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2023-01-23environments: don't replace relative view path with absolute path on ↵Harmen Stoppels4-4/+48
concretize/install (#34958) * environments: don't rewrite relative view path, expand path on cli ahead of time Currently if you have a spack.yaml that specifies a view by relative path, Spack expands it to an absolute path on `spack -e . install` and persists that to disk. This is rather annoying when you have a `spack.yaml` file inside a git repo, cause you want to use relative paths to make it relocatable, but you constantly have to undo the changes made to spack.yaml by Spack. So, as an alternative: 1. Always stick to paths as they are provided in spack.yaml, never replace them with a canonicalized version 2. Turn relative paths on the command line into absolute paths before storing to spack.yaml. This way you can do `spack env create --dir ./env --with-view ./view` and both `./env` and `./view` are resolved to the current working dir, as expected (not `./env/view`). This corresponds to the old behavior of `spack env create`. * create --with-view always takes a value
2023-01-23apptainer: add v1.1.5 (#35075)Massimiliano Culpo1-0/+1
2023-01-23e4s: add cusz +cuda (#35004)eugeneswalker1-0/+1
2023-01-23`py-pytest-mock`: add v3.10.0 (#35074)Thomas Bouvier1-1/+7
2023-01-22`py-datasets`: add v2.8.0 (#35069)Thomas Bouvier1-6/+17
* `py-datasets`: add v2.8.0 * Add missing +http variant + fix wrong dependency versions
2023-01-22axom: need to specify +rocm as part of dependency constraints (#35066)eugeneswalker1-6/+8
* axom: need to specify +cuda, +rocm as part of dependency constraints * remove lines 120, 128 * fix line length, spack style issue
2023-01-22`arrow`: don't use `when` as a keyword argument to filter_file() (#35065)Thomas Bouvier1-13/+13
Co-authored-by: thomas-bouvier <thomas-bouvier@users.noreply.github.com>
2023-01-21Add --exclude option to 'spack external find' (#35013)Alex Richert3-1/+25
* Add --exclude option to 'spack external find' to ignore user-specified external packages * Update bash completion arg order for external find Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2023-01-21`py-wandb`: add v0.13.9 (#35059)Thomas Bouvier1-12/+39
* `py-wandb`: add v0.13.9 * `py-wandb`: mark v0.10.1 as deprecated * Fixes suggested by @adamjstewart * No platform-specific requirements
2023-01-21py-numba: fix py-numpy version dependencies (#35054)Dylan Simon1-1/+1
as per #34362 comments
2023-01-21gmake: bootstrap without make (#35050)Harmen Stoppels1-11/+17
2023-01-21fms: add 32bit variant, add protections (#35010)Matthew Thompson1-7/+13
The GEOS Earth System Model currently requires the 32-bit variant of FMS. This PR adds that variant.
2023-01-20Windows/testing: enable tests for "spack find" (#33588)markus-ferrell3-15/+25
2023-01-20Identify Windows support with tags (#35027)John W. Parent27-29/+34
All packages with explicit Windows support can be found with `spack list --tags=windows`. This also removes the documentation which explicitly lists supported packages on Windows (which is currently out of date and is now unnecessary with the added tags). Note that if a package does not appear in this list, it *may* still build on Windows, but it likely means that no explicit attempt has been made to support it.
2023-01-20netlib-lapack: Fix Fortran detection for XL (#35048)QuellynSnead1-1/+1
* PR 30738 introduced changes in how we access compiler info. Looks like the XL case got missed.
2023-01-20libbsd: bump (#35029)Harmen Stoppels1-0/+2
2023-01-20Add package `py-imagehash` (#35015)Thomas Bouvier1-0/+23
* Add package `py-imagehash` * Use virtual package for `py-pillow`
2023-01-20flex%oneapi@2023.0.0: -Wno-error=implicit-function-declaration (#34900)eugeneswalker1-0/+4
2023-01-20Allocate more memory for generate jobs in all stacks (#35040)Zack Galbreath1-11/+2
* Allocate more memory for generate jobs in all stacks * Add a 60 minute timeout on generate jobs
2023-01-20ca-certificates-mozilla: 2023-01-10 (#35018)Harmen Stoppels1-0/+5
2023-01-20libiconv: bump (#35035)Harmen Stoppels1-0/+1
2023-01-20ncurses: bump (#35033)Harmen Stoppels1-0/+1
2023-01-20sqlite: bump (#35032)Harmen Stoppels1-0/+1
2023-01-20hypre: add option for sycl variant (#34987)eugeneswalker1-0/+13
* hypre: add option for sycl variant * hypre +sycl conflicts with @:2.23 * hypre +sycl: raise InstallError for unsupported compiler
2023-01-20Add nf-core-tools, and three remainder deps (#34466)Marco De La Pierre8-1/+199
* nextflow recipe: added latest stable version * tower-cli recipe: added latest release * recipes tower-agent and tower-cli renamed to nf-tower-agent and nf-tower-cli * recipes nf-tower-agent and nf-tower-cli: small fix * nf-core-tools recipe: added most py- dependencies * nf-core-tools: recipe without galaxy-tool-util (for testing) * fixed typos in py-yacman recipe * fixed typos in py-pytest-workflow recipe * fixed typo in nf-core-tools recipe * fixed typos in py-yacman recipe * fixes in recipes for py-questionary and py-url-normalize * fixes to py-yacman recipe * style fixes to py- packages that are dependencies to nf-core-tools * fix in py-requests-cache recipe * added missing dep in py-requests-cache recipe * nf-core-tools deps: removed redundant python dep for py packages oyaml and piper * nf-core-tools recipe: final, incl dep on py-galaxy-tool-util * nf-core-tools: new version with extra dependency * added py-galaxy-util, draft: added some required dep versions, still have to add 40+ deps * nextflow and nf-core-tools packages: added my self as maintainer * style fixes * style fix for nf-core-tools recipe * added license to py-logmuse recipe * audit fixes * style fix after audit fix * py-galaxy-tool-util: added deps 1st bunch * audit/style fixes, including adding missing dep package * more audit/style fixes * more more audit/style fixes * moooore audit fixes * py-galaxy-tool-util: dependencies 2nd chunk * silly audit fix * py-galaxy-util deps: 3rd bunch - first 20 done * fixes * style fix * py-galaxy-tool-util: 4th bunch of deps * stashing dep recipe backbones for py-galaxy-tool-util * nf-core-tools: using pre-built wheel for dependency py-galaxy-tool-util * nf-core-tools: adding also py-galaxy-util, as wheel * fix * nextflow: added latest bugfix version * Update var/spack/repos/builtin/packages/nf-core-tools/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/nf-core-tools/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * nf-core-tools pr: 1st bunch of review edits * nf-core-tools: 2nd bunch of review edits * adding back tower-agent and tower-cli as deprecated * nf-core-tools: 3rd bunch of review edits * small style fix * prepping py-galaxy-tool-util for further work * nf-core-tools: last bunch of deps, except for galaxy-tool-util and pulsar * audit fixes * updates to py-galaxy-tool-util and its deps, still 2 to work on * one style fix * updated recipe for py-galaxy-util * updated recipe for py-pulsar-galaxy-lib * typo fix * shasum fixes * updated py-sqlalchemy from develop * added newest versions (today) for nf-tower-agent and nf-tower-cli * Update var/spack/repos/builtin/packages/py-requests-cache/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-requests-cache/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * adding 2nd bunch of nf-core deps from update/nextflow-tools * adding 3rd bunch of nf-core deps from update/nextflow-tools * 4th chunk of nf-core deps from update/nextflow-tools * Update var/spack/repos/builtin/packages/py-dnspython/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-dnspython/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-dnspython/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pastedeploy/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pebble/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-fastapi/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-fastapi/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-gunicorn/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-starlette/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-starlette/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-starlette/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-parsley/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-paste/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-paste/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * py-gxformat2: added comment * py-lagom: now using github tarballs * fix for py-lagom * adding missing deps to py-fastapi-utils * another fix to py-lagom * Update var/spack/repos/builtin/packages/py-dnspython/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-lagom/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-supervisor/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-social-auth-core/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * fixes from PR review * adding missing deps, from PR review * py-galaxy2cwl from github tarball, as per PR review * fix to py-tuswsgi, as per PR review * nf-tools: edits from PR review * adding 3x more galaxy deps * fix * fixing circular dep of py-poetry-plugin-export with py-poetry * added newest nf-core-tools version * Update var/spack/repos/builtin/packages/py-galaxy-util/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * fix in py-poetry-plugin-export Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-20file: zstd support (#35041)Harmen Stoppels1-1/+4
2023-01-20Add type hints to DependencySpec (#35021)Massimiliano Culpo2-16/+18
* DependencySpec: add type hints * DependencySpec: make deptypes a keyword only argument
2023-01-20libidn2: bump (#35034)Harmen Stoppels1-0/+4
2023-01-19libffi: bump (#35030)Harmen Stoppels1-0/+1
2023-01-19Fix string append in OpenCV package (#35008)Tal Ben-Nun1-3/+5
* Fix string append in OpenCV package * style
2023-01-19qmcpack: enable linking with armpl-gcc and acfl for BLAS and FFT (#34496)Annop Wongwathanarat1-0/+11
2023-01-20e4s: ecp-data-vis-sdk +rocm: remove redundant amdgpu_target specification ↵eugeneswalker1-1/+1
(#35022)
2023-01-19libunistring: bump to 1.1 (#35031)Harmen Stoppels1-0/+2
2023-01-19py-pandas: add v1.5.3 (#35025)Adam J. Stewart1-0/+1
2023-01-19nmap: don't depend on py2 (ndiff and zenmap); add 7.93 (#34851)David Zmick1-5/+33
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-01-19file: bump (#35028)Harmen Stoppels1-0/+2
2023-01-19pfunit: fix max_array_rank variant (#34952)fMatthew Thompson1-3/+7
2023-01-19HDF5: supports external detection (#34940)Brian Van Essen1-0/+75
2023-01-19buildcache create: make "file exists" less verbose (#35019)Harmen Stoppels1-3/+3
Currently we print 3 lines of "file exist" warning per tarball, this is a bit excessive. Instead, it can be a simple single-line tty.warn message.
2023-01-19python: remove `CPATH` from `setup_run_environment` (#34727)Todd Gamblin1-3/+0
Currently, the `python` package tries to set `CPATH` in `setup_run_environment()`. We no longer set `CPATH` and other destructive environment variables (like `LD_LIBRARY_PATH`) in modules, so we shouldn't do something special for Python. Also, the way `python` sets `CPATH` causes issues. Because it does a header search to find directories containing headers, if you bootstrap `mypy` or other style tools on a fresh Ubuntu image with *no* python devel headers installed, you'll get an error like this when trying to load the thing you just installed: ```console [root@980de539843d /]# spack -b load py-mypy ==> Error: Unable to locate python headers in any of these locations: /usr/include/python3.6m /usr/include/3.6 /usr/Headers ``` The headers and includes aren't needed to get `mypy` in the path or for `mypy` to work, so we're failing unnecessarily here. - [x] remove `setup_run_environment()` from `python/package.py`
2023-01-19[py-numpy, py-scipy] Enable MKL & ARMpl (#34979)Stephen Sachs3-10/+15
2023-01-19depfile: --make-target-prefix -> --make-prefix (#35009)Harmen Stoppels4-22/+22
Since SPACK_PACKAGE_IDS is now also "namespaced" with <prefix>, it makes more sense to call the flag `--make-prefix` and alias the old flag `--make-target-prefix` to it.
2023-01-19git: bump. CVE-2022-41903 / CVE-2022-23521 (#35014)Harmen Stoppels1-8/+64
Co-Authored-By: Alec Scott <scott112@llnl.gov> Co-authored-by: Alec Scott <scott112@llnl.gov>
2023-01-18hpctoolkit: update cray support (#34995)Mark W. Krentel1-17/+33
1. add variant cray-static, older crays build hpcprof-mpi static, newer ones build dynamic. 2. move URL patches from github to gitlab. 3. add workaround for a bug where a file is mistakenly overwritten. 4. add conflict for hpcprof-mpi at 2022.10.01. * [@spackbot] updating style on behalf of mwkrentel Co-authored-by: mwkrentel <mwkrentel@users.noreply.github.com>
2023-01-18e4s ci: clean up unnecessary constraints (#35006)eugeneswalker1-17/+11
2023-01-18e4s: add sz3 (#35007)eugeneswalker1-0/+1
2023-01-18e4s ci: add veloc (#35003)eugeneswalker1-0/+1
2023-01-18VTK: fix 9.1–9.2 builds (#34589)Adam J. Stewart1-7/+12
* VTK: add missing dependencies * Deal with missing verdict dep * http -> https * Add patch to fix failing cmake * Update netcdf-cxx usage in build recipe * netcdf-cxx4 doesn't work
2023-01-18Bugfix: External Python Extensions (#34202)Greg Becker4-20/+207
Normally when using external packages in concretization, Spack ignores all dependencies of the external. #33777 updated this logic to attach a Python Spec to external Python extensions (most py-* packages), but as implemented there were a couple issues: * this did not account for concretization groups and could generate multiple different python specs for a single DAG * in some cases this created a fake Python spec with insufficient details to be usable (concretization/installation of the extension would fail) This PR addresses both of these issues: * For environment specs that are concretized together, external python extensions in those specs will all be assigned the same Python spec * If Spack needs to "invent" a Python spec, then it will have all the needed details (e.g. compiler/architecture)
2023-01-18license year bump (#34921)Harmen Stoppels7749-7777/+7780
* license bump year * fix black issues of modified files * mypy * fix 2021 -> 2023
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