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2023-02-01fastqc: Use the spack built perl (#35276)Glenn Johnson1-8/+3
The fastqc script was using the system perl. This PR sets the script to use the spack built/provided perl. This PR also removes the code that adds the java path. That should be handled by module loading as far as I know.
2023-02-01Add hdf5 versions 1.14.0, develop-1.14 and update develop version from ↵Larry Knox4-14/+58
develop-1.13 to develop-1.15 (#34734) * Add HDF5 version 1.13.3. * Remove maintainers no longer with The HDFGroup. * Add version hdf5-vol-async@1.4 * Add HDF5 version 1.14.0, develop-1.14, develop-1.15. Add missing conflicts for api version and develop versions. * Add conflicts statement to hdf5/package.py to avoid building hdf5 with MPICH 4.0.x versions with bug that causes testphdf5 test to fail. * Add patch to call find_package(MPI) for dependent packages not finding it, not having called it themselves. * Remove language components from find_package(MPI) in hdf5_1_14_0_config_find_mpi.patch. * Add HDF5 version 1.14.0, develop-1.14, develop-1.15. Add missing conflicts for api version and develop versions. * Add conflicts statement to hdf5/package.py to avoid building hdf5 with MPICH 4.0.x versions with bug that causes testphdf5 test to fail. * Add patch to call find_package(MPI) for dependent packages not finding it, not having called it themselves. * Remove language components from find_package(MPI) in hdf5_1_14_0_config_find_mpi.patch. * Don't guard ParaView patch on HDF5 variant ParaView always needsd HDF5 and ignores the variant. * py-h5py: Newer versions of HDF5 introduce breaking API changes --------- Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
2023-02-01Pin black to 22.12.0 to avoid spurious style changes (#35282)Massimiliano Culpo2-2/+2
We need to sync changes on major versions with spackbot, to avoid the bot saying everything is allright and have CI failing nonetheless.
2023-02-01py-equation: new package (#35198)Erik Heeren1-0/+23
* py-equation: new package * py-equation: add variants for extra dependencies
2023-01-31`nccl`: v2.15.5-1, v2.16.2-1 (#35248)Thomas Bouvier1-0/+2
* `nccl`: v2.15.5-1, v2.16.2-1 * Fix wrong sha256 * Revert checksums (after GitHub has algorithm change reverted)
2023-01-31libffi: New version 3.4.4 (#35087)Erik Schnetter1-0/+1
2023-01-31Revert "flex%oneapi@2023.0.0: -Wno-error=implicit-function-declaration ↵eugeneswalker1-4/+0
(#34900)" (#35181) This reverts commit 62f83dfb6dbc86eace56495aa59587ac1942dc20.
2023-01-31Adding rocm-opencl prefix lib path to LD_LIBRARY_PATH for run_environment ↵renjithravindrankannath1-0/+1
(#35011)
2023-01-31Fix awscli and deps (#35158)Harmen Stoppels4-7/+27
* py-docutils/py-pyyaml specify python 3.11 compat * bump awscli / py-botocore * fix botocore again * review fixes * .
2023-01-31Add trilinos-solvers variant to nalu-wind package. (#35267)Alan Williams1-2/+9
* Add trilinos-solvers variant to nalu-wind package. This allows nalu-wind to be built against a trilinos installation which doesn't have amesos2, belos, ifpack2, or muelu enabled, if the nalu-wind user provides the spec 'nalu-wind@master~trilinos-solvers' Support for these solver-packages remains on by default. * Fixed a style issue reported by CI. * Incorporate change in wording suggested from review comments. ... to clarify that at least one, or both, of hypre and/or trilinos-solvers must be enabled. The error condition is if both are disabled. * That style checker is picky... * It really did want a trailing comma...
2023-01-31py-munkres: new package (#35259)Erik Heeren1-0/+19
2023-01-31strumpack +rocm: set CMAKE_CXX_COMPILER to hipcc (#35153)eugeneswalker2-0/+30
* strumpack +rocm: set CMAKE_CXX_COMPILER to hipcc * strumpack@7.0.1+rocm^mpich: patch in upstream commit
2023-01-31py-matplotlibscalebar: new package (#35242)Erik Heeren1-0/+24
* py-matplotlibscalebar: new package * py-matplotlibscalebar: style * py-matplotlib-scalebar: review remarks
2023-01-31py-jinja2-cli: new package (#35238)Erik Heeren1-0/+20
* py-jinja2-cli: new package * Update var/spack/repos/builtin/packages/py-jinja2-cli/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-30[py-protoc-gen-swagger] new package (#35241)Jen Herting1-0/+18
* [py-protoc-gen-swagger] new package * [@spackbot] updating style on behalf of qwertos --------- Co-authored-by: qwertos <qwertos@users.noreply.github.com>
2023-01-30Update `py-docker` package (#35217)Jean-Baptiste Skutnik1-2/+13
* Add py-docker@5: * [@spackbot] updating style on behalf of spoutn1k * Ignore `tls` variant * Update var/spack/repos/builtin/packages/py-docker/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * `py-docker`: `py-paramiko` version fix --------- Co-authored-by: spoutn1k <spoutn1k@users.noreply.github.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-30arm-forge: add 22.1.3 (#35200)kent-cheung-arm1-0/+9
2023-01-30py-fiona: add v1.9.0 (#35247)Adam J. Stewart2-12/+21
2023-01-30HDF5 static (#34577)Alex Richert1-2/+0
* Add HDF5 static support for netcdf-c * Update var/spack/repos/builtin/packages/hdf5/package.py Apply pkgconfig fix for all libraries, not just lz Co-authored-by: Sergey Kosukhin <skosukhin@gmail.com> * Update package.py Fix pkg config templates * remove subprocess+2 lines * Try netcdf-c changes only Co-authored-by: Sergey Kosukhin <skosukhin@gmail.com>
2023-01-30py-torchgeo: add v0.4.0 (#35155)Adam J. Stewart2-18/+37
* py-torchgeo: add v0.4.0 * Add missing java dep
2023-01-30py-protobuf: various updates (#35188)Adam J. Stewart2-18/+4
2023-01-30py-shapely: add v2.0.1 (#35246)Adam J. Stewart1-7/+8
2023-01-30py-mariadb: new package (#35240)Erik Heeren1-0/+26
* py-mariadb: new package * py-mariadb: style
2023-01-30py-hjson: fix typo in latest version (#35234)Erik Heeren1-1/+1
2023-01-30Bugfix: Update Petsc Python dependency (#35216)Tamara Dahlgren1-1/+3
* Bugfix: Update Petsc python dependency for at least 3.18: * Update var/spack/repos/builtin/packages/petsc/package.py Co-authored-by: Satish Balay <balay@mcs.anl.gov>
2023-01-30e4s: add and prefer boost +python +filesystem +iostreams +system (#35180)eugeneswalker1-0/+3
2023-01-30rocblas: remove unnecessary conflicts (#35232)Cory Bloor1-2/+0
The gfx906:xnack- and gfx908:xnack- targets were introduced in ROCm 4.1 and replaced gfx906 and gfx908 as default build targets, but the library can still be built for gfx906 and gfx908 if requested.
2023-01-30mpich: add 4.0.3 and 4.1 releases (#35218)Ken Raffenetti1-0/+2
2023-01-30montage: fixing compilation issues for newer gcc versions (#35220)snehring1-0/+7
2023-01-30apptainer: update constraint on go dependency (#35230)simonleary-umass-edu1-0/+2
2023-01-30hypre: Update URL using citation instructions from ↵Satish Balay1-3/+1
https://github.com/hypre-space/hypre/wiki/Citing-hypre (#35225)
2023-01-30adios2: allow building on Windows (#35102)John W. Parent1-6/+17
2023-01-30OmpSs: add v2022.11 (#35228)aleixrocks1-5/+13
2023-01-29e4s oneapi: use oneapi@2023.0.0 (#34634)eugeneswalker3-83/+104
2023-01-29gmake: Fix too many levels of symbolic links error (#35224)Alec Scott1-0/+3
* gedit: Fix too many levels of symlinks error * Fix package formatting with black
2023-01-29e4s: add power stack (#32710)eugeneswalker3-317/+477
* e4s: restore builds builds * gitlab ci: allow UO to build protected binaries for signing * use newer image; comment out failing builds * gitlab-ci: Some tweaks for e4s power builds - fix tags (no longer require generate jobs to run on aws) - fix resource requests for generation jobs resource requests - remove SPACK_SIGNING_KEY from protected power build jobs - update UO signing key path - change the CDash build group to reflect stack name - retry pipeline generation jobs *always* * correct double packages: section * gitlab-ci:script: modernize * remove new gnu make, not for ppc64le --------- Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
2023-01-28freetype: add CMake support (#35107)John W. Parent1-2/+20
2023-01-28xz: add 5.4.1 and 5.2.10 (#35172)Michael Kuhn1-0/+2
2023-01-27Added newer versions of PyAMG and added dependencies for 4.2 and later. (#35185)Ben Cowan1-4/+8
* Added newer versions of PyAMG and added dependencies for 4.2 and later. * Fixed dependencies.
2023-01-27New Spack package: Palace (#35189)Sebastian Grimberg1-0/+120
2023-01-27Added e4s-cl package (#35117)Jean-Baptiste Skutnik7-1/+95
* Added e4s-cl package * Version order change * Added e4s-cl dependencies * Added python-sotools dependency * [@spackbot] updating style on behalf of spoutn1k * Add missing versions to py- packages * Fix style * [@spackbot] updating style on behalf of spoutn1k * Update var/spack/repos/builtin/packages/e4s-cl/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/e4s-cl/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-python-sotools/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Add docker removing patch for e4s-cl Co-authored-by: spoutn1k <spoutn1k@users.noreply.github.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-27py-nexusforge: add with dependencies (#35208)Erik Heeren9-3/+187
* py-nexusforge: add with dependencies * py-pyshacl, py-sseclient: more style * py-hjson, py-nexus-sdk, py-nexusforge, py-puremagic: more style * py-pyshacl: license update * py-nexusforge, py-prettytable, py-pyshacl: review remarks * py-nexusforge: make the variant mean something Too hasty to commit...
2023-01-27Py ipyparallel (#35178)Erik Heeren1-3/+4
* py-ipyparallel: add 8.4.1, which builds with py-hatchling * py-ipyparallel: copyright and redundant py-setuptools dependency * py-ipyparallel: py-packaging was dropped after 8.0.0
2023-01-27New patch release SLEPc 3.18.2 (#35176)Jose E. Roman2-1/+3
2023-01-27libblastrampoline: Add v5.3.0 and v5.4.0 (#35194)Mosè Giordano1-0/+2
2023-01-27Add a `maintainers` directive (#35083)Massimiliano Culpo9-27/+114
fixes #34879 This commit adds a new maintainer directive, which by default extend the list of maintainers for a given package. The directive is backward compatible with the current practice of having a "maintainers" list declared at the class level.
2023-01-26py-nptyping, py-typish: add package (#35126)Erik Heeren2-0/+42
* py-typish: add package * py-typish: style fix * py-nptyping: new package * py-nptyping, py-typish: review remarks * py-nptying: style * py-nptyping: generic url, avoid pypi for now
2023-01-26py-deap: add 1.3.3 (#35175)Erik Heeren1-0/+1
2023-01-26py-rasterio: add v1.3.5 (#35167)Adam J. Stewart1-0/+1
2023-01-26Cleanup of binary text relocation (#34188)Harmen Stoppels8-484/+561
Move the relocation of binary text in its own class Drop threaded text replacement, since the current bottleneck is decompression. It would be better to parallellize over packages, instead of over files per package. A small improvement with separate classes for text replacement is that we now compile the regex in the constructor; previously it was compiled per binary to be relocated.
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