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* environments: allow sigils to apply to entire reference
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If spack is checked out in a git worktree (see [1]), all git-related
commands fail because the `spack_is_git_repo()`-check is not thorough
enough.
When developing in a feature-branch in a seperate worktree, this is
annoying as all unittests regarding git-related spack commands fail,
cluttering the test results with false-positives.
[1]: https://git-scm.com/docs/git-worktree
Change-Id: I94b573a2c0e058e9ccc169e7ee6561626fbb06fd
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This was breaking tests on develop.
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* For tests that use the real Spack package repository, the config
needs to avoid using MPI providers that are not intended to be
installed by Spack. Without this, it is possible that Spack tests
which concretize the MPI virtual will end up trying to use an
implementation that it shouldn't (e.g. one that is always
provided externally). See #15666 for an example.
* The mutable_config test fixture was not initializing the scope
roots to the right directories (so the resulting config was empty).
* The current_host fixture in the concretize.py tests was using the
config fixture rather than mutable_config, and was polluting the
config cache for other tests.
* One test in concretize.py was clearing a nonexistent cache
(PackagePrefs._packages_config_cache). This reference has been
removed.
* The test 'test_preferred_compilers' was was depending on cross
test config pollution to succeed. The initial spec before
concretization has been updated to updated to be explicit about
the desired result.
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* dev-build: --drop-in <shell>
Add a `--drop-in <shell>` option to `spack dev-build`.
This option will automatically run a
`spack build-env <spec> -- <shell>` at the end of a `dev-build`, e.g.
to quickly drop-and-devel into a build phase of a package.
Example usage:
```
spack dev-build --before cmake --drop-in bash openpmd-api@develop
```
* build_env: drop in unit test
Co-authored-by: Greg Becker <becker33@llnl.gov>
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Generally speaking, errors that are encountered when attempting to load
command extensions now terminate the running Spack instance.
* Added new exceptions `spack.cmd.PythonNameError` and
`spack.cmd.CommandNameError`.
* New functions `spack.cmd.require_python_name(pname)` and
`spack.cmd.require_cmd_name(cname)` check that `pname` and `cname`
respectively meet requirements, throwing the appropriate error if not.
* `spack.cmd.get_module()` uses `require_cmd_name()` and passes through
exceptions from module load attempts.
* `spack.cmd.get_command()` uses `require_cmd_name()` and invokes
`get_module()` with the correct command-name form rather than the
previous (incorrect) Python name.
* Added New exceptions `spack.extensions.CommandNotFoundError` and
`spack.extensions.ExtensionNamingError`.
* `_extension_regexp` has a new leading underscore to indicate expected
privacy.
* `spack.extensions.extension_name()` raises an `ExtensionNamingError`
rather than using `tty.warn()`.
* `spack.extensions.load_command_extension()` checks command source
existence early and bails out if missing. Also, exceptions raised by
`load_module_from_file()` are passed through.
* `spack.extensions.get_module()` raises `CommandNotFoundError` as
appropriate.
* Spack `main()` allows `parser.add_command()` exceptions to cause
program end.
Tests:
* More common boilerplate has been pulled out into fixtures including
`sys.modules` dictionary cleanup and resource-managed creation of a
simple command extension with specified contents in the source file
for a single named command.
* "Hello, World!" test now uses a command named `hello-world` instead of
`hello` in order to verify correct handling of commands with hyphens.
* New tests for:
* Missing (or misnamed) command.
* Badly-named extension.
* Verification that errors encountered during import of a command are
propagated upward.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
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* prefix gets removed when adding additional configure options
* Update waf documentation to reflect the new change
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Add `-b,--before` option to dev-build command to stop before the phase in question.
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Update the travis CI docs: limiting the microarch is essential
for caching.
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This was an oversight in #15654 since `os.path.isfile`
checks that the something is a file in the current
filesystem.
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This PR introduces trivial refactoring in:
- `get_existing_elf_rpaths`
- `get_relative_elf_rpaths`
- `get_normalized_elf_rpaths`
- `set_placeholder`
mainly to be more consistent with practices used in other
parts of the code and to simplify functions locally. It also
adds or reworks unit tests for these functions and extends
their docstrings.
Co-authored-by: Patrick Gartung <gartung@fnal.gov>
Co-authored-by: Peter J. Scheibel <scheibel1@llnl.gov>
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print a note on how to activate a newly created environment
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Packages in Spack are classes, and we need to be able to execute class
methods on mock packages. The previous design used instances of a single
MockPackage class; this version gives each package its own class that can
spider depenencies. This allows us to implement class methods like
`possible_dependencies()` on mock packages.
This design change moves mock package creation into the
`MockPackageMultiRepo`, and mock packages now *must* be created from a
repo. This is required for us to mock `possible_dependencies()`, which
needs to be able to get dependency packages from the package repo.
Changes include:
* `MockPackage` is now `MockPackageBase`
* `MockPackageBase` instances must now be created with
`MockPackageMultiRepo.add_package()`
* add `possible_dependencies()` method to `MockPackageBase`
* refactor tests to use new code structure
* move package mocking infrastructure into `spack.util.mock_package`,
as it's becoming a more sophisticated class and it gets lots in `conftest.py`
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The variants table in `spack info` is cramped, as the *widest* it can be
is 80 columns. And that's actually only sort of true -- the padding
calculation is off, so it still wraps on terminals of size 80 because it
comes out *slightly* wider.
This change looks at the terminal size and calculates the width of the
description column based on it. On larger terminals, the output looks
much nicer, and on small terminals, the output no longer wraps.
Here's an example for `spack info qmcpack` with 110 columns.
Before:
Name [Default] Allowed values Description
==================== ==================== ==============================
afqmc [off] on, off Install with AFQMC support.
NOTE that if used in
combination with CUDA, only
AFQMC will have CUDA.
build_type [Release] Debug, Release, The build type to build
RelWithDebInfo
complex [off] on, off Build the complex (general
twist/k-point) version
cuda [off] on, off Build with CUDA
After:
Name [Default] Allowed values Description
==================== ==================== ========================================================
afqmc [off] on, off Install with AFQMC support. NOTE that if used in
combination with CUDA, only AFQMC will have CUDA.
build_type [Release] Debug, Release, The build type to build
RelWithDebInfo
complex [off] on, off Build the complex (general twist/k-point) version
cuda [off] on, off Build with CUDA
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fixes #16184
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(#16221)
Update compiler config with bootstrapped compiler when it was already installed and added config defaults to code so mutable_config test fixture works.
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To specify an environment for a comment, the user can specify
"spack -e <env>". The documentation incorrectly specified "-E" (which
is actually used to ignore any implicit use of environments).
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Document the nice `msg=` argument in conflicts. Super useful
for less generic conflict guidance.
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If the Spack compiler wrapper encounters any "-isystem" option, then
when adding include directories for Spack dependencies, Spack will
use "-isystem" instead of "-I". This prevents Spack-generated "-I"
options from overriding the "-isystem" options generated by the build
system. To ensure that build-system "-isystem" directories are
searched first, Spack places all of its inserted "-isystem"
directories after.
The new ordering of -isystem includes is:
* -isystem from build system (not system directories)
* -isystem from Spack
* -isystem from build system (for directories like /usr/include)
The prior order of "-I" arguments is preserved (although as of this
commit Spack no longer generates -I if -isystem is detected):
* -I from build system (not system directories)
* -I from Spack (only if there are no "-isystem" options)
* -I from build system (for directories like /usr/include)
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Since #16132, we've consolidated the setting of FORCE_UNSAFE_CONFIGURE to
`autotools.py`, so we don't need to use it in packages like `coreutils`,
in our commands, or in our container recipes.
- [x] Remove FORCE_UNSAFE_CONFIGURE from packages
- [x] Remove FORCE_UNSAFE_CONFIGURE from container recipes
- [x] Remove FORCE_UNSAFE_CONFIGURE from `spack ci` command
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This commit sets the `FORCE_UNSAFE_CONFIGURE` environment variable to 1 in autotools builds.
We see a lot of builds popping up and complaining about `FORCE_UNSAFE_CONFIGURE`. This behavior is not actually part of `autoconf` per se. It comes from this patch to `mknod.m4`, which is used by a lot of autoconf builds:
* https://lists.gnu.org/archive/html/bug-gnulib/2010-07/msg00282.html
Which originated from this problem that someone had on AIX:
* https://lists.gnu.org/archive/html/bug-gnulib/2010-07/msg00279.html
The gist of the problem seems to be that they want to check whether `mknod` can do something as root, but instead of checking whether they're running as root and using `su` or something to test this, they just made it harder to run `configure` as root.
This seems very ad hoc and this is one of many checks that are run as root in `configure`. Many of them run before this check, so it's not clear that the `FORCE_UNSAFE_CONFIGURE` thing is even preventing bad things from happening.
So:
1. This only happens in `autotools` builds, so we should go ahead and put it into `autotools.py` instead of in the global build environment, and
2. The variable does too little and provides a false sense of security in the first place, so we'll just disable it and avoid the nuisance. If we really feel strongly about this we can put some warnings in Spack about running as root, but at the top level, not in the middle of an already running script like `configure`.
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* Language-specific PIC flags
* Add tests for every compiler flag
* Fix bad rebase
* pic_flag -> cxx_pic_flag
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* SourceForge: Mirror Mixin
Add a mixing class for direct `CNAME`s to sourceforge mirrors.
Since the main gateway servers are often down, this could reduce
timeouts and fetch errors for sourceforge.net hosted software.
* SourceForge: unspectacular mirror replacement
add mirrors to all sourceforge packages with trivial
download logic.
tested fetch of latest version of each of these packages
with various mirrors before committing.
* SourceForge: xz
the author homepage is chronocially overrun and this is the offical
upload with many mirrors.
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`DYLD_LIBRARY_PATH` can frequently break builtin macOS software when
pointed at Spack libraries. This is because it takes *higher* precedence
than the default library search paths, which are used by system software.
`DYLD_FALLBACK_LIBRARY_PATH`, on the other hand, takes lower precedence.
At first glance, this might seem bad, because the software installed by
Spack in an environment needs to find *its* libraries, and it should not
use the defaults. However, Spack's isntallations are always `RPATH`'d,
so they do not have this problem.
`DYLD_FALLBACK_LIBRARY_PATH` is thus useful for things built in an
environment that need to use Spack's libraries, that don't set *their*
RPATHs correctly for whatever reason. We now prefer it to
`DYLD_LIBRARY_PATH` in modules and in environments because it helps a
little bit, and it is much less intrusive.
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provided (#15662).
Prior to this fix, the checked Spec object would not be populated, and
concretization would fail.
Co-authored-by: Marc Allen <mrcall@amazon.com>
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Currently, tags are case sensitive, which is unintuitive:
```console
$ spack list -t hpc
==> 2 packages.
nek5000 nektools
$ spack list -t HPC
==> 1 packages.
mfem
$ spack list -t Hpc
==> 0 packages.
```
This change makes them case insensitive:
```console
$ spack list -t hpc
==> 3 packages.
mfem nek5000 nektools
$ spack list -t HPC
==> 3 packages.
mfem nek5000 nektools
$ spack list -t Hpc
==> 3 packages.
mfem nek5000 nektools
```
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`spack test` has a spurious '[+] ' in the output:
```
lib/spack/spack/test/install.py .........[+] ......
```
Output is properly suppressed:
```
lib/spack/spack/test/install.py ...............
```
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Makes the following changes:
* (Fixes #15620) tty configuration was failing when stdout was
redirected. The implementation now creates a pseudo terminal for
stdin and checks stdout properly, so redirections of stdin/out/err
should be handled now.
* Handles terminal configuration when the Spack process moves between
the foreground and background (possibly multiple times) during a
build.
* Spack adjusts terminal settings to allow users to to enable/disable
build process output to the terminal using a "v" toggle, abnormal
exit cases (like CTRL-C) could leave the terminal in an unusable
state. This is addressed here with a special-case handler which
restores terminal settings.
Significantly extend testing of process output logger:
* New PseudoShell object for setting up a master and child process
and configuring file descriptor inheritance between the two
* Tests for "v" verbosity toggle making use of the added PseudoShell
object
* Added `uniq` function which takes a list of elements and replaces
any consecutive sequence of duplicate elements with a single
instance (e.g. "112211" -> "121")
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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The performance improvements done in #14693 where leaving the DB in an inconsistent state when specs were removed from it. This PR updates the DB internal state whenever the DB is written to a file.
Note that we still cannot properly enumerate installed dependents, so there is a TODO in this code. Fixing that will require the dependents dictionaries in specs to be re-keyed (either by hash, or not keyed at all -- a list would do). See #11983 for details.
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Reading the database repeatedly can be quite slow. We need a way to speed
up Spack when it reads the DB multiple times, but the DB has not been
modified between reads (which is nearly all the time).
- [x] Add a file containing a unique uuid that is regenerated at database
write time. Use this uuid to suppress re-parsing the database
contents if we know a previous uuid and the uuid has not changed.
- [x] Fix mutable_database fixture so that it resets the last seen
verifier when it resets.
- [x] Enable not rereading the database immediately after a write. Make
the tests reset the last seen verifier in between tests that use the
database fixture.
- [x] make presence of uuid module optional
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Removed the code that was converting the old index.yaml format into
index.json. Since the change happened in #2189 it should be
considered safe to drop this (untested) code.
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* only override spec prefix for non-external packages
* add test that environment shell modifications respect explicitly-specified prefixes for external packages
* add clarifying comment
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spack.util.environment_after_sourcing_files compares the local
environment against a shell environment after having sourced a
file; but this ends up including the default shell profile and
rc, which might differ from the local environment.
To change this, compare against the default shell environment,
expressed here as 'source /dev/null'.
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fixes #15775
Add all the variables listed here:
https://lmod.readthedocs.io/en/latest/090_configuring_lmod.html
to the list of those blacklisted when constructing environment
modifications by sourcing files.
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According to my nightly CI/CD tests, x.org is another large provider
of software in common build chains that is often down.
Added a hand-selected amount of mirrors that is well up-to-sync.
Tested with `util-macros` that has a quite "recent" patch release.
Other packages to follow in an individual PR.
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Makes the following changes:
* (Fixes #15620) tty configuration was failing when stdout was
redirected. The implementation now creates a pseudo terminal for
stdin and checks stdout properly, so redirections of stdin/out/err
should be handled now.
* Handles terminal configuration when the Spack process moves between
the foreground and background (possibly multiple times) during a
build.
* Spack adjusts terminal settings to allow users to to enable/disable
build process output to the terminal using a "v" toggle, abnormal
exit cases (like CTRL-C) could leave the terminal in an unusable
state. This is addressed here with a special-case handler which
restores terminal settings.
Significantly extend testing of process output logger:
* New PseudoShell object for setting up a master and child process
and configuring file descriptor inheritance between the two
* Tests for "v" verbosity toggle making use of the added PseudoShell
object
* Added `uniq` function which takes a list of elements and replaces
any consecutive sequence of duplicate elements with a single
instance (e.g. "112211" -> "121")
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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* Moved link to the right place in the docs
* Fixed a few minor issues in extensions docs
Fixed a typo, added a subsubsection for better
navigation, reworded "modules in Python" as
"Python packages"
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sourceware.org is often quite overrun and times out or results in
certificate errors.
Since libffi, bzip2, elfutils, etc. are quite fundamental in
build chains, lets add some official mirrors.
libffi, bzip2, elfutils, lvm2, valgrind: add mirrors
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The performance improvements done in #14693 where leaving the DB in an inconsistent state when specs were removed from it. This PR updates the DB internal state whenever the DB is written to a file.
Note that we still cannot properly enumerate installed dependents, so there is a TODO in this code. Fixing that will require the dependents dictionaries in specs to be re-keyed (either by hash, or not keyed at all -- a list would do). See #11983 for details.
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* Skip collection of compiler link paths if compiler does not define a verbose flag
* modules config bug: allow user to configure a compiler without an explicit entry for loaded modules
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