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2021-11-19otf: specify zlib prefix explicitly (#27491)Michael Kuhn1-2/+6
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.
2021-11-19Adding --reuse to dev-build command. (#27487)Michael Davis2-3/+3
2021-11-19nextflow: add v21.10.1 (#27538)Diego Alvarez1-0/+1
2021-11-19VisIt: update for building with 3.2.1. (#27036)Eric Brugger4-15/+84
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.
2021-11-19Remove spurious debug print (#27541)Massimiliano Culpo1-1/+0
2021-11-19thepeg: fix version condition bug (#27501)haralmha1-1/+1
2021-11-18py-rapidjson: add version 1.5 (#27527)iarspider1-0/+2
2021-11-18py-ply: get sources from pypi (#27526)Manuela Kuhn1-2/+5
* py-ply: use pypi * Add py-setuptools dependency
2021-11-18Refactor bootstrap of "spack style" dependencies (#27485)Massimiliano Culpo4-156/+156
Remove the "get_executable" function from the spack.bootstrap module. Now "flake8", "isort", "mypy" and "black" will use the same bootstrapping method as GnuPG.
2021-11-18Fix cyrus-sasl recipe: requires groff to build documentation (#27522)iarspider1-0/+1
2021-11-18Allow recent pytest versions to be used with Spack (#25371)Massimiliano Culpo95-32/+80
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
2021-11-18ci: run style unit tests only if we target develop (#27472)Harmen Stoppels5-12/+28
Some tests assume the base branch is develop, but this branch may not have been checked out.
2021-11-18Add Clingo v5.5.1 (#27512)Alec Scott1-0/+1
2021-11-17new package: py-scikit-learn-extra (#27439)Glenn Johnson1-0/+27
* new package: py-scikit-learn-extra * Remove extra blank line * Add missing py-cython dependency
2021-11-17py-envisage: add 6.0.1 (#27517)Manuela Kuhn1-3/+6
2021-11-17py-pygraphviz: Add version 1.7 (#26712)haralmha1-0/+21
* Add version 1.7 * Fixup! Add version 1.7
2021-11-17llvm: introduce [build/link]_llvm_dylib (#27450)Harmen Stoppels3-7/+16
Apart from building a single dylib for LLVM, users should also be able to link tools against it.
2021-11-17Add Htslib v1.14, Samtools v1.14, and Bcftools v1.14 (#27515)Alec Scott3-0/+7
2021-11-17openPMD-validator: 1.1.0.2 (#27514)Axel Huebl1-1/+5
Add the latest versions.
2021-11-17Add LMOD v8.5.27 (#27513)Alec Scott1-0/+1
2021-11-17Updated Repository Information (#27496)Ben Bergen1-2/+2
2021-11-17New patch release SLEPc 3.16.1 (#27509)Jose E. Roman2-2/+4
2021-11-17py-ipykernel: add 5.5.6 (#27498)Manuela Kuhn1-0/+1
2021-11-17llvm: use LIBCXX_ENABLE_STATIC_ABI_LIBRARY=ON (#27448)Harmen Stoppels1-16/+6
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.
2021-11-17openblas: add a symbol suffix variant (#27500)Harmen Stoppels1-0/+18
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.
2021-11-17qt+webkit: Build needs Py2, but mesa/Meson needs Py3 (#27466)Bernhard Kaindl1-2/+17
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>
2021-11-17New version of Spack and new conflicts (#27384)Harmen Stoppels1-5/+10
2021-11-17Fix overly generic exceptions in log parser (#27413)Harmen Stoppels1-4/+0
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
2021-11-17Add ReFrame 3.9.1 (#27493)Vasileios Karakasis1-0/+1
2021-11-16New version: py-pytest-cov 3.0.0; add 'toml' variant to py-coverage (#27478)iarspider2-0/+7
* New version: py-pytest-cov 3.0.0; add 'toml' variant to py-coverage * Update package.py
2021-11-16New version: py-pylint 2.8.2; new package py-platformdirs (#27473)iarspider2-1/+30
* 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>
2021-11-16llvm: maintainers (#27482)Harmen Stoppels1-1/+1
2021-11-16cdo: new release cdo-2.0.0 (#27457)Brian Spilner1-0/+1
2021-11-16Intel mpi: allow use of external libfabric (#27292)Robert Cohn3-19/+23
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.
2021-11-16New versions: py-pyasn1 0.4.8, py-pyasn1-modules 0.2.8 (#27453)iarspider2-1/+3
* New versions: py-pyasn1 0.4.8, py-pyasn1-modules 0.2.8 * Update package.py
2021-11-16Add py-h5py 3.6.0 (#27476)Thomas Kluyver1-0/+1
2021-11-16New version: py-pyrsistent 0.18.0 (#27477)iarspider1-1/+4
* 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>
2021-11-16py-pyqt-builder: add new package (#27484)Manuela Kuhn1-0/+20
2021-11-16New version: py-pytest 6.2.5 (#27481)iarspider1-4/+6
* 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>
2021-11-16Bump curl (#27471)Harmen Stoppels1-0/+2
2021-11-16New version: py-pu 1.11.0 (#27452)iarspider1-1/+4
2021-11-16New version: py-pycuda 2021.1 (#27458)iarspider1-2/+3
2021-11-16New version: py-pycurl 7.44.1 (#27470)iarspider1-0/+3
2021-11-16New version: py-pymongo 3.12.1 (#27474)iarspider1-0/+1
2021-11-16llvm: flang implies mlir (#27449)Harmen Stoppels1-0/+2
2021-11-16Add Python 3.9.9 (#27475)Harmen Stoppels1-0/+1
2021-11-16Add a symbol suffix option to LLVM (#27445)Harmen Stoppels1-0/+6
2021-11-16racket: fix URL extrapolation (#27459)Arjun Guha1-1/+4
2021-11-16mesa: Use the llvm-config of spec['llvm'] for '+llvm' (#27235)Bernhard Kaindl1-0/+10
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.
2021-11-16Add a maintainer for Intel packages (#27465)Robert Cohn5-0/+10