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
* [mfem] A few updates: add 'strumpack' variant; add 'zlib'
variant (same as 'gzstream'); fix optmization flag
for v4.0.
* [mfem] flake8 fix
* [mfem] Add version 4.1
* [mfem] Add/tweak some 'conflicts' directives.
* [gslib] Add new release versions + 'develop' version.
* [petsc] Restrict hdf5 version to <= 1.10.99 since 1.12.0 fails
* [metis] Use the original metis url for v4.0.3.
* [conduit] Remove restrictions to the used hdf5 variant to allow
building with other packages that use hdf5, e.g. petsc.
* [mfem] Few updates:
* Replace the 'gzstream' variant with 'zlib' variant.
* Do not add system library paths with -L flags.
* Allow '+pumi+shared' variant.
* Update the 'test_builds.sh' script.
* [occa] Add version 1.0.9.
* [mfem] Some OCCA and RAJA updates.
* [gslib] Fix the build for new versions of the library.
* [mfem] Add 'gslib' variant for GSLIB.
* [mfem] Add 'cuda' variant.
* [mfem] Add 'libceed' variant + a few more tweaks.
* [mfem] Add 'umpire' variant.
* [ceed] Add a draft for v3.0. Not tested. Just made sure that
concretization works for 'ceed' and 'ceed+cuda'.
* [nek] Fix Nek5000/NekCEM
* [nek] Add Nek5000-v19 & polishing Nek packages
* [flake8] Fix flake8 failure
* petsc: use of HDF5 does not care about +hl+fortran
* [petsc] Temporarily allow any hypre version with petsc@develop.
[ceed] Remove the requirement for hypre@develop.
* [libceed] Do not explicitly set NVCCFLAGS for v0.5 and later.
* [laghos] Add version 3.0, pointing to dev branch for now.
Do not set CXX at the make command line.
Simplify the dependecy directives a little.
[ceed] Use laghos v3.0 for ceed v3.0.0.
* [laghos] Keep the injection of CXX in the makefile for laghos
versions <= 2.0.
* [nekcem] Recovert hash-versions used by older versions of the
'ceed' package.
* [occa] Disable hip autodetection because it fails on some machines.
* [laghos] Update v3.0 with the actual release source.
* [suite-sparse] Explicitly add the c11 flag to CFLAGS.
* Update package.py (#15749)
* [magma] Add forgotten specification of the 'cuda_arch' variant.
* [ceed] Use magma v2.5.3 for ceed v3.0.
* libceed-0.6
* mfem: depend on libceed 0.6:, not 0.6.0:
* [libceed] Add 'magma' variant -- enable MAGMA backend.
* [ceed] In v3.0, use '+magma' variant of libceed when cuda is enabled.
* Initial package for Remhos (needs to be updated with actual sha256
* Adding Remhos to CEED-3.0, for now @develop
* petsc: add 3.13.0 (using petsc-lite) and 3.12.5
* ceed: update to petsc@3.13.0:3.13.99
* Temporary fix
* [nekcem] Add hash-version for ceed v3.0.
* [nek5000] Simplify source urls.
* [nektools] Use the same sources and versions as in nek5000.
* [ceed] Update Nek-related package versions.
* libceed: add v0.6 portabilty fix
* libceed: better v0.6 portabilty fix
* Adding Remhos 1.0 release in CEED-3.0
* Updating hash for Remhos-1.0
* [petsc] Add cuda variant.
* [libceed] Flake8 fix.
* [petsc] Add cuda variant.
* [ceed] Fix the OCCA version to 1.0.9. Enable petsc+cuda when
compiling ceed@3.0.0+cuda.
* nek5000: fix python 2.7+ syntax
* [laghos] Fix testing.
* [remhos] Fix testing.
* [remhos] For testing use the 'tests' target instead of 'test'.
* Add/update the maintainers for ceed, libceed, mfem, laghos, and remhos.
* [ceed] Remove unnecessary dependencies.
* libceed: activate AVX when supported
Co-authored-by: Thilina Rathnayake <thilinarmtb@gmail.com>
Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: Stan Tomov <tomov@eecs.utk.edu>
Co-authored-by: Tzanio <tzanio@llnl.gov>
* Throw an error at spack install invocation instead of most of the way through the build process when cuda_arch is unspecified.
* Clean-up of CMake booleans. No actual change.
* Use CMake variables for hwloc and libelf installation directories and avoid injecting extra flags into CMAKE_CXX_FLAGS
* Conflict should only exist for +cuda variant.
* Biopandas python package
* Update var/spack/repos/builtin/packages/py-biopandas/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-biopandas/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* remove scipy dependency
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
At least the v2.0.2.0 tar ball contains compiled object files etc, which
cause the build to fail on other architectures (ppc64le in particular), so
this patch adds a `make clean` after configuring first.
* 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.
* macOS: Fix emacs Linking
Fix linking issue of emacs on macOS (clang and gcc).
Applies the same work-around as conda-forge:
b051f6c928/recipe/build.sh
Homebrew avoids this by linking against the system ncurses lib:
https://github.com/Homebrew/homebrew-core/blob/master/Formula/emacs.rb
* ncurses: fix outdated variant comment
this comment was build on the assumption that gnutls
triggers a termlib dependency in emacs. that's not the
case, ncurses itself depends on termlib when build with
this feature.
libpng still has its sourceforge page but is actively been
developed on github.
since the sourceforge urls are too often down (as seen in
my nightly CI/CD tests), just switch the download source to
GitHub instead.
Mesa links against libtinfo so needs to depend on ncurses. It also needs
a little help finding the library directory so an LDFLAGS configure
option is added.
* MPark.Variant: GCC 7.3.1 Conflict
Due to an ICE in this specific patch-release of GCC, compile
errors in downstream packages should be avoided with a clean
conflict.
* Fix superfluous spaces
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Fix typo
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add Cubist
* enhance recipe
* Not using OS module anymore
* remove white space
* Fix build shell
* make Flake8 happy
* use bash shell for build
* Convert it To MakefilePackage as per peer-review
* Update var/spack/repos/builtin/packages/neo4j/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Add new package: neo4j
* refine neo4j package
* fix flake8 warning
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* update: memsurfer with python3
* flake8 compliance
* Update var/spack/repos/builtin/packages/memsurfer/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/memsurfer/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/memsurfer/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* removed build_type preferences at adamjstewart's suggestion
* Added build/run dependency on python3.7
as suggested by adam stewart
* more flake8 horror!
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* sonLib package as required by the HAL toolkit
* cleanup
* Update var/spack/repos/builtin/packages/sonlib/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/sonlib/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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.
* MAINT: Charliecloud OSX error
* raise an appropriate error when attempting to build
Charliecloud on Mac OSX, since it will otherwise fail
with a more confusing configure stage link check failure
* Update var/spack/repos/builtin/packages/charliecloud/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* MAINT: PR 16049 revision
* remove an unused import
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* pfft: fix to handle 'precision' variant in fftw
pfft had been checking for +double, etc. in fftw spec, which no longer
are present (replaced by Multivalued variant precision).
* pfft: fix to handle 'precision' variant in fftw
pfft had been checking for +double, etc. in fftw spec, which no
longer are present (replaced by Multivalued variant precision).
(amended to use more idiomatic checks as suggested by @alalazo)
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
* Patch Mathematica
Mathematica installer moves all files and directories from installation directory to a backup one. The problem is that it also moves .spack to this backup location. Once it's done it does not move .spack back where it was.
My patch creates a copy of .spack to /tmp then moves it back right before exiting the install call.
* Make lint happy
* Use Spack native copy()
As suggested in peer-review let's:
- Copy .spack to stage directory so I don't have to use random
- Use Spack native copy() to do these operations
* Use join_path to create paths
As per peer-review suggestion:
- Use join_path to create paths
- Use copy_tree since we're copying a directory that could have sub-directories
* Update package.py to include py-notebook 6.0.3 and sha
* Update package.py
* [py-notebook] updated py-tornado version requirements
* [py-notebook] reworked and reordered for readability
* [py-notebook] updated version requirement for py-jupyter-client
* [py-notebook] updated version requirements for py-jupyter-core
Co-authored-by: ehdeec <ehdeec@rit.edu>
* new package: BART
This PR adds the BART (Berkeley Advanced Reconstruction Toolset)
package.
Despite the presence of CMake files, this package builds with a
Makefile. It looks like the project is moving away from cmake. The patch
for MKL has been committed upstream so should only be necessary for this
version of BART. The Makefile patch is meant for working with Spack and
would not be useful upstream. The bart scripts are still setup to use
bart with the subcommands being individual binaries. This patches those
to use the single binary with built-in subcommands and assumes that
spack is providing the TOOLBOX environment variable and setting PATH.
* Update var/spack/repos/builtin/packages/bart/package.py
Yes, '==' make more sense for a single string.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* The python dependencies are run time only.
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* New patch release SLEPc 3.13.1
* Update var/spack/repos/builtin/packages/slepc/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* new package: py-youtube-dl + fixes for dependencies
This PR adds the py-youtube-dl program. In addition, there are a couple
of dependency packages that needed to be updated.
* ffmpeg
This is needed by py-youtube-dl. However, the spack ffmpeg recipe does
not include a lot of options, specifically, a dependency on openssl for
working with the https protocol.
- Added updated version.
- Added variants for the different licensing options.
- Added "meta" variants for X and drawtext. These turn on/off several
options.
- Set variants and dependencies for many options. The defaults are based
on the configuration settings in ffmpeg.
- Set dependencies that were missing or that will likely get pulled in
from the system.
* libxml2
The ffmpeg+libxml2 variant initially failed to build. The issue is that
libxml2 sets the headers property to
include_dir = self.spec.prefix.include.libxml2
The ffmpeg configure looks for prefix.include and fills in the rest.
This could probably be patched in ffmpeg but the headers property in the
libxml2 recipe is not consistent with the environment module or the
pkgconfig file, both of which set the headers path to prefix.include.
This PR sets the libxml2 headers property to
include_dir = self.spec.prefix.include
A spot check of a few libxml2 dependents did not rreveal any problems
with this change.
* Comment out libxml2 dependency in ffmpeg
The header property issue of the spack libxml2 package will need to be
resolved in another PR before libxml2 can be enabled in ffmpeg.
* new package: openmm
* dependency adjustments
* 1. modify dependencies
2. openmm dynamically compiles cuda kernels during runtime,
attempt to set up an environment that will work.
* Update var/spack/repos/builtin/packages/openmm/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This adds a boolean 'libtirpc' variant to the hdf package.
Default is false, which will reproduce previous behavior (which
was to rely either on system xdr headers/library, or have hdf use
it's builtin xdr lib/headers (which are only for 32 bit))
If true, a dependency is added on 'libtirpc', and the LIBS and
CPPFLAGS are updated in the configure command to find the libtirpc
library and xdr.h header.
This is needed as RHEL8 (and presumably other distros have or will be)
removed xdr.h from glib-headers package,which was breaking the previous
behavior of using system xdr headers.
* opencv: assorted fixes
1. depends on blas when +lapack
2. set cuda nvcc flags for cuda_arch
3. let cuda/contrib builds work
4. depends on hdf5 when cuda/contrib
5. depends on ant when +java
6. allow protobuf version to be different
7. let opencv recompile it's protoc files.
* ant is a build-time dependency
* register +cuda~contrib as impossible.
The old api is found in version 0.3.0 which uses a different release
name, so the url function was updated to properly find the older
releases. Also, this removes the boost constraint on the 0.3.0 version
which does not need it.
* meson: Add 0.54.0
This change also improves the rpath patch we are using. Instead of never
removing the rpath, we now only keep it if running within Spack to
guarantee consistent behavior of Meson.
* meson: Make ninja a hard dependency
* Update doxygen package
* Add new version releases 1.8.16 and 1.8.17
* Add mscgen as an optional dependency.
* Update doxygen package.py
Fix typo in mscgen dependency specification
* Remove whitespace for flake8
* primer3: move to github, add 2.5.0, fix 2.3.7
- The Primer3 project moved to GitHub.
- update the URL
- compare the tarballs 2.3.7 from Sourceforge and github, no
significant differences (e.g. the Sourceforge tarball contained a
couple of "tmp" files).
- update the signature for the 2.3.7 tarball.
- @2.3.7 doesn't build with gcc@8.4.0, there's a dubious pointer/int
comparison that causes an error. It was fixed upstream in newer
versions, apply simple patch to this version so that it continues to
be build-able with newer compilers. See:
- https://github.com/primer3-org/primer3/issues/2
- https://github.com/primer3-org/primer3/issues/3
- Add info for @2.5.0, which builds cleanly.
* Flake8 cleanup
* [gtk-doc] created template
* [gtk-doc] using custom url to standardize on dotted version
* [gtk-doc] added description and homepage
* [gtk-doc] added dependencies and added pdf variant
* [gtk-doc] commented out pdf variant
* [gtk-doc] cleaned up leftover fixmes
* [gtk-doc] flake8
* [gtk-doc] readded url
* [gtk-doc] python packages are build and run dependencies
* py-torch: Fix v1.4.0 by adding v1.4.1
version/tag hack so that 1.4.0 is still workable.
see pytorch/pytorch#35149
* delete/disable fbgemm support in 1.4.0
* moved conflict
Newer versions of glib require Meson, so this PR adds support for that
using a hybrid approach. glib@5.28: will be built using Meson, older
versions still make use of Autotools.
The most recent change to the openjdk package set expand=False for all versions
of the package. This means only the unexpanded archive will be installed, which is not correct.
* Update dependencies and support variant for Fortran Intermediate Representation.
* Add Cmake flags that toggle Fortran Intermediate Representation on/off. Exclude Flang tests for now.
* f18+fir variant needs next release of llvm or master.
* Only build tests if you are pass in --test to spack install
* New package: py-tensorboard
* some basic dependencies based on requirements.txt
remove the older version that doesn't build
* requested changes
* add additional dependencies
* more dependency changes
* py-onnx: only use py-typing if python < 3.5
avoids a 'Callable has no attribute __abc_registry' error. See
onnx/onnx#2199 and python/typing#573
* add version 1.6.0 while we're here.
Add new version 4.5.0 and update quarantine variable list to also
include LD_PRELOAD in addition to LD_LIBRARY_PATH (to avoid side-effect
when the first depends on the latter).
- Add info for version 0.68.3
- Add variant to package that enables the "extended" features. It
works with both of the existing versions (not sure how far back it
goes, but confirmed that it's valid fro 0.53).
Tested on OS X with go@1.14.1.
