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2023-10-30tty: flush immediately (#40774)Harmen Stoppels1-0/+1
2023-10-30freesurfer: fix support for linux (#39864)marcost21-2/+23
* Load the script file during enviroment setup so that all the enviroment variables are set properly * Patch csh/tcsh so that it uses spacks via env * Update SHA for latest version * Extend shebang to perl and fix up the regex
2023-10-30must: remove release candidates (#40476)Alec Scott1-4/+1
2023-10-30spectre: add v2023.10.11 (#40463)SXS Bot1-0/+3
Co-authored-by: nilsvu <nilsvu@users.noreply.github.com>
2023-10-30Get utilities necessary for successful PIO build (#40502)Brian Vanderwende1-0/+5
2023-10-30linaro-forge: add v23.0.4 (#40772)RichardBuntLinaro1-0/+9
2023-10-30binary_distribution.py: fix type annotation singleton (#40572)Harmen Stoppels4-27/+21
Convince the language server it's really just a BinaryCacheIndex, otherwise it defaults to thinking it's Singleton, and can't autocomplete etc.
2023-10-30Fetch recola from gitlab and add a new version of collier (#40651)Juan Miguel Carceller2-4/+12
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-10-30ISPC: Drop ncurses workaround in favor of patch (#39662)kwryankrattiger1-2/+7
ISPC had a bug in their lookup for NCurses, this was fixed upstream and backported here.
2023-10-30pegtl: add v3.2.7 (#35687)Federico Ficarelli1-0/+1
2023-10-30justbuild: add version 1.2.2 (#40701)Alberto Sartori1-0/+1
2023-10-30aluminum: make network variants "sticky" (#40715)Brian Van Essen1-0/+2
2023-10-30acts: new variant +binaries when +examples (#40738)Wouter Deconinck1-0/+4
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2023-10-30RAJA: add "plugins" variant (#40750)wspear1-0/+2
2023-10-30Fix an issue with using the environment variable `MACHTYPE` which is not ↵Veselin Dobrev2-2/+6
always defined (#40733) * Fix an issue reported here: https://github.com/spack/spack/pull/36154#issuecomment-1781854894 * [@spackbot] updating style on behalf of v-dobrev
2023-10-30py-pandas: add v2.1.2 (#40734)Adam J. Stewart1-2/+4
2023-10-30PyTorch: build with external fp16 (#40760)Adam J. Stewart2-28/+6
2023-10-30pcl: checksum new versions (#39039)Martin Aumüller1-1/+18
2023-10-30exago: fix exago missing on PYTHONPATH when `+python` (#40748)Cameron Rutherford1-0/+4
2023-10-30mfem: support petsc+rocm with spack-installed rocm (#40768)Veselin Dobrev1-1/+7
2023-10-30ASP-based solver: avoid cycles in clingo using hidden directive (#40720)Massimiliano Culpo3-50/+4
The code should be functonally equivalent to what it was before, but now to avoid cycles by design we are using a "hidden" feature of clingo
2023-10-29acts: add v28.1.0:30.3.2 (#40723)Wouter Deconinck1-0/+16
* acts: new version from 28.1.0 to 30.3.1 * acts: new version 30.3.2 * acts: new variant +podio
2023-10-29py-numcodecs: fix broken sse / avx2 variables (#40754)Harmen Stoppels1-4/+5
2023-10-29Add liggght patched for newer compiler (#38685)Aoba4-6/+350
* Add liggght patched for newer compiler Add C++ 17 support Add Clang and Oneapi support * Add maintainers * Fix format in liggghts * Fix maintainers before versions Co-authored-by: Alec Scott <alec@bcs.sh> * Fix style and user to usr * Update package.py --------- Co-authored-by: Alec Scott <alec@bcs.sh>
2023-10-28mercury: add v2.3.1 (#40749)Jerome Soumagne1-0/+1
2023-10-28py-moarchiving: new package (#40558)Lydéric Debusschère1-0/+25
* [add] py-moarchiving: new package * py-moarchiving: update from review: description, variant default value is False, switch when and type --------- Co-authored-by: LydDeb <lyderic.debusschere@eolen.com>
2023-10-28py-generateds: new package (#40555)Lydéric Debusschère1-0/+27
* [add] py-generateds: new package * py-generateds: Update from review Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com> * py-generateds: add versions 2.41.5, 2.42.1, 2.42.2, 2.43.1 and 2.43.2 --------- Co-authored-by: LydDeb <lyderic.debusschere@eolen.com> Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
2023-10-28NCCL: Add version 2.19.3-1 (#40704)Rémi Lacroix1-0/+1
2023-10-28New version of py-langsmith (#40674)Jen Herting1-0/+1
Co-authored-by: Benjamin Meyers <bsmits@rit.edu>
2023-10-28py-bluepyemodel: opensourcing with dependencies (#40592)Erik Heeren9-0/+266
* py-bluepyemodel: new package with dependencies * py-morphio: add MPI as dependency to avoid failing builds * Formatting * py-bluepyefe: no need to set NEURON_INIT_MPI * py-morphio: unifurcation branch is ancient history * py-bluepyopt: only set NEURON_INIT_MPI with +neuron * py-efel: get rid of old version * py-morph{-tool,io}: rename develop to master to match branch * py-bluepyefe: unset PMI_RANK is also neuron-related * py-bluepyopt: PMI_RANK is also neuron-related * Implement review remarks * py-morph-tool, py-neurom: small fixes * py-morphio: reword dependencies
2023-10-28py-comm: add 0.1.4 (#40669)Manuela Kuhn1-1/+4
2023-10-28py-numpy: add v1.26 (#40057)Adam J. Stewart8-156/+202
2023-10-27MSVC: detection from registry (#38500)John W. Parent3-55/+168
Typically MSVC is detected via the VSWhere program. However, this may not be available, or may be installed in an unpredictable location. This PR adds an additional approach via Windows Registry queries to determine VS install location root. Additionally: * Construct vs_install_paths after class-definition time (move it to variable-access time). * Skip over keys for which a user does not have read permissions when performing searches (previously the presence of these keys would have caused an error, regardless of whether they were needed). * Extend helper functionality with option for regex matching on registry keys vs. exact string matching. * Some internal refactoring: remove boolean parameters in some cases where the function was always called with the same value (e.g. `find_subkey`)
2023-10-27hipsycl: restrict compatibility with llvm for v0.8.0 (#40736)Mosè Giordano1-0/+3
2023-10-27e4s ci stacks: add exago specs (#40712)eugeneswalker4-1/+7
* e4s ci: add exago +cuda, +rocm builds * exago: rename 5-18-2022-snapshot to snapshot.5-18-2022 * disable exago +rocm for non-external rocm ci install * note that hiop +rocm fails to find hip libraries when they are spack-installed
2023-10-27mgard@2020-10-01 %oneapi@2023: turn of c++11-narrowing via cxxflags (#40743)eugeneswalker1-0/+6
2023-10-27External finding: update default paths; treat .bat as executable on Windows ↵John W. Parent4-82/+89
(#39850) .bat or .exe files can be considered executable on Windows. This PR expands the regex for detectable packages to allow for the detection of packages that vendor .bat wrappers (intel mpi for example). Additional changes: * Outside of Windows, when searching for executables `path_hints=None` was used to indicate that default path hints should be provided, and `[]` was taken to mean that no defaults should be chosen (in that case, nothing is searched); behavior on Windows has now been updated to match. * Above logic for handling of `path_hints=[]` has also been extended to library search (for both Linux and Windows). * All exceptions for external packages were documented as timeout errors: this commit adds a distinction for other types of errors in warning messages to the user.
2023-10-27OCI buildcache (#38358)Harmen Stoppels24-242/+3479
Credits to @ChristianKniep for advocating the idea of OCI image layers being identical to spack buildcache tarballs. With this you can configure an OCI registry as a buildcache: ```console $ spack mirror add my_registry oci://user/image # Dockerhub $ spack mirror add my_registry oci://ghcr.io/haampie/spack-test # GHCR $ spack mirror set --push --oci-username ... --oci-password ... my_registry # set login credentials ``` which should result in this config: ```yaml mirrors: my_registry: url: oci://ghcr.io/haampie/spack-test push: access_pair: [<username>, <password>] ``` It can be used like any other registry ``` spack buildcache push my_registry [specs...] ``` It will upload the Spack tarballs in parallel, as well as manifest + config files s.t. the binaries are compatible with `docker pull` or `skopeo copy`. In fact, a base image can be added to get a _runnable_ image: ```console $ spack buildcache push --base-image ubuntu:23.04 my_registry python Pushed ... as [image]:python-3.11.2-65txfcpqbmpawclvtasuog4yzmxwaoia.spack $ docker run --rm -it [image]:python-3.11.2-65txfcpqbmpawclvtasuog4yzmxwaoia.spack ``` which should really be a game changer for sharing binaries. Further, all content-addressable blobs that are downloaded and verified will be cached in Spack's download cache. This should make repeated `push` commands faster, as well as `push` followed by a separate `update-index` command. An end to end example of how to use this in Github Actions is here: **https://github.com/haampie/spack-oci-buildcache-example** TODO: - [x] Generate environment modifications in config so PATH is set up - [x] Enrich config with Spack's `spec` json (this is allowed in the OCI specification) - [x] When ^ is done, add logic to create an index in say `<image>:index` by fetching all config files (using OCI distribution discovery API) - [x] Add logic to use object storage in an OCI registry in `spack install`. - [x] Make the user pick the base image for generated OCI images. - [x] Update buildcache install logic to deal with absolute paths in tarballs - [x] Merge with `spack buildcache` command - [x] Merge #37441 (included here) - [x] Merge #39077 (included here) - [x] #39187 + #39285 - [x] #39341 - [x] Not a blocker: #35737 fixes correctness run env for the generated container images NOTE: 1. `oci://` is unfortunately taken, so it's being abused in this PR to mean "oci type mirror". `skopeo` uses `docker://` which I'd like to avoid, given that classical docker v1 registries are not supported. 2. this is currently `https`-only, given that basic auth is used to login. I _could_ be convinced to allow http, but I'd prefer not to, given that for a `spack buildcache push` command multiple domains can be involved (auth server, source of base image, destination registry). Right now, no urllib http handler is added, so redirects to https and auth servers with http urls will simply result in a hard failure. CAVEATS: 1. Signing is not implemented in this PR. `gpg --clearsign` is not the nicest solution, since (a) the spec.json is merged into the image config, which must be valid json, and (b) it would be better to sign the manifest (referencing both config/spec file and tarball) using more conventional image signing tools 2. `spack.binary_distribution.push` is not yet implemented for the OCI buildcache, only `spack buildcache push` is. This is because I'd like to always push images + deps to the registry, so that it's `docker pull`-able, whereas in `spack ci` we really wanna push an individual package without its deps to say `pr-xyz`, while its deps reside in some `develop` buildcache. 3. The `push -j ...` flag only works for OCI buildcache, not for others
2023-10-27octopus: split netcdf-c and netcdf-fortran dependency (#40685)Ashwin Kumar Karnad1-2/+3
2023-10-27strumpack: add version 7.2.0 (#40732)Satish Balay1-0/+1
2023-10-27gromacs: default to external blas & lapack (#40490)Harmen Stoppels1-28/+8
* gromacs: default to external blas & lapack * drop vendored lapack/blas altogether
2023-10-27ci: spack compiler find should list extra config scopes (#40727)Harmen Stoppels1-1/+6
otherwise it detected pre-configured compilers in an potentially different way.
2023-10-27Fixes and options for package spglib (#40684)dmt41-1/+6
* Fix cmake_args for spglib v2.1.0+ * Add option to build fortran interface in package spglib * fix style as sugested by ci/prechecks/style * Enable fortran variant from v1.16.4 as suggested Co-authored-by: Rocco Meli <r.meli@bluemail.ch> --------- Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
2023-10-27gromacs: fix version branch in intel fftw (#40489)Harmen Stoppels1-1/+1
2023-10-27akantu: use f-strings (#40466)Alec Scott1-6/+4
Co-authored-by: Nicolas Richart <nrichart@users.noreply.github.com>
2023-10-26plasma: add version 23.8.2 (#40728)Satish Balay1-0/+2
2023-10-26itk: misc fixes (#39832)Carlos Bederián1-2/+7
* itk: patch missing include for newer compilers * itk: The package doesn't use MPI * itk: package requires the high-level hdf5 api * itk: patch url with ?full_index=1 * itk: point to 4041 commit in master * itk: don't constrain hdf5 with ~mpi
2023-10-26ldak: add v5.2 & add maintainer (#40710)snehring1-18/+55
* ldak: update to 5.2, add maintainer * ldak: use compiler.openmp_flag
2023-10-26dataTransferKit: add v3.1.1, v3.1.0 (#40556)Daniel Arndt1-2/+5
* Update DataTransferKit for 3.1.1 release * Require Trilinos-14 for 3.1.0 and higher
2023-10-26PythonPackage: allow archive_files to be overridden (#40694)Adam J. Stewart1-1/+1