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2023-06-20[mochi-margo] margo version 0.14.0 added (#38473)Matthieu Dorier1-0/+1
2023-06-20[WRF] Always use compiler wrappers for FFLAGS/FCFLAGS (#38470)Stephen Sachs1-12/+3
`FFLAGS` and `FCFLAGS` are being ignored by WRF build system. Not only in version `3.9.1.1`, but also `4.x`. Also, I see no reason to explicitly add `-w` and `-O2` to compile lines when using `gcc@10:`. Tested for version `3.9.1.1`, `4.2.2`, & `4.5.0`. Tagging original authors of this part @MichaelLaufer and @giordano in case they want to chime in.
2023-06-20fastjet: add v3.4.1, update patch (#38467)Valentin Volkl1-1/+8
2023-06-20mpiwrapper: New version 2.10.4 (#38448)Erik Schnetter1-0/+1
2023-06-20mpitrampoline: New version 5.3.1 (#38449)Erik Schnetter1-0/+1
2023-06-20ncbi-rmblastn: switching urls from ftp to https (#38490)snehring1-3/+7
2023-06-20ncbi-rmblastn: patching to support building with %gcc@13: (#38382)George Young2-0/+13
* ncbi-rmblastn: patching to support building with %gcc@13: * ncbi-rmblastn: patching to build with %gcc@13: --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-20py-umi-tools: add 1.1.4, add py-pybktree dependency (#38394)George Young1-2/+2
* py-umi-tools: add 1.1.4, add py-pybktree dependency * remove python spec * Remove `six` dependency --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-20apptainer: adding version 1.1.9 (#38492)snehring1-0/+1
2023-06-20py-pybids: add 0.16.1 (#38480)Manuela Kuhn1-5/+16
2023-06-20root: fix variant detection (#38436)Valentin Volkl1-2/+5
2023-06-19py-pre-commit: add 3.3.3 (#38468)Manuela Kuhn1-11/+16
* py-pre-commit: add 3.3.3 * Update var/spack/repos/builtin/packages/py-pre-commit/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-19py-nodeenv: add 1.8.0 (#38383)Manuela Kuhn1-1/+2
* py-nodeenv: add 1.8.0 * Remove python@3.7 restriction
2023-06-19py-pkginfo: add 1.9.6 (#38434)Manuela Kuhn1-2/+2
* py-pkginfo: add 1.9.6 * Remove py-setuptools as run dependency
2023-06-19gsl: set GSL_ROOT_DIR (#38464)Juan Miguel Carceller1-0/+5
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com> Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-06-19repeatmasker: adding version 4.1.5 (#38445)snehring1-0/+1
2023-06-19py-pooch: add 1.7.0 (#38466)Manuela Kuhn1-3/+11
2023-06-19spdlog: patch for fmt::basic_runtime when ^fmt@10 (#38082)Wouter Deconinck1-0/+7
2023-06-18py-vermin: add latest version 1.5.2 (#38460)Morten Kristensen1-3/+3
* py-vermin: add latest version 1.5.2 * Removed obsolete dep and setuptools is only for build-time - setuptools are not used as runtime - py27 isn't strictly necessary
2023-06-17Add latest enzyme release (#38442)William Moses1-3/+5
2023-06-16py-aiohttp: add 3.8.4 (#38451)Manuela Kuhn1-15/+18
2023-06-16millepede: add v04-13-03 (#38141)Alec Scott1-0/+1
2023-06-16WarpX 23.06 (#38303)Axel Huebl3-24/+61
* WarpX 23.06 Update WarpX and related Python packages to the lastest releases. WarpX 23.06 introduces multi-dimension support in a single package, which will ease deployment in E4S et al. that can ship now a single, full-feature module/package that is NOT incompatible with itself anymore. * e4s ci stacks: multiple specs for each dim variant no longer required * [@spackbot] updating style on behalf of ax3l * WarpX: Update CMake CLI and Test/Check * Add Missing `build-directory` * [@spackbot] updating style on behalf of ax3l * Remove `build_directory` again --------- Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com> Co-authored-by: ax3l <ax3l@users.noreply.github.com>
2023-06-15Remove experimental hdf5 versions 1.13.x and add hdf5 version 1.10.10. (#38013)Larry Knox5-12/+8
* Remove experimental hdf5 versions 1.13.x. Upgrade to 1.14 or remove dependencies on hdf5 1.13.x. * Revert change to netcdf-c/package.py.
2023-06-15star: add 2.7.10 (#38197)George Young1-4/+15
* star: add 2.7.10 * star: fix building for non-avx2 arch processors * convert to MakefilePackage, second take at fixing for aarch64 * style --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-15perl-gd: update to 2.77, update urls (#38413)George Young1-1/+9
* perl-gd: update to 2.77, update urls --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-15MXNet: fix flag versions (#38402)Adam J. Stewart1-2/+2
2023-06-15Create package.py file for NIMROD abstract accelerated infrastructure. (#38405)Jacob King1-0/+58
Co-authored-by: jacobrking <jacobrking@users.noreply.github.com>
2023-06-15py-nibabel: add 5.1.0 (#38379)Manuela Kuhn1-2/+12
2023-06-15podio: Add py-tabulate as new run and test dependency (#38409)Thomas Madlener1-0/+1
2023-06-15py-numba: add 0.57.0, update dependency ranges (#38390)George Young1-5/+7
* py-numba: add 0.57.0, update dependency ranges * Update var/spack/repos/builtin/packages/py-numba/package.py Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com> * Update var/spack/repos/builtin/packages/py-numba/package.py Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com> * Update package.py --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
2023-06-15py-datalad: add 0.18.4 (#37936)Manuela Kuhn1-1/+3
2023-06-15tests/py-horovod: convert to new stand-alone test process (#38366)Tamara Dahlgren1-3/+4
2023-06-15tests/py-libensemble: convert to new stand-alone test process (#38344)Tamara Dahlgren1-20/+16
2023-06-15tests/py-eccodes: convert to new stand-alone test process (#38346)Tamara Dahlgren1-9/+4
2023-06-15py-neurora: add 1.1.6.10 (#38378)Manuela Kuhn1-0/+1
2023-06-14test/dust: convert to new stand-alone test process (#38367)Tamara Dahlgren1-9/+5
2023-06-14py-nbclient: add 0.8.0 (#38325)Manuela Kuhn1-1/+3
2023-06-14py-nbconvert: add 7.4.0 (#38326)Manuela Kuhn1-19/+20
* py-nbconvert: add 7.4.0 * Move historical dependencies after variant
2023-06-14py-docutils: re-add python@3.7 (#38336)Manuela Kuhn1-0/+1
2023-06-14magma@master: add python dependency (#38341)Satish Balay1-0/+1
2023-06-14edm4hep: Add version 0.9 (#38205)Thomas Madlener1-0/+1
2023-06-14fairmq: Add v1.6.0 (#38392)Dennis Klein1-0/+7
2023-06-14ltp: add v20230516 (#38138)Alec Scott1-0/+1
2023-06-14subread: add 2.0.6, update download paths (#38200)George Young1-4/+4
* subread: add 2.0.6, update download paths * Update var/spack/repos/builtin/packages/subread/package.py --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-06-14openradioss-starter,engine: new package (#38291)kjrstory2-0/+256
* openradioss-starter,engine: new package * openradioss-engine: change version name develop to main * openradioss-starter: change version name develop to main
2023-06-14freeipmi: add v1.6.9 (#38349)Alec Scott1-0/+1
2023-06-14Add Binder spackage (#38371)Kim Liegeois1-0/+54
* Add Binder spackage * Format binder recipe * Format binder recipe
2023-06-14add bioconductor-ebseq (#38380)pabloaledo1-0/+29
* add buiconductor-ebseq Signed-off-by: Pablo <pablo.aledo@seqera.io> --------- Signed-off-by: Pablo <pablo.aledo@seqera.io>
2023-06-14ctffind: Add a patch to fix incorrect return types. (#38085)Rémi Lacroix2-0/+35
Prevent the code from crashing (cf. https://grigoriefflab.umassmed.edu/comment/1696#comment-1696).
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