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2023-01-20ca-certificates-mozilla: 2023-01-10 (#35018)Harmen Stoppels1-0/+5
2023-01-20libiconv: bump (#35035)Harmen Stoppels1-0/+1
2023-01-20ncurses: bump (#35033)Harmen Stoppels1-0/+1
2023-01-20sqlite: bump (#35032)Harmen Stoppels1-0/+1
2023-01-20hypre: add option for sycl variant (#34987)eugeneswalker1-0/+13
* hypre: add option for sycl variant * hypre +sycl conflicts with @:2.23 * hypre +sycl: raise InstallError for unsupported compiler
2023-01-20Add nf-core-tools, and three remainder deps (#34466)Marco De La Pierre8-1/+199
* nextflow recipe: added latest stable version * tower-cli recipe: added latest release * recipes tower-agent and tower-cli renamed to nf-tower-agent and nf-tower-cli * recipes nf-tower-agent and nf-tower-cli: small fix * nf-core-tools recipe: added most py- dependencies * nf-core-tools: recipe without galaxy-tool-util (for testing) * fixed typos in py-yacman recipe * fixed typos in py-pytest-workflow recipe * fixed typo in nf-core-tools recipe * fixed typos in py-yacman recipe * fixes in recipes for py-questionary and py-url-normalize * fixes to py-yacman recipe * style fixes to py- packages that are dependencies to nf-core-tools * fix in py-requests-cache recipe * added missing dep in py-requests-cache recipe * nf-core-tools deps: removed redundant python dep for py packages oyaml and piper * nf-core-tools recipe: final, incl dep on py-galaxy-tool-util * nf-core-tools: new version with extra dependency * added py-galaxy-util, draft: added some required dep versions, still have to add 40+ deps * nextflow and nf-core-tools packages: added my self as maintainer * style fixes * style fix for nf-core-tools recipe * added license to py-logmuse recipe * audit fixes * style fix after audit fix * py-galaxy-tool-util: added deps 1st bunch * audit/style fixes, including adding missing dep package * more audit/style fixes * more more audit/style fixes * moooore audit fixes * py-galaxy-tool-util: dependencies 2nd chunk * silly audit fix * py-galaxy-util deps: 3rd bunch - first 20 done * fixes * style fix * py-galaxy-tool-util: 4th bunch of deps * stashing dep recipe backbones for py-galaxy-tool-util * nf-core-tools: using pre-built wheel for dependency py-galaxy-tool-util * nf-core-tools: adding also py-galaxy-util, as wheel * fix * nextflow: added latest bugfix version * Update var/spack/repos/builtin/packages/nf-core-tools/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/nf-core-tools/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * nf-core-tools pr: 1st bunch of review edits * nf-core-tools: 2nd bunch of review edits * adding back tower-agent and tower-cli as deprecated * nf-core-tools: 3rd bunch of review edits * small style fix * prepping py-galaxy-tool-util for further work * nf-core-tools: last bunch of deps, except for galaxy-tool-util and pulsar * audit fixes * updates to py-galaxy-tool-util and its deps, still 2 to work on * one style fix * updated recipe for py-galaxy-util * updated recipe for py-pulsar-galaxy-lib * typo fix * shasum fixes * updated py-sqlalchemy from develop * added newest versions (today) for nf-tower-agent and nf-tower-cli * Update var/spack/repos/builtin/packages/py-requests-cache/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-requests-cache/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * adding 2nd bunch of nf-core deps from update/nextflow-tools * adding 3rd bunch of nf-core deps from update/nextflow-tools * 4th chunk of nf-core deps from update/nextflow-tools * Update var/spack/repos/builtin/packages/py-dnspython/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-dnspython/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-dnspython/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pastedeploy/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pebble/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-fastapi/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-fastapi/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-gunicorn/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-starlette/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-starlette/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-starlette/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-parsley/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-paste/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-paste/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * py-gxformat2: added comment * py-lagom: now using github tarballs * fix for py-lagom * adding missing deps to py-fastapi-utils * another fix to py-lagom * Update var/spack/repos/builtin/packages/py-dnspython/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-lagom/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-supervisor/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-social-auth-core/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * fixes from PR review * adding missing deps, from PR review * py-galaxy2cwl from github tarball, as per PR review * fix to py-tuswsgi, as per PR review * nf-tools: edits from PR review * adding 3x more galaxy deps * fix * fixing circular dep of py-poetry-plugin-export with py-poetry * added newest nf-core-tools version * Update var/spack/repos/builtin/packages/py-galaxy-util/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * fix in py-poetry-plugin-export Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-20file: zstd support (#35041)Harmen Stoppels1-1/+4
2023-01-20libidn2: bump (#35034)Harmen Stoppels1-0/+4
2023-01-19libffi: bump (#35030)Harmen Stoppels1-0/+1
2023-01-19Fix string append in OpenCV package (#35008)Tal Ben-Nun1-3/+5
* Fix string append in OpenCV package * style
2023-01-19qmcpack: enable linking with armpl-gcc and acfl for BLAS and FFT (#34496)Annop Wongwathanarat1-0/+11
2023-01-19libunistring: bump to 1.1 (#35031)Harmen Stoppels1-0/+2
2023-01-19py-pandas: add v1.5.3 (#35025)Adam J. Stewart1-0/+1
2023-01-19nmap: don't depend on py2 (ndiff and zenmap); add 7.93 (#34851)David Zmick1-5/+33
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-01-19file: bump (#35028)Harmen Stoppels1-0/+2
2023-01-19pfunit: fix max_array_rank variant (#34952)fMatthew Thompson1-3/+7
2023-01-19HDF5: supports external detection (#34940)Brian Van Essen1-0/+75
2023-01-19python: remove `CPATH` from `setup_run_environment` (#34727)Todd Gamblin1-3/+0
Currently, the `python` package tries to set `CPATH` in `setup_run_environment()`. We no longer set `CPATH` and other destructive environment variables (like `LD_LIBRARY_PATH`) in modules, so we shouldn't do something special for Python. Also, the way `python` sets `CPATH` causes issues. Because it does a header search to find directories containing headers, if you bootstrap `mypy` or other style tools on a fresh Ubuntu image with *no* python devel headers installed, you'll get an error like this when trying to load the thing you just installed: ```console [root@980de539843d /]# spack -b load py-mypy ==> Error: Unable to locate python headers in any of these locations: /usr/include/python3.6m /usr/include/3.6 /usr/Headers ``` The headers and includes aren't needed to get `mypy` in the path or for `mypy` to work, so we're failing unnecessarily here. - [x] remove `setup_run_environment()` from `python/package.py`
2023-01-19[py-numpy, py-scipy] Enable MKL & ARMpl (#34979)Stephen Sachs2-10/+13
2023-01-19git: bump. CVE-2022-41903 / CVE-2022-23521 (#35014)Harmen Stoppels1-8/+64
Co-Authored-By: Alec Scott <scott112@llnl.gov> Co-authored-by: Alec Scott <scott112@llnl.gov>
2023-01-18hpctoolkit: update cray support (#34995)Mark W. Krentel1-17/+33
1. add variant cray-static, older crays build hpcprof-mpi static, newer ones build dynamic. 2. move URL patches from github to gitlab. 3. add workaround for a bug where a file is mistakenly overwritten. 4. add conflict for hpcprof-mpi at 2022.10.01. * [@spackbot] updating style on behalf of mwkrentel Co-authored-by: mwkrentel <mwkrentel@users.noreply.github.com>
2023-01-18VTK: fix 9.1–9.2 builds (#34589)Adam J. Stewart1-7/+12
* VTK: add missing dependencies * Deal with missing verdict dep * http -> https * Add patch to fix failing cmake * Update netcdf-cxx usage in build recipe * netcdf-cxx4 doesn't work
2023-01-18license year bump (#34921)Harmen Stoppels7148-7169/+7172
* license bump year * fix black issues of modified files * mypy * fix 2021 -> 2023
2023-01-18hdf5@1.8.21 %oneapi@2023.0.0: -Wno-error=int-conversion (#34983)eugeneswalker1-0/+2
2023-01-18npm: Add latest version, update build (#34947)Todd Gamblin1-17/+75
* npm: Add latest version, update build The `npm` package had gotten a bit long in the tooth and only suported the last version for which running `configure` / `make` / `make install` actually worked. - [x] Update the package to support npm@9, in which `npm install .` works properly and installation is easier. - [x] Update the package so that `npm@6:8` also install successfullly. The incantation that is *supposed* to work on these versions is `node bin/npm-cli.js install $(node bin/npm-cli.js pack . | tail -1)`, but depending on the version one of `npm install` or `npm pack` will fail when run straight from the install directory. So now we just manually copies things over. This seems to make the `npm` install much more reliable for all of `npm@6:9` (at least for me). udpates the `npm` build to support versions 6-9 and fixes the install for all of them on macos. * update for review
2023-01-18lammps: enable linking with armpl-gcc FFT (#34980)Annop Wongwathanarat1-0/+6
2023-01-18[armpl-gcc] Make pkg-config files available (#34978)Stephen Sachs1-1/+12
* [armpl-gcc] Make pkg-config files available ARMpl pkgconfig files are located in a non-default location and do not have the .pc extension. Changing those both helps pkgconfig pick them up correctly, e.g. in the meson build of `py-scipy`. * Address @annop-w comments * symlink instead of cp. Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2023-01-18acfl: update hash for 22.1 on RHEL-7 (#34997)Annop Wongwathanarat1-1/+1
2023-01-18py-pytorch-lightning: add v1.9.0 (#34996)Adam J. Stewart2-3/+11
2023-01-18Add tiny profile cmake support (#34993)Nate deVelder1-0/+2
2023-01-17Subclass PythonExtension instead of custom test method (#34985)Adam J. Stewart3-82/+3
2023-01-17py-itk: add version 5.3.0 (#34968)Glenn Johnson1-3/+71
* py-itk: add version 5.3.0 * Remove wheels for unsupported python versions * Fill out the version specs * Drop th 'm' from the cp37 version strings
2023-01-17py-h5py %oneapi@2023.0.0: ↵eugeneswalker1-0/+7
-Wno-error=incompatible-function-pointer-types,pointer-types-discards-qualifiers (#34984)
2023-01-17py-sphinx-immaterial: new package (#34948)Todd Gamblin1-0/+29
* py-sphinx-immaterial: new package This is a new-ish theme for Sphinx that's based on MkDocs's `immaterial` theme. More on the theme here: https://jbms.github.io/sphinx-immaterial/, but it seems to be very clear and readable. We *might* consider switching to it for Spack's docs. * Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * add note about node.js requirements Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-17rempi: patch rempi_message_manager.h: include string (#34982)eugeneswalker2-3/+15
2023-01-17Forward lookup of "test_log_file" and "test_failures" (#34882)Massimiliano Culpo1-2/+4
* Forward lookup of "test_log_file" and "test_failures" refers #34531 closes #34487 fixes #34440 * Add unit test * py-libensemble: fix tests * Support stand-alone tests with cached files as install-time tests Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
2023-01-17cp2k: enable linking with armpl-gcc for BLAS and FFT (#34981)Annop Wongwathanarat1-0/+4
2023-01-17python: 3.11.1, use -flto=thin when clang (#34951)Harmen Stoppels1-1/+6
2023-01-17Bump gnupg & libksba, (CVE) (#34976)Harmen Stoppels2-6/+34
* gnupg: 2.4.0 * libksba: 1.6.3 (CVE-2022-47629)
2023-01-17faiss: fixed error when importing faiss python package (#34672)Loïc Pottier1-1/+7
This is only a work-around for the actual problem that Python is used to install libraries instead of CMake, so we end up with BUILD_RPATH not INSTALL_RPATHs. Signed-off-by: Loïc Pottier <pottier1@llnl.gov> Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-01-17bubblewrap: 0.7.0 (#34975)Harmen Stoppels1-0/+1
2023-01-17perl-file-temp: add 0.2311 (#34866)Christopher Christofi1-0/+15
2023-01-17libcroco: Get the `doc` variant working (#34735)Glenn Johnson1-7/+29
2023-01-17mvapich: add new package in preparation for v3.0 (#34276)MatthewLieber1-0/+293
* Add new file for MVAPICH 3.0a release Creating this as a new package since it requires some new configuration options and because we are moving to the name "MVAPICH" and droping the 2 (following a similar move by MPICH). Co-authored-by: Nat Shineman <shineman.5@osu.edu> Co-authored-by: Matthew Lieber <lieber.31@osu.edu>
2023-01-17flexiblas: add versions up to v3.3.0 (#34874)Ashwin Kumar1-0/+4
2023-01-17New version for openCARP packages, v12.0 (#34710)Marie Houillon3-2/+12
Co-authored-by: openCARP consortium <info@opencarp.org>
2023-01-17mfem: support pumi w/zoltan and parmetis (#34864)Cameron Smith1-1/+14
2023-01-17crtm: overhaul package, add crtm-fix (#34715)Dom Heinzeller2-2/+125
Update crtm from JCSDA-EMC spack fork, add crtm-fix
2023-01-17ncview: bypass compiler check against netcdf-c compiler (#34580)Dom Heinzeller1-9/+10
2023-01-17OpenCV: checksum for 4.5.5, make contrib optional (#34313)iarspider1-5/+11
* OpenCV: checksum for 4.5.5, make contrib optional * [@spackbot] updating style on behalf of iarspider * Add conflicts for contrib modules * Fix typo * Implement changes from review * Update var/spack/repos/builtin/packages/opencv/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: iarspider <iarspider@users.noreply.github.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
generated by cgit v1.2.3-70-g09d2 (git 2.46.0) at 2024-08-27 04:08:50 +0000