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2022-10-18mothur: add v1.48.0 and variants (#33326)snehring1-20/+63
2022-10-18build(deps): bump docker/setup-buildx-action from 2.1.0 to 2.2.0 (#33384)dependabot[bot]1-1/+1
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.1.0 to 2.2.0. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/95cb08cb2672c73d4ffd2f422e6d11953d2a9c70...c74574e6c82eeedc46366be1b0d287eff9085eb6) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-10-18intel-oneapi-compilers: fix Python 2.7 compliance (#33383)Massimiliano Culpo1-2/+2
2022-10-17py-fiona: add v1.8.22 (#33372)Adam J. Stewart1-1/+2
2022-10-17e4s ci stack: add trilinos +rocm (#31601)eugeneswalker1-0/+5
2022-10-17lz4: add 1.9.4 (#33334)Michael Kuhn1-0/+1
2022-10-17Bugfix HIP and aluminum rocm build (#33344)Brian Van Essen2-7/+31
* Fixed two bugs in the HIP package recipe. The first is that the HIP_PATH was being set to the actual spec, and not the spec prefix. The second bug is that HIP is expected to be in /opt/rocm-x.y.z/hip but it's libraries can exist at both /opt/rocm-x.y.z/hip/lib and /opt/rocm-x.y.z/lib. This means that the external detection logic may find it in either and it turns out that some modules only expose one of those two locations. Logic is added to ensure that the internal HIP_PATH and associated ROCM_PATH are correctly set in both cases. * Added support for Aluminum to use the libfabric plugin with either RCCL or NCCL.
2022-10-17grid: reference `fftw-api` instead of `fftw` (#33374)Mosè Giordano1-1/+1
This makes it possible to compile with, e.g., `cray-fftw`, not just `fftw`.
2022-10-17New packages: libbigwig, methyldackel (#33273)snehring2-0/+66
* libbigwig: adding new package libbigwig * methyldackel: adding new package methyldackel * libbigwig: tighten up curl variant
2022-10-17Initial contribution of LibPressio ecosystem (#32630)Robert Underwood35-26/+1410
* Add libpressio and dependencies; some of these packages are maintained as forks of the original repositories and in those cases the docstring mentions this. * Add optional dependency in adios2 on libpressio * cub package: set CUB_DIR environment variable for dependent installations * Clear R_HOME/R_ENVIRON before Spack installation (avoid sources outside of Spack from affecting the installation in Spack) * Rename dlib to dorian3d-dlib and update dependents; add new dlib implementation. Pending an official policy on how to handle packages with short names, reviewer unilaterally decided that the rename was acceptable given that the new Spack dlib package is referenced more widely (by orders of magnitude) than the original Co-authored-by: Samuel Li <shaomeng@users.noreply.github.com>
2022-10-17py-xopen: version bump to 1.6.0 (#33231)Luke Diorio-Toth2-1/+28
* version bump to 1.6.0 * added py-isal, updated URL
2022-10-17Classic Intel compilers do not support gcc-toolchain (#33281)Stephen Sachs1-15/+26
* Classic Intel compilers do not support gcc-toolchain This fix removes `--gcc-toolchain=` from the ~.fcg` files for the classic Intel compilers. AFAIK this option is only supported for Clang based compilers. This lead to an issue when installing cmake. Reproducer: ``` spack install cmake@3.24.2%intel@2021.7.0~doc+ncurses+ownlibs~qt build_type=Release arch=linux-amzn2-skylake_avx512 ``` Tagging maintainer @rscohn2 * Add `-gcc-name` for icc .. and `-gxx-name` for icpc. AFAIK this is used for modern C++ support, so we can ignore `ifort`. Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2022-10-17database: don't warn adding missing build deps (#33361)Harmen Stoppels1-27/+48
When installing an individual spec `spack --only=package --cache-only /xyz` from a buildcache, Spack currently issues tons of warnings about missing build deps (and their deps) in the database. This PR disables these warnings, since it's fine to have a spec without its build deps in the db (they are just "missing").
2022-10-17py-horovod: add v0.26 (#33311)Adam J. Stewart2-0/+6
* py-horovod: add v0.26 * py-petastorm: add v0.12.0
2022-10-17installer.py: traverse_dependencies has local deptype (#33367)Harmen Stoppels1-9/+19
Currently `traverse_dependencies` fixes deptypes to traverse once and for all in the recursion, but this is incorrect, since deptypes depend on the node (e.g. if it's a dependency and cache-only, don't follow build type edges, even if the parent is build from sources and needs build deps.)
2022-10-17GnuPG: add v2.3.8 and update stack (#33368)Massimiliano Culpo6-1/+12
2022-10-17Add checksum for py-ipykernel 6.15.2 (#33360)iarspider1-0/+1
2022-10-17Add checksum for py-secretstorage 3.3.3 (#33366)iarspider1-0/+1
2022-10-17python: add 3.10.7, 3.9.14, 3.8.14, 3.7.14 (#32623)Carlos Bederián1-2/+6
2022-10-17Support spackbot rebuilding all specs from source (#32596)Scott Wittenburg2-21/+66
Support spackbot rebuilding all specs from source when asked (with "rebuild everything") - Allow overriding --prune-dag cli opt with env var - Use job variable to optionally prevent rebuild jobs early exit behavior - ci rebuild: Use new install argument to insist deps are always installed from binary, but package is only installed from source. - gitlab: fix bug w/ untouched pruning - ci rebuild: install from hash rather than json file - When doing a "rebuild everything" pipeline, make sure that each install job only consumes binary dependencies from the mirror being populated by the current pipeline. This avoids using, e.g. binaries from develop, when rebuilding everything on a PR. - When running a pipeline to rebuild everything, do not die because we generated a hash on the broken specs list. Instead only warn in that case. - bugfix: Replace broken no-args tty.die() with sys.exit(1)
2022-10-17Github Discussions can be used for Q&A (#33364)Harmen Stoppels1-0/+1
2022-10-17hypre 2.26.0 (#33299)Rui Peng Li1-0/+1
2022-10-17Add checksum for py-prompt-toolkit 3.0.31 (#33362)iarspider1-0/+1
2022-10-17Add checksum for py-grpcio-tools 1.48.1 (#33358)iarspider1-2/+5
2022-10-17installer.py: fix/test get_deptypes (#33363)Harmen Stoppels2-1/+40
Fixing an oversight in https://github.com/spack/spack/pull/32537 `get_deptypes` should depend on new `package/dependencies_cache_only` props.
2022-10-17gitlab ci: Do not force protected build jobs to run on aws runners (#33314)Scott Wittenburg1-1/+1
2022-10-17Add checksum for py-astroid 2.12.7, py-astroid 2.12.10, py-setuptools ↵iarspider4-30/+46
62.6.0, py-wrapt 1.14.1, py-pylint 2.15.0 (#32976) * Add checksum for py-astroid 2.12.7, py-setuptools 62.6.0 * Also add checksum for py-wrapt * Update package.py * Update package.py (#57) * Update package.py * Update package.py * Update package.py
2022-10-17installer.py: show timers for binary install (#33305)Harmen Stoppels1-23/+57
Print a message of the form ``` Fetch mm:ss. Build: mm:ss. Total: mm:ss ``` when installing from buildcache. Previously this only happened for source builds.
2022-10-17py-jupyterlab-pygments: install from wheel to avoid cyclic dependency (#33278)iarspider1-7/+21
* py-jupyterlab-pygments: avoid cyclic dependency * Fix style * Update package.py * Update package.py * [@spackbot] updating style on behalf of iarspider * Update package.py * Flake-8 * fix Co-authored-by: iarspider <iarspider@users.noreply.github.com>
2022-10-17py-numpy: add v1.23.4 (#33260)Adam J. Stewart1-0/+1
2022-10-17Add checksum for py-sniffio 1.3.0 (#32975)iarspider1-0/+2
2022-10-17py-tensorflow-hub: zlib, again. (#33359)Harmen Stoppels2-5/+31
2022-10-17mariadb-c-client: add 3.3.2, 3.2.7, 3.1.18, 3.0.10 (#33335)Michael Kuhn1-0/+4
2022-10-17sdl2: add v2.0.22 and v2.24.1 (#33351)Wouter Deconinck1-0/+4
2022-10-17nextflow: add v20.10.0 (#33354)Diego Alvarez1-0/+5
2022-10-17libblastrampoline: Add versions 5.1.1, 5.2.0 (#33352)Mosè Giordano1-0/+2
2022-10-17py-setuptools: add v65.5.0 (#33353)Adam J. Stewart1-0/+5
2022-10-16py-sphinx: add v5.3 and v5.2 (#33356)Adam J. Stewart1-0/+4
2022-10-16octopus: upgrade to 12.1 (#33343)Hans Fangohr1-0/+1
2022-10-16tasmanian: disable openmp by default (#33345)Miroslav Stoyanov1-2/+1
2022-10-16py-meson-python: add new versions (#33294)Adam J. Stewart1-1/+10
2022-10-16py-tensorflow: fix zlib (#33349)Harmen Stoppels2-1/+16
* py-tensorflow: fix zlib * [@spackbot] updating style on behalf of haampie Co-authored-by: haampie <haampie@users.noreply.github.com>
2022-10-16meson: update OneAPI compiler support patch (#33293)Adam J. Stewart2-6/+163
2022-10-15CI: allow multiple matches to combine tags (#32290)Jonathon Anderson20-13/+76
Currently "spack ci generate" chooses the first matching entry in gitlab-ci:mappings to fill attributes for a generated build-job, requiring that the entire configuration matrix is listed out explicitly. This unfortunately causes significant problems in environments with large configuration spaces, for example the environment in #31598 (spack.yaml) supports 5 operating systems, 3 architectures and 130 packages with explicit size requirements, resulting in 1300 lines of configuration YAML. This patch adds a configuraiton option to the gitlab-ci schema called "match_behavior"; when it is set to "merge", all matching entries are applied in order to the final build-job, allowing a few entries to cover an entire matrix of configurations. The default for "match_behavior" is "first", which behaves as before this commit (only the runner attributes of the first match are used). In addition, match entries may now include a "remove-attributes" configuration, which allows matches to remove tags that have been aggregated by prior matches. This only makes sense to use with "match_behavior:merge". You can combine "runner-attributes" with "remove-attributes" to effectively override prior tags.
2022-10-15Add checksum for py-seaborn 0.12.0 (#33145)iarspider1-5/+19
* Add checksum for py-seaborn 0.12.0 * Update package.py * Update package.py * [@spackbot] updating style on behalf of iarspider * Update package.py Co-authored-by: iarspider <iarspider@users.noreply.github.com>
2022-10-14rocksdb: add 7.7.3 (#33341)Michael Kuhn1-0/+1
2022-10-15depfile: update docs (#33279)Harmen Stoppels1-9/+37
2022-10-14glib: add 2.74.0 and 2.72.4 (#33332)Michael Kuhn1-2/+6
2022-10-14gptl: new version 8.1.1; use the correct mpi fortran compiler (#33235)WuK1-0/+5
* gptl: new version 8.1.1; use the correct `mpifc` * add `F90` and `$F77`
2022-10-14seacas: update to latest release (#33330)Greg Sjaardema1-0/+3
Add checksum for latest tag/release