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Bumps [isort](https://github.com/pycqa/isort) from 5.12.0 to 5.13.2.
- [Release notes](https://github.com/pycqa/isort/releases)
- [Changelog](https://github.com/PyCQA/isort/blob/main/CHANGELOG.md)
- [Commits](https://github.com/pycqa/isort/compare/5.12.0...5.13.2)
---
updated-dependencies:
- dependency-name: isort
dependency-type: direct:production
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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Bumps [isort](https://github.com/pycqa/isort) from 5.12.0 to 5.13.2.
- [Release notes](https://github.com/pycqa/isort/releases)
- [Changelog](https://github.com/PyCQA/isort/blob/main/CHANGELOG.md)
- [Commits](https://github.com/pycqa/isort/compare/5.12.0...5.13.2)
---
updated-dependencies:
- dependency-name: isort
dependency-type: direct:production
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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Since views use symlinks, all compiler binaries were skipped in this
case. Instead, only skip them if their target does not exist.
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Can also be an environment root, or programatically
`Spec("x").concretized()`.
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Convert the 'develop' section of an environment to a dedicated configuration section.
This means for example that instead of having to define `develop` specs in the
`spack.yaml`, the environment can `include:` another `develop.yaml` configuration
which specifies which specs should be developed in the environment.
This change is not expected to be disruptive given that existing environment `spack.yaml`
files will conform to the new schema.
(Update 11/28/2023) I have implemented the `develop`/`undevelop` commands in terms
of more-generic modification functions added to the `config` module: `change_or_add`
and `update_all`. It is assumed that the semantics added here (described in 11/18 update)
would be desirable to extend to other config update actions (e.g. adding compilers,
changing package requirements, adding mirrors).
(Update 11/18/2023) I have updated this such that `spack develop`, and
`spack undevelop` to potentially modify all writable scopes, like
https://github.com/spack/spack/pull/41147. https://github.com/spack/spack/pull/35307
will be useful for modifying included scopes, but generally speaking specifying a
`--scope` will not be required for `spack develop`: `spack develop` will add new
develop specs to whatever scope already has develop specs defined, or to the
highest-priority writable scope (which should be the env scope).
TODOs:
- [x] If you `spack undevelop` a package which is mentioned at multiple layers of
configuration, then currently this would only modify one of them. That's not
technically a new issue (has always existed for configuration modification), but
may be confusing to users when presented via an interface other than `spack config set`
- [x] Need to add (or confirm) the ability to modify individual config files by providing
a path (rather than using a scope identifier as a key to retrieve associated config).
- [x] `spack develop` adds new develop specs to the scope that defines them
(potentially skipping higher priority scopes to e.g. augment included scope files)
---------
Co-authored-by: scheibelp <scheibelp@users.noreply.github.com>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
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* py-plum-dispatch: add new package
* Update var/spack/repos/builtin/packages/py-plum-dispatch/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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* py-htgettoken: use os.environ, avoid AttributeError
This avoids the following error:
```
Warning: could not load runtime environment due to AttributeError: 'EnvironmentModifications' object has no attribute 'get'
```
* py-htgettoken: allow for undefined variables
* py-htgettoken: use dict get()
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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* Update for v0.7.2
* Dependency fix
* Dep type fix
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* py-optax: add new package with version 0.1.7
* Update var/spack/repos/builtin/packages/py-optax/package.py
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
---------
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
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Add pygame to spack
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* py-poetry: Add version 1.6.1
* py-poetry-core: Add version 1.7.0
* py-dulwich: Add version 0.21.6
* py-installer: Add version 0.7.0
* py-keyring: Add version 24.3.0
* py-poetry-plugin-export: Add version 1.6.0
* py-cachecontrol: Add version 0.13.0
* py-xattr: Add version 0.10.1, py-poetry dependence on darwin platform
* py-cachecontrol: fix typo
* py-cachecontrol: add version 0.13.1
* py-dulwich: remove version constraint on python, sort dependences, add py-typing-extensions dependence
* py-poetry-core: add version constraint on python
* py-poetry-plugin-export: fix python dependence, sort dependences
* py-poetry: sort dependences, fix dependences with respect to reviewing
* py-cachecontrol: fix typo
* py-poetry-plugin-export: comment py-poetry dependence; py-poetry: fix py-build dependence
---------
Co-authored-by: LydDeb <lyderic.debusschere@eolen.com>
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* libfabric: Add uring variant
* Remove tcp fabric requirement for uring
* Fix style and use spec.satisfies
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Adds Rose::Object
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Adds Compress::LZO
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* mpifileutils: add DAOS variant
* mpifileutils: Add daos dep when +daos
Add dependency on DAOS when +daos
Pass DAOS prefix to ensure correct DAOS is found by during configuration
* Change in to satisfies for boolean variants
---------
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
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Co-authored-by: github-actions <github-actions@users.noreply.github.com>
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Adds Test::Base
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* perl-datetime-format-strptime: New package
Adds package:
- perl-datetime-format-strptime
And adds these because they are test dependencies:
- perl-test-file-sharedir
- perl-test2-plugin-nowarnings
- perl-test2-suite
And modifies these to enable build time tests:
- perl-b-hooks-endofscope
- perl-class-singleton
- perl-datetime-locale
- perl-datetime-timezone
- perl-file-sharedir
- perl-namespace-autoclean
- perl-namespace-clean
- perl-params-validationcompiler
- perl-specio
* Add myself as maintainer
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* add new cpp compiler version
* empty ftn for 2023.2.3
* OLD ftn in 2023.2.3 version
* tolerate missing fortran compiler
---------
Co-authored-by: Robert Cohn <robert.s.cohn@intel.com>
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This adds a small (~5%) performance improvement to Spec parsing.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
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(#41640)
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* geant4: new version 11.2.0
* geant4: depends_on geant4-data@11.2:
* geant4-data: new version 11.2.0
* g4abla: new version 3.3
* g4emlow: new version 8.4
* g4incl: new version 1.1
* geant4: depends_on vecgeom@1.2.6:
* geant4: depends_on qt@5.9: when @11.2: +qt
* vecgeom: new version 1.2.6
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This PR does several things:
- [x] Allow any character to appear in the quoted values of variants and flags.
- [x] Allow easier passing of quoted flags on the command line, e.g. `cflags="-O2 -g"`.
- [x] Handle quoting better in spec output, using single quotes around double
quotes and vice versa.
- [x] Disallow spaces around `=` and `==` when parsing variants and flags.
## Motivation
This PR is motivated by the issues above and by ORNL's
[tips for launching at scale on Frontier](https://docs.olcf.ornl.gov/systems/frontier_user_guide.html#tips-for-launching-at-scale).
ORNL recommends using `sbcast --send-libs` to broadcast executables and their
libraries to compute nodes when running large jobs (e.g., 80k ranks). For an
executable named `exe`, `sbcast --send-libs` stores the needed libraries in a
directory alongside the executable called `exe_libs`. ORNL recommends pointing
`LD_LIBRARY_PATH` at that directory so that `exe` will find the local libraries and
not overwhelm the filesystem.
There are other ways to mitigate this problem:
* You could build with `RUNPATH` using `spack config add config:shared_linking:type:runpath`,
which would make `LD_LIBRARY_PATH` take precedence over Spack's `RUNPATHs`.
I don't recommend this one because `RUNPATH` can cause many other things to go wrong.
* You could use `spack config add config:shared_linking:bind:true`, added in #31948, which
will greatly reduce the filesystem load for large jobs by pointing `DT_NEEDED` entries in
ELF *directly* at the needed `.so` files instead of relying on `RPATH` search via soname.
I have not experimented with this at 80,000 ranks, but it should help quite a bit.
* You could use [Spindle](https://github.com/hpc/Spindle) (as LLNL does on its machines)
which should transparently fix this without any changes to your executable and without
any need to use `sbcast` or other tools.
But we want to support the `sbcast` use case as well.
## `sbcast` and Spack
Spack's `RPATHs` break the `sbcast` fix because they're considered with higher precedence
than `LD_LIBRARY_PATH`. So Spack applications will still end up hitting the shared filesystem
when searching for libraries. We can avoid this by injecting some `ldflags` in to the build, e.g.,
if were were going to launch, say, `LAMMPS` at scale, we could add another `RPATH`
specifically for use with `sbcast`:
spack install lammps ldflags='-Wl,-rpath=$ORIGIN/lmp_libs'
This will put the `lmp_libs` directory alongside `LAMMPS`'s `lmp` executable first in the
`RPATH`, so it will be searched before any directories on the shared filesystem.
## Issues with quoting
Before this PR, the command above would've errored out for two reasons:
1. `$` wasn't an allowed character in our spec parser.
2. You would've had to double quote the flags to get them to pass through correctly:
spack install lammps ldflags='"-Wl,-rpath=$ORIGIN/lmp_libs"'
This is ugly and I don't think many users will easily figure it out. The behavior was added in
#29282, and it improved parsing of specs passed as a single string, e.g.:
spack install 'lammps ldflags="-Wl,-rpath=$ORIGIN/lmp_libs"'
but a lot of users are naturally going to try to quote arguments *directly* on the command
line, without quoting their entire spec. #29282 used a heuristic to detect unquoted flags
and warn the user, but the warning could be confusing. In particular, if you wrote
`cflags="-O2 -g"` on the command line, it would break the flags up, warn, and tell you
that you could fix the issue by writing `cflags="-O2 -g"` even though you just wrote
that. It's telling you to *quote* that value, but the user has to know to double quote.
## New heuristic for quoted arguments from the CLI
There are only two places where we allow arbitrary quoted strings in specs: flags and
variant values, so this PR adds a simpler heuristic to the CLI parser: if an argument in
`sys.argv` starts with `name=...`, then we assume the whole argument is quoted.
This means you can write:
spack install bzip2 cflags="-O2 -g"
directly on the command line, without multiple levels of quoting. This also works:
spack install 'bzip2 cflags="-O2 -g"'
The only place where this heuristic runs into ambiguity is if you attempt to pass
anonymous specs that start with `name=...` as one large string. e.g., this will be
interpreted as one large flag value:
spack find 'cflags="-O2 -g" ~bar +baz'
This sets `cflags` to `"-O2 -g" ~bar +baz`, which is likely not what you wanted. You
can fix this easily by either removing the quotes:
spack find cflags="-O2 -g" ~bar +baz
Or by adding a space at the start, which has the same effect:
spack find ' cflags="-O2 -g" ~bar +baz'
You may wonder why we don't just look for quotes inside of flag arguments, and the
reason is that you *might* want them there. If you are passing arguments like:
spack install zlib cppflags="-D DEBUG_MSG1='quick fox' -D DEBUG_MSG2='lazy dog'"
You *need* the quotes there. So we've opted for one potentially confusing, but easily
fixed outcome vs. limiting what you can put in your quoted strings.
## Quotes in formatted spec output
In addition to being more lenient about characters accepted in quoted strings, this PR fixes
up spec formatting a bit. We now format quoted strings in specs with single quotes, unless
the string has a single quote in it, in which case we JSON-escape the string (i.e., we add
`\` before `"` and `\`).
zlib cflags='-D FOO="bar"'
zlib cflags="-D FOO='bar'"
zlib cflags="-D FOO='bar' BAR=\"baz\""
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* adding necessary headers, to fix https://github.com/spack/spack/issues/41398
* deleting something imported by accident
* [@spackbot] updating style on behalf of yizeyi18
* undo commit 7688fed according to suggestion from @msimberg
* patching camp@:2022.10.1 for compatibility with gcc-13
* adding the patch
* fixing paths in the patch
* [@spackbot] updating style on behalf of yizeyi18
* Update camp patch using LLNL/camp@05e1c35
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
* changing patch name
---------
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
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`setup_dependent_package` is not a build phase, it should just set
globals for a package.
It's called during setup of runtime environment of packages, and there
have been reports of it actually failing due to a read only file system
(not sure under what exact conditions that is possible).
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