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2022-12-29Change regex in bacio patch to avoid python re bug (#34668)Alex Richert1-1/+1
2022-12-28bugfix: make texinfo build properly with gettext (#34312)Todd Gamblin1-0/+7
`texinfo` depends on `gettext`, and it builds a perl module that uses gettext via XS module FFI. Unfortunately, the XS modules build asks perl to tell it what compiler to use instead of respecting the one passed to configure. Without this change, the build fails with this error: ``` parsetexi/api.c:33:10: fatal error: 'libintl.h' file not found ^~~~~~~~~~~ ``` We need the gettext dependency and the spack wrappers to ensure XS builds properly. - [x] Add needed `gettext` dependency to `texinfo` - [x] Override XS compiler with `PERL_EXT_CC` Co-authored-by: Paul Kuberry <pakuber@sandia.gov>
2022-12-28Consolidate how Spack uses `git` (#34700)Todd Gamblin26-162/+138
Local `git` tests will fail with `fatal: transport 'file' not allowed` when using git 2.38.1 or higher, due to a fix for `CVE-2022-39253`. This was fixed in CI in #33429, but that doesn't help the issue for anyone's local environment. Instead of fixing this with git config in CI, we should ensure that the tests run anywhere. - [x] Introduce `spack.util.git`. - [x] Use `spack.util.git.get_git()` to get a git executable, instead of `which("git")` everywhere. - [x] Make all `git` tests use a `git` fixture that goes through `spack.util.git.get_git()`. - [x] Add `-c protocol.file.allow=always` to all `git` invocations under `pytest`. - [x] Revert changes from #33429, which are no longer needed.
2022-12-27CPMD: Remove now unused "import"Rémi Lacroix1-2/+0
2022-12-27CPMD: Update for open-source releaseRémi Lacroix1-38/+3
CPMD has been open-sourced on GitHub so manual download is no longer needed. The patches have been included in the new 4.3 release.
2022-12-27spack graph: rework to use Jinja templates and builders (#34637)Massimiliano Culpo6-214/+253
`spack graph` has been reworked to use: - Jinja templates - builder objects to construct the template context when DOT graphs are requested. This allowed to add a new colored output for DOT graphs that highlights both the dependency types and the nodes that are needed at runtime for a given spec.
2022-12-26types: fix type annotations and remove novm annootations for llnl moduleTodd Gamblin2-18/+13
Apparently I forgot to do this in #34305.
2022-12-26timer: pick a single unit based on max duration.Harmen Stoppels3-17/+25
2022-12-26`spack solve`: use consistent units for timeTodd Gamblin2-5/+5
`spack solve` is supposed to show you times you can compare. setup, ground, solve, etc. all in a list. You're also supposed to be able to compare easily across runs. With `pretty_seconds()` (introduced in #33900), it's easy to miss the units, e.g., spot the bottleneck here: ```console > spack solve --timers tcl setup 22.125ms load 16.083ms ground 8.298ms solve 848.055us total 58.615ms ``` It's easier to see what matters if these are all in the same units, e.g.: ``` > spack solve --timers tcl setup 0.0147s load 0.0130s ground 0.0078s solve 0.0008s total 0.0463s ``` And the units won't fluctuate from run to run as you make changes. -[x] make `spack solve` timings consistent like before
2022-12-26qt-base: ~network by default (#34688)Adam J. Stewart1-1/+1
2022-12-24py-pytest-datadir: Init at 1.4.1 (#34692)Rohit Goswami1-0/+21
* py-pytest-datadir: Init at 1.4.1 * py-pytest-data-dir: Fix missing dep Co-authored-by: "Adam J. Stewart" <ajstewart426@gmail.com> Co-authored-by: "Adam J. Stewart" <ajstewart426@gmail.com>
2022-12-24py-uvw: added v0.5.0 (#34677)Lucas Frérot1-0/+1
2022-12-23Update py-meson-python (0.11.0, 0.12.0) and meson (0.64.1, 1.0.0) (#34675)Ralf Gommers2-6/+14
* Update py-meson-python versions (0.11.0, 0.12.0) * Update `meson` to version 0.64.1 * Add Meson 1.0.0 * Apply code review suggestions
2022-12-24tmux: add 3.3a (#34671)David Zmick1-0/+1
2022-12-23QMakeBuilder: fix bug introduced during multi-bs refactor (#34683)Adam J. Stewart1-1/+1
2022-12-22py-kornia: add v0.6.9 (#34652)Adam J. Stewart1-3/+4
2022-12-22libelf: fix build on macOS x86_64 (#34646)Adam J. Stewart1-5/+5
2022-12-22bacio: fix typo in patch method (#34663)Alex Richert1-1/+1
2022-12-22sherpa: add v2.2.13 (#34628)Wouter Deconinck1-0/+1
2022-12-22ML CI: Linux x86_64 (#34299)Adam J. Stewart4-256/+283
* ML CI: Linux x86_64 * Update comments * Rename again * Rename comments * Update to match other arches * No compiler * Compiler was wrong anyway * Faster TF
2022-12-22added py-dynim package (#34651)Loïc Pottier1-0/+26
Signed-off-by: Loïc Pottier <48072795+lpottier@users.noreply.github.com> Signed-off-by: Loïc Pottier <48072795+lpottier@users.noreply.github.com>
2022-12-22Restrict a patch of rhash to versions >=1.3.6 (#34310)Andrew Wood1-1/+1
2022-12-22Fix combine_phase_logs text encoding issues (#34657)Harmen Stoppels2-5/+20
Avoid text decoding and encoding when combining log files, instead combine in binary mode. Also do a buffered copy which is sometimes faster for large log files.
2022-12-22neve: add new package (#34596)Wladimir Arturo Garces Carrillo1-0/+43
Co-authored-by: WladIMirG <WladIMirG@users.noreply.github.com>
2022-12-22Add `--fresh` to docs to actually upgrade spack environments (#34433)Alec Scott1-5/+40
2022-12-22docs: show module documentation before submodules (#34258)Todd Gamblin1-0/+1
Currently, the Spack docs show documentation for submodules *before* documentation for submodules on package doc pages. This means that if you put docs in `__init__.py` in some package, the docs in there will be shown *after* the docs for all submodules of the package instead of at the top as an intro to the package. See, e.g., [the lockfile docs](https://spack.readthedocs.io/en/latest/spack.environment.html#module-spack.environment), which should be at the [top of that page](https://spack.readthedocs.io/en/latest/spack.environment.html). - [x] add the `--module-first` option to sphinx so that it generates module docs at top of page.
2022-12-22docs: remove monitors and analyzers (#34358)Todd Gamblin3-434/+0
These experimental features were removed in #31130, but the docs were not. - [x] remove the `spack monitor` and `spack analyze` docs
2022-12-22librsvg: add 2.40.21, which does not require rust (#34585)Benjamin S. Kirk1-2/+15
* librsvg: add 2.40.21, which does not require rust and has some security backports https://download.gnome.org/sources/librsvg/2.40/librsvg-2.40.21.news * librsvg: prevent finding broken gtkdoc binaries when ~doc is selected. On my CentOS7 hosts, ./configure finds e.g. /bin/gtkdoc-rebase even when ~doc is selected. These tools use Python2, and fail with an error: "ImportError: No module named site" So prevent ./configure from finding these broken tools when not building the +doc variant.
2022-12-22openbabel: add 3.1.0 and 3.1.1 (#34631)Rocco Meli1-0/+4
2022-12-22reframe: rework recipe, add v4.0.0-dev4 (#34584)Vasileios Karakasis1-11/+19
2022-12-22quantum-espresso: enable linking with armpl-gcc and acfl for BLAS and FFT ↵Annop Wongwathanarat1-0/+9
(#34416)
2022-12-22index.json.hash, no fatal error if key cannot be fetched (#34643)Harmen Stoppels2-19/+20
2022-12-22kokkos: add v3.7.01 (#34645)Benjamin Fovet1-1/+2
Co-authored-by: Benjamin Fovet <benjamin.fovet@cea.fr>
2022-12-22py-pytorch-lightning: add v1.8.6 (#34647)Adam J. Stewart1-0/+1
2022-12-22perl-config-simple: add 4.58 (#34649)Christopher Christofi1-0/+15
2022-12-22Using corresponding commit ids of hiprand for each releases (#34545)renjithravindrankannath1-2/+28
2022-12-22bacio: patch for v2.4.1 (#34575)Alex Richert1-0/+4
2022-12-21add py-psij-python and py-pystache packages (#34357)Andre Merzky3-0/+49
* add psij package and deps * update hashes, URLs * linting * Update var/spack/repos/builtin/packages/py-psij-python/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pystache/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pystache/package.py Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> * Update package.py apply suggested change * Update package.py apply suggested change * Update package.py ensure maintainer inheritance * add psij to exaworks meta-package Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-12-21paraview: patch catalyst etc. to build with oneapi (#33562)Howard Pritchard2-0/+48
without this patch, build of paraview has a meltdown when reaching 3rd party catalyst and other packages with these types of errors: 335 /tmp/foo/spack-stage/spack-stage-paraview-5.10.1-gscoqxhhakjyyfirdefuhmi2bzw4scho/spack-src/VTK/ThirdParty/fmt/vtkfmt/vtkfmt/format.h:1732:11: error: cannot capture a bi t-field by reference 336 if (sign) *it++ = static_cast<Char>(data::signs[sign]); 337 ^ Signed-off-by: Howard Pritchard <howardp@lanl.gov> Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2022-12-21json: remove python 2 only code (#34615)Harmen Stoppels3-45/+5
2022-12-21py-cartopy: older versions don't support Python 3.10 (#34626)Adam J. Stewart1-14/+2
2022-12-21podio: add v0.16.2 (#34606)Thomas Madlener1-0/+1
2022-12-21relion: add v4.0.0 (#34600)Hector Martinez-Seara1-8/+5
2022-12-21glib: add 2.74.3 (#34603)Michael Kuhn1-0/+1
2022-12-21rocm: make amdgpu_target sticky (#34591)Cory Bloor11-11/+14
The sticky property will prevent clingo from changing the amdgpu_target to work around conflicts. This is the same behaviour as was adopted for cuda_arch in 055c9d125d29606947f2fd88a06e279667a74648.
2022-12-21eckit: skip broken test (#34610)Sergey Kosukhin1-1/+20
2022-12-21hpctoolkit: replace filter_file with upstream patch (#34604)Mark W. Krentel1-15/+7
Replace the filter_file for older configure with rocm 5.3 with an upstream patch. Further, the patch is no longer needed for develop or later releases.
2022-12-21dashan-runtime,darshan-util,py-darshan: update package versions for ↵shanedsnyder3-3/+12
darshan-3.4.2 (#34583)
2022-12-21arm-forge: add 22.1.2 (#34569)louisespellacy-arm1-0/+9
2022-12-21starpu: add conflict for ~blocking +simgrid (#34616)lpoirel1-0/+1
see https://gitlab.inria.fr/starpu/starpu/-/commit/1f5a911d43ba8e49f7229ab16f5dafdfdd596bd2