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2022-12-06Bootstrap most of Spack dependencies using environments (#34029)Massimiliano Culpo5-3/+69
This commit reworks the bootstrapping procedure to use Spack environments as much as possible. The `spack.bootstrap` module has also been reorganized into a Python package. A distinction is made among "core" Spack dependencies (clingo, GnuPG, patchelf) and other dependencies. For a number of reasons, explained in the `spack.bootstrap.core` module docstring, "core" dependencies are bootstrapped with the current ad-hoc method. All the other dependencies are instead bootstrapped using a Spack environment that lives in a directory specific to the interpreter and the architecture being used.
2022-12-05Update packages (#34344)Sam Grayson2-1/+10
2022-12-05graphite2: add dependency on freetype (#34292)Glenn Johnson1-0/+1
2022-12-05berkeleygw: add back python dependencies and tweak testsuite (#34125)Miguel Dias Costa1-5/+28
* slightly raise tolerance of some tests
2022-12-05SWIG: new version 4.1.0 (#34250)Seth R. Johnson2-14/+39
2022-12-05psrcat: fixed typo/undefined variable problem (#34334)downloadico1-1/+1
replaced the reference to the undefined "bindir" variable with prefix.bin
2022-12-05pharokka and py-phanotate: new packages (#34333)Luke Diorio-Toth2-0/+55
* pharokka and py-phanotate: new packages * move libxcrypt edit I don't need libxcrypt when not building dev infernal. Moving to a different PR
2022-12-05jellyfish: add variants for python and ruby bindings (#33832)Bernhard Kaindl1-7/+22
Co-authored-by: teachers-uk-net <stuart.morrison@kcl.ac.uk>
2022-12-05cray-mpich: fix dependencies for externals from manifest (#34231)Peter Scheibel1-0/+3
The cray manifest shows dependency information for cray-mpich, which we never previously cared about because it can only be used as an external. This updates Spack's dependency information to make cray-mpich specs read in from the cray external manifest usable.
2022-12-05redis: newer version and added TLS support (#34230)Loïc Pottier1-1/+33
Signed-off-by: Loïc Pottier <pottier1@llnl.gov> Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-12-05py-nodeenv: add 1.7.0 (#34314)Manuela Kuhn1-0/+2
2022-12-05py-num2words: add 0.5.12 (#34315)Manuela Kuhn1-0/+1
2022-12-05Drop support for older rocm releases - 4.5.0 till 5.0.2 (#34264)Sreenivasa Murthy Kolam46-192/+955
* initial changes for rocm recipes * drop support for older releases * drop support for older rocm releases - add more recipes * drop support for older releases * address style issues * address style error * fix errors * address review comments
2022-12-05Added plumed version 2.8.1 including gromacs compatibility (#34268)Hector Martinez-Seara2-2/+14
* Added plumed version 2.8.1 including gromacs compatibility * Corrected ~mpi and +mpi variants in new depends * Fixed regression logic plumed+gromacs@2020.6 support
2022-12-05LAMMPS: Add new versions (#32522)Richard Berger1-27/+142
* LAMMPS: Add version 20220803 and 20220623.1 * LAMMPS: Add 20220915, 20221103, and 20220623.2
2022-12-05feat(Hermes)!: add yaml-cpp dependency (#34330)H. Joe Lee1-0/+1
The 0.9.0-beta requires yaml-cpp for parsing the configuration file format in YAML. P.S. I'm using https://www.conventionalcommits.org/en/v1.0.0/#specification for this commit message.
2022-12-05Add packages related to the LWA software stack (#34112)downloadico4-0/+171
* epsic: add epsic package to spack * psrcat: add psrcat to spack * psrchive: add psarchive to spack * tempo: add tempo package to spack
2022-12-05clingo: add version 5.6.2 (#34317)Todd Gamblin1-1/+1
See release notes at https://github.com/potassco/clingo/releases/tag/v5.6.2
2022-12-05Add the very first version of cernlib package (#33911)andriish1-0/+28
* Add the very first version of cernlib * Update package.py * Update package.py Co-authored-by: Andrii Verbytskyi <andriish@pcatlas18.mpp.mpg.de>
2022-12-05py-nbclassic: add 0.4.8 and new package py-notebook-shim (#34320)Manuela Kuhn2-2/+46
* py-nbclassic: add 0.4.8 and new package py-notebook-shim * Add missing dependencies
2022-12-05py-llvmlite: add 0.39.1 (#34318)Manuela Kuhn1-0/+2
2022-12-05spectre: add v2022.12.02 (#34277)SXS Bot1-0/+3
Co-authored-by: sxs-bot <sxs-bot@users.noreply.github.com>
2022-12-05Thermo4PFM: new package (#34287)Jean-Luc Fattebert1-0/+19
2022-12-05gurobi: add v10.0.0, v9.5.2 (#34291)Glenn Johnson1-0/+2
2022-12-05freeglut: add dependency on libxxf86vm (#34293)Glenn Johnson1-0/+1
2022-12-05wannier90: gfortran-10 support and libs property (#34278)Glenn Johnson1-0/+10
2022-12-05helics: add v3.3.2 (#34297)HELICS-bot1-0/+1
Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
2022-12-05mmseqs2: new package (#34189)Luke Diorio-Toth1-0/+39
2022-12-05py-torch: fix patching on ppc64le (#34283)Adam J. Stewart1-14/+21
2022-12-05Add conflicts between gcc@12.2.0 and rocblas@5.2.1:5.2.3 (#34217)Auriane R1-0/+4
* Add conflicts with gcc@12.2.0 * Add more links for reference
2022-12-05py-mne: add 1.2.2, 1.2.3 and dependency packages (#34295)Manuela Kuhn3-4/+66
* py-mne: add 1.2.2 and depencendy packages * py-mne: add 1.2.3 * Remove unnecessary when statement
2022-12-04py-torchmetrics: add v0.11.0 (#34220)Adam J. Stewart1-2/+2
2022-12-03py-tensorflow: patch for cuBLAS error (#34279)Glenn Johnson1-0/+13
2022-12-02Use correct method for selecting compiler names. (#34175)wspear1-4/+3
2022-12-02aws-parallelcluster: Add v2.11.9 (#34270)Enrico Usai1-1/+2
2022-12-02doxygen: add build-tools tag (#34249)Seth R. Johnson1-0/+4
* doxygen: add build-tool tag This allows it to be included automatically as an external. No one links against doxygen so this should be ok. * doxygen: add self as maintainer
2022-12-02vecgeom: add new 1.2.1 version (#34240)Ben Morgan1-0/+6
* vecgeom: add new 1.2.1 version * vecgeom: introduce conflict between gcc/cuda Recent tests of vecgeom in Spack environments have shown that the build with +cuda fails with GCC >= 11.3 and CUDA < 11.7 with error ...lib/gcc/x86_64-pc-linux-gnu/11.3.0/include/serializeintrin.h(41): error: identifier "__builtin_ia32_serialize" is undefined 1 error detected in the compilation of ".../VecGeom/source/BVHManager.cu". Other GCC/CUDA combinations appear o.k. Avoid this error in spack, and document it for users, with a conflict directive to express the restriction.
2022-12-02add mochi-margo 0.11.1 point release (#34271)Phil Carns1-0/+1
2022-12-02libvips: adding version 8.13.3 (#34228)snehring1-0/+1
2022-12-02py-alphafold: update to 2.2.4, update dependencies (#33876)Andrew W Elble7-23/+86
* py-alphafold: update to 2.2.4, update dependencies * style
2022-12-02py-nilearn: fix dependency version (#34284)Manuela Kuhn1-1/+1
2022-12-02ROOT: add math/gsl conflict and change version-dependent features to ↵Seth R. Johnson1-10/+7
conditional variants (#34244) * ROOT: add GSL/math dependency * ROOT: use conditional variants instead of conflicts
2022-12-02py-neurokit2: add 0.2.2 (#34267)Manuela Kuhn1-0/+2
2022-12-02feat(Hermes): update version to 0.9.0-beta. (#34243)H. Joe Lee1-3/+3
* feat(Hermes): update version to 0.9.0-beta. This is the latest release. * feat(Hermes): fix checksum. Credit: @tldahlgren
2022-12-02py-keyrings-alt: add 4.2.0 (#34262)Manuela Kuhn1-0/+5
* py-keyrings-alt: add 4.2.0 * Add missing py-jaraco-classes dependency
2022-12-02Add checksum for py-hatchling 1.8.1 (#34260)iarspider1-0/+1
2022-12-01py-flask: add 2.2.2 and fix dependencies for py-werkzeug and py-markupsafe ↵Manuela Kuhn3-5/+13
(#32849) * py-flask: add 2.2.2, py-werkzeug: add 2.2.2, py-markupsafe: add 2.1.1 * Remove py-dataclasses dependency
2022-12-01Herwig3: make njet, vbfnlo dependencies optional... (#33941)iarspider1-8/+17
* Herwig3: make njet, vbfnlo dependencies optional... also drop openloops dependency when building on PowerPC * Update package.py
2022-12-01py-twine: add 4.0.1, py-readme-renderer: add 37.3 (#34203)Manuela Kuhn2-3/+22
* py-twine: add 4.0.1 * Remove py-setuptools as run dependency
2022-12-01acfl: add post-installation check by running examples (#34172)Annop Wongwathanarat1-0/+9