* py-fenics-instant: new package for legacy fenics 2016 and 2017 versions
* Update var/spack/repos/builtin/packages/py-fenics-instant/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The signature for configure_args in the template for new
RPackage packages was incorrect (different than what is
defined and used in lib/spack/spack/build_systems/r.py)
See issue #21774
Keep spack.store.store and spack.store.db consistent in unit tests
* Remove calls to monkeypatch for spack.store.store and spack.store.db:
tests that used these called one or the other, which lead to
inconsistencies (the tests passed regardless but were fragile as a
result)
* Fixtures making use of monkeypatch with mock_store now use the
updated use_store function, which sets store.store and store.db
consistently
* subprocess_context.TestState now transfers the serializes and
restores spack.store.store (without the monkeypatch changes this
would have created inconsistencies)
Since signals are fundamentally racy, We can't bound the amount of time
that the `test_foreground_background_output` test will take to get to
'on', we can only observe that it transitions to 'on'. So instead of
using an arbitrary limit, just adjust the test to allow either 'on' or
'off' followed by 'on'.
This should eliminate the spurious errors we see in CI.
Follow-up to #17110
### Before
```bash
CC=/Users/Adam/spack/lib/spack/env/clang/clang; export CC
SPACK_CC=/usr/bin/clang; export SPACK_CC
PATH=...:/Users/Adam/spack/lib/spack/env/apple-clang:/Users/Adam/spack/lib/spack/env/case-insensitive:/Users/Adam/spack/lib/spack/env:...; export PATH
```
### After
```bash
CC=/Users/Adam/spack/lib/spack/env/clang/clang; export CC
SPACK_CC=/usr/bin/clang; export SPACK_CC
PATH=...:/Users/Adam/spack/lib/spack/env/clang:/Users/Adam/spack/lib/spack/env/case-insensitive:/Users/Adam/spack/lib/spack/env:...; export PATH
```
`CC` and `SPACK_CC` were being set correctly, but `PATH` was using the name of the compiler `apple-clang` instead of `clang`. For most packages, since `CC` was set correctly, nothing broke. But for packages using `Makefiles` that set `CC` based on `which clang`, it was using the system compilers instead of the compiler wrappers. Discovered when working on `py-xgboost@0.90`.
An alternative fix would be to copy the symlinks in `env/clang` to `env/apple-clang`. Let me know if you think there's a better way to do this, or to test this.
The dependencies needed a little clean up as several dependencies are
only needed for the +X variant. This PR consolidates all of the
dependencies that actually require +X and explicitly disables them when
~X to prevent accidentally picking up system libraries.
- modified the description of the +X variant
- arranges dependencies to group them
- added missing dependency on xz
- removed unneeded dependencies
- freetype
- glib
- set dependencies when +X
- cairo
- jpeg
- libpng
- libtiff
- tcl/tk
- R uses tcl/tk together, so only tk needs to be depended on, and only
when +X
- moved tcl/tk resources to with/without-x test
- added explicit with/without settings for
- cairo
- jpeglib
- libpng
- libtiff
- tcltk
The fixture was introduced in #19690 maybe accidentally.
It's not used in unit tests, and though it should be
mutable it seems an exact copy of it's immutable version.
Before this change, in pipeline environments where runners do not have access
to persistent shared file-system storage, the only way to pass buildcaches to
dependents in later stages was by using the "enable-artifacts-buildcache" flag
in the gitlab-ci section of the spack.yaml. This change supports a second
mechanism, named "temporary-storage-url-prefix", which can be provided instead
of the "enable-artifacts-buildcache" feature, but the two cannot be used at the
same time. If this prefix is provided (only "file://" and "s3://" urls are
supported), the gitlab "CI_PIPELINE_ID" will be appended to it to create a url
for a mirror where pipeline jobs will write buildcache entries for use by jobs
in subsequent stages. If this prefix is provided, a cleanup job will be
generated to run after all the rebuild jobs have finished that will delete the
contents of the temporary mirror. To support this behavior a new mirror
sub-command has been added: "spack mirror destroy" which can take either a
mirror name or url.
This change also fixes a bug in generation of "needs" list for each job. Each
jobs "needs" list is supposed to only contain direct dependencies for scheduling
purposes, unless "enable-artifacts-buildcache" is specified. Only in that case
are the needs lists supposed to contain all transitive dependencies. This
changes fixes a bug that caused the needs lists to always contain all transitive
dependencies, regardless of whether or not "enable-artifacts-buildcache" was
specified.
* py-typing: new version, avoid issues with newer versions of python
https://pypi.org/project/typing/
"For package maintainers, it is preferred to use
typing;python_version<"3.5" if your package requires it to support
earlier Python versions."
* update conflict version / more message detail
* change the depends_on, leave a comment suggesting correct usage
The actual, documented minimum version of the cfitsio dependency,
v3.181, is now neither available for (easy) download from NASA, nor as
a Spack package. No upper bound on version number exists (at this time).
