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2023-01-09openfoam: OneAPI is only supported from 2106 onwards (#34797)Stephen Sachs1-1/+4
Also, adios2 fortran bindings are not necessary. This circumvents https://github.com/spack/spack/issues/31817 Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2023-01-08adding 3rd bunch of nf-core deps from update/nextflow-tools (#34563)Marco De La Pierre17-0/+359
* adding 2nd bunch of nf-core deps from update/nextflow-tools * adding 3rd bunch 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> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-07GDAL: add v3.6.2 (#34823)Adam J. Stewart1-0/+1
2023-01-07acts: new version 22.0.0 (#34826)Wouter Deconinck1-0/+1
No build system changes.
2023-01-06Adding recipes for py-qutip and py-qutip-qip (#34835)Marco De La Pierre2-0/+51
* added recipes for py-qutip and py-qutip-qip * small fix * updated qutip 2x versions * py-qutip-qip: tarball url from github * style fix in py-qutip-qip * Update var/spack/repos/builtin/packages/py-qutip-qip/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-qutip-qip/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-qutip-qip/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-qutip/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-qutip/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-06Adding py-pennylane from Xanadu (#34838)Marco De La Pierre3-0/+80
* draft for py-pennylane recipe * first draft for py-strawberryfields recipe * minimal fix * small fixes * accounting for circular dep in py-pennylane and py-pennylane-lightning * removing py-strawberryfields from this branch * updated versions for py-pennylane 2x * needs cmake * py-pennylane-lightning using github tarball * Update var/spack/repos/builtin/packages/py-autoray/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pennylane-lightning/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-06kripke: add cuda and rocm support (#34257)Verinder Rana1-12/+60
2023-01-06py-instrain and py-drep: new version and added maintainer (#34581)Luke Diorio-Toth2-0/+5
2023-01-06mpiwrapper: New version 2.10.0 (#34795)Erik Schnetter1-0/+2
2023-01-06cni-plugins: New version 1.1.1 (#34809)Erik Schnetter1-0/+1
2023-01-06conmon: New version 2.1.5 (#34810)Erik Schnetter1-0/+1
2023-01-06go-md2man: New version 2.0.2 (#34811)Erik Schnetter1-0/+1
2023-01-06go: New version 1.19.4 (#34812)Erik Schnetter1-0/+1
2023-01-06libseccomp: New version 2.5.4 (#34814)Erik Schnetter1-0/+1
2023-01-06slirp4netns: New version 1.2.0 (#34816)Erik Schnetter1-3/+4
2023-01-06podman: New version 4.3.1 (#34817)Erik Schnetter2-0/+25
2023-01-06mpitrampoline: New version 5.2.0 (#34796)Erik Schnetter1-0/+2
2023-01-06Fix the version number for the fmt dep of pika package (#34839)Auriane R1-2/+2
* Fix the version number for the fmt dep of pika package * Add version constraint for fmt standard specification
2023-01-05cabana: version ranges (#34794)Harmen Stoppels1-1/+1
Co-authored-by: Sam Reeve <6740307+streeve@users.noreply.github.com>
2023-01-05cmake fails with icpc warning (#34774)Stephen Sachs1-0/+7
The Intel compiler isn't able to deal with noinline member functions of template classses defined in headers. As such it outputs ``` warning #2196: routine is both "inline" and "noinline" ``` cmake bootstrap will fail due to the word 'warning'. See spack/var/spack/repos/builtin/packages/protobuf/intel-v2.patch for reference. The issue does not appear with intel@2021.7.0 or later: ``` $~: compiler=/shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-12.2.0/intel-oneapi-compilers-2022.2.0-uqvb2553zy5toeapvoopacndd27x6p5m/compiler/2022.2.0/linux/bin/intel64/icpc $~: $compiler unique.c icpc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message. ``` This is a clean version of https://github.com/spack/spack/pull/34167 Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2023-01-05Typo in `arbor/package.py`: incorrect version (#34820)Brent Huisman1-1/+1
2023-01-04package/libproxy: fix py3 install (#34431)Sinan1-3/+15
* package/libproxy: fix py3 install * improve readability * fix bug * also add extend * make flake happy * [@spackbot] updating style on behalf of Sinan81 * Update var/spack/repos/builtin/packages/libproxy/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * python dependency implied by extends const. * disable python variant by default * add run_env, add py conflict * Update var/spack/repos/builtin/packages/libproxy/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * set env for macos as well * generalize lib dir detection Co-authored-by: sbulut <sbulut@3vgeomatics.com> Co-authored-by: Sinan81 <Sinan81@users.noreply.github.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-04add_new_package: py-file-magic (#34486)Sinan1-0/+18
* add_new_package: py-file-magic * re-order depends... * Update var/spack/repos/builtin/packages/py-file-magic/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * [@spackbot] updating style on behalf of Sinan81 Co-authored-by: sbulut <sbulut@3vgeomatics.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Sinan81 <Sinan81@users.noreply.github.com>
2023-01-04Add py-svgpath and py-trimesh (#34471)Erik Heeren4-0/+111
* Add py-svgpath and dependency * Update copyright expiration * [@spackbot] updating style on behalf of heerener * Process review remarks * Update var/spack/repos/builtin/packages/py-trimesh/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Fix style issue * py-trimesh: cleanup and optional dependencies * Fix formatting issue * py-trimesh: complete dependency list for easy variant Two new packages: py-mapbox-earcut and py-pycollada * Some more missing dependencies Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-04set PREFIX in make() for some packages (#34773)Harmen Stoppels2-2/+4
2023-01-04Fix libvterm and libtermkey packages (#34776)Alberto Invernizzi2-4/+15
* fix PREFIX for both libvterm and libtermkey * minor: use libtool from dependency * switch to command-line prefix instead of replacing it in Makefile
2023-01-03new package: py-kb-python + dependencies (#34737)Glenn Johnson4-0/+119
* new package: py-kb-python + dependencies - py-loompy - py-ngs-tools - py-numpy-groupies * Update var/spack/repos/builtin/packages/py-kb-python/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-03py-shortuuid: add version 1.0.11 (#34739)Glenn Johnson1-2/+5
* py-shortuuid: add version 1.0.11 * Update var/spack/repos/builtin/packages/py-shortuuid/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-03LLVM: Update HWLOC dep version (#34780)kwryankrattiger1-0/+1
2023-01-03jube: Add versions 2.5.0 and 2.5.1 (#34783)Sebastian Grabowski1-0/+12
* jube: Add 2.5.0 and 2.5.1 * jube: Depend on py-pyyaml
2023-01-03Windows: package defaults and MPI detection (#34614)John W. Parent1-4/+9
* Update packages config to indicate that MSVC is the preferred compiler * Update packages config to indicate that msmpi is the preferred MPI provider * Fix msmpi external detection
2023-01-03scr: require spath+mpi (#34775)Harmen Stoppels1-1/+1
It includes `spath_mpi.h` explicitly, and in some concretizations results in a build failure. (Don't ask me why the concretizer picks `spath~mpi`).
2023-01-02gmake: 4.4, remove alpha release (#34709)Harmen Stoppels1-22/+4
2023-01-02votca: add v2022.1 (#34650)Christoph Junghans1-0/+1
2023-01-02pixman: new versions 0.42.0, 0.42.2 (#34723)Wouter Deconinck1-0/+2
This fixes, [among other things](https://lists.freedesktop.org/archives/pixman/2022-October/004993.html), a [bug](https://issuetracker.google.com/issues/249834910) in 0.40.0 that prevents building with oneapi.
2023-01-02py-sphinx: add v6.0.0 (#34724)Adam J. Stewart1-8/+9
2023-01-02libxau: add libs property (#34288)Glenn Johnson1-0/+4
2023-01-02r-affyio: add zlib dependency (#34743)Glenn Johnson1-0/+1
2023-01-02r-cairo: add needed dependency on libxt (#34744)Glenn Johnson1-0/+1
2023-01-02r-hdf5array: add needed dependency on zlib (#34745)Glenn Johnson1-0/+1
2023-01-02r-rhdf5: add needed zlib dependency (#34746)Glenn Johnson1-0/+1
2023-01-02r-rhdf5filters: add needed zlib dependency (#34747)Glenn Johnson1-0/+1
2023-01-02r-rhdf5lib: add needed zlib dependency (#34748)Glenn Johnson1-0/+1
2023-01-02r-rjava: add needed zlib dependency (#34749)Glenn Johnson1-0/+1
2023-01-02r-rtracklayer: add zlib and openssl dependencies (#34750)Glenn Johnson1-0/+2
2023-01-02r-signac: added needed zlib dependency (#34751)Glenn Johnson1-0/+1
2023-01-02bcftools: add version 1.15.1 (#34752)Glenn Johnson1-0/+2
2023-01-02genrich: add needed zlib dependency (#34753)Glenn Johnson1-0/+2
2023-01-02mumax: Set NVCC_CCBIN to spack compiler wrapper (#34754)Glenn Johnson1-0/+1
2023-01-02openscenegraph: add dependency on fontconfig (#34755)Glenn Johnson1-0/+1
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