Commit Graph

1390 Commits

Author SHA1 Message Date
aleksana
571c71e6f7 treewide: migrate packages to pkgs/by-name, take 1
We are migrating packages that meet below requirements:

1. using `callPackage`
2. called path is a directory
3. overriding set is empty (`{ }`)
4. not containing path expressions other than relative path (to
makenixpkgs-vet happy)
5. not referenced by nix files outside of the directory, other
than`pkgs/top-level/all-packages.nix`
6. not referencing nix files outside of the directory
7. not referencing `default.nix` (since it's changed to `package.nix`)
8. `outPath` doesn't change after migration

The tool is here: https://github.com/Aleksanaa/by-name-migrate.
2024-11-09 20:04:51 +08:00
R. Ryantm
17926cc521 fastp: 0.23.4 -> 0.24.0 2024-11-08 14:14:48 +00:00
Reno Dakota
52bf1163fa
treewide: use getLib when accessing clang / libclang / stdenv.cc.cc
In preparation to eliminate the lib output for the unwrapped clang, use
`lib.getLib` to access the `lib` output.
2024-11-07 10:27:41 +00:00
Ramses
005be24458
gatk: 4.6.0.0 -> 4.6.1.0 (#352547) 2024-11-03 22:51:28 +01:00
Nick Cao
d441bf480d
seqkit: 2.8.2 -> 2.9.0 (#352925) 2024-11-02 09:17:28 -04:00
Sefa Eyeoglu
6f860c1245
jbrowse: 2.15.4 -> 2.16.0 (#352036) 2024-11-01 23:56:19 +01:00
R. Ryantm
269236bbd4 seqkit: 2.8.2 -> 2.9.0 2024-11-01 16:52:07 +00:00
R. Ryantm
ee0e666076 gatk: 4.6.0.0 -> 4.6.1.0 2024-10-31 06:46:36 +00:00
OTABI Tomoya
31ce2c564f
libcifpp: 7.0.4 -> 7.0.7; dssp: 4.4.8 -> 4.4.10 (#349679) 2024-10-29 18:00:21 +09:00
R. Ryantm
1779edf359 jbrowse: 2.15.4 -> 2.16.0 2024-10-29 06:25:09 +00:00
natsukium
afaf2aab04
bwa-mem2: fix build on x86_64-darwin 2024-10-26 15:48:16 +09:00
piegames
68927918d0 treewide: Fix indentation in strings
The indentation stripping semantics of strings are fairly bad and have a
few gotchas where the resulting string has not the intended indentation.
This commit fixes most if not all such instances in Nixpkgs.

I tried to strive a balance between keeping the diff small and
reformatting/refactoring the code to look better. In general,
reformatting should be left to Nixfmt.

Note that this causes a lot of rebuilds by design. All changes need to
be thoroughly vetted and reviewed for correctness. There is no automatic
way to prove correctness.

List of files to fix generated by running
https://gerrit.lix.systems/c/lix/+/2092 on Nixpkgs and looking at the
warnings.
2024-10-22 21:36:42 +02:00
R. Ryantm
3dd4dedc78 diamond: 2.1.9 -> 2.1.10 2024-10-19 14:23:13 +00:00
natsukium
1857e1080e
dssp: 4.4.8 -> 4.4.10
Diff: https://github.com/PDB-REDO/dssp/compare/refs/tags/v4.4.8...v4.4.10

Changelog: https://github.com/PDB-REDO/dssp/releases/tag/v4.4.10
2024-10-19 11:31:00 +09:00
R. Ryantm
dfcd56c83b last: 1550 -> 1592 2024-10-18 10:40:57 +00:00
Stanisław Pitucha
9f1d63f8d4 cmtk: darwin
Fix the Darwin build. It required the same c++ standard setting as other platforms.
Moved the options to cmake format too.
2024-10-15 18:48:24 +11:00
Nick Cao
63e9af1f34
stacks: 2.66 -> 2.68 (#348422) 2024-10-14 12:21:55 -04:00
R. Ryantm
62caef981e stacks: 2.66 -> 2.68 2024-10-14 03:53:28 +00:00
R. Ryantm
89f13435d2 subread: 2.0.6 -> 2.0.7 2024-10-14 03:01:38 +00:00
R. Ryantm
8eab3789cb picard-tools: 3.2.0 -> 3.3.0 2024-10-10 04:19:53 +00:00
R. Ryantm
ce83463c27 delly: 1.2.9 -> 1.3.1 2024-10-09 12:33:11 +00:00
R. Ryantm
2e9de92fe6 dssp: 4.4.7 -> 4.4.8 2024-10-07 12:45:50 +00:00
OTABI Tomoya
5d788ab3e8
jbrowse: 2.15.1 -> 2.15.4 (#344596) 2024-10-06 17:27:35 +09:00
Peder Bergebakken Sundt
c1d784a832
ezminc: unstable-2019-03-12 -> unstable-2023-10-06; unbreak (#342963) 2024-10-02 01:30:10 +02:00
Ben Darwin
797703d712 ezminc: unstable-2019-03-12 -> unstable-2023-10-06 2024-09-30 21:02:59 -04:00
R. Ryantm
a9275e71f8 delly: 1.2.6 -> 1.2.9 2024-09-27 00:59:40 +02:00
R. Ryantm
1a133b175d jbrowse: 2.15.1 -> 2.15.4 2024-09-26 07:44:23 +00:00
OTABI Tomoya
d917f5057c
messer-slim: 4.2.2 -> 4.3 (#342699) 2024-09-25 21:11:51 +09:00
OTABI Tomoya
4c4690e27b
jbrowse: 2.15.0 -> 2.15.1 (#341939) 2024-09-25 12:07:47 +09:00
Artturin
e0464e4788 treewide: replace stdenv.is with stdenv.hostPlatform.is
In preparation for the deprecation of `stdenv.isX`.

These shorthands are not conducive to cross-compilation because they
hide the platforms.

Darwin might get cross-compilation for which the continued usage of `stdenv.isDarwin` will get in the way

One example of why this is bad and especially affects compiler packages
https://www.github.com/NixOS/nixpkgs/pull/343059

There are too many files to go through manually but a treewide should
get users thinking when they see a `hostPlatform.isX` in a place where it
doesn't make sense.

```
fd --type f "\.nix" | xargs sd --fixed-strings "stdenv.is" "stdenv.hostPlatform.is"
fd --type f "\.nix" | xargs sd --fixed-strings "stdenv'.is" "stdenv'.hostPlatform.is"
fd --type f "\.nix" | xargs sd --fixed-strings "clangStdenv.is" "clangStdenv.hostPlatform.is"
fd --type f "\.nix" | xargs sd --fixed-strings "gccStdenv.is" "gccStdenv.hostPlatform.is"
fd --type f "\.nix" | xargs sd --fixed-strings "stdenvNoCC.is" "stdenvNoCC.hostPlatform.is"
fd --type f "\.nix" | xargs sd --fixed-strings "inherit (stdenv) is" "inherit (stdenv.hostPlatform) is"
fd --type f "\.nix" | xargs sd --fixed-strings "buildStdenv.is" "buildStdenv.hostPlatform.is"
fd --type f "\.nix" | xargs sd --fixed-strings "effectiveStdenv.is" "effectiveStdenv.hostPlatform.is"
fd --type f "\.nix" | xargs sd --fixed-strings "originalStdenv.is" "originalStdenv.hostPlatform.is"
```
2024-09-25 00:04:37 +03:00
R. Ryantm
d5a1271205
messer-slim: 4.2.2 -> 4.3 2024-09-18 08:31:41 -04:00
Nick Cao
086b39f8c4
veryfasttree: 4.0.3 -> 4.0.4 (#342630) 2024-09-18 08:16:41 -04:00
R. Ryantm
d8a3114831 veryfasttree: 4.0.3 -> 4.0.4 2024-09-17 20:29:50 +00:00
R. Ryantm
ee5a15d93e kallisto: 0.51.0 -> 0.51.1 2024-09-17 13:16:27 +00:00
Peder Bergebakken Sundt
b0330ee78d
muscle: compile with GCC for Darwin (#321551) 2024-09-17 01:20:26 +02:00
R. Ryantm
db5f567b79 jbrowse: 2.15.0 -> 2.15.1 2024-09-15 00:54:38 +00:00
R. Ryantm
7decc89f3e bcftools: 1.20 -> 1.21 2024-09-13 06:20:40 +00:00
Peder Bergebakken Sundt
f99890f31f
minc-tools: unstable-2020-07-25 -> 2.3.06-unstable-2023-08-12 (#340340) 2024-09-13 01:41:06 +02:00
Weijia Wang
d4d144b8f2
jbrowse: 2.14.0 -> 2.15.0 (#339549) 2024-09-11 00:24:42 +02:00
Weijia Wang
7127eff86d
iqtree: 2.3.5 -> 2.3.6 (#331537) 2024-09-09 23:31:22 +02:00
Ben Darwin
6718a1b70f minc-tools: unstable-2020-07-25 -> 2.3.06-unstable-2023-08-12 2024-09-07 13:57:40 -04:00
Ben Darwin
5297d8f429 minc-tools: apply nixfmt 2024-09-07 12:46:46 -04:00
Aleksana
6b045549f1
igv: only replace actual java commands with the full path (#338340) 2024-09-06 23:11:25 +08:00
R. Ryantm
17a622b98e jbrowse: 2.14.0 -> 2.15.0 2024-09-04 14:00:01 +00:00
Nick Cao
1cb6cb8df1
jbrowse: 2.13.1 -> 2.14.0 (#338101) 2024-09-03 15:17:57 -04:00
electric-castle
5d19a9ed86 Only replace actual java commands with the full path 2024-08-29 23:51:23 -07:00
Peder Bergebakken Sundt
ebc2389134 treewide: remove refs/tags/ from github release meta.changelog urls
diff of `jq <packages.json 'to_entries[]|"\(.key) \(.value.meta.changelog)"' -r`:

https://gist.github.com/pbsds/49b2e2ae5c9b967a0972bbc3c2597c12
2024-08-29 22:45:00 -04:00
R. Ryantm
747970800e jbrowse: 2.13.1 -> 2.14.0 2024-08-29 04:33:48 +00:00
Peder Bergebakken Sundt
925c7fa7b8
Merge pull request #331743 from r-ryantm/auto-update/kallisto
kallisto: 0.50.1 -> 0.51.0
2024-08-16 01:57:02 +02:00
R. Ryantm
ce2698d6c3 jbrowse: 2.12.3 -> 2.13.1 2024-08-07 10:53:57 +00:00