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Fixes #4026
#1167 updated Database.reindex to keep old installation records to
support external packages. However, when a user manually removes a
prefix and reindexes this kept the records so the packages were
still installed according to "spack find" etc. This adds a check
for non-external packages to ensure they are properly installed
according to the directory layout.
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* add relion package
* fix flake8
* add licence
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* Dia requires libxml2.
* Clean up dependencies for Dia (and add X11 deps).
+ Remove dependencies on cairo and libpng. The will be satisfied via gtkplus.
+ Add dependencies on X11 libraries: libsm, libuuid, libxinerama, libxrender.
+ From a dependency diagram, it doesn't appear that we need libxml2 since this
dependency should be come in through cairo (via gtkplus). However, Dia will
not build without it.
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* Separate build integration tests; simplify test scripts
- Move build tests out of the regular Travis unit tests, add more smoke
test packages to build.
- Run all test scripts with bash -e, which fails on error.
- Factor coverage out into a Travis environment variable, so it's more
obvious from .travis.yml which tests contribute to coverage and which
don't.
- Factor dependency checking and much of the front-matter in tests
scripts into a setup.sh script, which is sourced by all the test
scripts. Extra cruft in each tests script now reduced to 2 lines at
the beginning.
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* Hackery to get gtkplus to build
PR #3077 broke gtkplus by introducing gobject-introspection.
This big hack makes things work. It has problems.
1. Rather than deal with the nasty sbang fooey in the
g-ir-tool-template.in derived scripts, it just adds a python
dependency to each package that runs one of the scripts. This lets
the `/usr/bin/env python` sbang do the right thing.
2. It stuffs a several directories on to the XDG_DATA_DIRS environment
variable, which is used for (among other things) locating the .gir
files.
3. It avoids building the gtkplus demos because I can't make the bit
that calls `gdk-pixbuf-csource` work. It doesn't think that it can
load `.png` files and all of the google hits I found suggest a bad
`loader.cache` file. The file's fine and I can strace the command
and watch it read it in... Many, many hours wasted here.
In spite of the demo failing, the tests pass and an emacs built
with this lib seems to work.
* Fix sbang so everyone needn't depend_on python
Rather than have every package that
`depends_on('gobject-introspection')` also need to
`depend_on('python')`, this commit fixes the
scripts (e.g. `g-ir-scanner`).
The interesting bit is in the gobject-introspection package. There is
a beefy comment there that is included below.
The commit also removes the now un-necessary dependencies from various
packages.
I have two reservations about this commit:
1. How portable is the "insertion" sed command? I'm particularly
worried that some sed's might need the line to insert to be on a
different line, which I can't imagine how to cram into the
Makefile.in.
The solution I see to this is rather than extending the existing
sed command in the Makefile I could shim in another line in the
rule and e.g. call a bit of Perl (or Python, I suppose) which would
end up being much neater.
2. As written it always uses Spack's `.../bin/sbang`, which might or
might not be a good idea.
If I use "the solution" from number 1 above, then I can check the
line length before I munge it. Otherwise???
---
This package creates several scripts from |
toosl/g-ir-tool-template.in. In their original form these |
scripts end up with a sbang line like |
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`#!/usr/bin/env /path/to/spack/python`. |
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These scripts are generated and then used as part of the build |
(other packages also use the scripts after they've been |
installed). |
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The path to the spack python can become too long. Because these |
tools are used as part of the build, the normal hook that fixes |
this problem can't help us. |
This package fixes the problem in two steps: |
- it rewrites the g-ir-tool-template so that its sbang line |
refers directly to spack's python (filter_file step below); and |
- it patches the Makefile.in so that the generated Makefile has an |
extra sed expression in its TOOL_SUBSTITUTION that results in |
an `#!/bin/bash /path/to/spack/bin/sbang` unconditionally being |
inserted into the scripts as they're generated. |
* Cairo needs python when it's +X
Cairo needs to depend_on python when it's +X. I think it's an
indirect requirement that's coming in via libxcb).
* Flake8 cleanup
* Make cairo's dep on python be type=build
This seems to be the right thing and seems to produce a result
that works (I can build gtk+ and then emacs+X on top of it).
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* ghostscript: add version 9.21 and handle new URL format
* ghostscript: add url of latest version to fix `spack versions`
* ghostscript: use github for all versions our package provides (>= 9.18)
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- Sometimes you need something mindless to do.
- Sometimes it can be helpful, as well.
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* Add missing readline dependency to sqlite
* Fix typo
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* matplotlib and basemap require setuptools to run properly together
* flake 8 fix
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Commit-type: bug-fix
Funded-by: IDEAS
Project: xSDK
Reported-by: "Klinvex, Alicia Marie" <amklinv@sandia.gov>
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- add Version.__format__ to support new-style formatting.
- Python3 doesn't handle this well -- it delegates to
object.__format__(), which raises an error for fancy format strings.
- not sure why it doesn't call str(self).__format__ instead, but that's
hwo things are.
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* add kokkos package
* fix flake8
* add descriptions to kokkos variants
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zsh build will fail with
configure: error: "No terminal handling library was found on your system."
if ncurses is not found.
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* perl: provide +gdbm variant for use when system dbm is missing or buggy
* perl: remove gdbm variant; always depends on gdbm
* perl: pass gdbm paths as Configure arguments
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* Add API Docs for lib/spack/llnl
* Clean up after previous builds
* Better fix for purging API docs
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The blast+ configure script supports building
--with-{python,perl}=path and --without-{python,perl}.
This commit makes the use of those two languages configurable via
variants and adds dependencies and explicit --with-... or
--without-... flags to configure.
Python was a non-optional dependency, now it is a variant that
defaults to `True`.
Perl was not previously an explicit dependency but the configure
script was likely to discover one on your system (`/usr/bin/perl`).
It is now a variant that defaults to `True`.
I am unable to accurately determine what these flags to the configure
script enable. My users are frustrated by the dependency on Python in
particular because it constrains the other modules that they can have
loaded for new discernible benefit.
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* xSDK: a bundle/meta package that simple installs a series of packages with suitable specs
This is based on struggles with previous attempts at such a bundler
Funded-by: IDEAS
Project: IDEAS/xSDK
Time: 12 hours
* PETSc needs c++11 when built with Trilinos
* Added alquimia package
* remove direct setting of cpp in petsc/package.py since it doesn't work on some systems.
Funded-by: IDEAS
Project: IDEAS/xSDK
Time: .3 hours
Reported-by: Mark A. Berrill <berrillma@ornl.gov>
* provide the MPI compilers to PETSc configure with --with-cc etc instead of --with-mpi-dir
Funded-by: IDEAS
Project: IDEAS/xSDK
* Spack bug fix issue #3144
String could contain /n which resulting in spack generating warning message to stderr on each
use of compiler which configure interpreted as failing compiler
Thanks-to: Mark A. Berrill <berrillma@ornl.gov>
* Fixed alquimia package
Alquimia expects PETSC_DIR and PETSC_ARCH to be defined, and
refuses to install if they are not. Spack does not define PETSC_
ARCH, so Alquimia will not install. This patch does two things
to fix the alquimia build:
1. A patch has been added to remove the dependency on PETSC_ARCH.
2. Alquimia currently depends on old versions of PETSc and pflotran.
@ghammond86 updated the alquimia interfaces to use more recent
versions, but his patch is still sitting in an alquimia pull
request. As a result, the spack installer now uses his fork
of alquimia. This is a temporary fix until his pull request is
accepted.
* Need to pass to Alquimia the MPI compilers, not the raw compilers
Otherwise the PETSc tests do not produce executables that can run because they are not
linked against MPI libraries
Funded-by: IDEAS
Project: IDEAS/xSDK
Time: .5 hours
* Add alquimia to xSDK build
Funded-by: IDEAS
Project: IDEAS/xSDK
* Fix flake8 errors for xsdk packages
* Add xsdk support for xsdk version xsdk-0.2.0
Note that currently it is just dummy code, but will eventually use
a xsdk-0.2.0 tag for each package it installs.
Funded-by: IDEAS
Project: IDEAS/xSDK
Time: .7 hours
* Do not build Mumps by default for PETSc since it is not portable, for example to Cray
Allow alquimia to accept PETSc even if the PETSc test executable cannot run since this is a problem on Cray.
Reported-by: Alicia Marie Klinvex <amklinv@sandia.gov>
* Add xsdk-0.2.0-rc1 tag for xsdk-0.2.0 installs
* Switch alquimia download site back to standard location
since they have incorporated Glenn Hammond's fixes
Also it no longer needs the patch to the Alquimia cmake
Funded-by: IDEAS
Project: IDEAS/xSDK
Reported-by: Sergi Molins Rafa <smolins@lbl.gov>
* update hypre to use the latest release candidate for xsdk 0.2.0
Funded-by: IDEAS
Project: IDEAS/xSDK
Reported-by: Ulrike Meier Yang <yang11@llnl.gov>
* Re-added patch to alquimia
The patch was out of date and has been updated accordingly.
* Added Tpetra-free option to Trilinos
The Tpetra stack takes forever to build and is not used by any of the
IDEAS teams, so there should be an option to disable it. I have added
this option and updated the xSDK accordingly. I also disabled
xSDKTrilinos in the xSDK, since none of the apps teams currently use it,
and it's largely Tpetra-based.
* Removed alquimia patch from develop version
The patch has been incorporated into alquimia and is no longer
necessary for the develop version. The tagged version has not
been updated accordingly and still needs the patch for now.
(When the tagged version gets updated, the patch does need to be
removed from spack altogether, or it will break the build.)
* Removed patch from alquimia
It has been incorporated into alquimia, both the develop and
rc2 tagged versions. The 0.2.0 version of alquimia has been updated
to tag rc2 rather than rc1.
* update xsdk-0.2.0 to depend on PETSc xsdk-0.2.0-rc2 which fixes for Apple xcode 8.3
Commit-type: bug-fix
Funded-by: IDEAS
Project: IDEAS/xSDK
* import sys got lost in merge with develop
* Update xsdk packages to use xsdk-0.2.0 tag
Commit-type: feature
Funded-by: IDEAS
Project: ECP
* Fixes for Flake8
note, had to ignore some long lines due to a single string
* simple improvements to XDK packages as suggested by Spack pull request reviewers
Commit-type: style-fix
Funded-by: IDEAS
Project: xSDK
* Removed unneeded : after develop as requested by Denis Davydov in pull request review
Commit-type: style-fix
Funded-by: IDEAS
Project: xSDK
Thanks-to: Denis Davydov
* Removed change that may not be needed due to updates in PETSc spack file such as using mpicc etc directly
Commit-type: bug-fix
Funded-by: IDEAS
Project: xSDK
Thanks-to: Adam J. Stewart
* Do not turn on xSDKTrilinos for xSDK builds since it requires tpetra
Commit-type: bug-fix
Funded-by: IDEAS
Project: xSDK
* comment why MUMPS is disabled by default for PETSc so that others won't try to enable it when modifying petsc package next time
Commit-type: documentation
Funded-by: IDEAS
Project: xSDK
Thanks-to: Denis Davydov
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- Omit final paren from regular expressions in cmd/flake8.py
- Allows long directives to be exempted even if they are wrapped.
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* Properly ignore flake8 F811 redefinition errors
* Add unit tests for flake8 command
* Allow spack flake8 to work on systems with older git
* Skip flake8 unit tests for Python 2.6 and 3.3
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* legion: add mpi inoperability
* legion: make +mpi the default
* legion: add shared variant
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* Added magma package
* Incorporated Serban's change
* globalarrays: add global arrays package to Spack.
* globalarray: remove extreaneous comment from package file
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