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2022-11-30Fix recipe for py-onnx-runtime (#34130)iarspider1-3/+8
* Fix recipe * Update package.py * Update recipe following review * Update var/spack/repos/builtin/packages/py-onnx-runtime/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * remove unused imports * Update package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-11-30PMIx: enable python bindings (#34107)Sajid Ali1-0/+6
2022-11-30Deduplicate code to propagate module changes across MRO (#34157)Massimiliano Culpo2-50/+22
2022-11-30Single pass text replacement (#34180)Harmen Stoppels2-34/+88
2022-11-29py-bidscoin, py-multiecho: add new packages (#34168)Manuela Kuhn2-0/+55
2022-11-29debug: move "nonexistent config path" message to much higher verbosity level ↵Todd Gamblin1-2/+2
(#34201) We currently report that searched config paths don't exist at debug level 1, which clutters the output quite a bit: ```console > spack -d solve --fresh --show asp hdf5 > hdf5.lp ==> [2022-11-29-14:18:21.035133] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/darwin/concretizer.yaml ==> [2022-11-29-14:18:21.035151] Skipping nonexistent config path /Users/gamblin2/.spack/concretizer.yaml ==> [2022-11-29-14:18:21.035169] Skipping nonexistent config path /Users/gamblin2/.spack/darwin/concretizer.yaml ==> [2022-11-29-14:18:21.035238] Reading config from file /Users/gamblin2/src/spack/etc/spack/defaults/repos.yaml ==> [2022-11-29-14:18:21.035996] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/defaults/darwin/repos.yaml ==> [2022-11-29-14:18:21.036021] Skipping nonexistent config path /etc/spack/repos.yaml ==> [2022-11-29-14:18:21.036039] Skipping nonexistent config path /etc/spack/darwin/repos.yaml ==> [2022-11-29-14:18:21.036057] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/repos.yaml ==> [2022-11-29-14:18:21.036072] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/darwin/repos.yaml ==> [2022-11-29-14:18:21.036088] Skipping nonexistent config path /Users/gamblin2/.spack/repos.yaml ==> [2022-11-29-14:18:21.036105] Skipping nonexistent config path /Users/gamblin2/.spack/darwin/repos.yaml ==> [2022-11-29-14:18:21.071828] Reading config from file /Users/gamblin2/src/spack/etc/spack/defaults/config.yaml ==> [2022-11-29-14:18:21.081628] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/defaults/darwin/config.yaml ==> [2022-11-29-14:18:21.081669] Skipping nonexistent config path /etc/spack/config.yaml ==> [2022-11-29-14:18:21.081692] Skipping nonexistent config path /etc/spack/darwin/config.yaml ==> [2022-11-29-14:18:21.081712] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/config.yaml ==> [2022-11-29-14:18:21.081731] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/darwin/config.yaml ==> [2022-11-29-14:18:21.081748] Skipping nonexistent config path /Users/gamblin2/.spack/config.yaml ==> [2022-11-29-14:18:21.081764] Skipping nonexistent config path /Users/gamblin2/.spack/darwin/config.yaml ==> [2022-11-29-14:18:21.134909] Reading config from file /Users/gamblin2/src/spack/etc/spack/defaults/packages.yaml ==> [2022-11-29-14:18:21.148695] Reading config from file /Users/gamblin2/src/spack/etc/spack/defaults/darwin/packages.yaml ==> [2022-11-29-14:18:21.152555] Skipping nonexistent config path /etc/spack/packages.yaml ==> [2022-11-29-14:18:21.152582] Skipping nonexistent config path /etc/spack/darwin/packages.yaml ==> [2022-11-29-14:18:21.152601] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/packages.yaml ==> [2022-11-29-14:18:21.152620] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/darwin/packages.yaml ==> [2022-11-29-14:18:21.152637] Skipping nonexistent config path /Users/gamblin2/.spack/packages.yaml ==> [2022-11-29-14:18:21.152654] Skipping nonexistent config path /Users/gamblin2/.spack/darwin/packages.yaml ==> [2022-11-29-14:18:21.853915] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/defaults/compilers.yaml ==> [2022-11-29-14:18:21.853962] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/defaults/darwin/compilers.yaml ==> [2022-11-29-14:18:21.853987] Skipping nonexistent config path /etc/spack/compilers.yaml ==> [2022-11-29-14:18:21.854007] Skipping nonexistent config path /etc/spack/darwin/compilers.yaml ==> [2022-11-29-14:18:21.854025] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/compilers.yaml ==> [2022-11-29-14:18:21.854043] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/darwin/compilers.yaml ==> [2022-11-29-14:18:21.854060] Skipping nonexistent config path /Users/gamblin2/.spack/compilers.yaml ==> [2022-11-29-14:18:21.854093] Reading config from file /Users/gamblin2/.spack/darwin/compilers.yaml ``` It is very rare that I want to know this much information about config search, so I've moved this to level 3. Now at level 1, we can see much more clearly what configs were actually found: ```console > spack -d solve --fresh --show asp hdf5 > hdf5.lp ==> [2022-11-29-14:19:04.035457] Imported solve from built-in commands ==> [2022-11-29-14:19:04.035818] Imported solve from built-in commands ==> [2022-11-29-14:19:04.037626] Reading config from file /Users/gamblin2/src/spack/etc/spack/defaults/concretizer.yaml ==> [2022-11-29-14:19:04.040033] Reading config from file /Users/gamblin2/src/spack/etc/spack/defaults/repos.yaml ==> [2022-11-29-14:19:04.080852] Reading config from file /Users/gamblin2/src/spack/etc/spack/defaults/config.yaml ==> [2022-11-29-14:19:04.133241] Reading config from file /Users/gamblin2/src/spack/etc/spack/defaults/packages.yaml ==> [2022-11-29-14:19:04.147175] Reading config from file /Users/gamblin2/src/spack/etc/spack/defaults/darwin/packages.yaml ==> [2022-11-29-14:19:05.157896] Reading config from file /Users/gamblin2/.spack/darwin/compilers.yaml ``` You can still get the old messages with `spack -ddd` (to activate debug level 3).
2022-11-29add 15.0.5, 15.0.6 (#34194)Paul R. C. Kent1-0/+2
2022-11-29CI: Update Data and Vis SDK Stack (#34009)kwryankrattiger3-77/+107
* CI: Update Data and Vis SDK Stack * Update image to match target deployments (E4S) * Enable all packages * Test supported variants of ParaView and VisIt * Sensei: Update Python hint for newer cmake * Sensei: add Python3 hint
2022-11-29icc@2021.6.0 does not support gcc@12 headers (#34191)Stephen Sachs1-0/+3
Error message: ``` /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/gcc-12.2.0-4tairupdxg2tg2yhvjdlbs7xbd7wudl3/bin/../include/c++/12.2.0/bits/random.h(104): error: expected a declaration { extension using type = unsigned __int128; }; ^ ``` Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2022-11-29Dav sdk catalyst (#34010)kwryankrattiger2-2/+5
* SDK: Add Catalyst 1 and 2 support to the SDK * LibCatalyst: Remove unused python3 variant from package
2022-11-29evtgen: add v02.02.00 (#34187)Valentin Volkl1-1/+12
* evtgen: add v02.02.00 * format
2022-11-29Fix libxc cflag (#34000)Cristian Le1-1/+3
Using standard c99 should not be specific to intel compilers.
2022-11-29hiredis: updated package definition to use CMake (#33949)Loïc Pottier1-14/+45
2022-11-28Add maintainer to Exawind stack and Trilinos (#34174)psakievich4-4/+4
* Add maintainer to Nalu-Wind and Trilinos * Add to trilinos * Exawind too * amr-wind too
2022-11-28genfit: add v02-00-01 (#34159)Valentin Volkl1-0/+1
2022-11-28fix typo in path for sanity check (#34117)Hans Fangohr1-1/+1
- typo breaks install
2022-11-28Add new version of snakemake (#34041)Sam Grayson5-7/+116
* Add new version of snakemake * Add myself as a maintainer * py-retry -> py-reretry * Added snakemake variants for storage systems * Updated comments * Responded to Adam's comments * Fixed spack style * Add build/run dependency types
2022-11-28New package: py-statmorph (#34158)Benjamin Meyers4-1/+100
* New package py-statmorph w/ dependecies. Add py-astropy@5.1 * [@spackbot] updating style on behalf of meyersbs * [py-statmorph,py-astropy,py-pyerfa] minor fixes
2022-11-28New package: py-stui (#34156)Benjamin Meyers1-0/+22
* New package py-stui * [py-stui] add maintainer * [@spackbot] updating style on behalf of meyersbs * [py-stui] fix deps
2022-11-28Add checksum for py-rsa 4.9 (#34115)iarspider1-2/+5
* Add checksum for py-rsa 4.9 * Update package.py * Update var/spack/repos/builtin/packages/py-rsa/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-11-28omegah: new scorec version, fix cuda flags (#34169)Cameron Smith1-1/+9
2022-11-28e4s ci: add hdf5-vol-async; remove expired comments (#34110)eugeneswalker1-4/+1
2022-11-28petsc, py-petsc4py: add 3.18.2 (#34161)Satish Balay2-0/+2
2022-11-28py-bidskit: new package and dcm2niix: add 1.0.20220720 (#34162)Manuela Kuhn2-1/+31
* py-bidskit: new package and dcm2niix: add 1.0.20220720 * Remove list_url
2022-11-28Add checksum for py-traitlets 5.3.0 (#34127)iarspider1-0/+1
2022-11-28warn about removal of deprecated format strings (#34101)Greg Becker6-7/+19
* warn about removal of deprecated format strings Co-authored-by: becker33 <becker33@users.noreply.github.com>
2022-11-28py-dcm2bids: add new package (#34163)Manuela Kuhn1-0/+23
2022-11-28easi: update package, rework impalajit (#34032)Thomas-Ulrich3-64/+62
2022-11-28acfl: provides blas, lapack, and fftw-api@3 (#34154)Annop Wongwathanarat1-4/+85
2022-11-28texinfo: add v7.0 (#34150)Hector Martinez-Seara1-0/+1
2022-11-28Use a module-like object to propagate changes in the MRO, when setting build ↵Massimiliano Culpo2-18/+77
env (#34059) This fixes an issue introduced in #32340, which changed the semantics of the "module" object passed to the "setup_dependent_package" callback.
2022-11-28Revert "Revert "gitlab: Add shared PR mirror to places pipelines look for ↵Harmen Stoppels3-0/+17
binaries. (#33746)" (#34087)" (#34153) This reverts commit 63e440651436fdc30993ef58875279e71f4851d1.
2022-11-28armpl-gcc: add post-installation check by running examples (#34086)Annop Wongwathanarat1-15/+24
2022-11-28Add type hints to Prefix class (#34135)Adam J. Stewart1-21/+44
2022-11-28Add restic v0.14.0 (#34148)Alec Scott1-0/+2
2022-11-27direnv: add v2.32.2 (#34147)Alec Scott1-1/+2
2022-11-27rust: add 1.65.0 (#34124)Michael Kuhn1-0/+8
2022-11-27SingularityCE: Add conmon+squashfs as dependencies (#33891)Umashankar Sivakumar1-0/+4
2022-11-27pastix: add new version 6.2.2 (#34066)fpruvost1-2/+3
2022-11-27neovim: fix deptypes (#34060)Harmen Stoppels1-17/+17
2022-11-26py-fastpath: new package (#34142)Luke Diorio-Toth1-0/+21
* py-fastpath: new package * Update var/spack/repos/builtin/packages/py-fastpath/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-11-26emacs: add variant treesitter for Emacs 29+ (#34134)Eric Berquist1-0/+6
2022-11-26prmon: Add missing depends_on py-numpy, py-pandas when +plot (#34123)Wouter Deconinck1-0/+2
2022-11-26aragorn: add newer versions and URL (#34140)Luke Diorio-Toth1-3/+20
2022-11-26minced: add v0.4.2 (#34141)Luke Diorio-Toth1-0/+1
2022-11-26Octopus: branch for Octopus development is now "main" (#34128)Hans Fangohr1-1/+1
Historically, development of the Octopus code was done on the "develop" branch on https://gitlab.com/octopus-code/octopus but now development takes place on "main" (since Q3 2022). The suggestion in this PR to solve the issue is to keep the spack label `octopus@develop` as this better indicates this is the development branch on git than `octopus@main`, but of course to use the `main` branch (there is no choice here - the `develop` branch is not touched anymore). Sticking to `octopus@develop` as the version label also keeps backwards compatibility.
2022-11-26nvtop: Add 2.0.3, 2.0.4, 3.0.0 and 3.0.1 (#34145)marcost21-3/+8
* And add the option to compile support for Intel GPU's
2022-11-26Revert "`url_exists` related improvements (#34095)" (#34144)Satish Balay2-78/+64
This reverts commit d06fd26c9ac8dd525fc129096188e2ea9fd2d0d7. The problem is that Bitbucket's API forwards download requests to an S3 bucket using a temporary URL. This URL includes a signature for the request, which embeds the HTTP verb. That means only GET requests are allowed, and HEAD requests would fail verification, leading to 403 erros. The same is observed when using `curl -LI ...`
2022-11-26amdblis: symlink libblis-mt to libblis (#32819)Carlos Bederián1-0/+10
2022-11-25toml-f: add 0.2.4 and 0.3.1 (#34025)Sebastian Ehlert1-1/+3
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