summaryrefslogtreecommitdiff
AgeCommit message (Collapse)AuthorFilesLines
2022-07-20installer.py: require "explicit: True" in the install arguments to mark a ↵Harmen Stoppels2-1/+14
package "explicit" (#31646)
2022-07-18py-pip: 22.x (#31621)Harmen Stoppels1-0/+2
2022-07-18Update py-xdot to use python_purelib #31616 (#31628)Servesh Muralidharan1-1/+1
Issue discussed in https://github.com/spack/spack/issues/31616
2022-07-18rocblas: tighten tensile dependencies (#31414)Cory Bloor1-15/+10
* rocblas: make tensile dependencies conditional * Remove rocm-smi from the rocblas dependency list rocm-smi was added to the rocblas dependency list because Tensile was a dependency of rocBLAS and rocm-smi was a dependency of Tensile. However, that reasoning was not correct. Tensile is composed of three components: 1. A command-line tool for generating kernels, benchmarking them, and saving the parameters used for generating the best kernels (a.k.a. "Solutions") in YAML files. 2. A build system component that reads YAML solution files, generates kernel source files, and invokes the compiler to compile then into code object files (*.co, *.hsco). An index of the kernels and their associated parameters is also generated and stored in either YAML or MessagePack format (TensileLibrary.yaml or TensileLibrary.dat). 3. A runtime library that will load the TensileLibrary and code object files when asked to execute a GEMM and choose the ideal kernel for your specific input parameters. rocBLAS developers use (1) during rocBLAS development. This is when Tensile depends on rocm-smi. The GPU clock speed and temperature must be controlled to ensure consistency when doing the solution benchmarking. That control is provided by rocm-smi. When building rocBLAS, Tensile is used for (2). However, there is no need for control of the GPU at that point and rocm-smi is not a dependency. At runtime, the rocBLAS library uses Tensile for (3), but there is again no dependency on rocm-smi. tl;dr: rocm-smi is a dependency of the tensile benchmarking tool, which is not a build dependency or runtime dependency of rocblas.
2022-07-18e4s ci: add ginkgo +rocm (#31603)eugeneswalker1-0/+1
2022-07-18kraken2: add v2.1.2 (#31613)Luke Diorio-Toth1-0/+1
2022-07-18containerize: fix missing environment activation (#31596)Massimiliano Culpo1-2/+1
2022-07-18lhapdf: add gettext libs explicitly (#31555)haralmha1-1/+3
Co-authored-by: Valentin Volkl <valentin.volkl@cern.ch>
2022-07-18py-pyarrow: aarch64 patch no longer applies/required (#31609)Adam J. Stewart1-1/+1
2022-07-18py-kornia: add v0.6.6 (#31611)Adam J. Stewart1-0/+1
2022-07-18Fixes for kallisto package (#31617)Glenn Johnson4-2/+55
This PR contains several fixes for the kallisto package. - create hdf5 variant as hdf5 is optional beginning with 0.46.2 - provide patch for 0.43 to link against libz - provide patch for older versions to build again gcc-11 and up - patch and code to use autoconf-2.70 and up
2022-07-18Only hack botocore when needed (#31610)Jonathon Anderson1-6/+10
Newer versions of botocore (>=1.23.47) support the full IOBase interface, so the hacks added to supplement the missing attributes are no longer needed. Conditionally disable the hacks if they appear to be unnecessary based on the class hierarchy found at runtime.
2022-07-16py-phydms, py-pypdf2, and py-pyvolve: new packages (#31540)Luke Diorio-Toth4-2/+89
* py-panaroo: new package * moving panaroo to branch * py-phydms: new package * added dependencies and new packages * fixed py-pypdf2 dependencies
2022-07-16mizani, plotnine, and pystan: added more versions and variable dependencies ↵Luke Diorio-Toth4-36/+93
(#31541) * py-panaroo: new package * moving panaroo to branch * updated mizani, plotnine, and pystan versions and requirements * made suggested fixes * adding more requested fixes * added new versions of statsmodels and httpstan
2022-07-16py-horovod: add versions 0.22+, fix aarch64 build (#29310)FJ-NaokiMatsumura3-19/+754
* py-torch: add version 0.23.0 and fix to built on aarch64 * Add newer versions, fix build issues * Fix tests Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-07-15Qhull: fix RPATH on macOS (#31586)Adam J. Stewart1-0/+6
2022-07-15py-geocube: add v0.3.2 (#31588)Adam J. Stewart1-0/+1
2022-07-15tamaas: new version 2.5.0 (#31501)Lucas Frérot1-0/+2
* tamaas: new version 2.5.0 * tamaas: do not build/install documentation * tamaas: hash correction for v2.5.0.post1 Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-07-15gperftools: Add version 2.10 and add unwind to LDFLAGS (#31574)haralmha1-0/+5
* gperftools: Add version 2.10 and add unwind to LDFLAGS * Make unwind flag conditional on libunwind variant
2022-07-15Use lexists instead of exists during fetch (#31509)Harmen Stoppels1-11/+11
2022-07-14openssl: add patch for @1.1.1q. fixed issues #31545 (#31575)牟展佑1-0/+4
2022-07-14blight, fparser, typing_extensions (#31566)Elizabeth Sherrock4-5/+72
* Added fparser 0.0.16 * Created package * Change from GitHub download to pypi * py-typing-extensions: 4.3.0 * Added py-pdoc3 * Finished adding py-blight * Fixed typos * Fixed dependency specs * Fixed some things after PR review * Added @woodruffw as blight maintainer * Removed maintainer comment block from pdoc3
2022-07-14snappy: Update to version 1.1.9 (#31578)Erik Schnetter1-1/+3
2022-07-14update e4s to reflect june status (#31032)eugeneswalker2-182/+190
2022-07-14Bug/fix credentials s3 buildcache update (#31391)Joseph Snyder3-5/+14
* Add connection information to buildcache update command Ensure that the s3 connection made when attempting to update the content of a buildcache attempts to use the extra connection information from the mirror creation. * Add unique help for endpoint URL argument Fix copy/paste error for endpoint URL help which was the same as the access token * Re-work URL checking for S3 mirrors Due to the fact that nested bucket URLs would never match the string used for checking that the mirror is the same, switch the check used. Sort all mirror URLs by length to have the most specific cases first and see if the desired URL "starts with" the mirror URL. * Long line style fixes Add execptions for long lines and fix other style errors * Use format() function to rebuild URL Use the format command to rebuild the url instead of crafing a formatted string out of known values * Add early exit for URL checking When a valid mirror is found, break from the loop
2022-07-14Deprecate `blacklist`/`whitelist` in favor of `include`/`exclude` (#31569)Todd Gamblin23-135/+375
For a long time the module configuration has had a few settings that use `blacklist`/`whitelist` terminology. We've been asked by some of our users to replace this with more inclusive language. In addition to being non-inclusive, `blacklist` and `whitelist` are inconsistent with the rest of Spack, which uses `include` and `exclude` for the same concepts. - [x] Deprecate `blacklist`, `whitelist`, `blacklist_implicits` and `environment_blacklist` in favor of `exclude`, `include`, `exclude_implicits` and `exclude_env_vars` in module configuration, to be removed in Spack v0.20. - [x] Print deprecation warnings if any of the deprecated names are in module config. - [x] Update tests to test old and new names. - [x] Update docs. - [x] Update `spack config update` to fix this automatically, and include a note in the error that you can use this command.
2022-07-14[py-tensorflow-hub] full_index=1 caused checksum change (#31585)Jen Herting1-1/+1
2022-07-14interproscan: new version 5.56-89.0 (#31565)snehring1-0/+2
* interproscan: new version 5.56-89.0 * interproscan: add maintainer
2022-07-14py-statsmodels: add v0.13.2 (#31571)Adam J. Stewart1-0/+2
2022-07-14ADIOS2: 2.8.2 (#31564)Axel Huebl1-0/+1
Add the latest ADIOS2 release.
2022-07-13Decompression: use tar exe vs. built-in Python tarfile support (#31563)Peter Scheibel1-19/+4
Python's built-in tarfile support doesn't address some general cases of malformed tarfiles that are already handled by the system 'tar' utility; until these can be addressed, use that exclusively.
2022-07-13Add package py-devito and it's dependencies (#31495)Stephen Sachs6-0/+192
* [py-devito] Add package Also add dependencies: - py-nbval - py-cgen - py-codepy - py-contexttimer - py-pyrevolve * [py-devito] Fix some typos * [py-devito] Fix: include examples directory Upstream issue: https://github.com/devitocodes/devito/issues/1954 * [py-devito] clean up * [py-devito] clean up dependency packages * [py-devito] flake8: line too long * Address @adamjstewart comments * Make flake8 happy Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2022-07-13m4: Add build dependency on diffutils (#31232)Jonathon Anderson1-0/+1
2022-07-13GDAL: CMake support and dependency variants (#31197)Adam J. Stewart3-439/+516
Add support for CMake builds while preserving autotools support for older versions of GDAL * Add GDAL 3.5.0 * Remove GDAL 1 * Add support for new CMake build system * Change defaults to build all recommended dependencies * Simplify Autotools flag handling * Determine version range for drivers
2022-07-13ants: add version 2.4.0 (#31562)Ben Darwin1-1/+2
2022-07-13Add versions 4.3.0 and 4.3.1. Update boost reqs with component/versions. ↵Emil Briggs1-1/+4
(#31559)
2022-07-13mpitrampoline: New version 4.1.2 (#31560)Erik Schnetter1-0/+3
2022-07-13Cppcheck: fix install and convert to cmake build system (#31488)Chris White1-6/+17
* fix cppcheck install and convert to cmake build system * add white238 as a maintainer
2022-07-13ghostscript-fonts: fix URL (#31360)Rémi Lacroix1-2/+3
2022-07-13Hermes: add v0.7.0-beta, remove older versions (#31544)H. Joe Lee1-4/+5
2022-07-13vtk-m: add v1.8.0 (#31220)Vicente Bolea4-5/+5
2022-07-13py-ford: add v6.1.13 (#31483)Elizabeth Sherrock1-0/+1
2022-07-13Open3D: fix build with external fmt (#31547)Adam J. Stewart1-2/+4
2022-07-13py-pytorch-lightning: add v1.6.5 (#31548)Adam J. Stewart1-0/+1
2022-07-13Tower Agent / Tower CLI: new packages (#31539)Marco De La Pierre3-0/+64
2022-07-12`spack.repo.get()` can only be called on concrete specs (#31411)Massimiliano Culpo79-1560/+1239
The goal of this PR is to make clearer where we need a package object in Spack as opposed to a package class. We currently instantiate a lot of package objects when we could make do with a class. We should use the class when we only need metadata, and we should only instantiate and us an instance of `PackageBase` at build time. Modifications: - [x] Remove the `spack.repo.get` convenience function (which was used in many places, and not really needed) - [x] Use `spack.repo.path.get_pkg_class` wherever possible - [x] Try to route most of the need for `spack.repo.path.get` through `Spec.package` - [x] Introduce a non-data descriptor, that can be used as a decorator, to have "class level properties" - [x] Refactor unit tests that had to be modified to reduce code duplication - [x] `Spec.package` and `Repo.get` now require a concrete spec as input - [x] Remove `RepoPath.all_packages` and `Repo.all_packages`
2022-07-12trilinos: add new release 13.4.0 and use sha256 instead of commit hashes ↵Seth R. Johnson1-4/+5
(#31277)
2022-07-12spiner: update dependencies (#31486)Richard Berger1-2/+2
2022-07-12py-nbmake: add v1.3.0; py-nbclient: add v0.6.6, 0.5.13; py-traitlets: add ↵Adam J. Stewart3-11/+36
v5.3.0 (#31513) * py-nbmake: add v1.3.0 * Add newer versions
2022-07-12amdblis: add 3.2 (#31518)Carlos Bederián1-0/+1