There's a missing break in a switch statement that newer gcc's
dislike.
Our #4696 simply disallowed newer gcc's.
This fixes the problem instead.
It's been [PR'ed upstream](https://github.com/agordon/fastx_toolkit/pull/22).
Tested with gcc@5.5.0 and gcc@8.2.0 on CentOS.
The most recent release of bamutil that we support uses an embedded
copy of libStatGen that has several issues that keep it from building
with newer releases of gcc.
They've all been fixed upstream and the latest release of bamutil
would pick them up if/when we support it. The build process has
changed though, plus my team needs *this* version.
This commit backports those fixes.
- The nested directive implementation was broken for python 3
- directive results were not properly removed from the directive list
when it was processed in the DirectiveMeta metaclass.
- the issue was that remove_directives only descended into a list or
tuple, but in Python3, the initial value passed to the function is a
view of dictionary values.
- make it a list to fix things, and add a regression test.
- currently just looks at patches
- allows you to find out which package applied a patch to a spec
- intended to work with tarballs and resources in the future.
- add tab completion for `spack resource` and subcommands
- previously, if a concrete sub-DAG with patched specs was written out
and read back in, its patches would not be found because the dependent
that patched it was no longer in the DAG.
- Add a test to ensure that the PatchCache handles this case.
- Also add tests to ensure that patch objects are properly created from
Specs -- previously we only checked that the patches were on the Spec.
- this fixes a bug where if we save a concretized sug-DAG where a package
had been patched by a dependent, and the dependent was not in the DAG,
we would not read in all patches correctly.
- Rather than looking up patches in the DAG, we look them up globally
from an index created from the entire repository.
- The patch cache is a bit tricky for several reasons:
- we have to cache information from packages, specifically, the patch
level and working directory.
- FilePatches need to know which package owns them, so that they can
figure out where the patch lives. The repo can change locations from
run to run, so we have to store relative paths and restore them when
the cache is reloaded.
- Patch files can change underneath the cache, because repo indexes
only update on package changes. We currently punt on this -- there
are stub methods for needs_update() that will need to check patch
files when packages are loaded. There isn't an easy way to do this
at global indexing time without making the FastPackageChecker a lot
slower. This is TBD for a future commit.
- Currently, the same patch can only be used one way in a package. That
is, if it appears twice with different level/working_dir settings,
bad things will happen. There's no package that current uses the
same patch two different ways, so we've punted on this as well, but
we may need to fix this in the future by moving a lot of the metdata
(level, working dir) to the spec, and *only* caching sha256sums in
the PatchCache. That would require some much more complicated tweaks
to the Spec, so we're holding off on that til later.
- This required patches to be refactored somewhat -- the difference
between a UrlPatch and a FilePatch is still not particularly clean.
- indexes should use json, not YAML, to optimize for speed
- only use YAML in human-editable files
- this makes ProviderIndex consistent with other indexes
- virtual provider cache and tags were previously generated by nearly
identical but separate methods.
- factor out an Indexer interface for updating repository caches, and
provide implementations for each type of index (TagIndex,
ProviderIndex) so that more can be added if needed.
- Among other things, this allows all indexes to be updated at once.
This is an advantage because loading package files is the real
overhead, and building the indexes once the packages are loaded is
trivial. We avoid extra bulk read-ins by generating all package indexes
at once.
- This can be extended for dependents (reverse dependencies) and patches
later.
- cleanup patch.py:
- make patch.py constructors more understandable
- loosen coupling of patch.py with package
- in Package: make package_dir, module, and namespace class properties
- These were previously instance properties and couldn't be called from
directives, e.g. in patch.create()
- make them class properties so that they can be used in class definition
- also add some instance properties to delegate to class properties so
that prior usage on Package objects still works
* Always build glib with iconv
My early PR, #10165, which added a variant to configure glib to use
libiconv and defaulted to false, seems to be causing more trouble than
the knob is worth.
This changes the glib package to always depend on and use libiconv.
* libiconv depends_on is no longer conditional
* First draft for installing Stata 15
I've tested this works on my systems and gives a successful install of STATA 15.
* Flake8 cleanup
* Another Flake8
* Update license header
* Various improvements
A lot of improvements as suggested by @adamjstewart
* flake8 check
- When returning string output, use text_type and decode utf-8 in Python
2 instead of using `str`
- This properly handles unicode, whereas before we would pass bad strings
to colify in `spack blame` when reading git output
- add a test that round-trips some unicode through an Executable object
* paraview: adding variants to use external packages as internal do not compile
* paraview: add latest paraview version
* catalyst: fixed libvtkexpat undefined reference linking error in Catalyst 5.5
* catalyst: add latest catalyst version
* catalyst: added ParaView_DIR env variable to catalyst module
* add paraview, catalyst patches
- https://gitlab.kitware.com/vtk/vtk-m/merge_requests/1166
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2433
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2436
* - Handle updated library paths for catalyst.
Versions 5.4 and old places libraries under a paraview subdirectory.
Eg, "lib/paraview-5.4", they are now placed directly under "lib"
- Minor code style cleanup
* Handle update library and python paths for ParaView-5.5
* catalyst: added ParaView_DIR path to spack_env
* BUG: applied the patch to the extracted catalyst source files
* paraview: added missing self to a member variable
* paraview: added Paraview_DIR to env
* catalyst: added osmesa variant
* of-catalyst: added new package
* add (FOAM,WM)_PROJECT_DIR also to spack_env environment
* depends on first openfoam release supporting catalyst
* openfoam-com: added missing env variables to module generation
* openfoam: fixed flake8 errors
* of-catalyst: added full variant and openfoam version dependency
* paraview: adding variants to use external packages as internal do not compile
* catalyst: fixed libvtkexpat undefined reference linking error in Catalyst 5.5
* catalyst: added ParaView_DIR env variable to catalyst module
* add paraview, catalyst patches
- https://gitlab.kitware.com/vtk/vtk-m/merge_requests/1166
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2433
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2436
* - Handle updated library paths for catalyst.
Versions 5.4 and old places libraries under a paraview subdirectory.
Eg, "lib/paraview-5.4", they are now placed directly under "lib"
- Minor code style cleanup
* Handle update library and python paths for ParaView-5.5
* catalyst: added ParaView_DIR path to spack_env
* BUG: applied the patch to the extracted catalyst source files
* of-catalyst: added new package
* add (FOAM,WM)_PROJECT_DIR also to spack_env environment
* depends on first openfoam release supporting catalyst
* paraview: added missing self to a member variable
* openfoam-com: added missing env variables to module generation
* openfoam: fixed flake8 errors
* paraview: added Paraview_DIR to env
* catalyst: added osmesa variant
* of-catalyst: added full variant and openfoam version dependency
* paraview-catalyst: use always external expat and netcdf
* of-catalyst: reformatted package description
* paraview-catalyst: removed duplicated function
* catalyst: fixed flake8 error
* of-catalyst: fixed license header
* of-catalyst: minor changes
* of-catalyst: renamed gitrepo with git
* of-catalyst: removed useless gitrepo parameter
* Added a package for the MDAnalysis toolkit.
* Added python packages for breathe and m2r. Updated versions and URL
for the sphinx package.
* Fixed flake8 error
* Updated package requirements based on feedback.
* Updated with requirements from the setup.py
* Switched it back to pypi.
* py-pynio: new package
* Major re-working to add some of the optional dependencies, and make it conform to the approach described in the pynio setup.py comments. Much of it turned out to be too complicated, and I have added some notes in comments to explain this to future adventurers.
* Added variants for the hdf5 and gdal dependencies, which do seem to be genuinely optional. Also added absolute dependencies for jpeg and zlib, which setup.py says it wants, but were being found as the os-installed versions.
* Added descriptions for the new variants, and moved them to above the dependencies
