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2022-10-08new packages (py-metaphlan, py-hclust2, iqtree2) + updates to others ↵Luke Diorio-Toth6-15/+108
(py-dendropy, py-phylophlan, py-pkgconfig) (#32936) * added metaphlan v4, cleaned up phylophlan * added iqtree2 * fixed phylophlan, builds now * changed config.yaml to default * fixed style * py-jsonschema: add 4.16.0 and new package py-hatch-fancy-pypi-readme (#32929) * acfl: add v22.1 (#32915) Co-authored-by: Annop Wongwathanarat <annop.wongwathanarat@arm.com> * Fixup errors introduced by Clingo Pr: (#32905) * re2c depends on cmake on Windows * Winbison properly added to bootstrap package search list * Set CMAKE_HIP_ARCHITECTURES with the value of amdgpu_target (#32901) * libtiff: default to +zlib+jpeg (#32945) * octave: add version 7.2.0 (#32943) * simgrid new releases (#32920) * [rocksdb] Added rtti variant (#32918) * rvs binary path updated for 5.2 rocm release (#32892) * Add checksum for py-pytest-runner 6.0.0 (#32957) * py-einops: add v0.5.0 (#32959) * Replace repo with the NVIDIA one (#32951) * Add checksum for py-tomli 2.0.1 (#32949) * QMCPACK: add @3.15.0 (#32931) * Tidied up configure arguments to use special spack autotools features. (#32930) * casper: old domain fell off, adding github repo (#32928) * unifyfs: pin mercury version; add boost variant (#32911) Mercury has a new version (v2.2) releasing soon that UnifyFS does not build with and hasn't been tested with. This pins UnifyFS to the last version of Mercury used/tested. Add a variant to avoid building/using boost Append -std=gnu99 to cflags if building with gcc@4. Needed for mochi-margo to compile * trilinos: constrain superlu-dist version (#32889) * trilinos: constrain superlu-dist version for 13.x * syntax * FEniCSx: Updates for 0.5.1 (#32665) * Updates for DOLFINx 0.5.1 and associated packages * xtensor needed on anything less than main * Switch back to Python 3.7 minimum. * Might be good to point out in our README how to fix Python version? * Fix basix, xtensor dep * Add numba feature * Fix checksum * Make slepc optional Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> * simgrid: add variant and remove flag (#32797) * simgrid: remove std c++11 flag * simgrid: add msg variant * Axom: bring in changes from axom repo (#32643) * bring in changes from axom repo Co-authored-by: white238 <white238@users.noreply.github.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> * Add checksum for py-pyparsing 3.0.9 (#32952) * rdma-core: fix syntax for external discoverability (#32962) * Add checksum for py-flatbuffers 2.0.7 (#32955) * amrex: add v22.10 (#32966) * Remove CMakePackage.define alias from most packages (#32950) * Bug fix for `ca-certificates-mozilla/package.py` to enable `spack install --source` (#32953) * made suggested changes to iqtree2, py-dendropy, py-metaphlan, and py-pkgconfig. Poetry install still broken * reverted py-pkgconfig deps to poetry-core * made iqtree2 less dedundant, changes to py-dendropy and py-pkgconfig deps Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com> Co-authored-by: Annop Wongwathanarat <annop.wongwathanarat@gmail.com> Co-authored-by: Annop Wongwathanarat <annop.wongwathanarat@arm.com> Co-authored-by: John W. Parent <45471568+johnwparent@users.noreply.github.com> Co-authored-by: Auriane R <48684432+aurianer@users.noreply.github.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Kai Torben Ohlhus <k.ohlhus@gmail.com> Co-authored-by: Vinícius <viniciusvgp@gmail.com> Co-authored-by: Matthieu Dorier <mdorier@anl.gov> Co-authored-by: renjithravindrankannath <94420380+renjithravindrankannath@users.noreply.github.com> Co-authored-by: iarspider <iarspider@gmail.com> Co-authored-by: Paul R. C. Kent <kentpr@ornl.gov> Co-authored-by: Brian Van Essen <vanessen1@llnl.gov> Co-authored-by: snehring <7978778+snehring@users.noreply.github.com> Co-authored-by: Cameron Stanavige <stanavige1@llnl.gov> Co-authored-by: Cody Balos <balos1@llnl.gov> Co-authored-by: Jack S. Hale <mail@jackhale.co.uk> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Co-authored-by: Lucas Nesi <lucas31nesi@hotmail.com> Co-authored-by: Chris White <white238@llnl.gov> Co-authored-by: white238 <white238@users.noreply.github.com> Co-authored-by: Martin Pokorny <mpokorny@caltech.edu> Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov> Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>
2022-10-08New package: py-qudida (#33115)Jen Herting1-0/+24
* [py-qudida] New package * [@spackbot] updating style on behalf of qwertos Co-authored-by: qwertos <qwertos@users.noreply.github.com>
2022-10-08py-blis: fix environment settings (#32913)Qian Jianhua1-0/+4
2022-10-07Add checksum for py-jupyterlab-pygments 0.2.2 (#33081)iarspider1-1/+5
2022-10-07remove outdated comments (#33123)eugeneswalker1-8/+6
2022-10-07Add checksum for py-jupyter-core 4.11.1 (#33086)iarspider1-1/+4
2022-10-07autotools: extend patching of the libtool script (#30768)Sergey Kosukhin4-34/+208
* filter_file: introduce argument 'start_at' * autotools: extend patching of the libtool script * autotools: refactor _patch_usr_bin_file * autotools: improve readability of the filtering * autotools: keep the modification time of the configure scripts * autotools: do not try to patch directories * autotools: explain libtool patching for posterity Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2022-10-07Add checksum for py-nbclient 0.6.7 (#33083)iarspider1-0/+1
2022-10-07e4s ci: add variorum (#33113)eugeneswalker1-1/+1
2022-10-07e4s ci: add h5bench (#33114)eugeneswalker1-1/+1
2022-10-07[brotli] added version 1.0.9 (#33107)Jen Herting1-0/+1
2022-10-07New package: py-pathml (#32566)Jen Herting1-0/+34
* [py-pathml Farber] Created package * [pathml Farber] Dependencies added * [py-pathml] Corrected dependency * [py-pathml] Added types * [py-pathml] depends on py-h5py * [py-pathml] py-opencv-contrib-python -> opencv+python3+contrib * [py-pathml] added spack import and fixed setuptools type * [py-pathml] update import * [py-pathml] opencv no longer has +contrib * [@spackbot] updating style on behalf of qwertos Co-authored-by: James A Zilberman <jazrc@rit.edu> Co-authored-by: qwertos <qwertos@users.noreply.github.com>
2022-10-07fixed and added mrnet versions (#33120)Gregory Lee1-1/+3
2022-10-07Add checksum for py-onnxmltools 1.11.0 (#33104)iarspider3-0/+44
* Add checksum for py-onnxmltools 1.11.0 * Add checksum for py-onnxmltools 1.11.0 * Fix patch name * Update var/spack/repos/builtin/packages/py-onnx-runtime/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-10-07Add checksum for py-pkginfo 1.8.3 (#33094)iarspider1-0/+2
* Add checksum for py-pkginfo 1.8.3 * Update var/spack/repos/builtin/packages/py-pkginfo/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-10-07Add checksum for py-markdown 3.4.1 (#33098)iarspider1-7/+10
* Add checksum for py-markdown 3.4.1 * Update package.py
2022-10-07pythia6: set CMAKE_MACOSX_RPATH=True to build on macos (#33082)Laurent Aphecetche1-0/+2
2022-10-07Add checksum for py-pathlib2 2.3.7.poast1 (#33105)iarspider1-0/+4
* Add checksum for py-pathlib2 2.3.7.poast1 * [@spackbot] updating style on behalf of iarspider Co-authored-by: iarspider <iarspider@users.noreply.github.com>
2022-10-07Add checksum for py-python-ldap 3.4.2 (#33106)iarspider1-0/+2
2022-10-07Add checksum for py-networkx 2.8.6, py-pygraphviz 1.10 (#33102)iarspider2-8/+27
* Add checksum for py-networkx 2.8.6, py-pygraphviz 1.10 * [@spackbot] updating style on behalf of iarspider Co-authored-by: iarspider <iarspider@users.noreply.github.com>
2022-10-07Add checksum for py-mplhep 0.3.26 (#33101)iarspider1-1/+4
2022-10-07Add checksum for py-more-itertools 8.14.0 (#33100)iarspider1-1/+3
2022-10-07Add checksum for py-lz4 4.0.2 (#33097)iarspider1-0/+4
2022-10-07Add checksum for py-llvmlite 0.38.1 (#33096)iarspider1-0/+1
2022-10-07Add checksum for py-jupyter-console 6.4.4 (#33088)iarspider1-0/+2
2022-10-07Add checksum for py-jsonpickle 2.2.0 (#33087)iarspider1-0/+1
2022-10-07py-black: add v22.10.0 (#33077)Adam J. Stewart1-10/+12
2022-10-07e4s ci: add quantum-espresso (#33075)eugeneswalker1-0/+1
2022-10-07Rename p2300 to stdexec (#33099)Auriane R2-2/+2
* Rename p2300 package after renaming PR merged in stdexec https://github.com/NVIDIA/stdexec/pull/622 * Adapt pika to depend on stdexec
2022-10-07trilinos and xyce: fix fortran library handling (#33033)Paul Kuberry2-37/+84
* trilinos and xyce: fix fortran library handling xyce: - add pymi_static_blas variant and logic handles blas and hdf5 conflicts for Xyce-PyMi - make +isorropia and +zoltan conditional on mpi * xyce: clean up CMake options * xyce: change pymi_static_blas to pymi_static_tpls * xyce: made pymi_static_tpls only when +pymi
2022-10-07Add checksum for py-tornado 6.2, py-pyzmq 24.0.1, py-jupyter-client 7.3.5 ↵iarspider3-10/+22
(#33062)
2022-10-06geant3: new package (#33065)Laurent Aphecetche1-0/+43
* geant3: new package * fix copyright
2022-10-07add compatibility for rocky8 and rhel8 (#33068)MatthewLieber1-0/+3
2022-10-06oommf: update oommf package to version 2.0b0 (#33072)Hans Fangohr1-0/+10
- Official release mentioned on https://math.nist.gov/oommf/software-20.html - Tested at https://github.com/fangohr/oommf-in-spack/pull/39/files
2022-10-06cppgsl: add version 4.0.0 (#33060)Laurent Aphecetche1-0/+1
2022-10-06phist: add patch to resolve build issue #32111 with +fortran %oneapi (#32965)Jonas Thies2-1/+96
* phist: add patch to resolve build issue #32111 with +fortran %oneapi * phist: some lines of code were patched twice, make these patches orthogonal.
2022-10-06Add a warning on Python 2.7 deprecation (#33052)Massimiliano Culpo2-0/+9
Co-authored-by: alalazo <alalazo@users.noreply.github.com> Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2022-10-06ncbi-toolkit: adding version 26_0_1 (#33061)snehring1-0/+15
2022-10-06tcl module template: automatically unload automatically loaded modules (#32853)Sergey Kosukhin2-2/+2
Remove `module-info mode load` condition that prevents auto-unloading when autoloading is enabled. It looks like this condition was added to work around an issue in environment-modules that is no longer necessary. Add quotes to make is-loaded happy
2022-10-06Add checksum for py-executing 1.0.0 (#33059)iarspider1-0/+1
2022-10-06Add checksum for py-histogrammar 1.0.31 (#33045)iarspider1-0/+3
2022-10-06Add checksum for py-uhi 0.3.1 (#33043)iarspider1-1/+3
2022-10-06Add checksum for py-tqdm 4.64.1 (#33046)iarspider1-0/+1
2022-10-06Add checksum for py-zipp@3.8.1 (#33048)iarspider1-0/+2
2022-10-06Update py stack data (#33051)iarspider1-0/+1
* Add checksum for py-traitlets 5.3.0 * Add checksum for py-stack-data 0.5.0 * Remove extra file
2022-10-06geant4-vmc: unset MACOSX_DEPLOYMENT_TARGET (#32828)Laurent Aphecetche1-0/+4
2022-10-06ncl: enable building with recent versions of hdf5 (#32842)Sergey Kosukhin3-38/+32
2022-10-06Add checksum for py-urllib3 1.26.12 (#33019)iarspider2-0/+20
* Add checksum for py-urllib3 1.26.12 * Update var/spack/repos/builtin/packages/py-urllib3/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Fixes from review Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-10-06gmake: add 4.3.90 alpha release (#33044)Harmen Stoppels1-14/+26
GNU Make 4.3.90 supports jobserver through fifo, so it's nice to add the alpha release to Spack already.
2022-10-06py-docutils: add 0.19 (#32814)Manuela Kuhn1-1/+3
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