            'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink',
            'set_executable', 'copy_mode', 'unset_executable_mode',
-           'remove_dead_links', 'remove_linked_tree']
+           'remove_dead_links', 'remove_linked_tree', 'find_library_path']
 
 import os
 import sys
@@ -392,3 +392,18 @@ def remove_linked_tree(path):
             os.unlink(path)
         else:
             shutil.rmtree(path, True)
+
+
+def find_library_path(libname, *paths):
+    """Searches for a file called <libname> in each path.
+
+    Return:
+      directory where the library was found, if found.  None otherwise.
+
+    """
+    for path in paths:
+        library = join_path(path, libname)
+        if os.path.exists(library):
+            return path
+    return None
+
-- 
cgit v1.2.3-70-g09d2


From e049fc2840ba81cdff2ca7edd798c5e961ae94e9 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 27 Mar 2016 11:47:20 -0700
Subject: Run post-install hoooks before build stage is removed.

- Build will properly fail when post-install hoooks fail.

- Post-install hooks have a proper working directory set now.
---
 lib/spack/spack/package.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 9af3221837..c17bec4a14 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -926,6 +926,9 @@ class Package(object):
                      install(env_path, env_install_path)
                      dump_packages(self.spec, packages_dir)
 
+                # Run post install hooks before build stage is removed.
+                spack.hooks.post_install(self)
+
             # Stop timer.
             self._total_time = time.time() - start_time
             build_time = self._total_time - self._fetch_time
@@ -954,9 +957,6 @@ class Package(object):
         # the database, so that we don't need to re-read from file.
         spack.installed_db.add(self.spec, self.prefix)
 
-        # Once everything else is done, run post install hooks
-        spack.hooks.post_install(self)
-
 
     def sanity_check_prefix(self):
         """This function checks whether install succeeded."""
-- 
cgit v1.2.3-70-g09d2


From 5695e4c03d6c98fc187ec405923cd1dcf2fbdff6 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Sun, 27 Mar 2016 15:37:52 -0500
Subject: Wrap the long description of an environment module so it is more
 readable.

---
 lib/spack/spack/modules.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index d45fdde703..f6a11c92e3 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -278,6 +278,6 @@ class TclModule(EnvModule):
         # Long description
         if self.long_description:
             module_file.write('proc ModulesHelp { } {\n')
-            doc = re.sub(r'"', '\"', self.long_description)
-            module_file.write("puts stderr \"%s\"\n" % doc)
+            for line in textwrap.wrap(self.long_description, 72):
+                module_file.write("puts stderr \"%s\"\n" % line)
             module_file.write('}\n\n')
-- 
cgit v1.2.3-70-g09d2


From e0f463c4f99e4808b5647a2abae915ce0cb80561 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@googlemail.com>
Date: Sun, 27 Mar 2016 23:56:41 +0200
Subject: uninstall : added recursive option

---
 lib/spack/spack/cmd/uninstall.py | 151 ++++++++++++++++++++++++++-------------
 1 file changed, 101 insertions(+), 50 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py
index 350ef372cb..8da0fe1c4a 100644
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -23,19 +23,24 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from __future__ import print_function
-import sys
+
 import argparse
+import sys
 
 import llnl.util.tty as tty
-from llnl.util.tty.colify import colify
-
 import spack
 import spack.cmd
 import spack.repository
 from spack.cmd.find import display_specs
 from spack.package import PackageStillNeededError
 
-description="Remove an installed package"
+description = "Remove an installed package"
+
+error_message = """You can either:
+    a) Use a more specific spec, or
+    b) use spack uninstall -a to uninstall ALL matching specs.
+"""
+
 
 def setup_parser(subparser):
     subparser.add_argument(
@@ -44,10 +49,81 @@ def setup_parser(subparser):
     subparser.add_argument(
         '-a', '--all', action='store_true', dest='all',
         help="USE CAREFULLY. Remove ALL installed packages that match each " +
-        "supplied spec. i.e., if you say uninstall libelf, ALL versions of " +
-        "libelf are uninstalled. This is both useful and dangerous, like rm -r.")
+             "supplied spec. i.e., if you say uninstall libelf, ALL versions of " +
+             "libelf are uninstalled. This is both useful and dangerous, like rm -r.")
     subparser.add_argument(
-        'packages', nargs=argparse.REMAINDER, help="specs of packages to uninstall")
+        '-r', '--recursive', action='store_true', dest='recursive',
+        help='Uninstall all the packages that depends on the ones for which we required explicit removal.'
+
+    )
+    subparser.add_argument('packages', nargs=argparse.REMAINDER, help="specs of packages to uninstall")
+
+
+def concretize_specs(specs, allow_multiple_matches=False, force=False):
+    """
+    Returns a list of specs matching the non necessarily concretized specs given from cli
+
+    Args:
+        specs: list of specs to be matched against installed packages
+        allow_multiple_matches : boolean (if True multiple matches for each item in specs are admitted)
+
+    Return:
+        list of specs
+    """
+    specs_from_cli = []  # List of specs that match expressions given via command line
+    has_errors = False
+    for spec in specs:
+        matching = spack.installed_db.query(spec)
+        # For each spec provided, make sure it refers to only one package.
+        # Fail and ask user to be unambiguous if it doesn't
+        if not allow_multiple_matches and len(matching) > 1:
+            tty.error("%s matches multiple packages:" % spec)
+            print()
+            display_specs(matching, long=True)
+            print()
+            has_errors = True
+
+        # No installed package matches the query
+        if len(matching) == 0 and not force:
+            tty.error("%s does not match any installed packages." % spec)
+            has_errors = True
+
+        specs_from_cli.extend(matching)
+    if has_errors:
+        tty.die(error_message)
+
+    return specs_from_cli
+
+
+def installed_dependents(specs):
+    dependents = {}
+    for item in specs:
+        lst = [x for x in item.package.installed_dependents if x not in specs]
+        if lst:
+            dependents[item] = lst
+    return dependents
+
+
+def do_uninstall(specs, force):
+    specs = list(set(specs))  # Make specs unique
+    packages = []
+    for item in specs:
+        try:
+            # should work if package is known to spack
+            packages.append(item.package)
+        except spack.repository.UnknownPackageError as e:
+            # The package.py file has gone away -- but still
+            # want to uninstall.
+            spack.Package(item).do_uninstall(force=True)
+
+    # Sort packages to be uninstalled by the number of installed dependents
+    # This ensures we do things in the right order
+    def num_installed_deps(pkg):
+        return len(pkg.installed_dependents)
+
+    packages.sort(key=num_installed_deps)
+    for item in packages:
+        item.do_uninstall(force=force)
 
 
 def uninstall(parser, args):
@@ -56,50 +132,25 @@ def uninstall(parser, args):
 
     with spack.installed_db.write_transaction():
         specs = spack.cmd.parse_specs(args.packages)
+        # Gets the list of installed specs that match the ones give via cli
+        uninstall_list = concretize_specs(specs, args.all, args.force)  # takes care of '-a' is given in the cli
+        dependent_list = installed_dependents(uninstall_list)  # takes care of '-r'
 
-        # For each spec provided, make sure it refers to only one package.
-        # Fail and ask user to be unambiguous if it doesn't
-        pkgs = []
-        for spec in specs:
-            matching_specs = spack.installed_db.query(spec)
-            if not args.all and len(matching_specs) > 1:
-                tty.error("%s matches multiple packages:" % spec)
-                print()
-                display_specs(matching_specs, long=True)
-                print()
-                print("You can either:")
-                print("  a) Use a more specific spec, or")
-                print("  b) use spack uninstall -a to uninstall ALL matching specs.")
-                sys.exit(1)
-
-            if len(matching_specs) == 0:
-                if args.force: continue
-                tty.die("%s does not match any installed packages." % spec)
-
-            for s in matching_specs:
-                try:
-                    # should work if package is known to spack
-                    pkgs.append(s.package)
-                except spack.repository.UnknownPackageError as e:
-                    # The package.py file has gone away -- but still
-                    # want to uninstall.
-                    spack.Package(s).do_uninstall(force=True)
-
-        # Sort packages to be uninstalled by the number of installed dependents
-        # This ensures we do things in the right order
-        def num_installed_deps(pkg):
-            return len(pkg.installed_dependents)
-        pkgs.sort(key=num_installed_deps)
-
-        # Uninstall packages in order now.
-        for pkg in pkgs:
-            try:
-                pkg.do_uninstall(force=args.force)
-            except PackageStillNeededError as e:
-                tty.error("Will not uninstall %s" % e.spec.format("$_$@$%@$#", color=True))
+        # There are dependents but recursive uninstall wasn't a requirement
+        has_error = False
+        if dependent_list and not args.recursive and not args.force:
+            for spec, lst in dependent_list.items():
+                tty.error("Will not uninstall %s" % spec.format("$_$@$%@$#", color=True))
                 print('')
                 print("The following packages depend on it:")
-                display_specs(e.dependents, long=True)
+                display_specs(lst, long=True)
                 print('')
-                print("You can use spack uninstall -f to force this action.")
-                sys.exit(1)
+                has_error = True
+        elif args.recursive:
+            for key, lst in dependent_list.items():
+                uninstall_list.extend(lst)
+
+        if has_error:
+            tty.die('You can use spack uninstall -f to force this action')
+        # Uninstall everything on the list
+        do_uninstall(uninstall_list, args.force)
-- 
cgit v1.2.3-70-g09d2


From 7eca1284c81c3efc5a87b8a174a0974811656b3e Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sun, 27 Mar 2016 08:59:25 +0200
Subject: metis/parmetis/boost/oce/scalapack: correct install_name on Darwin
 via a global function.

---
 lib/spack/llnl/util/filesystem.py                  | 30 ++++++++++++-
 var/spack/repos/builtin/packages/boost/package.py  | 50 ++++++++++++----------
 var/spack/repos/builtin/packages/metis/package.py  |  6 ++-
 .../builtin/packages/netlib-scalapack/package.py   |  5 +++
 var/spack/repos/builtin/packages/oce/package.py    |  6 ++-
 .../repos/builtin/packages/parmetis/package.py     |  6 ++-
 6 files changed, 76 insertions(+), 27 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index c4665c284c..46ca03bec4 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -27,9 +27,10 @@ __all__ = ['set_install_permissions', 'install', 'install_tree', 'traverse_tree'
            'force_remove', 'join_path', 'ancestor', 'can_access', 'filter_file',
            'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink',
            'set_executable', 'copy_mode', 'unset_executable_mode',
-           'remove_dead_links', 'remove_linked_tree']
+           'remove_dead_links', 'remove_linked_tree', 'fix_darwin_install_name']
 
 import os
+import glob
 import sys
 import re
 import shutil
@@ -38,6 +39,7 @@ import errno
 import getpass
 from contextlib import contextmanager, closing
 from tempfile import NamedTemporaryFile
+import subprocess
 
 import llnl.util.tty as tty
 from spack.util.compression import ALLOWED_ARCHIVE_TYPES
@@ -392,3 +394,29 @@ def remove_linked_tree(path):
             os.unlink(path)
         else:
             shutil.rmtree(path, True)
+
+def fix_darwin_install_name(path):
+    """
+    Fix install name of dynamic libraries on Darwin to have full path.
+    There are two parts of this task:
+    (i) use install_name('-id',...) to change install name of a single lib;
+    (ii) use install_name('-change',...) to change the cross linking between libs.
+    The function assumes that all libraries are in one folder and currently won't
+    follow subfolders.
+
+    Args:
+        path: directory in which .dylib files are alocated
+
+    """
+    libs = glob.glob(join_path(path,"*.dylib"))
+    for lib in libs:
+        # fix install name first:
+        subprocess.Popen(["install_name_tool", "-id",lib,lib], stdout=subprocess.PIPE).communicate()[0]
+        long_deps = subprocess.Popen(["otool", "-L",lib], stdout=subprocess.PIPE).communicate()[0].split('\n')
+        deps = [dep.partition(' ')[0][1::] for dep in long_deps[2:-1]]
+        # fix all dependencies:
+        for dep in deps:
+            for loc in libs:
+                if dep == os.path.basename(loc):
+                    subprocess.Popen(["install_name_tool", "-change",dep,loc,lib], stdout=subprocess.PIPE).communicate()[0]
+                    break
diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index fb1f5daee7..82ce6fbb74 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -1,5 +1,6 @@
 from spack import *
 import spack
+import sys
 
 class Boost(Package):
     """Boost provides free peer-reviewed portable C++ source
@@ -45,34 +46,34 @@ class Boost(Package):
     version('1.34.1', '2d938467e8a448a2c9763e0a9f8ca7e5')
     version('1.34.0', 'ed5b9291ffad776f8757a916e1726ad0')
 
-    default_install_libs = set(['atomic', 
-        'chrono', 
-        'date_time', 
-        'filesystem', 
+    default_install_libs = set(['atomic',
+        'chrono',
+        'date_time',
+        'filesystem',
         'graph',
         'iostreams',
         'locale',
         'log',
-        'math', 
+        'math',
         'program_options',
-        'random', 
-        'regex', 
-        'serialization', 
-        'signals', 
-        'system', 
-        'test', 
-        'thread', 
+        'random',
+        'regex',
+        'serialization',
+        'signals',
+        'system',
+        'test',
+        'thread',
         'wave'])
 
-    # mpi/python are not installed by default because they pull in many 
-    # dependencies and/or because there is a great deal of customization 
+    # mpi/python are not installed by default because they pull in many
+    # dependencies and/or because there is a great deal of customization
     # possible (and it would be difficult to choose sensible defaults)
     default_noinstall_libs = set(['mpi', 'python'])
 
     all_libs = default_install_libs | default_noinstall_libs
 
     for lib in all_libs:
-        variant(lib, default=(lib not in default_noinstall_libs), 
+        variant(lib, default=(lib not in default_noinstall_libs),
             description="Compile with {0} library".format(lib))
 
     variant('debug', default=False, description='Switch to the debug version of Boost')
@@ -124,9 +125,9 @@ class Boost(Package):
 
         with open('user-config.jam', 'w') as f:
             compiler_wrapper = join_path(spack.build_env_path, 'c++')
-            f.write("using {0} : : {1} ;\n".format(boostToolsetId, 
+            f.write("using {0} : : {1} ;\n".format(boostToolsetId,
                 compiler_wrapper))
-            
+
             if '+mpi' in spec:
                 f.write('using mpi : %s ;\n' %
                     join_path(spec['mpi'].prefix.bin, 'mpicxx'))
@@ -155,7 +156,7 @@ class Boost(Package):
         linkTypes = ['static']
         if '+shared' in spec:
             linkTypes.append('shared')
-        
+
         threadingOpts = []
         if '+multithreaded' in spec:
             threadingOpts.append('multi')
@@ -163,12 +164,12 @@ class Boost(Package):
             threadingOpts.append('single')
         if not threadingOpts:
             raise RuntimeError("At least one of {singlethreaded, multithreaded} must be enabled")
-        
+
         options.extend([
             'toolset=%s' % self.determine_toolset(spec),
             'link=%s' % ','.join(linkTypes),
             '--layout=tagged'])
-        
+
         return threadingOpts
 
     def install(self, spec, prefix):
@@ -177,14 +178,14 @@ class Boost(Package):
             if "+{0}".format(lib) in spec:
                 withLibs.append(lib)
         if not withLibs:
-            # if no libraries are specified for compilation, then you dont have 
+            # if no libraries are specified for compilation, then you dont have
             # to configure/build anything, just copy over to the prefix directory.
             src = join_path(self.stage.source_path, 'boost')
             mkdirp(join_path(prefix, 'include'))
             dst = join_path(prefix, 'include', 'boost')
             install_tree(src, dst)
             return
-    
+
         # to make Boost find the user-config.jam
         env['BOOST_BUILD_PATH'] = './'
 
@@ -207,4 +208,7 @@ class Boost(Package):
         # Boost.MPI if the threading options are not separated.
         for threadingOpt in threadingOpts:
             b2('install', 'threading=%s' % threadingOpt, *b2_options)
-        
+
+        # The shared libraries are not installed correctly on Darwin; correct this
+        if (sys.platform == 'darwin') and ('+shared' in spec):
+            fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py
index 68b9f6fd30..9301135f9f 100644
--- a/var/spack/repos/builtin/packages/metis/package.py
+++ b/var/spack/repos/builtin/packages/metis/package.py
@@ -24,7 +24,7 @@
 ##############################################################################
 
 from spack import *
-import glob
+import glob,sys
 
 class Metis(Package):
     """
@@ -90,3 +90,7 @@ class Metis(Package):
             fs = glob.glob(join_path(source_directory,'GKlib',"*.h"))
             for f in fs:
                 install(f, GKlib_dist)
+
+            # The shared library is not installed correctly on Darwin; correct this
+            if (sys.platform == 'darwin') and ('+shared' in spec):
+                fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index c3e6822cdf..d59f8e41fe 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -41,6 +41,11 @@ class NetlibScalapack(Package):
             make()
             make("install")
 
+        # The shared libraries are not installed correctly on Darwin; correct this
+        if (sys.platform == 'darwin') and ('+shared' in spec):
+            fix_darwin_install_name(prefix.lib)
+
+
     def setup_dependent_package(self, module, dependent_spec):
         spec = self.spec
         lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py
index 06acb96736..4d5081ac9d 100644
--- a/var/spack/repos/builtin/packages/oce/package.py
+++ b/var/spack/repos/builtin/packages/oce/package.py
@@ -1,5 +1,5 @@
 from spack import *
-import platform
+import platform, sys
 
 class Oce(Package):
     """
@@ -45,3 +45,7 @@ class Oce(Package):
         cmake('.', *options)
 
         make("install/strip")
+
+        # The shared libraries are not installed correctly on Darwin; correct this
+        if (sys.platform == 'darwin'):
+            fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index f5b8b6de91..ff4370aa4b 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -24,7 +24,7 @@
 ##############################################################################
 
 from spack import *
-
+import sys
 
 class Parmetis(Package):
     """
@@ -83,3 +83,7 @@ class Parmetis(Package):
             cmake(source_directory, *options)
             make()
             make("install")
+
+            # The shared library is not installed correctly on Darwin; correct this
+            if (sys.platform == 'darwin') and ('+shared' in spec):
+                fix_darwin_install_name(prefix.lib)
-- 
cgit v1.2.3-70-g09d2


From f3dd889d4462d14c9f0233540bccbf6a9720bcf0 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 28 Mar 2016 03:51:05 -0700
Subject: Fix bug with lib64 RPATH setting in cc.

---
 lib/spack/env/cc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index c6a09724e9..17740250d1 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -293,9 +293,9 @@ for dep in "${deps[@]}"; do
     if [[ -d $dep/lib64 ]]; then
         # libraries+=("$dep/lib64")
         if [[ $mode = ccld ]]; then
-            args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
+            args=("-L$dep/lib64" "-Wl,-rpath,$dep/lib64" "${args[@]}")
         elif [[ $mode = ld ]]; then
-            args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
+            args=("-L$dep/lib64" "-rpath" "$dep/lib64" "${args[@]}")
         fi
     fi
 done
-- 
cgit v1.2.3-70-g09d2


From d8579a5b80efd8b09e5332a922dee533f2a0a55e Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 28 Mar 2016 03:51:41 -0700
Subject: Simplify cc: Remove old logic and add better tests.

- removed a lot of old logic that was only still needed for tests.

- Added better unit tests for dependency RPATH, -L, and -I args

- tests now check whether the compiler omits -I args in link mode.
---
 lib/spack/env/cc           | 138 +++++----------------------------------------
 lib/spack/spack/test/cc.py | 127 +++++++++++++++++++++++++++++++++++------
 2 files changed, 123 insertions(+), 142 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 17740250d1..4217159a25 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -114,7 +114,9 @@ case "$command" in
         ;;
 esac
 
-# If any of the arguments below is present then the mode is vcheck. In vcheck mode nothing is added in terms of extra search paths or libraries
+# If any of the arguments below is present then the mode is vcheck. In
+# vcheck mode nothing is added in terms of extra search paths or
+# libraries
 if [ -z "$mode" ]; then
     for arg in "$@"; do
         if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then
@@ -125,7 +127,6 @@ if [ -z "$mode" ]; then
 fi
 
 # Finish setting up the mode.
-
 if [ -z "$mode" ]; then
     mode=ccld
     for arg in "$@"; do
@@ -162,127 +163,18 @@ fi
 input_command="$@"
 args=("$@")
 
-# Dump parsed values for unit testing if asked for
-if [[ -n $SPACK_TEST_COMMAND ]]; then
-
-    #
-    # Now do real parsing of the command line args, trying hard to keep
-    # non-rpath linker arguments in the proper order w.r.t. other command line
-    # arguments.  This is important for things like groups.
-    #
-    includes=()
-    libraries=()
-    libs=()
-    rpaths=()
-    other_args=()
-
-    while [ -n "$1" ]; do
-        case "$1" in
-            -I*)
-                arg="${1#-I}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                includes+=("$arg")
-                ;;
-            -L*)
-                arg="${1#-L}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                libraries+=("$arg")
-                ;;
-            -l*)
-                arg="${1#-l}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                libs+=("$arg")
-                ;;
-            -Wl,*)
-                arg="${1#-Wl,}"
-                # TODO: Handle multiple -Wl, continuations of -Wl,-rpath
-                if [[ $arg == -rpath=* ]]; then
-                    arg="${arg#-rpath=}"
-                    for rpath in ${arg//,/ }; do
-                        rpaths+=("$rpath")
-                    done
-                elif [[ $arg == -rpath,* ]]; then
-                    arg="${arg#-rpath,}"
-                    for rpath in ${arg//,/ }; do
-                        rpaths+=("$rpath")
-                    done
-                elif [[ $arg == -rpath ]]; then
-                    shift; arg="$1"
-                    if [[ $arg != '-Wl,'* ]]; then
-                        die "-Wl,-rpath was not followed by -Wl,*"
-                    fi
-                    arg="${arg#-Wl,}"
-                    for rpath in ${arg//,/ }; do
-                        rpaths+=("$rpath")
-                    done
-                else
-                    other_args+=("-Wl,$arg")
-                fi
-                ;;
-            -Xlinker)
-                shift; arg="$1";
-                if [[ $arg = -rpath=* ]]; then
-                    rpaths+=("${arg#-rpath=}")
-                elif [[ $arg = -rpath ]]; then
-                    shift; arg="$1"
-                    if [[ $arg != -Xlinker ]]; then
-                        die "-Xlinker -rpath was not followed by -Xlinker <arg>"
-                    fi
-                    shift; arg="$1"
-                    rpaths+=("$arg")
-                else
-                    other_args+=("-Xlinker")
-                    other_args+=("$arg")
-                fi
-                ;;
-            *)
-                other_args+=("$1")
-                ;;
-        esac
-        shift
-    done
-
-    IFS=$'\n'
-    case "$SPACK_TEST_COMMAND" in
-        dump-includes)   echo "${includes[*]}";;
-        dump-libraries)  echo "${libraries[*]}";;
-        dump-libs)       echo "${libs[*]}";;
-        dump-rpaths)     echo "${rpaths[*]}";;
-        dump-other-args) echo "${other_args[*]}";;
-        dump-all)
-            echo "INCLUDES:"
-            echo "${includes[*]}"
-            echo
-            echo "LIBRARIES:"
-            echo "${libraries[*]}"
-            echo
-            echo "LIBS:"
-            echo "${libs[*]}"
-            echo
-            echo "RPATHS:"
-            echo "${rpaths[*]}"
-            echo
-            echo "ARGS:"
-            echo "${other_args[*]}"
-            ;;
-        *)
-            die "ERROR: Unknown test command"
-            ;;
-    esac
-    exit
-fi
-
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
+    # Prepend include directories
     if [[ -d $dep/include ]]; then
         if [[ $mode = cpp || $mode = cc || $mode = as || $mode = ccld ]]; then
             args=("-I$dep/include" "${args[@]}")
         fi
     fi
 
+    # Prepend lib and RPATH directories
     if [[ -d $dep/lib ]]; then
-        # libraries+=("$dep/lib")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
@@ -290,8 +182,8 @@ for dep in "${deps[@]}"; do
         fi
     fi
 
+    # Prepend lib64 and RPATH directories
     if [[ -d $dep/lib64 ]]; then
-        # libraries+=("$dep/lib64")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib64" "-Wl,-rpath,$dep/lib64" "${args[@]}")
         elif [[ $mode = ld ]]; then
@@ -302,18 +194,8 @@ done
 
 # Include all -L's and prefix/whatever dirs in rpath
 if [[ $mode = ccld ]]; then
-    # for dir in "${libraries[@]}"; do
-    #     if [[ dir = $SPACK_INSTALL* ]]; then
-    #         args=("-Wl,-rpath,$dir" "${args[@]}")
-    #     fi
-    # done
     args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
-    # for dir in "${libraries[@]}"; do
-    #     if [[ dir = $SPACK_INSTALL* ]]; then
-    #         args=("-rpath" "$dir" "${args[@]}")
-    #     fi
-    # done
     args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
@@ -345,6 +227,14 @@ export PATH
 
 full_command=("$command" "${args[@]}")
 
+# In test command mode, write out full command for Spack tests.
+if [[ $SPACK_TEST_COMMAND = dump-args ]]; then
+    echo "${full_command[@]}"
+    exit
+elif [[ -n $SPACK_TEST_COMMAND ]]; then
+    die "ERROR: Unknown test command"
+fi
+
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
diff --git a/lib/spack/spack/test/cc.py b/lib/spack/spack/test/cc.py
index f3f6d4a22e..0b1aeb2a8f 100644
--- a/lib/spack/spack/test/cc.py
+++ b/lib/spack/spack/test/cc.py
@@ -28,6 +28,8 @@ arguments correctly.
 """
 import os
 import unittest
+import tempfile
+import shutil
 
 from llnl.util.filesystem import *
 import spack
@@ -55,13 +57,40 @@ class CompilerTest(unittest.TestCase):
         self.ld = Executable(join_path(spack.build_env_path, "ld"))
         self.cpp = Executable(join_path(spack.build_env_path, "cpp"))
 
-        os.environ['SPACK_CC'] = "/bin/mycc"
-        os.environ['SPACK_PREFIX'] = "/usr"
+        self.realcc = "/bin/mycc"
+        self.prefix = "/spack-test-prefix"
+
+        os.environ['SPACK_CC'] = self.realcc
+        os.environ['SPACK_PREFIX'] = self.prefix
         os.environ['SPACK_ENV_PATH']="test"
         os.environ['SPACK_DEBUG_LOG_DIR'] = "."
         os.environ['SPACK_COMPILER_SPEC'] = "gcc@4.4.7"
         os.environ['SPACK_SHORT_SPEC'] = "foo@1.2"
 
+        # Make some fake dependencies
+        self.tmp_deps = tempfile.mkdtemp()
+        self.dep1 = join_path(self.tmp_deps, 'dep1')
+        self.dep2 = join_path(self.tmp_deps, 'dep2')
+        self.dep3 = join_path(self.tmp_deps, 'dep3')
+        self.dep4 = join_path(self.tmp_deps, 'dep4')
+
+        mkdirp(join_path(self.dep1, 'include'))
+        mkdirp(join_path(self.dep1, 'lib'))
+
+        mkdirp(join_path(self.dep2, 'lib64'))
+
+        mkdirp(join_path(self.dep3, 'include'))
+        mkdirp(join_path(self.dep3, 'lib64'))
+
+        mkdirp(join_path(self.dep4, 'include'))
+
+        if 'SPACK_DEPENDENCIES' in os.environ:
+            del os.environ['SPACK_DEPENDENCIES']
+
+
+    def tearDown(self):
+        shutil.rmtree(self.tmp_deps, True)
+
 
     def check_cc(self, command, args, expected):
         os.environ['SPACK_TEST_COMMAND'] = command
@@ -92,6 +121,10 @@ class CompilerTest(unittest.TestCase):
         self.check_cpp('dump-mode', [], "cpp")
 
 
+    def test_as_mode(self):
+        self.check_cc('dump-mode', ['-S'], "as")
+
+
     def test_ccld_mode(self):
         self.check_cc('dump-mode', [], "ccld")
         self.check_cc('dump-mode', ['foo.c', '-o', 'foo'], "ccld")
@@ -104,27 +137,85 @@ class CompilerTest(unittest.TestCase):
         self.check_ld('dump-mode', ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'], "ld")
 
 
-    def test_includes(self):
-        self.check_cc('dump-includes', test_command,
-                      "\n".join(["/test/include", "/other/include"]))
+    def test_dep_rpath(self):
+        """Ensure RPATHs for root package are added."""
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      ' '.join(test_command))
+
+
+    def test_dep_include(self):
+        """Ensure a single dependency include directory is added."""
+        os.environ['SPACK_DEPENDENCIES'] = self.dep4
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      '-I' + self.dep4 + '/include ' +
+                      ' '.join(test_command))
+
+
+    def test_dep_lib(self):
+        """Ensure a single dependency RPATH is added."""
+        os.environ['SPACK_DEPENDENCIES'] = self.dep2
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      '-L' + self.dep2 + '/lib64 ' +
+                      '-Wl,-rpath,' + self.dep2 + '/lib64 ' +
+                      ' '.join(test_command))
+
+
+    def test_all_deps(self):
+        """Ensure includes and RPATHs for all deps are added. """
+        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
+            self.dep1, self.dep2, self.dep3, self.dep4])
+
+        # This is probably more constrained than it needs to be; it
+        # checks order within prepended args and doesn't strictly have
+        # to.  We could loosen that if it becomes necessary
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+
+                      '-I' + self.dep4 + '/include ' +
+
+                      '-L' + self.dep3 + '/lib64 ' +
+                      '-Wl,-rpath,' + self.dep3 + '/lib64 ' +
+                      '-I' + self.dep3 + '/include ' +
+
+                      '-L' + self.dep2 + '/lib64 ' +
+                      '-Wl,-rpath,' + self.dep2 + '/lib64 ' +
+
+                      '-L' + self.dep1 + '/lib ' +
+                      '-Wl,-rpath,' + self.dep1 + '/lib ' +
+                      '-I' + self.dep1 + '/include ' +
+
+                      ' '.join(test_command))
 
 
-    def test_libraries(self):
-        self.check_cc('dump-libraries', test_command,
-                      "\n".join(["/test/lib", "/other/lib"]))
+    def test_ld_deps(self):
+        """Ensure no (extra) -I args or -Wl, are passed in ld mode."""
+        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
+            self.dep1, self.dep2, self.dep3, self.dep4])
 
+        self.check_ld('dump-args', test_command,
+                      'ld ' +
+                      '-rpath ' + self.prefix + '/lib ' +
+                      '-rpath ' + self.prefix + '/lib64 ' +
 
-    def test_libs(self):
-        self.check_cc('dump-libs', test_command,
-                      "\n".join(["lib1", "lib2", "lib3", "lib4"]))
+                      '-L' + self.dep3 + '/lib64 ' +
+                      '-rpath ' + self.dep3 + '/lib64 ' +
 
+                      '-L' + self.dep2 + '/lib64 ' +
+                      '-rpath ' + self.dep2 + '/lib64 ' +
 
-    def test_rpaths(self):
-        self.check_cc('dump-rpaths', test_command,
-                      "\n".join(["/first/rpath", "/second/rpath", "/third/rpath", "/fourth/rpath"]))
+                      '-L' + self.dep1 + '/lib ' +
+                      '-rpath ' + self.dep1 + '/lib ' +
 
+                      ' '.join(test_command))
 
-    def test_other_args(self):
-        self.check_cc('dump-other-args', test_command,
-                      "\n".join(["arg1", "-Wl,--start-group", "arg2", "arg3", "arg4",
-                                 "-Wl,--end-group", "arg5", "arg6"]))
-- 
cgit v1.2.3-70-g09d2


From 1141f1195572a81cb98e5fa439db6860fd326d43 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@googlemail.com>
Date: Tue, 29 Mar 2016 00:28:02 +0200
Subject: uninstall : added user confirmation

---
 lib/spack/spack/cmd/uninstall.py | 47 +++++++++++++++++++++++++++++++++++-----
 1 file changed, 42 insertions(+), 5 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py
index 8da0fe1c4a..7183817908 100644
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -24,15 +24,14 @@
 ##############################################################################
 from __future__ import print_function
 
-import argparse
 import sys
+import argparse
 
 import llnl.util.tty as tty
 import spack
 import spack.cmd
 import spack.repository
 from spack.cmd.find import display_specs
-from spack.package import PackageStillNeededError
 
 description = "Remove an installed package"
 
@@ -41,6 +40,16 @@ error_message = """You can either:
     b) use spack uninstall -a to uninstall ALL matching specs.
 """
 
+def ask_for_confirmation(message):
+    while True:
+        tty.msg(message + '[y/n]')
+        choice = raw_input().lower()
+        if choice == 'y':
+            break
+        elif choice == 'n':
+            sys.exit(1)
+        tty.warning('Please reply either "y" or "n"')
+
 
 def setup_parser(subparser):
     subparser.add_argument(
@@ -53,7 +62,11 @@ def setup_parser(subparser):
              "libelf are uninstalled. This is both useful and dangerous, like rm -r.")
     subparser.add_argument(
         '-r', '--recursive', action='store_true', dest='recursive',
-        help='Uninstall all the packages that depends on the ones for which we required explicit removal.'
+        help='Also uninstall any packages that depend on the ones given via command line.'
+    )
+    subparser.add_argument(
+        '-y', '--yes-to-all', action='store_true', dest='yes_to_all',
+        help='Assume "yes" is the answer to every confirmation asked to the user.'
 
     )
     subparser.add_argument('packages', nargs=argparse.REMAINDER, help="specs of packages to uninstall")
@@ -96,6 +109,15 @@ def concretize_specs(specs, allow_multiple_matches=False, force=False):
 
 
 def installed_dependents(specs):
+    """
+    Returns a dictionary that maps a spec with a list of its installed dependents
+
+    Args:
+        specs: list of specs to be checked for dependents
+
+    Returns:
+        dictionary of installed dependents
+    """
     dependents = {}
     for item in specs:
         lst = [x for x in item.package.installed_dependents if x not in specs]
@@ -105,7 +127,13 @@ def installed_dependents(specs):
 
 
 def do_uninstall(specs, force):
-    specs = list(set(specs))  # Make specs unique
+    """
+    Uninstalls all the specs in a list.
+
+    Args:
+        specs: list of specs to be uninstalled
+        force: force uninstallation (boolean)
+    """
     packages = []
     for item in specs:
         try:
@@ -136,7 +164,7 @@ def uninstall(parser, args):
         uninstall_list = concretize_specs(specs, args.all, args.force)  # takes care of '-a' is given in the cli
         dependent_list = installed_dependents(uninstall_list)  # takes care of '-r'
 
-        # There are dependents but recursive uninstall wasn't a requirement
+        # Process dependent_list and update uninstall_list
         has_error = False
         if dependent_list and not args.recursive and not args.force:
             for spec, lst in dependent_list.items():
@@ -149,8 +177,17 @@ def uninstall(parser, args):
         elif args.recursive:
             for key, lst in dependent_list.items():
                 uninstall_list.extend(lst)
+            uninstall_list = list(set(uninstall_list))
 
         if has_error:
             tty.die('You can use spack uninstall -f to force this action')
+
+        if not args.yes_to_all:
+            tty.msg("The following packages will be uninstalled : ")
+            print('')
+            display_specs(uninstall_list, long=True)
+            print('')
+            ask_for_confirmation('Do you want to proceed ? ')
+
         # Uninstall everything on the list
         do_uninstall(uninstall_list, args.force)
-- 
cgit v1.2.3-70-g09d2


From a14527ec0619151d6defc909a46aefd2a9378cb7 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 28 Mar 2016 15:34:25 -0700
Subject: Add command to compiler input log.

---
 lib/spack/env/cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 4217159a25..68cd8514f4 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -241,7 +241,7 @@ fi
 if [[ $SPACK_DEBUG = TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$input_command" >> $input_log
+    echo "$command $input_command" >> $input_log
     echo "$mode       ${full_command[@]}" >> $output_log
 fi
 
-- 
cgit v1.2.3-70-g09d2


From f80e839ff48809a5ba8b7343d2378133a3fbce82 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 29 Mar 2016 02:58:05 -0700
Subject: Handle Darwin's ld -r option properly

- ld -r doesn't work with RPATH on OS X.

- for GNU ld, the -r option only means 'relocatable',
  and doesn't affect RPATH.

- This adds special handling to omit RPATHs for ld -r on OS X
---
 lib/spack/env/cc | 35 +++++++++++++++++++++++++++--------
 1 file changed, 27 insertions(+), 8 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 68cd8514f4..2eb6f46afe 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -85,6 +85,10 @@ done
 #    ccld    compile & link
 #    vcheck  version check
 #
+# Depending on the mode, we may or may not add extra rpaths.
+# This variable controls whether they are added.
+add_rpaths=true
+
 command=$(basename "$0")
 case "$command" in
     cc|c89|c99|gcc|clang|icc|pgcc|xlc)
@@ -108,6 +112,17 @@ case "$command" in
         ;;
     ld)
         mode=ld
+
+        # Darwin's linker has a -r argument that merges object files
+        # together. It doesn't work with -rpath.
+        if [[ $OSTYPE = darwin* ]]; then
+            for arg in "$@"; do
+                if [ "$arg" = -r ]; then
+                    add_rpaths=false
+                    break
+	            fi
+            done
+        fi
         ;;
     *)
         die "Unkown compiler: $command"
@@ -176,27 +191,31 @@ for dep in "${deps[@]}"; do
     # Prepend lib and RPATH directories
     if [[ -d $dep/lib ]]; then
         if [[ $mode = ccld ]]; then
-            args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
+            $add_rpaths && args=("-Wl,-rpath,$dep/lib" "${args[@]}")
+            args=("-L$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
-            args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
+            $add_rpaths && args=("-rpath" "$dep/lib" "${args[@]}")
+            args=("-L$dep/lib" "${args[@]}")
         fi
     fi
 
     # Prepend lib64 and RPATH directories
     if [[ -d $dep/lib64 ]]; then
         if [[ $mode = ccld ]]; then
-            args=("-L$dep/lib64" "-Wl,-rpath,$dep/lib64" "${args[@]}")
+            $add_rpaths && args=("-Wl,-rpath,$dep/lib64" "${args[@]}")
+            args=("-L$dep/lib64" "${args[@]}")
         elif [[ $mode = ld ]]; then
-            args=("-L$dep/lib64" "-rpath" "$dep/lib64" "${args[@]}")
+            $add_rpaths && args=("-rpath" "$dep/lib64" "${args[@]}")
+            args=("-L$dep/lib64" "${args[@]}")
         fi
     fi
 done
 
 # Include all -L's and prefix/whatever dirs in rpath
 if [[ $mode = ccld ]]; then
-    args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
+    $add_rpaths && args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
-    args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
+    $add_rpaths && args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
 #
@@ -241,8 +260,8 @@ fi
 if [[ $SPACK_DEBUG = TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$command $input_command" >> $input_log
-    echo "$mode       ${full_command[@]}" >> $output_log
+    echo "[$mode] $command $input_command" >> $input_log
+    echo "[$mode] ${full_command[@]}" >> $output_log
 fi
 
 exec "${full_command[@]}"
-- 
cgit v1.2.3-70-g09d2


From dfc5cf288c1017ef62390489cb534848aef5a9a6 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 29 Mar 2016 04:35:41 -0700
Subject: Fix bug in restage

- Restage previously only removed the source directory from the stage.
- Now removes any other directories in stage as well.
---
 lib/spack/spack/fetch_strategy.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index 0d0a7db8a9..4ea87bea7e 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -289,8 +289,14 @@ class URLFetchStrategy(FetchStrategy):
         if not self.archive_file:
             raise NoArchiveFileError("Tried to reset URLFetchStrategy before fetching",
                                      "Failed on reset() for URL %s" % self.url)
-        if self.stage.source_path:
-            shutil.rmtree(self.stage.source_path, ignore_errors=True)
+
+        # Remove everythigng but the archive from the stage
+        for filename in os.listdir(self.stage.path):
+            abspath = os.path.join(self.stage.path, filename)
+            if abspath != self.archive_file:
+                shutil.rmtree(abspath, ignore_errors=True)
+
+        # Expand the archive again
         self.expand()
 
     def __repr__(self):
-- 
cgit v1.2.3-70-g09d2


From 653d7c52574b7a6e3795fb3beeeee553bd76b293 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@googlemail.com>
Date: Tue, 29 Mar 2016 17:28:46 +0200
Subject: uninstall : minor fixes

---
 lib/spack/spack/cmd/uninstall.py | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'lib')

diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py
index 7183817908..72ad132112 100644
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -40,6 +40,7 @@ error_message = """You can either:
     b) use spack uninstall -a to uninstall ALL matching specs.
 """
 
+
 def ask_for_confirmation(message):
     while True:
         tty.msg(message + '[y/n]')
@@ -122,6 +123,7 @@ def installed_dependents(specs):
     for item in specs:
         lst = [x for x in item.package.installed_dependents if x not in specs]
         if lst:
+            lst = list(set(lst))
             dependents[item] = lst
     return dependents
 
-- 
cgit v1.2.3-70-g09d2


From dd1c667d8d5d260146f81b0b90ad52c41160208e Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@googlemail.com>
Date: Wed, 30 Mar 2016 16:10:20 +0200
Subject: uninstall : changed error message

---
 lib/spack/spack/cmd/uninstall.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'lib')

diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py
index 72ad132112..7aadd254e8 100644
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -182,7 +182,7 @@ def uninstall(parser, args):
             uninstall_list = list(set(uninstall_list))
 
         if has_error:
-            tty.die('You can use spack uninstall -f to force this action')
+            tty.die('You can use spack uninstall -r to uninstall these dependencies as well')
 
         if not args.yes_to_all:
             tty.msg("The following packages will be uninstalled : ")
-- 
cgit v1.2.3-70-g09d2


From 4f6320a7eb14f7d09c1e31a92d224e54e32c3921 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@googlemail.com>
Date: Thu, 31 Mar 2016 13:22:48 +0200
Subject: uninstall : added unit tests

---
 lib/spack/spack/test/__init__.py      |  3 +-
 lib/spack/spack/test/cmd/__init__.py  |  0
 lib/spack/spack/test/cmd/uninstall.py | 37 ++++++++++++++++
 lib/spack/spack/test/database.py      | 82 +----------------------------------
 lib/spack/spack/test/mock_database.py | 78 +++++++++++++++++++++++++++++++++
 5 files changed, 119 insertions(+), 81 deletions(-)
 create mode 100644 lib/spack/spack/test/cmd/__init__.py
 create mode 100644 lib/spack/spack/test/cmd/uninstall.py
 create mode 100644 lib/spack/spack/test/mock_database.py

(limited to 'lib')

diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py
index cd842561e6..175a49428c 100644
--- a/lib/spack/spack/test/__init__.py
+++ b/lib/spack/spack/test/__init__.py
@@ -67,7 +67,8 @@ test_names = ['versions',
               'namespace_trie',
               'yaml',
               'sbang',
-              'environment']
+              'environment',
+              'cmd.uninstall']
 
 
 def list_tests():
diff --git a/lib/spack/spack/test/cmd/__init__.py b/lib/spack/spack/test/cmd/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/lib/spack/spack/test/cmd/uninstall.py b/lib/spack/spack/test/cmd/uninstall.py
new file mode 100644
index 0000000000..06a24e2958
--- /dev/null
+++ b/lib/spack/spack/test/cmd/uninstall.py
@@ -0,0 +1,37 @@
+import spack.test.mock_database
+
+from spack.cmd.uninstall import uninstall
+
+
+class MockArgs(object):
+    def __init__(self, packages, all=False, force=False, recursive=False):
+        self.packages = packages
+        self.all = all
+        self.force = force
+        self.recursive = recursive
+        self.yes_to_all = True
+
+
+class TestUninstall(spack.test.mock_database.MockDatabase):
+    def test_uninstall(self):
+        parser = None
+        # Multiple matches
+        args = MockArgs(['mpileaks'])
+        self.assertRaises(SystemExit, uninstall, parser, args)
+        # Installed dependents
+        args = MockArgs(['libelf'])
+        self.assertRaises(SystemExit, uninstall, parser, args)
+        # Recursive uninstall
+        args = MockArgs(['callpath'], all=True, recursive=True)
+        uninstall(parser, args)
+
+        all_specs = spack.install_layout.all_specs()
+        self.assertEqual(len(all_specs), 7)
+        # query specs with multiple configurations
+        mpileaks_specs = [s for s in all_specs if s.satisfies('mpileaks')]
+        callpath_specs = [s for s in all_specs if s.satisfies('callpath')]
+        mpi_specs = [s for s in all_specs if s.satisfies('mpi')]
+
+        self.assertEqual(len(mpileaks_specs), 0)
+        self.assertEqual(len(callpath_specs), 0)
+        self.assertEqual(len(mpi_specs),      3)
diff --git a/lib/spack/spack/test/database.py b/lib/spack/spack/test/database.py
index ce6e8a0552..465263d057 100644
--- a/lib/spack/spack/test/database.py
+++ b/lib/spack/spack/test/database.py
@@ -28,16 +28,12 @@ both in memory and in its file
 """
 import os.path
 import multiprocessing
-import shutil
-import tempfile
 
 import spack
 from llnl.util.filesystem import join_path
 from llnl.util.lock import *
 from llnl.util.tty.colify import colify
-from spack.database import Database
-from spack.directory_layout import YamlDirectoryLayout
-from spack.test.mock_packages_test import *
+from spack.test.mock_database import MockDatabase
 
 
 def _print_ref_counts():
@@ -75,80 +71,7 @@ def _print_ref_counts():
     colify(recs, cols=3)
 
 
-class DatabaseTest(MockPackagesTest):
-
-    def _mock_install(self, spec):
-        s = Spec(spec)
-        s.concretize()
-        pkg = spack.repo.get(s)
-        pkg.do_install(fake=True)
-
-
-    def _mock_remove(self, spec):
-        specs = spack.installed_db.query(spec)
-        assert(len(specs) == 1)
-        spec = specs[0]
-        spec.package.do_uninstall(spec)
-
-
-    def setUp(self):
-        super(DatabaseTest, self).setUp()
-        #
-        # TODO: make the mockup below easier.
-        #
-
-        # Make a fake install directory
-        self.install_path = tempfile.mkdtemp()
-        self.spack_install_path = spack.install_path
-        spack.install_path = self.install_path
-
-        self.install_layout = YamlDirectoryLayout(self.install_path)
-        self.spack_install_layout = spack.install_layout
-        spack.install_layout = self.install_layout
-
-        # Make fake database and fake install directory.
-        self.installed_db = Database(self.install_path)
-        self.spack_installed_db = spack.installed_db
-        spack.installed_db = self.installed_db
-
-        # make a mock database with some packages installed note that
-        # the ref count for dyninst here will be 3, as it's recycled
-        # across each install.
-        #
-        # Here is what the mock DB looks like:
-        #
-        # o  mpileaks     o  mpileaks'    o  mpileaks''
-        # |\              |\              |\
-        # | o  callpath   | o  callpath'  | o  callpath''
-        # |/|             |/|             |/|
-        # o |  mpich      o |  mpich2     o |  zmpi
-        #   |               |             o |  fake
-        #   |               |               |
-        #   |               |______________/
-        #   | .____________/
-        #   |/
-        #   o  dyninst
-        #   |\
-        #   | o  libdwarf
-        #   |/
-        #   o  libelf
-        #
-
-        # Transaction used to avoid repeated writes.
-        with spack.installed_db.write_transaction():
-            self._mock_install('mpileaks ^mpich')
-            self._mock_install('mpileaks ^mpich2')
-            self._mock_install('mpileaks ^zmpi')
-
-
-    def tearDown(self):
-        super(DatabaseTest, self).tearDown()
-        shutil.rmtree(self.install_path)
-        spack.install_path = self.spack_install_path
-        spack.install_layout = self.spack_install_layout
-        spack.installed_db = self.spack_installed_db
-
-
+class DatabaseTest(MockDatabase):
     def test_005_db_exists(self):
         """Make sure db cache file exists after creating."""
         index_file = join_path(self.install_path, '.spack-db', 'index.yaml')
@@ -157,7 +80,6 @@ class DatabaseTest(MockPackagesTest):
         self.assertTrue(os.path.exists(index_file))
         self.assertTrue(os.path.exists(lock_file))
 
-
     def test_010_all_install_sanity(self):
         """Ensure that the install layout reflects what we think it does."""
         all_specs = spack.install_layout.all_specs()
diff --git a/lib/spack/spack/test/mock_database.py b/lib/spack/spack/test/mock_database.py
new file mode 100644
index 0000000000..6fd05439bf
--- /dev/null
+++ b/lib/spack/spack/test/mock_database.py
@@ -0,0 +1,78 @@
+import shutil
+import tempfile
+
+import spack
+from spack.spec import Spec
+from spack.database import Database
+from spack.directory_layout import YamlDirectoryLayout
+from spack.test.mock_packages_test import MockPackagesTest
+
+
+class MockDatabase(MockPackagesTest):
+    def _mock_install(self, spec):
+        s = Spec(spec)
+        s.concretize()
+        pkg = spack.repo.get(s)
+        pkg.do_install(fake=True)
+
+    def _mock_remove(self, spec):
+        specs = spack.installed_db.query(spec)
+        assert(len(specs) == 1)
+        spec = specs[0]
+        spec.package.do_uninstall(spec)
+
+    def setUp(self):
+        super(MockDatabase, self).setUp()
+        #
+        # TODO: make the mockup below easier.
+        #
+
+        # Make a fake install directory
+        self.install_path = tempfile.mkdtemp()
+        self.spack_install_path = spack.install_path
+        spack.install_path = self.install_path
+
+        self.install_layout = YamlDirectoryLayout(self.install_path)
+        self.spack_install_layout = spack.install_layout
+        spack.install_layout = self.install_layout
+
+        # Make fake database and fake install directory.
+        self.installed_db = Database(self.install_path)
+        self.spack_installed_db = spack.installed_db
+        spack.installed_db = self.installed_db
+
+        # make a mock database with some packages installed note that
+        # the ref count for dyninst here will be 3, as it's recycled
+        # across each install.
+        #
+        # Here is what the mock DB looks like:
+        #
+        # o  mpileaks     o  mpileaks'    o  mpileaks''
+        # |\              |\              |\
+        # | o  callpath   | o  callpath'  | o  callpath''
+        # |/|             |/|             |/|
+        # o |  mpich      o |  mpich2     o |  zmpi
+        #   |               |             o |  fake
+        #   |               |               |
+        #   |               |______________/
+        #   | .____________/
+        #   |/
+        #   o  dyninst
+        #   |\
+        #   | o  libdwarf
+        #   |/
+        #   o  libelf
+        #
+
+        # Transaction used to avoid repeated writes.
+        with spack.installed_db.write_transaction():
+            self._mock_install('mpileaks ^mpich')
+            self._mock_install('mpileaks ^mpich2')
+            self._mock_install('mpileaks ^zmpi')
+
+    def tearDown(self):
+        super(MockDatabase, self).tearDown()
+        shutil.rmtree(self.install_path)
+        spack.install_path = self.spack_install_path
+        spack.install_layout = self.spack_install_layout
+        spack.installed_db = self.spack_installed_db
-- 
cgit v1.2.3-70-g09d2


From 63f824b218af9fcea4c13d7bef8b1d8ff31d09b2 Mon Sep 17 00:00:00 2001
From: Tom Scogland <scogland1@llnl.gov>
Date: Wed, 30 Dec 2015 11:53:27 -0800
Subject: add a path argument to the stage command

Allow users to use spack to stage a, potentially complex, package into a
given path.  This is nice for packages with multiple resources that must
be placed, for example LLVM with all sub-projects.
---
 lib/spack/spack/cmd/stage.py | 8 +++++++-
 lib/spack/spack/package.py   | 8 ++++++--
 2 files changed, 13 insertions(+), 3 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/cmd/stage.py b/lib/spack/spack/cmd/stage.py
index 5786780efb..749fa90868 100644
--- a/lib/spack/spack/cmd/stage.py
+++ b/lib/spack/spack/cmd/stage.py
@@ -35,6 +35,9 @@ def setup_parser(subparser):
     subparser.add_argument(
         '-n', '--no-checksum', action='store_true', dest='no_checksum',
         help="Do not check downloaded packages against checksum")
+    subparser.add_argument(
+        '-p', '--path', dest='path',
+        help="Path to stage package, does not add to spack tree")
 
     subparser.add_argument(
         'specs', nargs=argparse.REMAINDER, help="specs of packages to stage")
@@ -50,4 +53,7 @@ def stage(parser, args):
     specs = spack.cmd.parse_specs(args.specs, concretize=True)
     for spec in specs:
         package = spack.repo.get(spec)
-        package.do_stage()
+        if args.path:
+            package.do_stage(path=args.path)
+        else:
+            package.do_stage()
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 9af3221837..ce314b7b0a 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -709,14 +709,18 @@ class Package(object):
         if spack.do_checksum and self.version in self.versions:
             self.stage.check()
 
-
-    def do_stage(self, mirror_only=False):
+    def do_stage(self, mirror_only=False, path=None):
         """Unpacks the fetched tarball, then changes into the expanded tarball
            directory."""
+
         if not self.spec.concrete:
             raise ValueError("Can only stage concrete packages.")
 
         self.do_fetch(mirror_only)
+
+        if path is not None:
+            self.stage.path = path
+
         self.stage.expand_archive()
         self.stage.chdir_to_source()
 
-- 
cgit v1.2.3-70-g09d2


From 5d2151ed645f853a083cd445ae8631f9ed987559 Mon Sep 17 00:00:00 2001
From: Tom Scogland <scogland1@llnl.gov>
Date: Thu, 31 Mar 2016 10:20:55 -0700
Subject: reworked to deal with stage.path as property

This version actually pulls the path through the package to deliver it
to each stage on creation when passed through the command.  This is
necessary due to the new StageComposite class that makes setting the
path directly on the stage impractical, it also takes the logic out of
package for the most part, which seems like an improvement.
---
 lib/spack/spack/cmd/stage.py |  5 ++---
 lib/spack/spack/package.py   | 15 +++++++--------
 lib/spack/spack/stage.py     |  7 +++++--
 3 files changed, 14 insertions(+), 13 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/cmd/stage.py b/lib/spack/spack/cmd/stage.py
index 749fa90868..975bb54ef7 100644
--- a/lib/spack/spack/cmd/stage.py
+++ b/lib/spack/spack/cmd/stage.py
@@ -54,6 +54,5 @@ def stage(parser, args):
     for spec in specs:
         package = spack.repo.get(spec)
         if args.path:
-            package.do_stage(path=args.path)
-        else:
-            package.do_stage()
+            package.path = args.path
+        package.do_stage()
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index ce314b7b0a..9dcfbee661 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -335,6 +335,9 @@ class Package(object):
         if '.' in self.name:
             self.name = self.name[self.name.rindex('.') + 1:]
 
+        # Allow custom staging paths for packages
+        self.path=None
+
         # Sanity check attributes required by Spack directives.
         spack.directives.ensure_dicts(type(self))
 
@@ -445,7 +448,8 @@ class Package(object):
         resource_stage_folder = self._resource_stage(resource)
         resource_mirror = join_path(self.name, os.path.basename(fetcher.url))
         stage = ResourceStage(resource.fetcher, root=root_stage, resource=resource,
-                              name=resource_stage_folder, mirror_path=resource_mirror)
+                              name=resource_stage_folder, mirror_path=resource_mirror,
+                              path=self.path)
         return stage
 
     def _make_root_stage(self, fetcher):
@@ -455,7 +459,7 @@ class Package(object):
         s = self.spec
         stage_name = "%s-%s-%s" % (s.name, s.version, s.dag_hash())
         # Build the composite stage
-        stage = Stage(fetcher, mirror_path=mp, name=stage_name)
+        stage = Stage(fetcher, mirror_path=mp, name=stage_name, path=self.path)
         return stage
 
     def _make_stage(self):
@@ -709,18 +713,13 @@ class Package(object):
         if spack.do_checksum and self.version in self.versions:
             self.stage.check()
 
-    def do_stage(self, mirror_only=False, path=None):
+    def do_stage(self, mirror_only=False):
         """Unpacks the fetched tarball, then changes into the expanded tarball
            directory."""
-
         if not self.spec.concrete:
             raise ValueError("Can only stage concrete packages.")
 
         self.do_fetch(mirror_only)
-
-        if path is not None:
-            self.stage.path = path
-
         self.stage.expand_archive()
         self.stage.chdir_to_source()
 
diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py
index f88f82fc2d..d711752c20 100644
--- a/lib/spack/spack/stage.py
+++ b/lib/spack/spack/stage.py
@@ -89,7 +89,7 @@ class Stage(object):
     """
 
     def __init__(self, url_or_fetch_strategy,
-                 name=None, mirror_path=None, keep=False):
+                 name=None, mirror_path=None, keep=False, path=None):
         """Create a stage object.
            Parameters:
              url_or_fetch_strategy
@@ -135,7 +135,10 @@ class Stage(object):
 
         # Try to construct here a temporary name for the stage directory
         # If this is a named stage, then construct a named path.
-        self.path = join_path(spack.stage_path, self.name)
+        if path is not None:
+            self.path = path
+        else:
+            self.path = join_path(spack.stage_path, self.name)
 
         # Flag to decide whether to delete the stage folder on exit or not
         self.keep = keep
-- 
cgit v1.2.3-70-g09d2


From a670408617b76777d35185aa554eeaf3892e0188 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Thu, 31 Mar 2016 11:34:00 -0700
Subject: Quick fix for pkg diff.

---
 lib/spack/spack/cmd/pkg.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'lib')

diff --git a/lib/spack/spack/cmd/pkg.py b/lib/spack/spack/cmd/pkg.py
index cf478d3763..20a3fc5fc2 100644
--- a/lib/spack/spack/cmd/pkg.py
+++ b/lib/spack/spack/cmd/pkg.py
@@ -77,7 +77,8 @@ def get_git():
 
 def list_packages(rev):
     git = get_git()
-    relpath = spack.packages_path[len(spack.prefix + os.path.sep):] + os.path.sep
+    pkgpath = os.path.join(spack.packages_path, 'packages')
+    relpath = pkgpath[len(spack.prefix + os.path.sep):] + os.path.sep
     output = git('ls-tree', '--full-tree', '--name-only', rev, relpath,
                  output=str)
     return sorted(line[len(relpath):] for line in output.split('\n') if line)
-- 
cgit v1.2.3-70-g09d2


From 459aab628d73c7f6f1d4eecbf64b34ca334e0ada Mon Sep 17 00:00:00 2001
From: citibeth <rpf2116@columbia.edu>
Date: Fri, 1 Apr 2016 16:00:58 -0400
Subject: Added documentation for installing Environment Modules with Spack.

---
 lib/spack/docs/basic_usage.rst | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

(limited to 'lib')

diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst
index accf09cc2a..0727e12f6e 100644
--- a/lib/spack/docs/basic_usage.rst
+++ b/lib/spack/docs/basic_usage.rst
@@ -774,6 +774,34 @@ Environment modules
 Spack provides some limited integration with environment module
 systems to make it easier to use the packages it provides.
 
+
+Installing Environment Modules
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+In order to use Spack's generated environment modules, you must have
+installed the *Environment Modules* package.  On many Linux
+distributions, this can be installed from the vendor's repository.
+For example: ```yum install environment-modules``
+(Fedora/RHEL/CentOS).  If your Linux distribution does not have
+Environment Modules, you can get it with Spack:
+
+1. Install with::
+
+    spack install environment-modules
+
+2. Activate with::
+
+    MODULES_HOME=`spack location -i environment-modules`
+     MODULES_VERSION=`ls -1 $MODULES_HOME/Modules | head -1`
+     ${MODULES_HOME}/Modules/${MODULES_VERSION}/bin/add.modules
+
+This adds to your ``.bashrc`` (or similar) files, enabling Environment
+Modules when you log in.  It will ask your permission before changing
+any files.
+
+Spack and Environment Modules
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
 You can enable shell support by sourcing some files in the
 ``/share/spack`` directory.
 
-- 
cgit v1.2.3-70-g09d2


From 2f4d8a634d19debbe069f3c44b4d2d6822f693cb Mon Sep 17 00:00:00 2001
From: Elizabeth F <elizabeth.fischer@columbia.edu>
Date: Sun, 3 Apr 2016 15:45:09 -0400
Subject: Fix conditional extends (BUG #683)

---
 lib/spack/spack/modules.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index f6a11c92e3..d797af287d 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -163,9 +163,14 @@ class EnvModule(object):
         # package-specific modifications
         spack_env = EnvironmentModifications()
         for item in self.pkg.extendees:
-            package = self.spec[item].package
-            package.setup_dependent_package(self.pkg.module, self.spec)
-            package.setup_dependent_environment(spack_env, env, self.spec)
+            try:
+                package = self.spec[item].package
+                package.setup_dependent_package(self.pkg.module, self.spec)
+                package.setup_dependent_environment(spack_env, env, self.spec)
+            except:
+                # The extends was conditional, so it doesn't count here
+                # eg: extends('python', when='+python')
+                pass
 
         # Package-specific environment modifications
         self.spec.package.setup_environment(spack_env, env)
-- 
cgit v1.2.3-70-g09d2


From 401dcb363539409e7b94d8ce016bc1a2e70db3a1 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Mon, 4 Apr 2016 10:28:47 +0200
Subject: uninstall : renamed `--recursive` to `--dependents`

---
 lib/spack/spack/cmd/uninstall.py      | 6 +++---
 lib/spack/spack/test/cmd/uninstall.py | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py
index 7aadd254e8..231c6fe661 100644
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -62,7 +62,7 @@ def setup_parser(subparser):
              "supplied spec. i.e., if you say uninstall libelf, ALL versions of " +
              "libelf are uninstalled. This is both useful and dangerous, like rm -r.")
     subparser.add_argument(
-        '-r', '--recursive', action='store_true', dest='recursive',
+        '-d', '--dependents', action='store_true', dest='dependents',
         help='Also uninstall any packages that depend on the ones given via command line.'
     )
     subparser.add_argument(
@@ -168,7 +168,7 @@ def uninstall(parser, args):
 
         # Process dependent_list and update uninstall_list
         has_error = False
-        if dependent_list and not args.recursive and not args.force:
+        if dependent_list and not args.dependents and not args.force:
             for spec, lst in dependent_list.items():
                 tty.error("Will not uninstall %s" % spec.format("$_$@$%@$#", color=True))
                 print('')
@@ -176,7 +176,7 @@ def uninstall(parser, args):
                 display_specs(lst, long=True)
                 print('')
                 has_error = True
-        elif args.recursive:
+        elif args.dependents:
             for key, lst in dependent_list.items():
                 uninstall_list.extend(lst)
             uninstall_list = list(set(uninstall_list))
diff --git a/lib/spack/spack/test/cmd/uninstall.py b/lib/spack/spack/test/cmd/uninstall.py
index 06a24e2958..80efe06d36 100644
--- a/lib/spack/spack/test/cmd/uninstall.py
+++ b/lib/spack/spack/test/cmd/uninstall.py
@@ -4,11 +4,11 @@ from spack.cmd.uninstall import uninstall
 
 
 class MockArgs(object):
-    def __init__(self, packages, all=False, force=False, recursive=False):
+    def __init__(self, packages, all=False, force=False, dependents=False):
         self.packages = packages
         self.all = all
         self.force = force
-        self.recursive = recursive
+        self.dependents = dependents
         self.yes_to_all = True
 
 
@@ -22,7 +22,7 @@ class TestUninstall(spack.test.mock_database.MockDatabase):
         args = MockArgs(['libelf'])
         self.assertRaises(SystemExit, uninstall, parser, args)
         # Recursive uninstall
-        args = MockArgs(['callpath'], all=True, recursive=True)
+        args = MockArgs(['callpath'], all=True, dependents=True)
         uninstall(parser, args)
 
         all_specs = spack.install_layout.all_specs()
-- 
cgit v1.2.3-70-g09d2


From f40b0f52e0c8b8f076c2ab361edfeba9bc6768fb Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Mon, 4 Apr 2016 10:59:01 +0200
Subject: uninstall : updated documentation and error messages

---
 lib/spack/docs/basic_usage.rst   | 42 +++++++++++++++++++++++++++++-----------
 lib/spack/spack/cmd/uninstall.py |  9 ++++-----
 2 files changed, 35 insertions(+), 16 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst
index accf09cc2a..72a02802fb 100644
--- a/lib/spack/docs/basic_usage.rst
+++ b/lib/spack/docs/basic_usage.rst
@@ -149,26 +149,46 @@ customize an installation in :ref:`sec-specs`.
 ``spack uninstall``
 ~~~~~~~~~~~~~~~~~~~~~
 
-To uninstall a package, type ``spack uninstall <package>``.  This will
-completely remove the directory in which the package was installed.
+To uninstall a package, type ``spack uninstall <package>``.  This will ask the user for
+confirmation, and in case will completely remove the directory in which the package was installed.
 
 .. code-block:: sh
 
    spack uninstall mpich
 
 If there are still installed packages that depend on the package to be
-uninstalled, spack will refuse to uninstall it. You can override this
-behavior with ``spack uninstall -f <package>``, but you risk breaking
-other installed packages. In general, it is safer to remove dependent
-packages *before* removing their dependencies.
+uninstalled, spack will refuse to uninstall it.
 
-A line like ``spack uninstall mpich`` may be ambiguous, if multiple
-``mpich`` configurations are installed.  For example, if both
+To uninstall a package and every package that depends on it, you may give the
+`--dependents` option.
+
+.. code-block:: sh
+
+   spack uninstall --dependents mpich
+
+will display a list of all the packages that depends on `mpich` and, upon confirmation,
+will uninstall them in the right order.
+
+A line like
+
+.. code-block:: sh
+
+   spack uninstall mpich
+
+may be ambiguous, if multiple ``mpich`` configurations are installed.  For example, if both
 ``mpich@3.0.2`` and ``mpich@3.1`` are installed, ``mpich`` could refer
 to either one. Because it cannot determine which one to uninstall,
-Spack will ask you to provide a version number to remove the
-ambiguity.  As an example, ``spack uninstall mpich@3.1`` is
-unambiguous in this scenario.
+Spack will ask you either to provide a version number to remove the
+ambiguity or use the ``--all`` option to uninstall all of the matching packages.
+
+You may force uninstall a package with the `--force` option
+
+.. code-block:: sh
+
+   spack uninstall --force mpich
+
+but you risk breaking other installed packages. In general, it is safer to remove dependent
+packages *before* removing their dependencies or use the `--dependents` option.
 
 
 Seeing installed packages
diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py
index 231c6fe661..1ff3d8db5f 100644
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -24,7 +24,6 @@
 ##############################################################################
 from __future__ import print_function
 
-import sys
 import argparse
 
 import llnl.util.tty as tty
@@ -48,8 +47,8 @@ def ask_for_confirmation(message):
         if choice == 'y':
             break
         elif choice == 'n':
-            sys.exit(1)
-        tty.warning('Please reply either "y" or "n"')
+            raise SystemExit('Operation aborted')
+        tty.warn('Please reply either "y" or "n"')
 
 
 def setup_parser(subparser):
@@ -164,7 +163,7 @@ def uninstall(parser, args):
         specs = spack.cmd.parse_specs(args.packages)
         # Gets the list of installed specs that match the ones give via cli
         uninstall_list = concretize_specs(specs, args.all, args.force)  # takes care of '-a' is given in the cli
-        dependent_list = installed_dependents(uninstall_list)  # takes care of '-r'
+        dependent_list = installed_dependents(uninstall_list)  # takes care of '-d'
 
         # Process dependent_list and update uninstall_list
         has_error = False
@@ -182,7 +181,7 @@ def uninstall(parser, args):
             uninstall_list = list(set(uninstall_list))
 
         if has_error:
-            tty.die('You can use spack uninstall -r to uninstall these dependencies as well')
+            tty.die('You can use spack uninstall --dependents to uninstall these dependencies as well')
 
         if not args.yes_to_all:
             tty.msg("The following packages will be uninstalled : ")
-- 
cgit v1.2.3-70-g09d2


From bb968fc5a2bf2ceb585676646f68ec2029a298b1 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 4 Apr 2016 02:52:38 -0700
Subject: Fix #620, Resolve #664. Fix issues with build environment.

- Also added better regression tests for build environment.
---
 lib/spack/spack/build_environment.py               | 41 ++++------
 lib/spack/spack/test/install.py                    | 29 +++++--
 .../builtin.mock/packages/cmake-client/package.py  | 89 ++++++++++++++++++++++
 .../repos/builtin.mock/packages/cmake/package.py   | 69 +++++++++++++++++
 4 files changed, 197 insertions(+), 31 deletions(-)
 create mode 100644 var/spack/repos/builtin.mock/packages/cmake-client/package.py
 create mode 100644 var/spack/repos/builtin.mock/packages/cmake/package.py

(limited to 'lib')

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 640db0c1d1..f4f8037ac0 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -213,7 +213,7 @@ def set_module_variables_for_package(pkg, module):
     # TODO: of build dependencies, as opposed to link dependencies.
     # TODO: Currently, everything is a link dependency, but tools like
     # TODO: this shouldn't be.
-    m.cmake = which("cmake")
+    m.cmake = Executable('cmake')
 
     # standard CMake arguments
     m.std_cmake_args = ['-DCMAKE_INSTALL_PREFIX=%s' % pkg.prefix,
@@ -278,21 +278,6 @@ def parent_class_modules(cls):
     return result
 
 
-def setup_module_variables_for_dag(pkg):
-    """Set module-scope variables for all packages in the DAG."""
-    for spec in pkg.spec.traverse(order='post'):
-        # If a user makes their own package repo, e.g.
-        # spack.repos.mystuff.libelf.Libelf, and they inherit from
-        # an existing class like spack.repos.original.libelf.Libelf,
-        # then set the module variables for both classes so the
-        # parent class can still use them if it gets called.
-        spkg = spec.package
-        modules = parent_class_modules(spkg.__class__)
-        for mod in modules:
-            set_module_variables_for_package(spkg, mod)
-        set_module_variables_for_package(spkg, spkg.module)
-
-
 def setup_package(pkg):
     """Execute all environment setup routines."""
     spack_env = EnvironmentModifications()
@@ -316,20 +301,26 @@ def setup_package(pkg):
 
     set_compiler_environment_variables(pkg, spack_env)
     set_build_environment_variables(pkg, spack_env)
-    setup_module_variables_for_dag(pkg)
 
-    # Allow dependencies to modify the module
+    # traverse in postorder so package can use vars from its dependencies
     spec = pkg.spec
-    for dependency_spec in spec.traverse(root=False):
-        dpkg = dependency_spec.package
-        dpkg.setup_dependent_package(pkg.module, spec)
+    for dspec in pkg.spec.traverse(order='post'):
+        # If a user makes their own package repo, e.g.
+        # spack.repos.mystuff.libelf.Libelf, and they inherit from
+        # an existing class like spack.repos.original.libelf.Libelf,
+        # then set the module variables for both classes so the
+        # parent class can still use them if it gets called.
+        spkg = dspec.package
+        modules = parent_class_modules(spkg.__class__)
+        for mod in modules:
+            set_module_variables_for_package(spkg, mod)
+        set_module_variables_for_package(spkg, spkg.module)
 
-    # Allow dependencies to set up environment as well
-    for dependency_spec in spec.traverse(root=False):
-        dpkg = dependency_spec.package
+        # Allow dependencies to modify the module
+        dpkg = dspec.package
+        dpkg.setup_dependent_package(pkg.module, spec)
         dpkg.setup_dependent_environment(spack_env, run_env, spec)
 
-    # Allow the package to apply some settings.
     pkg.setup_environment(spack_env, run_env)
 
     # Make sure nothing's strange about the Spack environment.
diff --git a/lib/spack/spack/test/install.py b/lib/spack/spack/test/install.py
index 8297893f01..fc5b7e67df 100644
--- a/lib/spack/spack/test/install.py
+++ b/lib/spack/spack/test/install.py
@@ -64,7 +64,14 @@ class InstallTest(MockPackagesTest):
         shutil.rmtree(self.tmpdir, ignore_errors=True)
 
 
-    def test_install_and_uninstall(self):
+    def fake_fetchify(self, pkg):
+        """Fake the URL for a package so it downloads from a file."""
+        fetcher = FetchStrategyComposite()
+        fetcher.append(URLFetchStrategy(self.repo.url))
+        pkg.fetcher = fetcher
+
+
+    def ztest_install_and_uninstall(self):
         # Get a basic concrete spec for the trivial install package.
         spec = Spec('trivial_install_test_package')
         spec.concretize()
@@ -73,11 +80,7 @@ class InstallTest(MockPackagesTest):
         # Get the package
         pkg = spack.repo.get(spec)
 
-        # Fake the URL for the package so it downloads from a file.
-
-        fetcher = FetchStrategyComposite()
-        fetcher.append(URLFetchStrategy(self.repo.url))
-        pkg.fetcher = fetcher
+        self.fake_fetchify(pkg)
 
         try:
             pkg.do_install()
@@ -85,3 +88,17 @@ class InstallTest(MockPackagesTest):
         except Exception, e:
             pkg.remove_prefix()
             raise
+
+
+    def test_install_environment(self):
+        spec = Spec('cmake-client').concretized()
+
+        for s in spec.traverse():
+            self.fake_fetchify(s.package)
+
+        pkg = spec.package
+        try:
+            pkg.do_install()
+        except Exception, e:
+            pkg.remove_prefix()
+            raise
diff --git a/var/spack/repos/builtin.mock/packages/cmake-client/package.py b/var/spack/repos/builtin.mock/packages/cmake-client/package.py
new file mode 100644
index 0000000000..a5d3ef156a
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/cmake-client/package.py
@@ -0,0 +1,89 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+import os
+
+def check(condition, msg):
+    """Raise an install error if condition is False."""
+    if not condition:
+        raise InstallError(msg)
+
+
+class CmakeClient(Package):
+    """A dumy package that uses cmake."""
+    homepage  = 'https://www.example.com'
+    url       = 'https://www.example.com/cmake-client-1.0.tar.gz'
+
+    version('1.0', '4cb3ff35b2472aae70f542116d616e63')
+
+    depends_on('cmake')
+
+
+    def setup_environment(self, spack_env, run_env):
+        spack_cc    # Ensure spack module-scope variable is avaiabl
+        check(from_cmake == "from_cmake",
+              "setup_environment couldn't read global set by cmake.")
+
+        check(self.spec['cmake'].link_arg == "test link arg",
+              "link arg on dependency spec not readable from setup_environment.")
+
+
+    def setup_dependent_environment(self, spack_env, run_env, dspec):
+        spack_cc    # Ensure spack module-scope variable is avaiable
+        check(from_cmake == "from_cmake",
+              "setup_dependent_environment couldn't read global set by cmake.")
+
+        check(self.spec['cmake'].link_arg == "test link arg",
+              "link arg on dependency spec not readable from setup_dependent_environment.")
+
+
+    def setup_dependent_package(self, module, dspec):
+        spack_cc    # Ensure spack module-scope variable is avaiable
+        check(from_cmake == "from_cmake",
+              "setup_dependent_package couldn't read global set by cmake.")
+
+        check(self.spec['cmake'].link_arg == "test link arg",
+              "link arg on dependency spec not readable from setup_dependent_package.")
+
+
+
+    def install(self, spec, prefix):
+        # check that cmake is in the global scope.
+        global cmake
+        check(cmake is not None, "No cmake was in environment!")
+
+        # check that which('cmake') returns the right one.
+        cmake = which('cmake')
+        check(cmake.exe[0].startswith(spec['cmake'].prefix.bin),
+              "Wrong cmake was in environment: %s" % cmake)
+
+        check(from_cmake == "from_cmake",
+              "Couldn't read global set by cmake.")
+
+        check(os.environ['from_cmake'] == 'from_cmake',
+              "Couldn't read env var set in envieonmnt by dependency")
+
+        mkdirp(prefix.bin)
+        touch(join_path(prefix.bin, 'dummy'))
diff --git a/var/spack/repos/builtin.mock/packages/cmake/package.py b/var/spack/repos/builtin.mock/packages/cmake/package.py
new file mode 100644
index 0000000000..deb44c2bf7
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/cmake/package.py
@@ -0,0 +1,69 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+import os
+
+def check(condition, msg):
+    """Raise an install error if condition is False."""
+    if not condition:
+        raise InstallError(msg)
+
+
+class Cmake(Package):
+    """A dumy package for the cmake build system."""
+    homepage  = 'https://www.cmake.org'
+    url       = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz'
+
+    version('3.4.3',    '4cb3ff35b2472aae70f542116d616e63',
+            url='https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz')
+
+
+    def setup_environment(self, spack_env, run_env):
+        spack_cc    # Ensure spack module-scope variable is avaiable
+        spack_env.set('for_install', 'for_install')
+
+    def setup_dependent_environment(self, spack_env, run_env, dspec):
+        spack_cc    # Ensure spack module-scope variable is avaiable
+        spack_env.set('from_cmake', 'from_cmake')
+
+
+    def setup_dependent_package(self, module, dspec):
+        spack_cc    # Ensure spack module-scope variable is avaiable
+
+        self.spec.from_cmake = "from_cmake"
+        module.from_cmake = "from_cmake"
+
+        self.spec.link_arg = "test link arg"
+
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+
+        check(os.environ['for_install'] == 'for_install',
+              "Couldn't read env var set in compile envieonmnt")
+
+        cmake_exe = join_path(prefix.bin, 'cmake')
+        touch(cmake_exe)
+        set_executable(cmake_exe)
-- 
cgit v1.2.3-70-g09d2


From 7bc28cc334ea8b64ad4722dda2997871c27dc01a Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Mon, 4 Apr 2016 14:33:48 -0400
Subject: Clean up cc script

---
 lib/spack/env/cc | 65 ++++++++++++++++++++++++++++----------------------------
 1 file changed, 33 insertions(+), 32 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 2eb6f46afe..6445edf839 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -84,13 +84,12 @@ done
 #    ld      link
 #    ccld    compile & link
 #    vcheck  version check
-#
-# Depending on the mode, we may or may not add extra rpaths.
-# This variable controls whether they are added.
-add_rpaths=true
 
 command=$(basename "$0")
 case "$command" in
+    cpp)
+        mode=cpp
+        ;;
     cc|c89|c99|gcc|clang|icc|pgcc|xlc)
         command="$SPACK_CC"
         language="C"
@@ -107,22 +106,8 @@ case "$command" in
         command="$SPACK_F77"
         language="Fortran 77"
         ;;
-    cpp)
-        mode=cpp
-        ;;
     ld)
         mode=ld
-
-        # Darwin's linker has a -r argument that merges object files
-        # together. It doesn't work with -rpath.
-        if [[ $OSTYPE = darwin* ]]; then
-            for arg in "$@"; do
-                if [ "$arg" = -r ]; then
-                    add_rpaths=false
-                    break
-	            fi
-            done
-        fi
         ;;
     *)
         die "Unkown compiler: $command"
@@ -130,11 +115,11 @@ case "$command" in
 esac
 
 # If any of the arguments below is present then the mode is vcheck. In
-# vcheck mode nothing is added in terms of extra search paths or
-# libraries
-if [ -z "$mode" ]; then
+# vcheck mode, nothing is added in terms of extra search paths or
+# libraries.
+if [[ -z $mode ]]; then
     for arg in "$@"; do
-        if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then
+        if [[ $arg = -v || $arg = -V || $arg = --version || $arg = -dumpversion ]]; then
             mode=vcheck
             break
     fi
@@ -142,16 +127,16 @@ if [ -z "$mode" ]; then
 fi
 
 # Finish setting up the mode.
-if [ -z "$mode" ]; then
+if [[ -z $mode ]]; then
     mode=ccld
     for arg in "$@"; do
-        if [ "$arg" = -E ]; then
+        if [[ $arg = -E ]]; then
             mode=cpp
             break
-        elif [ "$arg" = -S ]; then
+        elif [[ $arg = -S ]]; then
             mode=as
             break
-        elif [ "$arg" = -c ]; then
+        elif [[ $arg = -c ]]; then
             mode=cc
             break
         fi
@@ -159,7 +144,7 @@ if [ -z "$mode" ]; then
 fi
 
 # Dump the version and exit if we're in testing mode.
-if [ "$SPACK_TEST_COMMAND" = "dump-mode" ]; then
+if [[ $SPACK_TEST_COMMAND = dump-mode ]]; then
     echo "$mode"
     exit
 fi
@@ -170,10 +155,23 @@ if [[ -z $command ]]; then
     die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
 fi
 
-if [ "$mode" == vcheck ] ; then
+if [[ $mode == vcheck ]]; then
     exec ${command} "$@"
 fi
 
+# Darwin's linker has a -r argument that merges object files together.
+# It doesn't work with -rpath.
+# This variable controls whether they are added.
+add_rpaths=true
+if [[ mode = ld && $OSTYPE = darwin* ]]; then
+    for arg in "$@"; do
+        if [[ $arg = -r ]]; then
+            add_rpaths=false
+            break
+	fi
+    done
+fi
+
 # Save original command for debug logging
 input_command="$@"
 args=("$@")
@@ -234,11 +232,14 @@ IFS=':' read -ra spack_env_dirs <<< "$SPACK_ENV_PATH"
 spack_env_dirs+=("" ".")
 PATH=""
 for dir in "${env_path[@]}"; do
-    remove=""
-    for rm_dir in "${spack_env_dirs[@]}"; do
-        if [[ $dir = $rm_dir ]]; then remove=True; fi
+    addpath=true
+    for env_dir in "${spack_env_dirs[@]}"; do
+        if [[ $dir = $env_dir ]]; then
+            addpath=false
+            break
+        fi
     done
-    if [[ -z $remove ]]; then
+    if $addpath; then
         PATH="${PATH:+$PATH:}$dir"
     fi
 done
-- 
cgit v1.2.3-70-g09d2


From 83d6e04d39ce81376c96cf6b4aa3261ff9e6fbc9 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Mon, 4 Apr 2016 15:38:21 -0400
Subject: Convert `=` to `==` in tests; untabify

---
 lib/spack/env/cc | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 6445edf839..b845de8a2b 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -119,7 +119,7 @@ esac
 # libraries.
 if [[ -z $mode ]]; then
     for arg in "$@"; do
-        if [[ $arg = -v || $arg = -V || $arg = --version || $arg = -dumpversion ]]; then
+        if [[ $arg == -v || $arg == -V || $arg == --version || $arg == -dumpversion ]]; then
             mode=vcheck
             break
     fi
@@ -130,13 +130,13 @@ fi
 if [[ -z $mode ]]; then
     mode=ccld
     for arg in "$@"; do
-        if [[ $arg = -E ]]; then
+        if [[ $arg == -E ]]; then
             mode=cpp
             break
-        elif [[ $arg = -S ]]; then
+        elif [[ $arg == -S ]]; then
             mode=as
             break
-        elif [[ $arg = -c ]]; then
+        elif [[ $arg == -c ]]; then
             mode=cc
             break
         fi
@@ -144,7 +144,7 @@ if [[ -z $mode ]]; then
 fi
 
 # Dump the version and exit if we're in testing mode.
-if [[ $SPACK_TEST_COMMAND = dump-mode ]]; then
+if [[ $SPACK_TEST_COMMAND == dump-mode ]]; then
     echo "$mode"
     exit
 fi
@@ -163,12 +163,12 @@ fi
 # It doesn't work with -rpath.
 # This variable controls whether they are added.
 add_rpaths=true
-if [[ mode = ld && $OSTYPE = darwin* ]]; then
+if [[ mode == ld && $OSTYPE == darwin* ]]; then
     for arg in "$@"; do
-        if [[ $arg = -r ]]; then
+        if [[ $arg == -r ]]; then
             add_rpaths=false
             break
-	fi
+        fi
     done
 fi
 
@@ -181,17 +181,17 @@ IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
     # Prepend include directories
     if [[ -d $dep/include ]]; then
-        if [[ $mode = cpp || $mode = cc || $mode = as || $mode = ccld ]]; then
+        if [[ $mode == cpp || $mode == cc || $mode == as || $mode == ccld ]]; then
             args=("-I$dep/include" "${args[@]}")
         fi
     fi
 
     # Prepend lib and RPATH directories
     if [[ -d $dep/lib ]]; then
-        if [[ $mode = ccld ]]; then
+        if [[ $mode == ccld ]]; then
             $add_rpaths && args=("-Wl,-rpath,$dep/lib" "${args[@]}")
             args=("-L$dep/lib" "${args[@]}")
-        elif [[ $mode = ld ]]; then
+        elif [[ $mode == ld ]]; then
             $add_rpaths && args=("-rpath" "$dep/lib" "${args[@]}")
             args=("-L$dep/lib" "${args[@]}")
         fi
@@ -199,10 +199,10 @@ for dep in "${deps[@]}"; do
 
     # Prepend lib64 and RPATH directories
     if [[ -d $dep/lib64 ]]; then
-        if [[ $mode = ccld ]]; then
+        if [[ $mode == ccld ]]; then
             $add_rpaths && args=("-Wl,-rpath,$dep/lib64" "${args[@]}")
             args=("-L$dep/lib64" "${args[@]}")
-        elif [[ $mode = ld ]]; then
+        elif [[ $mode == ld ]]; then
             $add_rpaths && args=("-rpath" "$dep/lib64" "${args[@]}")
             args=("-L$dep/lib64" "${args[@]}")
         fi
@@ -210,9 +210,9 @@ for dep in "${deps[@]}"; do
 done
 
 # Include all -L's and prefix/whatever dirs in rpath
-if [[ $mode = ccld ]]; then
+if [[ $mode == ccld ]]; then
     $add_rpaths && args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
-elif [[ $mode = ld ]]; then
+elif [[ $mode == ld ]]; then
     $add_rpaths && args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
@@ -234,7 +234,7 @@ PATH=""
 for dir in "${env_path[@]}"; do
     addpath=true
     for env_dir in "${spack_env_dirs[@]}"; do
-        if [[ $dir = $env_dir ]]; then
+        if [[ $dir == $env_dir ]]; then
             addpath=false
             break
         fi
@@ -248,7 +248,7 @@ export PATH
 full_command=("$command" "${args[@]}")
 
 # In test command mode, write out full command for Spack tests.
-if [[ $SPACK_TEST_COMMAND = dump-args ]]; then
+if [[ $SPACK_TEST_COMMAND == dump-args ]]; then
     echo "${full_command[@]}"
     exit
 elif [[ -n $SPACK_TEST_COMMAND ]]; then
@@ -258,7 +258,7 @@ fi
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
-if [[ $SPACK_DEBUG = TRUE ]]; then
+if [[ $SPACK_DEBUG == TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
     echo "[$mode] $command $input_command" >> $input_log
-- 
cgit v1.2.3-70-g09d2


From 0ff059e388b856d7eed86d27a665a48b65bfa65f Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Mon, 4 Apr 2016 16:00:09 -0400
Subject: Clean up comments and output messages

---
 lib/spack/env/cc | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index b845de8a2b..aa1e0dbe29 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -39,7 +39,7 @@
 #
 
 # This is the list of environment variables that need to be set before
-# the script runs.  They are set by routines in spack.build_environment
+# the script runs. They are set by routines in spack.build_environment
 # as part of spack.package.Package.do_install().
 parameters="
 SPACK_PREFIX
@@ -50,7 +50,7 @@ SPACK_SHORT_SPEC"
 
 # The compiler input variables are checked for sanity later:
 #   SPACK_CC, SPACK_CXX, SPACK_F77, SPACK_FC
-# Debug flag is optional; set to true for debug logging:
+# Debug flag is optional; set to "TRUE" for debug logging:
 #   SPACK_DEBUG
 # Test command is used to unit test the compiler script.
 #   SPACK_TEST_COMMAND
@@ -66,11 +66,10 @@ function die {
 
 for param in $parameters; do
     if [[ -z ${!param} ]]; then
-        die "Spack compiler must be run from spack!  Input $param was missing!"
+        die "Spack compiler must be run from Apack! Input '$param' is missing."
     fi
 done
 
-#
 # Figure out the type of compiler, the language, and the mode so that
 # the compiler script knows what to do.
 #
@@ -78,12 +77,12 @@ done
 # 'command' is set based on the input command to $SPACK_[CC|CXX|F77|F90]
 #
 # 'mode' is set to one of:
+#    vcheck  version check
 #    cpp     preprocess
 #    cc      compile
 #    as      assemble
 #    ld      link
 #    ccld    compile & link
-#    vcheck  version check
 
 command=$(basename "$0")
 case "$command" in
@@ -114,8 +113,8 @@ case "$command" in
         ;;
 esac
 
-# If any of the arguments below is present then the mode is vcheck. In
-# vcheck mode, nothing is added in terms of extra search paths or
+# If any of the arguments below are present, then the mode is vcheck.
+# In vcheck mode, nothing is added in terms of extra search paths or
 # libraries.
 if [[ -z $mode ]]; then
     for arg in "$@"; do
-- 
cgit v1.2.3-70-g09d2


From 0296f96c7b5279b2dd9cf585a493f21e3344fe2b Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 4 Apr 2016 13:56:15 -0700
Subject: Resolves #739. Don't call setup_dependent_* for package itself.

---
 lib/spack/spack/build_environment.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'lib')

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index f4f8037ac0..eb72f2a6b4 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -304,7 +304,7 @@ def setup_package(pkg):
 
     # traverse in postorder so package can use vars from its dependencies
     spec = pkg.spec
-    for dspec in pkg.spec.traverse(order='post'):
+    for dspec in pkg.spec.traverse(order='post', root=False):
         # If a user makes their own package repo, e.g.
         # spack.repos.mystuff.libelf.Libelf, and they inherit from
         # an existing class like spack.repos.original.libelf.Libelf,
@@ -321,6 +321,7 @@ def setup_package(pkg):
         dpkg.setup_dependent_package(pkg.module, spec)
         dpkg.setup_dependent_environment(spack_env, run_env, spec)
 
+    set_module_variables_for_package(pkg, pkg.module)
     pkg.setup_environment(spack_env, run_env)
 
     # Make sure nothing's strange about the Spack environment.
-- 
cgit v1.2.3-70-g09d2


From 4ce03b75bc628bd80a9798300043f3ec0a2ed7fa Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 5 Apr 2016 07:42:23 -0400
Subject: Correct typo

---
 lib/spack/env/cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'lib')

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index aa1e0dbe29..18fd8f7bdb 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -66,7 +66,7 @@ function die {
 
 for param in $parameters; do
     if [[ -z ${!param} ]]; then
-        die "Spack compiler must be run from Apack! Input '$param' is missing."
+        die "Spack compiler must be run from Spack! Input '$param' is missing."
     fi
 done
 
-- 
cgit v1.2.3-70-g09d2


From 73b6214a13339f11dbc33b0e068c13499f139b6f Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Tue, 22 Mar 2016 15:23:46 +0100
Subject: module files : proper cleanup on uninstall fixes #216

Conflicts:
	lib/spack/spack/test/database.py
---
 lib/spack/spack/cmd/module.py | 10 ++--------
 lib/spack/spack/modules.py    |  6 +++++-
 2 files changed, 7 insertions(+), 9 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py
index 315d9fc926..a67f5c0c13 100644
--- a/lib/spack/spack/cmd/module.py
+++ b/lib/spack/spack/cmd/module.py
@@ -22,21 +22,16 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import sys
 import os
 import shutil
-import argparse
+import sys
 
 import llnl.util.tty as tty
-from llnl.util.lang import partition_list
-from llnl.util.filesystem import mkdirp
-
 import spack.cmd
+from llnl.util.filesystem import mkdirp
 from spack.modules import module_types
 from spack.util.string import *
 
-from spack.spec import Spec
-
 description ="Manipulate modules and dotkits."
 
 
@@ -98,7 +93,6 @@ def module_refresh():
             cls(spec).write()
 
 
-
 def module(parser, args):
     if args.module_command == 'refresh':
         module_refresh()
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index d797af287d..61624fbd70 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -211,7 +211,11 @@ class EnvModule(object):
     def remove(self):
         mod_file = self.file_name
         if os.path.exists(mod_file):
-            shutil.rmtree(mod_file, ignore_errors=True)
+            try:
+                os.remove(mod_file)  # Remove the module file
+                os.removedirs(os.path.dirname(mod_file))  # Remove all the empty directories from the leaf up
+            except OSError:
+                pass  # removedirs throws OSError on first non-empty directory found
 
 
 class Dotkit(EnvModule):
-- 
cgit v1.2.3-70-g09d2


From 400166398239be0880c025672dd3e5eb6c8bac7f Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@googlemail.com>
Date: Wed, 6 Apr 2016 22:19:07 +0200
Subject: leftover from cherry-pick

---
 lib/spack/spack/test/mock_database.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'lib')

diff --git a/lib/spack/spack/test/mock_database.py b/lib/spack/spack/test/mock_database.py
index 6fd05439bf..82ba59fc48 100644
--- a/lib/spack/spack/test/mock_database.py
+++ b/lib/spack/spack/test/mock_database.py
@@ -17,7 +17,7 @@ class MockDatabase(MockPackagesTest):
 
     def _mock_remove(self, spec):
         specs = spack.installed_db.query(spec)
-        assert(len(specs) == 1)
+        assert len(specs) == 1
         spec = specs[0]
         spec.package.do_uninstall(spec)
 
@@ -71,6 +71,8 @@ class MockDatabase(MockPackagesTest):
             self._mock_install('mpileaks ^zmpi')
 
     def tearDown(self):
+        for spec in spack.installed_db.query():
+            spec.package.do_uninstall(spec)
         super(MockDatabase, self).tearDown()
         shutil.rmtree(self.install_path)
         spack.install_path = self.spack_install_path
-- 
cgit v1.2.3-70-g09d2


From 1af88be3712d1b6090a2dde5d7a68405f7372ca7 Mon Sep 17 00:00:00 2001
From: Matthew LeGendre <legendre1@llnl.gov>
Date: Fri, 8 Apr 2016 11:06:14 -0700
Subject: Spack was no longer using $TMPDIR for its stage area at LLNL. Spack's
 directory search was unnecessarily putting candidates that contained your
 username at the end of its search list.

---
 lib/spack/spack/__init__.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

(limited to 'lib')

diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py
index aee11f061f..9108e1d0e3 100644
--- a/lib/spack/spack/__init__.py
+++ b/lib/spack/spack/__init__.py
@@ -136,9 +136,7 @@ for path in _tmp_candidates:
     # don't add a second username if it's already unique by user.
     if not _tmp_user in path:
         tmp_dirs.append(join_path(path, '%u', 'spack-stage'))
-
-for path in _tmp_candidates:
-    if not path in tmp_dirs:
+    else:
         tmp_dirs.append(join_path(path, 'spack-stage'))
 
 # Whether spack should allow installation of unsafe versions of
-- 
cgit v1.2.3-70-g09d2