Commit graph

23893 commits

Author SHA1 Message Date
iarspider
3db918b1cd
New version: py-pytools 2021.2.9 (#27531) 2021-11-19 02:23:03 -07:00
Michael Kuhn
eefff81289
otf: specify zlib prefix explicitly (#27491)
This causes `otfconfig` to also list zlib's library directory.
Otherwise, `-lz` cannot be found. Also remove `--with-zlibsymbols`,
which doesn't seem to be supported anymore.
2021-11-19 09:37:27 +01:00
Michael Davis
3375db12a5
Adding --reuse to dev-build command. (#27487) 2021-11-19 09:25:45 +01:00
Diego Alvarez
4d059ead8c
nextflow: add v21.10.1 (#27538) 2021-11-19 09:21:14 +01:00
Eric Brugger
4cf71b2c7f
VisIt: update for building with 3.2.1. (#27036)
Include several several patches to vtk 8.1 for building on a 
system with no system install X11 libraries or include files.

Specify specific versions of dependent packages that are known to work with 3.2.1.

Tested on spock.olcf.ornl.gov. The GUI came up and rendered images 
and an image was successfully saved using off screen rendering from 
data from curv2d.silo.
2021-11-19 09:05:13 +01:00
Massimiliano Culpo
57d3b02800
Remove spurious debug print (#27541) 2021-11-19 09:02:22 +01:00
haralmha
4d1f09c752
thepeg: fix version condition bug (#27501) 2021-11-19 08:56:00 +01:00
iarspider
c183111a61
py-rapidjson: add version 1.5 (#27527) 2021-11-18 17:52:06 -08:00
Manuela Kuhn
0b6ce17dc4
py-ply: get sources from pypi (#27526)
* py-ply: use pypi

* Add py-setuptools dependency
2021-11-18 16:52:51 -07:00
Massimiliano Culpo
e3cd91af53
Refactor bootstrap of "spack style" dependencies (#27485)
Remove the "get_executable" function from the
spack.bootstrap module. Now "flake8", "isort",
"mypy" and "black" will use the same
bootstrapping method as GnuPG.
2021-11-18 15:23:09 +01:00
iarspider
d0c4aeb0c0
Fix cyrus-sasl recipe: requires groff to build documentation (#27522) 2021-11-18 15:10:37 +01:00
Massimiliano Culpo
f981682bdc
Allow recent pytest versions to be used with Spack (#25371)
Currently Spack vendors `pytest` at a version which is three major 
versions behind the latest (3.2.5 vs. 6.2.4). We do that since v3.2.5 
is the latest version supporting Python 2.6. Remaining so much 
behind the currently supported versions though might introduce 
some incompatibilities and is surely a technical debt.

This PR modifies Spack to:
- Use the vendored `pytest@3.2.5` only as a fallback solution, 
  if the Python interpreter used for Spack doesn't provide a newer one
- Be able to parse `pytest --collect-only` in all the different output 
  formats from v3.2.5 to v6.2.4 and use it consistently for `spack unit-test --list-*`
- Updating the unit tests in Github Actions to use a more recent `pytest` version
2021-11-18 15:08:59 +01:00
Harmen Stoppels
8f7640dbef
ci: run style unit tests only if we target develop (#27472)
Some tests assume the base branch is develop, but this branch may not
have been checked out.
2021-11-18 13:00:39 +01:00
Alec Scott
7ee736a158
Add Clingo v5.5.1 (#27512) 2021-11-18 06:27:01 +01:00
Glenn Johnson
b260efd9c4
new package: py-scikit-learn-extra (#27439)
* new package: py-scikit-learn-extra

* Remove extra blank line

* Add missing py-cython dependency
2021-11-17 23:13:19 -06:00
Manuela Kuhn
b4fcb4d43c
py-envisage: add 6.0.1 (#27517) 2021-11-17 23:12:28 -06:00
haralmha
301a506aa2
py-pygraphviz: Add version 1.7 (#26712)
* Add version 1.7

* Fixup! Add version 1.7
2021-11-17 23:08:56 -06:00
Harmen Stoppels
40a6ac62d3
llvm: introduce [build/link]_llvm_dylib (#27450)
Apart from building a single dylib for LLVM, users should also be able
to link tools against it.
2021-11-17 20:10:59 -07:00
Alec Scott
d24d13559b
Add Htslib v1.14, Samtools v1.14, and Bcftools v1.14 (#27515) 2021-11-17 14:30:18 -08:00
Axel Huebl
367c3d8a83
openPMD-validator: 1.1.0.2 (#27514)
Add the latest versions.
2021-11-17 14:26:23 -08:00
Alec Scott
684d9cef23
Add LMOD v8.5.27 (#27513) 2021-11-17 14:21:57 -08:00
Ben Bergen
c459adbf6a
Updated Repository Information (#27496) 2021-11-17 10:02:41 -08:00
Jose E. Roman
d9a39d6128
New patch release SLEPc 3.16.1 (#27509) 2021-11-17 09:57:53 -08:00
Manuela Kuhn
26c5001ec4
py-ipykernel: add 5.5.6 (#27498) 2021-11-17 11:06:08 -06:00
Harmen Stoppels
c05746eac2
llvm: use LIBCXX_ENABLE_STATIC_ABI_LIBRARY=ON (#27448)
The previous workaround of using CMAKE_INSTALL_RPATH=ON was used to
avoid CMake trying to write an RPATH into the linker script libcxx.so,
which is nonsensical. See commit f86ed1e.

However, CMAKE_INSTALL_RPATH=ON seems to disable the build RPATH, which
breaks LLVM during the build when it has to locate its build-time shared
libraries (e.g. libLLVM.so). That required yet another workaround, where
some shared libraries were installed "by hand", so that they were picked
up from the install libdir. See commit 8a81229.

This was a dirty workaround, and also makes it impossible to use ninja,
since we explicitly invoked make.

This commit removes the two old workaround, and sets
LIBCXX_ENABLE_STATIC_ABI_LIBRARY=ON, so that libc++abi.a is linked into
libc++.so, which makes it enough to link with -lc++ or invoke clang++
with -stdlib=libc++, so that our install succeeds and linking LLVM's c++
standard lib is still easy.
2021-11-17 09:14:05 -07:00
Harmen Stoppels
d900abe7e1
openblas: add a symbol suffix variant (#27500)
Some packages use a 64_ or _64 symbol suffix for the ilp64 (= 64-bit
integers) intefrace for BLAS. In particular if we want to support shim
libraries like libopenblastrampoline supporting both the 32 and 64 bit
integer version of blas, it must be possible to distinguish between the
two.
2021-11-17 08:52:56 -07:00
Bernhard Kaindl
2765861705
qt+webkit: Build needs Py2, but mesa/Meson needs Py3 (#27466)
mesa inherits MesonPackage (since October 2020) which depends on Py@3.
The conflicts('mesa') enables a regular build of `qt@5.7:5.15+webkit`
without having to specify the exact version by causing the concretizer
to select mesa18 which does not depend on python@3.

Co-authored-by: Bernhard Kaindl <bernhard.kaindl@ait.ac.at>
2021-11-17 07:42:49 -05:00
Harmen Stoppels
ac8993ac38
New version of Spack and new conflicts (#27384) 2021-11-17 11:25:33 +01:00
Harmen Stoppels
cc62689504
Fix overly generic exceptions in log parser (#27413)
This type of error is skipped:

make[1]: *** [Makefile:222: /tmp/user/spack-stage/.../spack-src/usr/lib/julia/libopenblas64_.so.so] Error 1

but it's useful to have it, especially when a package sets a variable
incorrectly in makefiles
2021-11-17 11:24:14 +01:00
Vasileios Karakasis
9260c38408
Add ReFrame 3.9.1 (#27493) 2021-11-17 00:44:59 +00:00
iarspider
b4ac385d70
New version: py-pytest-cov 3.0.0; add 'toml' variant to py-coverage (#27478)
* New version: py-pytest-cov 3.0.0; add 'toml' variant to py-coverage

* Update package.py
2021-11-16 17:16:59 -07:00
iarspider
85a98fc758
New version: py-pylint 2.8.2; new package py-platformdirs (#27473)
* New version: py-pylint 2.8.2; new package py-platformdirs

* Update var/spack/repos/builtin/packages/py-platformdirs/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pylint/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-16 17:10:52 -07:00
Harmen Stoppels
0221639e8a
llvm: maintainers (#27482) 2021-11-16 15:41:02 -07:00
Brian Spilner
7ad9fc7fdb
cdo: new release cdo-2.0.0 (#27457) 2021-11-16 22:08:43 +01:00
Robert Cohn
67cba372e8
Intel mpi: allow use of external libfabric (#27292)
Intel mpi comes with an installation of libfabric (which it needs as a
dependency). It can use other implementations of libfabric at runtime
though, so if you install a package that depends on `mpi` and
`libfabric`, you can specify `intel-mpi+external-libfabric` and ensure
that the Spack-built instance is used (both by `intel-mpi` and the
root).

Apply analogous change to intel-oneapi-mpi.
2021-11-16 12:55:24 -08:00
iarspider
b194b957ce
New versions: py-pyasn1 0.4.8, py-pyasn1-modules 0.2.8 (#27453)
* New versions: py-pyasn1 0.4.8, py-pyasn1-modules 0.2.8

* Update package.py
2021-11-16 13:52:56 -07:00
Thomas Kluyver
df5892ac89
Add py-h5py 3.6.0 (#27476) 2021-11-16 13:28:08 -06:00
iarspider
a432d971b1
New version: py-pyrsistent 0.18.0 (#27477)
* New version: py-pyrsistent 0.18.0

* Update package.py

* Update var/spack/repos/builtin/packages/py-pyrsistent/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-16 12:20:04 -07:00
Manuela Kuhn
85cf8af026
py-pyqt-builder: add new package (#27484) 2021-11-16 12:11:30 -07:00
iarspider
a867320021
New version: py-pytest 6.2.5 (#27481)
* New version: py-pytest 6.2.5

* Update var/spack/repos/builtin/packages/py-pytest/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-16 12:11:08 -07:00
Harmen Stoppels
a70d917da6
Bump curl (#27471) 2021-11-16 10:30:28 -08:00
iarspider
b9314fd887
New version: py-pu 1.11.0 (#27452) 2021-11-16 11:49:42 -06:00
iarspider
de916bd27b
New version: py-pycuda 2021.1 (#27458) 2021-11-16 11:46:23 -06:00
iarspider
9f6dd08e1c
New version: py-pycurl 7.44.1 (#27470) 2021-11-16 11:40:43 -06:00
iarspider
db307f9946
New version: py-pymongo 3.12.1 (#27474) 2021-11-16 11:39:28 -06:00
Harmen Stoppels
7c3b146789
llvm: flang implies mlir (#27449) 2021-11-16 10:08:07 -07:00
Harmen Stoppels
54fc26bf34
Add Python 3.9.9 (#27475) 2021-11-16 10:17:23 -06:00
Harmen Stoppels
a780f96a25
Add a symbol suffix option to LLVM (#27445) 2021-11-16 06:06:07 -08:00
Arjun Guha
bb54e9a4be
racket: fix URL extrapolation (#27459) 2021-11-16 08:38:47 +01:00
Bernhard Kaindl
ada598668b
mesa: Use the llvm-config of spec['llvm'] for '+llvm' (#27235)
Fix builds on hosts where /usr/bin/llvm-config-* is found and provides an
incompatible version: Ensure that the llvm-config of spec['llvm'] is used.
2021-11-16 08:07:48 +01:00