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2022-11-11remove activate/deactivate support in favor of environments (#29317)Harmen Stoppels2-129/+1
Environments and environment views have taken over the role of `spack activate/deactivate`, and we should deprecate these commands for several reasons: - Global activation is a really poor idea: - Install prefixes should be immutable; since they can have multiple, unrelated dependents; see below - Added complexity elsewhere: verification of installations, tarballs for build caches, creation of environment views of packages with unrelated extensions "globally activated"... by removing the feature, it gets easier for people to contribute, and we'd end up with fewer bugs due to edge cases. - Environment accomplish the same thing for non-global "activation" i.e. `spack view`, but better. Also we write in the docs: ``` However, Spack global activations have two potential drawbacks: #. Activated packages that involve compiled C extensions may still need their dependencies to be loaded manually. For example, ``spack load openblas`` might be required to make ``py-numpy`` work. #. Global activations "break" a core feature of Spack, which is that multiple versions of a package can co-exist side-by-side. For example, suppose you wish to run a Python package in two different environments but the same basic Python --- one with ``py-numpy@1.7`` and one with ``py-numpy@1.8``. Spack extensions will not support this potential debugging use case. ``` Now that environments are established and views can take over the role of activation non-destructively, we can remove global activation/deactivation.
2022-11-10Fixed a bug where the external HIP library is found in a nested directory, ↵Brian Van Essen1-1/+6
even on newer releases of ROCm. (#33772)
2022-11-11emacs: Add version 28.2 (#33255)Pranith1-0/+1
2022-11-11global: add --with-ncurses with prefix to configure (#33136)Yang Zongze2-5/+18
2022-11-11go-bootstrap: improve error message for Monterey (#31800)Seth R. Johnson1-1/+5
Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
2022-11-10redis-plus-plus: added initial support (#33803)Loïc Pottier1-0/+54
* redis-plus-plus: added initial support * redis-plus-plus: use cmake arg provided by Spack * redis-plus-plus: oups tiny typo Signed-off-by: Loïc Pottier <pottier1@llnl.gov> Signed-off-by: Loïc Pottier <lpottier@arnor> Co-authored-by: Loïc Pottier <lpottier@arnor>
2022-11-11Delete directory with vestigial configuration file (#33825)Massimiliano Culpo1-40/+0
2022-11-10adding sha for 7.0 release (#33823)MatthewLieber1-1/+2
Co-authored-by: Matthew Lieber <lieber.31@osu.edu>
2022-11-10xsdk: deprecate 0.6.0, and remove older deprecated releases (#33815)Satish Balay2-97/+7
xsdk-examples: deprecate @0.2.0, remove @0.1.0 in sync with older xsdk releases
2022-11-10Cran updates (#33819)Glenn Johnson124-14/+333
* add version 1.7-20 to r-ade4 * add version 1.1-13 to r-adephylo * add version 0.3-20 to r-adespatial * add version 1.2-0 to r-afex * add version 0.8-19 to r-amap * add version 0.1.8 to r-aplot * add version 2.0.8 to r-biasedurn * add version 2.4-4 to r-bio3d * add version 1.30.19 to r-biocmanager * add version 1.2-9 to r-brobdingnag * add version 0.4.1 to r-bslib * add version 3.7.3 to r-callr * add version 3.1-1 to r-car * add version 0.3-62 to r-clue * add version 1.2.0 to r-colourpicker * add version 1.8.1 to r-commonmark * add version 0.4.3 to r-cpp11 * add version 1.14.4 to r-data-table * add version 1.34 to r-desolve * add version 2.4.5 to r-devtools * add version 0.6.30 to r-digest * add version 0.26 to r-dt * add version 1.7-12 to r-e1071 * add version 1.8.2 to r-emmeans * add version 1.1.16 to r-exomedepth * add version 0.1-8 to r-expint * add version 0.4.0 to r-fontawesome * add version 1.5-2 to r-fracdiff * add version 1.10.0 to r-future-apply * add version 3.0.1 to r-ggmap * add version 3.4.0 to r-ggplot2 * add version 2.1.0 to r-ggraph * add version 0.6.4 to r-ggsignif * add version 0.6-7 to r-gmp * add version 2022.10-2 to r-gparotation * add version 0.8.3 to r-graphlayouts * add version 1.8.8 to r-grbase * add version 2.1-0 to r-gstat * add version 0.18.6 to r-insight * add version 1.3.1 to r-irkernel * add version 1.8.3 to r-jsonlite * add version 1.7.0 to r-lava * add version 1.1-31 to r-lme4 * add version 5.6.17 to r-lpsolve * add version 5.5.2.0-17.9 to r-lpsolveapi * add version 1.2.9 to r-mapproj * add version 3.4.1 to r-maps * add version 1.1-5 to r-maptools * add version 1.3 to r-markdown * add version 6.0.0 to r-mclust * add version 4.2-2 to r-memuse * add version 1.8-41 to r-mgcv * add version 1.2.5 to r-minqa * add version 0.3.7 to r-nanotime * add version 2.4.1.1 to r-nfactors * add version 3.1-160 to r-nlme * add version 2.7-1 to r-nmof * add version 0.60-16 to r-np * add version 2.0.4 to r-openssl * add version 4.2.5.1 to r-openxlsx * add version 0.3-8 to r-pbdzmq * add version 2.0-3 to r-pcapp * add version 0.7.0 to r-philentropy * add version 2.0.3 to r-pkgcache * add version 1.3.1 to r-pkgload * add version 1.10-4 to r-polyclip * add version 3.8.0 to r-processx * add version 1.7.2 to r-ps * add version 2.12.1 to r-r-utils * add version 1.2.4 to r-ragg * add version 3.7 to r-rainbow * add version 0.0.20 to r-rcppannoy * add version 0.3.3.9.3 to r-rcppeigen * add version 0.3.12 to r-rcppgsl * add version 1.0.2 to r-recipes * add version 1.1.10 to r-rmutil * add version 0.10.24 to r-rmysql * add version 2.4.8 to r-rnexml * add version 4.1.19 to r-rpart * add version 1.7-2 to r-rrcov * add version 0.8.28 to r-rsconnect * add version 0.25 to r-servr * add version 1.7.3 to r-shiny * add version 3.0-0 to r-spatstat-data * add version 3.0-3 to r-spatstat-geom * add version 3.0-1 to r-spatstat-random * add version 3.0-0 to r-spatstat-sparse * add version 3.0-1 to r-spatstat-utils * add version 1.8.0 to r-styler * add version 3.4.1 to r-sys * add version 1.5-2 to r-tclust * add version 0.0.9 to r-tfmpvalue * add version 1.2.0 to r-tidyselect * add version 0.10-52 to r-tseries * add version 4.2.2 to r-v8 * add version 0.5.0 to r-vctrs * add version 2.6-4 to r-vegan * add version 0.7.0 to r-wk * add version 0.34 to r-xfun * add version 1.0.6 to r-xlconnect * add version 3.99-0.12 to r-xml * add version 0.12.2 to r-xts * add version 1.0-33 to r-yaimpute * add version 2.3.6 to r-yaml * add version 2.2.2 to r-zip * add version 2.2-7 to r-deoptim * add version 4.3.1 to r-ergm * add version 0.18 to r-evaluate * add version 1.29.0 to r-future * add version 0.0.8 to r-ggfun * add version 0.9.2 to r-ggrepel * add version 1.9.0 to r-lubridate * add version 4.10.1 to r-plotly * add version 0.2.12 to r-rcppcctz * add version 1.2 to r-rook * add version 1.6-1 to r-segmented * add version 4.2.1 to r-seurat * add version 4.1.3 to r-seuratobject * add version 1.0-9 to r-sf * add version 1.5-1 to r-sp * add version 1.8.1 to r-styler * new package: r-timechange * new package: r-stars * new package: r-sftime * new package: r-spatstat-explore Co-authored-by: glennpj <glennpj@users.noreply.github.com>
2022-11-10pandoc: add version 2.19.2 (#33811)Rémi Lacroix1-0/+9
2022-11-10add utilities and examples variants to conduit (#33804)Chris White1-0/+15
2022-11-10octave: new version 7.3.0 (#33788)Olivier Cessenat1-0/+1
2022-11-10gcc: drop target bootstrap flags for aarch64 (#33813)Harmen Stoppels1-1/+3
See https://github.com/spack/spack/issues/31184 GCC bootstrap logic adds `-mpcu` for libatomic (iirc), which conflicts with the `-march` flag we provide.
2022-11-10elpa: Fix build on ppc64le (#33639)Dave Love1-2/+4
2022-11-10pybind11: v2.10.1 (#33645)Axel Huebl1-1/+2
Add the latest release of pybind11: https://github.com/pybind/pybind11/releases/tag/v2.10.1
2022-11-10py-einops: add v0.6.0 (#33799)Adam J. Stewart1-0/+1
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2022-11-10dcap: add variant ~plugins: Disables the build of plugins (#33524)iarspider1-0/+6
2022-11-10cpu-features: Add variant to enable BUILD_SHARED_LIBS=True (#33809)iarspider1-0/+3
* Allow building shared libraries for cpu-features
2022-11-09py-mpi4py: add version 3.1.4 (#33805)Satish Balay1-0/+1
2022-11-10udunits: Add libs property to recipe to find libudunits2 (#33764)Glenn Johnson1-0/+4
2022-11-10ucx: fix int overflow: use ssize_t (#33784)Harmen Stoppels2-0/+34
2022-11-10New Package: stressapptest (#33736)Saqib Khan1-0/+23
Signed-off-by: saqibkh <saqibkhan@utexas.edu>
2022-11-10New Package: y-cruncher (#33754)Saqib Khan1-0/+25
y-cruncher is a program that can compute Pi and other constants to trillions of digits. Signed-off-by: saqibkh <saqibkhan@utexas.edu>
2022-11-09updates and fixes for libpressio (#33789)Robert Underwood6-2/+77
* updates and fixes for libpressio * differentiate between standalone and build tests * add e4s tags Co-authored-by: Robert Underwood <runderwood@anl.gov>
2022-11-09New package: py-darshan (#33430)Jean Luca Bez1-0/+45
* include py-darshan * include requested changes * fix required versions * fix style * fix style * Update package.py * Update var/spack/repos/builtin/packages/py-darshan/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-11-09Adding libpfm 4.12.0 (#33779)Filippo Spiga1-1/+2
2022-11-09sentieon-genomics: adding version 202112.06 (#33786)snehring1-0/+1
2022-11-09Update package.py (#33787)James Willenbring1-1/+1
Proposing to add myself as a maintainer of the Trilinos Spack package after a related conversation with @kuberry.
2022-11-09Boost: Change comment to conflict for MPI/Python (#33767)kwryankrattiger1-4/+7
Boost 1.64.0 has build errors when building the python and MPI modules. This was previously just a comment in the package.py which allowed broken specs to concretize. The comments are now expressed in conflicts to prevent this.
2022-11-09postgresql: fix weird spack message (#33770)snehring1-1/+1
2022-11-08MFEM: more updates for v4.5 (#33603)Veselin Dobrev3-48/+113
* [mfem] updates related to building with cuda * [hypre] tweak to support building with external ROCm/HIP * [mfem] more tweaks related to building with +rocm * [mfem] temporary (?) workaround for issue #33684 * [mfem] fix style * [mfem] fix +shared+miniapps install
2022-11-08Add checksum for py-protobuf 4.21.7, protobuf 21.7; remove protobuf and ↵iarspider4-175/+59
py-protobuf 2.x (#32977) * Add checksum for py-protobuf 4.21.7, protobuf 21.7 * Update var/spack/repos/builtin/packages/protobuf/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py * Update var/spack/repos/builtin/packages/protobuf/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/protobuf/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py * Update package.py * Delete protoc2.5.0_aarch64.patch * Update package.py * Restore but deprecate py-protobuf 3.0.0a/b; deprecate py-tensorflow 0.x * Fix audit Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-11-08Patch `fmt` for hipcc/dpcpp (#33733)Mikael Simberg1-0/+8
* Patch fmt for hipcc/dpcpp * Add msimberg as fmt maintainer
2022-11-08environment-modules: add version 5.2.0 (#33762)Xavier Delaruelle1-1/+2
2022-11-08hepmc3: new version 3.2.5 (#33748)Wouter Deconinck1-0/+1
Changelog at https://gitlab.cern.ch/hepmc/HepMC3/-/tags/3.2.5 Maintainer: @vvolkl
2022-11-08hypre +rocm: needs explicit rocprim dep (#33745)eugeneswalker1-0/+1
2022-11-08python: 3.11.0 (#33507)Harmen Stoppels3-8/+293
2022-11-08cosma: Add shared option (#33751)Dave Love1-4/+6
2022-11-08gromacs: enable linking with armpl-gcc FFT (#33750)Annop Wongwathanarat1-0/+7
2022-11-08r: fix order of execution for Makeconf filtering (#33752)Massimiliano Culpo1-2/+3
fixes #33747
2022-11-07intel oneapi classic bootstrapping (#31285)Greg Becker3-4/+71
The `intel` compiler at versions > 20 is provided by the `intel-oneapi-compilers-classic` package (a thin wrapper around the `intel-oneapi-compilers` package), and the `oneapi` compiler is provided by the `intel-oneapi-compilers` package. Prior to this work, neither of these compilers could be bootstrapped by Spack as part of an install with `install_missing_compilers: True`. Changes made to make these two packages bootstrappable: 1. The `intel-oneapi-compilers-classic` package includes a bin directory and symlinks to the compiler executables, not just logical pointers in Spack. 2. Spack can look for bootstrapped compilers in directories other than `$prefix/bin`, defined on a per-package basis 3. `intel-oneapi-compilers` specifies a non-default search directory for the compiler executables. 4. The `spack.compilers` module now can make more advanced associations between packages and compilers, not just simple name translations 5. Spack support for lmod hierarchies accounts for differences between package names and the associated compiler names for `intel-oneapi-compilers/oneapi`, `intel-oneapi-compilers-classic/intel@20:`, `llvm+clang/clang`, and `llvm-amdgpu/rocmcc`. - [x] full end-to-end testing - [x] add unit tests
2022-11-07mpich: patch @3.4 to fix checking whether the datatype is contiguous (#33328)Sergey Kosukhin2-1/+144
Co-authored-by: Thomas Jahns <jahns@dkrz.de> Co-authored-by: Thomas Jahns <jahns@dkrz.de>
2022-11-07PyTorch: add v1.13.0 (#33596)Adam J. Stewart7-65/+186
* PyTorch: add v1.13.0 * py-torchaudio: add v0.13.0 * py-torchaudio: add all versions * py-torchvision: jpeg required for all backends * py-torchtext: add v0.14.0 * py-torchtext: fix build * py-torchaudio: fix build * py-torchtext: update version tag * Use Spack-built sox * Explicitly disable sox build * https -> http
2022-11-07Add zstd support for elfutils (#33695)Cédric Chevalier1-0/+4
* Add zstd support for elfutils Not defining `+zstd` implies `--without-zstd` flag to configure. This avoids automatic library detection and thus make the build only depends on Spack installed dependencies. * Use autotools helper "with_or_without" * Revert use of with_or_without Using `with_or_without()` with `variant` keyword does not seem to work.
2022-11-08Fix missing "*.spack*" files in views (#30980)Jordan Galby1-0/+46
All files/dirs containing ".spack" anywhere their name were ignored when generating a spack view. For example, this happened with the 'r' package.
2022-11-072022.3.1 oneAPI release promotion (#33742)akhursev15-0/+95
2022-11-07eckit: fix underlinking (#33739)Sergey Kosukhin1-0/+8
2022-11-07Rust: don't apply constraints to nightly/beta versions (#33723)Adam J. Stewart2-4/+6
2022-11-07quantum-espresso: improve concretization for intel libraries (#33312)Laura Bellentani1-0/+1
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