Full merge from upstream 2023-09-21 #192
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* cgns: Add -fPIC to Fortan/C compilation flags This should fix spack#39699 * cgns: Add -fPIC compilation flags when +fortran Incorporating suggestions of @aumuell with addition of making +pic required when +fortran
* seacas: Set TPL_ENABLE_Pthread=ON when +thread_safe This should fix spack#39702 Basically, following suggestion of error message and setting TPL_ENABLE_Pthread to the value of the boolean spack variant thread_safe * seacas: Fix style issue Add space after comment #
The condition probably did not get updated when the behavior of the version specifier changed.
* r-tinytiger: Add tinytiger R package. * Fix homepage. --------- Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Add Figcone Package * Fix the style * add url * fix style removing whitespace of a blanck line * remove versions
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Unzip required during build otherwise configuration of luarocks fails during installation of lua@5.3.6 on ubuntu 22.04 w/o system unzip.
…k#39855) Co-authored-by: github-actions <github-actions@users.noreply.github.com>
* neko: add v0.6.1 and fix package * Change to a conditional variant for gslib
* allow to build latest version of cp2k with cmake * apply black
Edit configuration file to use the Spack compiler wrappers.
* Write timing information for installs from cache * CI: aggregate and upload install_times.json to artifacts * CI: Don't change root directory for artifact generation * Flat event based timer variation Event based timer allows for easily starting and stopping timers without wiping sub-timer data. It also requires less branching logic when tracking time. The json output is non-hierarchical in this version and hierarchy is less rigidly enforced between starting and stopping. * Add and write timers for top level install * Update completion * remove unused subtimer api * Fix unit tests * Suppress timing summary option * Save timers summaries to user_data artifacts * Remove completion from fish * Move spack python to script section * Write timer correctly for non-cache installs * Re-add hash to timer file * Fish completion updates * Fix null timer yield value * fix type hints * Remove timer-summary-file option * Add "." in front of non-package timer name --------- Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com> Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
* Docs/Packaging guide: Add BundlePackage * Adjusted version ordering note to reflect convention.
…k#39883) Bumps [pytest](https://github.com/pytest-dev/pytest) from 7.4.1 to 7.4.2. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@7.4.1...7.4.2) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Perform external spec detection with multiple workers The logic to perform external spec detection has been refactored into classes. These classes use the GoF "template" pattern to account for the small differences between searching for "executables" and for "libraries", while unifying the larger part of the algorithm. A ProcessPoolExecutor is used to parallelize the work. * Speed-up external find by tagging detectable packages automatically Querying packages by tag is much faster than inspecting the repository, since tags are cached. This commit adds a "detectable" tag to every package that implements the detection protocol, and external detection uses it to search for packages. * Pass package names instead of package classes to workers The slowest part of the search is importing the Python modules associated with candidate packages. The import is done serially before we distribute the work to the pool of executors. This commit pushes the import of the Python module to the job performed by the workers, and passes just the name of the packages to the executors. In this way imports can be done in parallel. * Rework unit-tests for Windows Some unit tests were doing a full e2e run of a command just to check a input handling. Make the test more focused by just stressing a specific function. Mark as xfailed 2 tests on Windows, that will be fixed by a PR in the queue. The tests are failing because we monkeypatch internals in the parent process, but the monkeypatching is not done in the "spawned" child process.
Smart alias completion introduced in spack#39499 wasn't as smart as it needed to be, and would complete any invalid command prefix and some env names with alias names. - [x] don't complete aliases if there are no potential completions e.g., don't convert `spack isnotacommand` -> `spack concretize` - [x] don't complete with an aliases if we're not looking at a top-level subcommand.
Extensionless archives requiring two-stage decompression and extraction require intermediate archives to be renamed after decompression/extraction to prevent collision. Prior behavior attempted to cleanup the intermediate archive with the original name, this PR ensures the renamed folder is cleaned instead. Co-authored-by: Dan Lipsa <dan.lipsa@khq.kitware.com> Co-authored-by: John Parent <john.parent@kitware.com>
* Cloverleaf-ref: proposal for a -ref version only * Cloverleaf-ref: fixing typo. --------- Co-authored-by: fpanichi <fpanichi@amd.com>
…#39875) Enclose variable tracking root in quotes.
* updates for VELOC 1.6 * veloc: add v1.7 --------- Co-authored-by: Bogdan Nicolae <bogdan.nicolae@acm.org>
* [add] py-ansimarkup: new recipe required by py-cylc-flow * py-ansimarkup: remove version constraint on python, add version 2.1.0
Co-authored-by: sbulut <sbulut@3vgeomatics.com>
Put back normalization of the "virtuals" input as a sorted tuple. Without this we might get edges that differ just for the order of virtuals, or that have lists, which are not hashable. Add unit-tests to prevent regressions.
…ured
This looks to me like the best compromise regarding externals in a
buildcache. I wouldn't want `spack install` on my machine to install
specs that were marked external on another. At the same time there are
centers that control the target systems on which spack is used, and
would want to use external in buildcaches.
As a solution, reuse concretization will now consider those externals
used in buildcaches that match a locally configured external in
packages.yaml.
So for example person A installs and pushes specs with this config:
```yaml
packages:
ncurses:
externals:
- spec: ncurses@6.0.12345 +feature
prefix: /usr
```
and person B concretizes and installs using that buildcache with the
following config:
```yaml
packages:
ncurses:
externals:
- spec: ncurses@6
prefix: /usr
```
the spec will be reused (or rather, will be considered for reuse...)
…tream-merge-2023-09-21
…utation (spack#39868) Co-authored-by: matooley <phil.tooley@amd.com>
Fixes spack#39622 Add a timeout to compiler detection and allow Spack to proceed when this timeout occurs. In all cases, the timeout is 120 seconds: it is assumed any compiler invocation we do for the purposes of verifying it would resolve in that amount of time. Also refine executables that are tested as being possible MSVC instances, and limit where we try to detect MSVC. In more detail: * Compiler detection should timeout after a certain period of time. Because compiler detection executes arbitrary executables on the system, we could encounter a program that just hangs, or even a compiler that hangs on a license key or similar. A timeout prevents this from hanging Spack. * Prevents things like cl-.* from being detected as potential MSVC installs. cl is always just cl in all cases that Spack supports. Change the MSVC class to indicate this. * Prevent compilers unsupported on certain platforms from being detected there (i.e. don't look for MSVC on systems other than Windows). The first point alone is sufficient to address spack#39622, but the next two reduce the likelihood of timeouts (which is useful since those slow down the user even if they are survivable).
…39991) * [add] py-graphql-ws: new recipe, required by py-cylc-uiserver * py-graphql-ws: remove constraint on version for python
* py-nanobind add cmake path * fix style --------- Co-authored-by: Robert Underwood <runderwood@anl.gov>
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Add missing `linux` platform in Charm++ when building for `arm8`.
…ck#40125) * py-fenics-dolfinx: add upper bound on Python version * Small fix * Update var/spack/repos/builtin/packages/py-fenics-dolfinx/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
…ream-merge-2023-09-21
Be less specific about gettext with ~libxml2 can use libc+iconv or gettext with or without libxml2 initial round of ups compatability from prev release readonly bootstrap (cvmfs) workaround package updates from fnal-develop added ups compat files more missing files moderncmakedomain package per_os_scope Redo of FNALssi/spack spack#94 redo of FNALssi spack#162 Revert "redo of FNALssi spack#162" This reverts commit f92ed6e. Someone fixed the geant4 recipe with a for loop in the recipe instead, so not doing this after all. redo of FNALssi spack#161 more cleanups from fnal-develop More lib64 fun speling of startswith version
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There are issues with binary_distribiution.py. |
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Argh. I was fixing those! Just going to force-remerge. |
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Full merge of upstream into fnal-develop as of 2023-09-21.