Commit graph

35954 commits

Author SHA1 Message Date
Harmen Stoppels
5e9c702fa7 gcc: use -idirafter for libc headers (#44081)
GCC C++ headers like cstdlib use `#include_next <stdlib.h>` to wrap libc
headers. We're using `-isystem` for libc, which puts those headers too
early in the search path. `-idirafter` fixes this so `include_next`
works.
2024-05-08 20:45:39 +02:00
Harmen Stoppels
965bb4d3c0 gitlab ci: tutorial: add julia and vim (#44073) 2024-05-08 14:19:22 +02:00
Todd Gamblin
354f98c94a r: patch R-CVE-2024-27322 for r@3.5:4.3.3 (#44050)
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
2024-05-08 14:19:22 +02:00
Tamara Dahlgren
5dce480154 Remove dead environment creation code (#44065) 2024-05-08 14:19:22 +02:00
Richarda Butler
f634d48b7c Include concrete environments with include_concrete (#33768)
Add the ability to include any number of (potentially nested) concrete environments, e.g.:

```yaml
   spack:
     specs: []
     concretizer:
         unify: true
     include_concrete:
     - /path/to/environment1
     - /path/to/environment2
```

or, from the CLI:

```console
   $ spack env create myenv
   $ spack -e myenv add python
   $ spack -e myenv concretize
   $ spack env create --include-concrete myenv included_env
```

The contents of included concrete environments' spack.lock files are
included in the environment's lock file at creation time. Any changes
to included concrete environments are only reflected after the environment
is re-concretized from the re-concretized included environments.

- [x] Concretize included envs
- [x] Save concrete specs in memory by hash
- [x] Add included envs to combined env's lock file
- [x] Add test
- [x] Update documentation

    Co-authored-by: Kayla Butler <<butler59@llnl.gov>
    Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.co
m>
    Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
    Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
2024-05-08 14:19:22 +02:00
Massimiliano Culpo
4daee565ae Update the tutorial command to point to releases/v0.22 (#44056) 2024-05-08 14:19:22 +02:00
Massimiliano Culpo
8e4dbdc2d7 Bump removal version in deprecation messages (#44064) 2024-05-08 14:19:22 +02:00
Harmen Stoppels
4f6adc03cd gitlab: dont build paraview for neoverse v2 (#44060) 2024-05-08 14:19:22 +02:00
Massimiliano Culpo
f7afd67a26
Remove spurious ASP debug lines (#44051) 2024-05-07 11:28:38 +02:00
psakievich
d22bdc1c4e
certs: fix interpolation and disallow relative paths (#44030) 2024-05-07 11:16:32 +02:00
Mikael Simberg
540f9eefb7
mold: Add 2.30.0 and 2.31.0 (#44034) 2024-05-07 10:41:13 +02:00
Massimiliano Culpo
2db5bca778
Warn users of the future removal of platform=cray (#43980) 2024-05-07 10:30:23 +02:00
Harmen Stoppels
bcd05407b8
llnl.util.tty.color._force_color: init in global scope (#44036)
Currently SPACK_COLOR=always is not respected in the build process on
macOS, because the global `_force_color` is re-evaluated in global scope
during module setup, where it is always `None`.

So, move global init bits from main.py to the module itself.
2024-05-07 09:49:46 +02:00
John W. Parent
b35ec605fe
python-venv: use correct python name for which call (#44048) 2024-05-07 09:32:44 +02:00
Massimiliano Culpo
0a353abc42
Fix issues in packages with the new release of archspec (#44037) 2024-05-07 09:20:34 +02:00
Massimiliano Culpo
e178c58847
Respect requests when filtering reused specs (#44042)
Some specs which were excluded from reuse,
are currently added back to the solve when
we traverse dependencies of other reusable
specs.

This fixes the issue by keeping track of what
we can explicitly reuse.
2024-05-07 09:06:51 +02:00
Massimiliano Culpo
d7297e67a5
Maintenance for the "bootstrap" workflow in CI (#44031)
Removed a lot of duplication.

Fixed an issue in containers, leading to false negative
2024-05-07 08:49:53 +02:00
snehring
ee8addf04a
neic-finitefault: adding new package and dependencies (#44032)
* neic-finitefault: adding new package
* py-obspy: adding new package
* py-okada-wrapper: adding new package
* py-pygmt: adding new package
* py-pyrocko: adding new package

---------

Signed-off-by: Shane Nehring <snehring@iastate.edu>
2024-05-06 15:45:32 -07:00
Jon Rood
fd3cd3a1c6
amr-wind: updates and fixes (#43993)
* Updates and fixes for AMR-Wind.

* Add versions and update openfast constraints.

* Style.

* Fix version.
2024-05-06 13:31:29 -06:00
Garth N. Wells
e585aeb883
(py)-fenics-dolfinx: version update (#44002)
* Update DOLFINx to v0.8
* Fix typo
2024-05-06 12:11:02 -07:00
James Taliaferro
1f43384db4
Add LSP client extension for Kakoune (#44000)
* new package: kakoune-lsp
* blacken
* add myself as a maintainer
2024-05-06 11:18:45 -07:00
Adam J. Stewart
814b328fca
py-torchmetrics: add v1.4.0 (#44027) 2024-05-06 10:21:20 -07:00
Harmen Stoppels
125206d44d
python: always use a venv (#40773)
This commit adds a layer of indirection to improve build isolation with 
and without external Python, as well as usability of environment views.

It adds `python-venv` as a dependency to all packages that `extends("python")`, 
which has the following advantages:

1. Build isolation: only `PYTHONPATH` is considered in builds, not 
   user / system packages
2. Stable install layout: fixes the problem on Debian, RHEL and Fedora where 
   external / system python produces `bin/local` subdirs in Spack install prefixes. 
3. Environment views are Python virtual environments (and if you add 
   `py-pip` things like `pip list` work)

Views work whether they're symlink, hardlink or copy type.

This commit additionally makes `spec["python"].command` return 
`spec["python-venv"].command`. The rationale is that packages in repos we do 
not own do not pass the underlying python to the build system, which could still 
result in incorrectly computed install layouts.

Other attributes like `libs`, `headers` should be on `python` anyways and need no change.
2024-05-06 16:17:35 +02:00
John W. Parent
a081b875b4
proj: patch for modern cmake (#43780) 2024-05-06 16:01:10 +02:00
Harmen Stoppels
a16ee3348b
Do not cache indices in Gitlab (#44029) 2024-05-06 15:54:21 +02:00
Massimiliano Culpo
d654d6b1f4
Remove Fedora 37 and 38, Ubuntu 18 from CI (#44006) 2024-05-06 15:51:45 +02:00
Harmen Stoppels
9b4ca0be40
clingo bootstrap: remove 3.12 patch and concretizer workarounds (#44028) 2024-05-06 15:00:41 +02:00
Harmen Stoppels
dc71dcfdc2
bootstrap: lazy bootstrapping of clingo and GnuPG (#44026)
Currently bootstrapping from source fails because clingo requires gnupg
requires clingo.

This commit stops eager bootstrapping. We don't need `patchelf` nor `gnupg`
generally. They're bootstrapped when needed.
2024-05-06 14:02:39 +02:00
Greg Becker
1f31c3374c
External package detection for compilers (#43464)
This creates shared infrastructure for compiler packages to implement the 
detailed search capabilities from the `spack compiler find` command for the 
`spack external find` command.

After this commit, `spack compiler find` can be replaced with 
`spack external find --tag compiler`, with the exception of mixed toolchains.
2024-05-06 10:33:33 +02:00
Massimiliano Culpo
27aeb6e293
Update vendored archspec to v0.2.4 (#44005) 2024-05-06 10:20:56 +02:00
Harmen Stoppels
715214c1a1
spack env create <env>: dir if dir-like (#44024)
A named env cannot contain `.` and `/`.

So when a user runs `spack env create ./here` do not error but treat it
as `spack env create -d ./here`.

Also fix help string of `spack env create`, which seems to have been
copied from `activate` incorrectly.
2024-05-06 02:00:23 -06:00
dependabot[bot]
b471d62dbd
build(deps): bump black from 24.4.0 to 24.4.2 in /lib/spack/docs (#43878)
Bumps [black](https://github.com/psf/black) from 24.4.0 to 24.4.2.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/24.4.0...24.4.2)

---
updated-dependencies:
- dependency-name: black
  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>
2024-05-06 09:55:43 +02:00
Massimiliano Culpo
a5f62889ca
archspec: add v0.2.4 (#44022) 2024-05-06 09:51:01 +02:00
Alec Scott
2a942d98e3
pkgconf: add v2.2.0 (#44008) 2024-05-06 09:31:41 +02:00
Alec Scott
4a4077d4ef
rust: add v1.78.0 (#44012) 2024-05-06 09:30:34 +02:00
Alec Scott
c0fcccc232
go: add v1.22.2 (#44013) 2024-05-06 09:30:13 +02:00
Alec Scott
0b2cbfefce
ncurses: add v6.5 (#44015) 2024-05-06 09:30:00 +02:00
Massimiliano Culpo
c499514322
libgpg-error: add v1.49 (#44023) 2024-05-06 09:28:31 +02:00
Alec Scott
ae392b5935
pcre2: add v10.43 (#44020) 2024-05-06 09:25:11 +02:00
Alec Scott
62e9bb5d51
libunistring: add v1.2 (#44018) 2024-05-06 09:24:12 +02:00
Alec Scott
6cd948184e
libidn2: add v2.3.7 (#44017) 2024-05-06 09:23:50 +02:00
Alec Scott
44ff24f558
openssl: v3.3.0 (#44019) 2024-05-06 09:22:15 +02:00
Alec Scott
c657dfb768
gettext: v0.22.5 (#44014) 2024-05-05 06:57:42 -06:00
Pranav Sivaraman
f2e410d95a
lazygit: add v0.41.0 (#43903) 2024-05-04 17:18:30 -06:00
dependabot[bot]
df443a38d6
build(deps): bump actions/checkout from 4.1.2 to 4.1.4 (#43831)
Bumps [actions/checkout](https://github.com/actions/checkout) from 4.1.2 to 4.1.4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](9bb56186c3...0ad4b8fada)

---
updated-dependencies:
- dependency-name: actions/checkout
  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>
2024-05-04 15:49:26 -07:00
dependabot[bot]
74fe498cb8
build(deps): bump mypy from 1.9.0 to 1.10.0 in /lib/spack/docs (#43834)
Bumps [mypy](https://github.com/python/mypy) from 1.9.0 to 1.10.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/1.9.0...v1.10.0)

---
updated-dependencies:
- dependency-name: mypy
  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>
2024-05-04 15:48:49 -07:00
Carlos Bederián
5f13a48bf2
mesa: add 23.3.6 (#43736) 2024-05-04 15:46:39 -07:00
Jon Rood
c4824f7fd2
ccls: add new versions (#43923) 2024-05-04 15:42:07 -07:00
dependabot[bot]
49a8634584
build(deps): bump codecov/codecov-action from 4.3.0 to 4.3.1 (#43945)
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4.3.0 to 4.3.1.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](84508663e9...5ecb98a3c6)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  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>
2024-05-04 15:39:42 -07:00
Seth Bromberger
eac5ea869f
tmux: add v3.4 and missing yacc build dep (#43975) 2024-05-04 22:33:19 +02:00