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2022-11-11docs: updates related to extensions (#33837)Harmen Stoppels4-44/+78
2022-11-11Update CHANGELOG.md for v0.19.0Todd Gamblin1-3/+271
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2022-11-11Update SECURITY.md for v0.19Todd Gamblin1-2/+2
2022-11-11Version is now v0.19.0.Todd Gamblin1-1/+1
2022-11-11remove activate/deactivate support in favor of environments (#29317)Harmen Stoppels24-1708/+34
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.
2022-11-10remove deprecated top-level module config (#33828)Greg Becker3-66/+2
* remove deprecated top-level module config per deprecation in 0.18
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>
2022-11-11remove deprecated `concretization` environment key (#33774)Greg Becker3-90/+6
2022-11-10Use bfs order in spack find --deps tree (#33782)Harmen Stoppels2-9/+11
* Use bfs order in spack find --deps tree * fix printing tests
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
2022-11-10spack location: fix attribute lookup after multiple build systems (#33791)Massimiliano Culpo1-2/+4
fixes #33785
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>
2022-11-09always use the cxx compiler as a host compiler (#33771)Chris White1-7/+1
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
2022-11-09Revert "fix racy sbang (#33549)" (#33778)Harmen Stoppels3-65/+43
This reverts commit 4d28a6466188ea9fe3b55a4c3d7690dd66e0dc8f.
2022-11-09ensure external PythonPackages have python deps (#33777)Greg Becker5-0/+54
Currently, external `PythonPackage`s cause install failures because the logic in `PythonPackage` assumes that it can ask for `spec["python"]`. Because we chop off externals' dependencies, an external Python extension may not have a `python` dependency. This PR resolves the issue by guaranteeing that a `python` node is present in one of two ways: 1. If there is already a `python` node in the DAG, we wire the external up to it. 2. If there is no existing `python` node, we wire up a synthetic external `python` node, and we assume that it has the same prefix as the external. The assumption in (2) isn't always valid, but it's better than leaving the user with a non-working `PythonPackage`. The logic here is specific to `python`, but other types of extensions could take advantage of it. Packages need only define `update_external_dependencies(self)`, and this method will be called on externals after concretization. This likely needs to be fleshed out in the future so that any added nodes are included in concretization, but for now we only bolt on dependencies post-concretization. Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2022-11-08Account for patchelf binaries when creating local bootstrap mirror (#33776)Massimiliano Culpo1-0/+2
This was overlooked when we added binary patchelf buildcaches
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
2022-11-08fix racy sbang (#33549)Harmen Stoppels3-43/+65
Spack currently creates a temporary sbang that is moved "atomically" in place, but this temporary causes races when multiple processes start installing sbang. Let's just stick to an idempotent approach. Notice that we only re-install sbang if Spack updates it (since we do file compare), and sbang was only touched 18 times in the past 6 years, whereas we hit the sbang tempfile issue frequently with parallel install on a fresh spack instance in CI. Also fixes a bug where permissions weren't updated if config changed but the latest version of the sbang file was already installed.
2022-11-08hypre +rocm: needs explicit rocprim dep (#33745)eugeneswalker1-0/+1
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