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2022-03-21relion: add dependency on libpng for version 4 (#29615)Glenn Johnson1-0/+1
2022-03-21r-future: add v1.24.0 (#29616)Glenn Johnson1-0/+2
2022-03-21r-jsonlite: add v1.8.0 (#29618)Glenn Johnson1-0/+1
2022-03-21r-philentropy: add v0.6.0 (#29619)Glenn Johnson2-1/+23
This also adds r-poorman as a new package.
2022-03-21r-pillar: add v1.7.0 (#29620)Glenn Johnson1-0/+2
2022-03-21r-rcurl: add v1.98-1.6 (#29622)Glenn Johnson1-0/+1
2022-03-21crmc: new package (#29371)haralmha1-0/+48
2022-03-21ftjam: add new package (#29320)haralmha1-0/+18
2022-03-21xyce: switch to Trilinos 13.2.0 and add dependencies for +pymi (#29331)Paul Kuberry1-8/+9
* xyce: switch to Trilinos 13.2.0 and add dependencies for +pymi * xyce: clean up Trilinos dependency logic
2022-03-21py-torchgeo: add v0.2.1 (#29632)Adam J. Stewart1-1/+5
2022-03-21python: add v3.10.3 (#29640)Jörg Behrmann1-0/+1
From the release announcement: "This is a special bugfix release ahead of schedule to address a memory leak that was happening on certain function calls when using Cython. The memory leak consisted of a small constant amount of bytes in certain function calls from Cython code. Although in most cases this was not very noticeable, it was very impactful for long-running applications and certain usage patterns. Check bpo-46347 for more information."
2022-03-21libtree: add upperbound for elfio (#29637)Harmen Stoppels1-1/+1
2022-03-20cmake: 3.21.x, 3.22.x bump (#29633)Harmen Stoppels1-0/+3
2022-03-20rivet: fix dependency build types (#29358)Valentin Volkl1-12/+9
* rivet: fix dependency build types If it isn't a python package, there is no good reason to change the default build type to remove link * rivet: turn swig into build dependency
2022-03-20dealii: new version and restrict sundials version (#29631)Luca Heltai1-1/+3
2022-03-20py-torch: set INTEL_MKL_DIR (#29613)Glenn Johnson1-0/+5
Add the INTEL_MKL_DIR variable so py-torch can find mkl if provided by intel-oneapi-mkl.
2022-03-20OpenJDK: add 11.0.14.1, 17.0.2 (#29167)Diego Alvarez1-2/+19
* Added OpenJDK 11.0.14.1 and 17.0.2 * Fix preferred_defined change.
2022-03-20rust: new version 1.58.1 and deprecate older (#29322)Vivian Hafener1-33/+40
* Added rust version 1.58.1 * Fixed flake8 style errors Co-authored-by: Viv Eric Hafener <vehrc@sporcbuild.rc.rit.edu>
2022-03-20botan: new versions 2.18.2, 2.19.0 and 2.19.1 (#29361)Martin Aumüller1-0/+3
2022-03-19GDAL: add v3.4.2 (#29496)Adam J. Stewart1-3/+6
2022-03-19py-torch-sparse: add missing dependency on py-torch (#29612)Glenn Johnson1-0/+1
2022-03-19Revert "Add command for reading a json-based DB description (#24894)" (#29603)Nils Vu3-41/+0
This reverts commit 531b1c5c3dcc9bc7bec27e223608aed477e94dbd.
2022-03-19py-pysam: update to version 0.18.0 (#29609)Glenn Johnson1-0/+2
2022-03-19mmg: add vtk variant (#29533)Carlos Bederián1-4/+4
2022-03-19py-rasterio: add v1.2.10 (#29497)Adam J. Stewart1-7/+14
2022-03-19ants: add version 20220205 (#29500)Ben Darwin1-1/+3
A new release hasn't been tagged in over a year.
2022-03-19WRF: Update AOCC patches for latest WRF version. (#29529)Timothy Brown1-2/+2
2022-03-19EVE: new version 2022.03.0 (#29511)Joel Falcou1-2/+3
2022-03-19opencl-c-headers and opencl-clhpp: add new versions (#29535)lorddavidiii2-0/+2
- these versions are a synchronization with the OpenCL v3.0.10 specification release.
2022-03-18dicom3tools: fix build error with Fujitsu compiler (#29435)Qian Jianhua1-0/+8
2022-03-18Add command for reading a json-based DB description (#24894)Peter Scheibel3-0/+41
Adds `spack external read-cray-manifest`, which reads a json file that describes a set of package DAGs. The parsed results are stored directly in the database. A user can see these installed specs with `spack find` (like any installed spec). The easiest way to use them right now as dependencies is to run `spack spec ... ^/hash-of-external-package`. Changes include: * `spack external read-cray-manifest --file <path/to/file>` will add all specs described in the file to Spack's installation DB and will also install described compilers to the compilers configuration (the expected format of the file is described in this PR as well including examples of the file) * Database records now may include an "origin" (the command added in this PR registers the origin as "external-db"). In the future, it is assumed users may want to be able to treat installs registered with this command differently (e.g. they may want to uninstall all specs added with this command) * Hash properties are now always preserved when copying specs if the source spec is concrete * I don't think the hashes of installed-and-concrete specs should change and this was the easiest way to handle that * also specs that are concrete preserve their `.normal` property when copied (external specs may mention compilers that are not registered, and without this change they would fail in `normalize` when calling `validate_or_raise`) * it might be this should only be the case if the spec was installed - [x] Improve testing - [x] Specifically mark DB records added with this command (so that users can do something like "uninstall all packages added with `spack read-external-db`) * This is now possible with `spack uninstall --all --origin=external-db` (this will remove all specs added from manifest files) - [x] Strip variants that are listed in json entries but don't actually exist for the package Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2022-03-18hdf5-vol-log: new version 1.1 (#29553)Larry Knox1-2/+4
2022-03-18PETSc: split install() into configure(), build(), install() (#29126)JDBetteridge1-5/+18
2022-03-18hepmcanalysis: propagate cxxstd from root (#29512)haralmha1-8/+5
* Use same cxx value as root * Remove pointer syntax from non-pointer type in source * Run patch function before build * Use raw string in filter_file and merge edit function with patch * Escape parentheses * Use gDirectory from ROOT instead of CurrentDirectory function
2022-03-18mmg: add 5.6.0 (#29534)Carlos Bederián1-0/+1
2022-03-17Make boost minimal and composable (Original PR#22303) (#28623)Abhik Sarkar190-104/+1117
* Make boost composable Currently Boost enables a few components through variants by default, which means that if you want to use only what you need and no more, you have to explicitly disable these variants, leading to concretization errors whenever a second package explicitly needs those components. For instance if package A only needs `+component_a` it might depend on `boost +component_a ~component_b`. And if packge B only needs `+component_b` it might depend on `boost ~component_a +component_b`. If package C now depends on both A and B, this leads to unsatisfiable variants and hence a concretization error. However, if we default to disabling all components, package A can simply depend on `boost +component_a` and package B on `boost +component_b` and package C will concretize to depending on `boost +component_a +component_b`, and whatever you install, you get the bare minimum. * Fix style * Added composable boost dependencies for folly * fixing akantu merge issue * hpctoolkit boost dependencies already defined * Fix Styles * Fixup style once more * Adding isort fix * isort one more time * Fix for package audit issue Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com> Co-authored-by: Ryan O'Malley <rd.omalley@comcast.net>
2022-03-17clinfo: add new versions (#29537)lorddavidiii1-0/+2
2022-03-17New package: py-jaconv (#29548)Jen Herting1-0/+19
* [py-jaconv] created template * [py-jaconv] - added homepage - added description - depends on setuptools - removed fixmes
2022-03-17octa: new package. (#29333)Toyohisa Kameyama4-0/+185
2022-03-17Windows Support: Testing Suite integrationJohn Parent7-58/+38
Broaden support for execution of the test suite on Windows. General bug and review fixups
2022-03-17"spack commands --update-completion"John Parent8-137/+128
2022-03-17Expand external find for Windows (#27588)John Parent5-33/+30
* Incorporate new search location * Add external user option * proper doc string * Explicit commands in getting started * raise during chgrp on Win recover installer changes Notate admin privleges Windows phase install hooks Find external python and install ninja (#23496) Allow external find python to find windows python and spack install ninja Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Betsy McPhail <betsy.mcphail@kitware.com>
2022-03-17Spack on Windows package portsJohn Parent11-139/+549
CMake - Windows Bootstrap (#25825) Remove hardcoded cmake compiler (#26410) Revert breaking cmake changes Ensure no autotools on Windows Perl on Windows (#26612) Python source build windows (#26313) Reconfigure sysconf for Windows Python2.6 compatibility Fxixup new sbang tests for windows Ruby support (#28287) Add NASM support (#28319) Add mock Ninja package for testing
2022-03-17Windows: VS and CMake supportBetsy McPhail1-7/+4
Fix: Building packages with CMake is broken (#24241) vsInstallPaths needs to be renamed vs_install_paths (#24297)
2022-03-17Packaging of netlib-lapack for windows (#24993)Jared Popelar3-20/+102
MSVC's internal CMake and Ninja now detected by spack external find and added to packages.yaml Saving progress on packaging zlib for Windows Fixing the shared CMake flag * Loading Intel's ifx Fortran compiler into MSVC; if there are multiple versions of MSVC installed and detected, ifx will only be placed into the first block written in compilers.yaml. The version number of ifx can be detected using MSVC's version flag (instead of /QV) by using ignore_version_errors. This commit also provides support for detection of Intel compilers in their own compiler block by adding ifx.exe to the fc/f77_name blocks inside intel.py * Giving CMake a Fortran compiler argument * Adding patch file for removing duplicated mangling header for versions 3.9.1 and older; static and shared now successfully building on Windows * Have netlib-lapack depend on ninja@1.10 Co-authored-by: John R. Cary <cary@txcorp.com> Co-authored-by: Jared Popelar <jpopelar@txcorp.com> Making a default config.yaml for Windows Small path length for build_stage Provide more prerequisite details, mention default config.yaml Killing an unnecessary setvars call Replacing some lost changes, proofreading, updating windows-supported package list Co-authored-by: John Parent <john.parent@kitware.com>
2022-03-17Workarounds for install errors on Windows (#21890)Betsy McPhail1-2/+11
1. Forwarding sys.stdin, e.g. use input_multiprocess_fd, gives an error on Windows. Skipping for now 3. subprocess_context needs to serialize for Windows, like it does for Mac. Co-authored-by: lou.lawrence@kitware.com <lou.lawrence@kitware.com> Co-authored-by: John Parent <john.parent@kitware.com>
2022-03-17assimp: depends on pkgconfig; disable bundled dependencies (#29551)Wouter Deconinck1-0/+4
* [assimp] depends_on pkgconfig and disable hunter, build zlib/minizip
2022-03-17openssh: Update to version 8.9 (#29539)Erik Schnetter1-0/+1
2022-03-17fastjet: use mirror for sources (#29357)Valentin Volkl1-1/+5
as a workaround for https://github.com/spack/spack/issues/20050
2022-03-17Add intermediate folder in lib to LD_LIBRARY_PATH (#29519)haralmha1-0/+3