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2024-09-06Replace `if ... in spec` with `spec.satisfies` in f* and g* packages (#46127)Auriane R.79-280/+280
* Replace if ... in spec with spec.satisfies in f* and g* packages * gromacs: ^amdfftw -> ^[virtuals=fftw-api] amdfftw * flamemaster: add virtuals lapack for the amdlibflame dependency --------- Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
2024-09-06py-pandas: relax build dependencies (#46229)Adam J. Stewart1-5/+5
2024-09-06py-torchgeo: zipfile-deflate64 no longer required (#46233)Adam J. Stewart1-1/+1
2024-09-06Require a newer version of cudnn for cupy (#46248)Robert Underwood0-0/+0
cupy 12 needs a newer version of cudnn as documented here. Supercedes #46128 Co-authored-by: Robert Underwood <runderwood@anl.gov>
2024-09-06Use an HTTP git url for libpressio-opt (#46249)Robert Underwood1-1/+1
superceds #46128 Co-authored-by: Robert Underwood <runderwood@anl.gov>
2024-09-06Mixed-source cflags (#41049)Peter Scheibel8-174/+732
Allow flags from different sources (compilers, `require:`, command-line specs, and `depends_on`) to be merged together, and enforce a consistent order among them. The order is based on the sources, e.g. flags on specs from the command line always come last. Some flag order consistency issues are fixed: 1. Flags from `compilers.yaml` and the command line were always intra- and inter-source order consistent. 2. Flags from dependents and packages.yaml (introduced via `require:`) were not: for `-a -b` from one source and `-c` from another, the final result might rearrange `-a -b`, and would also be inconsistent in terms of whether `-c` came before or after. (1) is/was handled by going back to the original source, i.e., flags are retrieved directly from the command line spec rather than the solver. (2) is addressed by: * Keeping track of grouped flags in the solver * Keeping track of flag sources in the solver on a per-flag basis The latter info is used in this PR to enforce DAG ordering on flags applied from multiple dependents to the same package, e.g., for this graph: ``` a /|\ b | c \|/ d ``` If `a`, `b`, and `c` impose flags on `d`, the combined flags on `d` will contain the flags of `a`, `b`, and `c` -- in that order. Conflicting flags are allowed (e.g. -O2 and -O3). `Spec.satisifes()` has been updated such that X satisfies Y as long as X has *at least* all of the flags that Y has. This is also true in the solver constraints. `.satisfies` does not account for how order can change behavior (so `-O2 -O3` can satisfy `-O3 -O2`); it is expected that this can be addressed later (e.g. by prohibiting flag conflicts). `Spec.constrain` and `.intersects` have been updated to be consistent with this new definition of `.satisfies`.
2024-09-06sleef: add the PIC flag (#46217)Juan Miguel Carceller1-1/+4
2024-09-06pthreadpool: add the PIC flag (#46216)Juan Miguel Carceller1-0/+1
2024-09-06Bootstrap GnuPG and `file` on Windows (#41810)John W. Parent14-90/+243
Spack can now bootstrap two new dependencies on Windows: GnuPG, and file. These dependencies are modeled as a separate package, and they install a cross-compiled binary. Details on how they binaries are built are in https://github.com/spack/windows-bootstrap-resources
2024-09-06fish: use shlex.quote instead of custom quote (#46251)Harmen Stoppels2-115/+88
2024-09-06py-pybind11: add v2.13.0-v2.13.4 and new conflict (#45872)Stephen Nicholas Swatman1-0/+8
This PR adds py-pybind11 versions 2.13.0, 2.13.1, 2.13.2, 2.13.3, and 2.13.4. It also adds a new conflict between gcc 14 and pybind versions up to and including 2.13.1.
2024-09-06db: more type hints (#46242)Harmen Stoppels1-23/+23
2024-09-05Require a newer version of cudnn for cupy (#46247)Robert Underwood1-1/+2
cupy 12 needs a newer version of cudnn as documented here. Supercedes #46128 Co-authored-by: Robert Underwood <runderwood@anl.gov>
2024-09-05Allow deprecating more than one property in config (#46221)Massimiliano Culpo4-58/+70
* Allow deprecating more than one property in config This internal change allows the customization of errors and warnings to be printed when deprecating a property. Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> * fix Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> * Use a list comprehension for "issues" Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> --------- Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2024-09-05Windows: Update pytest with echo and remove others (#45620)Nicole C.12-21/+7
* Windows: Update pytest with echo and remove others * Fix style * Remove unused pytest import in undevelop * Update test_test_part_pass to be Window compatible * Style
2024-09-05py-contourpy: add v1.3.0 (#46225)Adam J. Stewart1-9/+23
2024-09-05expat: Add 2.6.3 with security fixes + deprecate vulnerable 2.6.2 (#46208)Sebastian Pipping1-2/+10
2024-09-05Bug fixes for building py-netcdf4 and py-ruamel-yaml-clib with ↵Dom Heinzeller2-2/+2
apple-clang@15 (#46184) * Fix compiler flags in py-netcdf4 for apple-clang@15: * Fix compiler flags in py-ruamel-yaml-clib for apple-clang@15:
2024-09-05npb: fix mpi rank mismatch errors (#46075)Fernando Ayats1-1/+5
MPI variant has several rank mismatch errors, which are silently ignored. This downgrades the errors to warnings.
2024-09-05PyTorch: update ecosystem (#46220)Adam J. Stewart3-0/+5
2024-09-05awscli-v2: remove upperbound on cryptography (#46222)Adam J. Stewart1-1/+3
2024-09-05py-imageio: add v2.35.1 (#46227)Adam J. Stewart1-0/+1
2024-09-05py-laspy: add v2.3.5 (#46228)Adam J. Stewart1-0/+1
2024-09-05py-pyvista: add v0.44.1 (#46231)Adam J. Stewart1-0/+2
2024-09-05py-tifffile: add v2024 (#46232)Adam J. Stewart1-0/+1
2024-09-05Add when's to some tau dependencies (#46212)Alex Richert1-8/+24
* Add when's to some tau dependencies * [@spackbot] updating style on behalf of AlexanderRichert-NOAA
2024-09-05[rocm-openmp-extras] - Add support for flang-legacy in 6.1.2 (#46130)estewart082-12/+70
* [rocm-openmp-extras] - Add support for flang-legacy in 6.1.2 * [rocm-openmp-extras] - Remove unused variable flang_legacy_dir * [rocm-openmp-extras] - Limit flang-legacy build to 6.1 and newer ROCm versions
2024-09-05PLUMED: Using a C compiler variable (#46082)etiennemlb1-2/+2
* Using a C compiler variable * homogeneity
2024-09-05Avoid best-effort expansion of stacks (#40792)Massimiliano Culpo3-144/+35
fixes #40791 Currently stacks behave differently if used in unify:false environments, which leads to inconsistencies during concretization. For instance, we might have two abstract user specs that do not intersect with each other map to the same concrete spec in the environment. This is clearly wrong. This PR removes the best effort expansion, so that user specs are always applied strictly.
2024-09-05gaudi: Specify boost dependencies explicitly and cleanup package (#46194)Thomas Madlener4-239/+17
* gaudi: Specify boost components and add +fiber for v39 * gaudi: Limit fmt version to allow building master branch * Make boost dependencies a bit more readable * Remove patches for no longer existing versions
2024-09-05reindex: ensure database is empty before reindex (#46199)Harmen Stoppels1-5/+18
fixes two tests that did not clear the in-memory bits of a database before calling reindex.
2024-09-05pika: Add 0.28.0 (#46207)Mikael Simberg2-0/+4
* pika: Add 0.28.0 * Add conflict between pika 0.28.0 and dla-future
2024-09-05Pass Database layout in constructor (#46219)Harmen Stoppels12-117/+96
Ensures that Database instances do not reference a global `spack.store.STORE.layout`. Simplify Database.{add,reindex} signature.
2024-09-05Remove `test_external_package_module` (#46218)Massimiliano Culpo1-14/+0
This test was possibly meant for the Cray platform, and currently is a no-op. Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2024-09-05spack deprecate: deprecate --link-type flag (#46202)Harmen Stoppels2-11/+6
2024-09-04Replace `if ... in spec` with `spec.satisfies` in d* and e* packages (#46126)Auriane R.49-193/+195
* Replace if ... in spec with spec.satisfies in d* and e* packages * Use virtuals for different mpi implementations in esmf * esmf: ^[virtuals=mpi] mpt * extrae: ^[virtuals=mpi] intel-oneapi-mpi --------- Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
2024-09-04libfabric: Add CUDA variant (#46203)Jack Morrison1-1/+4
Signed-off-by: Jack Morrison <jack.morrison@cornelisnetworks.com>
2024-09-04seacas: require +metis and +mpi instead of +parmetis (#46205)mvlopri1-1/+1
This change aligns the build condition for parmetis with the depends_on condition. The current build condition of parmetis looks for "+parmetis" in the spec which is not added by the depends_on as that adds "^parmetis" instead.
2024-09-04py-schema: add v0.7.7 (#46210)Pranav Sivaraman1-1/+4
* py-schema: add v0.7.7 * py-schema: fix when spec Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> --------- Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
2024-09-04boost: Conditionally include/exclude Boost.Json depending on Boost version ↵Mikael Simberg1-0/+3
(#46200)
2024-09-04py-misk: add new package (#46153)Pranav Sivaraman1-0/+21
2024-09-04Added jump package (#46164)Felix Thaler1-0/+23
2024-09-04py-trieregex: new package (#46154)Pranav Sivaraman1-0/+20
* py-trieregex: new package
2024-09-04amrex: add v24.09 (#46171)Weiqun Zhang1-0/+1
2024-09-04rocm-openmp-extras: Avoiding registration of duplicate check-targets and fix ↵renjithravindrankannath2-0/+36
for the failure in hostexec (#45658) * Adding addtional check for omptarget library for amdgpu in nvidia environment * Avoiding registration of duplicate when built on cuda * Adding hsa library path in LD_LIBRARY_PATH * Correction in hsa prefix library path in LD_LIBRARY_PATH
2024-09-04Automated deployment to update package flux-core 2024-09-04 (#46191)Vanessasaurus1-0/+2
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2024-09-04goaccess: new package (#46193)Harmen Stoppels1-0/+25
2024-09-04py-rasterio: add v1.3.11 (#46195)Adam J. Stewart1-22/+28
* py-rasterio: add v1.3.11 * Use default_args
2024-09-04py-fiona: add v1.10.0 (#46196)Adam J. Stewart1-26/+31
2024-09-04py-numpy: add v2.1.1 (#46197)Adam J. Stewart1-0/+1