After final improvements to the official formatter implementation,
this commit now performs the first treewide reformat of Nix files using it.
This is part of the implementation of RFC 166.
Only "inactive" files are reformatted, meaning only files that
aren't being touched by any PR with activity in the past 2 months.
This is to avoid conflicts for PRs that might soon be merged.
Later we can do a full treewide reformat to get the rest,
which should not cause as many conflicts.
A CI check has already been running for some time to ensure that new and
already-formatted files are formatted, so the files being reformatted here
should also stay formatted.
This commit was automatically created and can be verified using
nix-build a08b3a4d19.tar.gz \
--argstr baseRev b32a094368
result/bin/apply-formatting $NIXPKGS_PATH
The aged perlPackages.NetSNMP library does not support modern SHA algorithms for authentication.
It's possible to enable support for these newer protocols with a patch.
The patch is taken from the OpenBSD ports tree:
https://github.com/openbsd/ports/blob/master/net/p5-Net-SNMP/patches/patch-lib_Net_SNMP_Security_USM_pm
It enables support for SHA 224, 256, 384, and 512.
Tests are also include in the patch for these additional algorithms.
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"
```
The nixpkgs-unstable channel's programs.sqlite was used to identify
packages producing exactly one binary, and these automatically added
to their package definitions wherever possible.
Perl interface to manipulate BigWig and BigBeg files (for genomics)
This will be used to package VEP : uttps://www.ensembl.org/info/docs/tools/vep/script/vep_download.html
For that, only kent version 335 works at the moment.
For this commit, 2 commits for kent are needed
- e027a5d836 : packaging kent header
- 2b2c6f4c28 : enabling patches in kent
t/css-dom.t was deactivated because it failed due to deprecated syntax. This
commit uses an upstream patch to fix the syntax and activate the test again.
