Commit Graph

11 Commits

Author SHA1 Message Date
Alexis Praga
17d6f0757e hap-py: fix python3 compatibility
pipes is no longer supported in python3 and require
a change of imports.
2026-05-16 22:21:15 +02:00
Alexis Praga
e44bc94266 hap-py: compile with latest nixpkgs
Avoid removal by #490615. Changes
- fix missing header
- add missing library
- comile with latest Boost
2026-03-06 23:23:49 +01:00
Gaetan Lepage
dab389b79a hap-py: cleanup, fix cmake 4 compatibility 2025-12-07 23:29:26 +00:00
Winter
a19cd4ffb1 Revert "treewide: replace rev with tag"
This reverts commit 65a333600d.

This wasn't tested for correctness with something like fodwatch [0],
and should not have been (self-)merged so quickly, especially without
further review.

It also resulted in the breakage of at least one package [1] (and that's
the one we know of and was caught).

A few packages that were updated in between this commit and this revert
were not reverted back to using `rev`, but other than that, this is a
1:1 revert.

[0]: https://codeberg.org/raphaelr/fodwatch
[1]: https://github.com/NixOS/nixpkgs/pull/396904 / 758551e458
2025-04-08 02:57:25 -04:00
Pol Dellaiera
65a333600d treewide: replace rev with tag 2025-04-07 16:57:22 +02:00
Peder Bergebakken Sundt
357d2530e5 treewide: substitute pname for strings
Inspired by https://github.com/NixOS/nixpkgs/pull/387725#issuecomment-2704943777, script is based on https://github.com/NixOS/nixpkgs/pull/336172 using what i learned in https://github.com/NixOS/nixpkgs/pull/386865, part of https://github.com/NixOS/nixpkgs/issues/346453

Should be zero rebuilds.

All candidates were made using:

```shell

export NIXPKGS_ALLOW_UNFREE=1
export NIXPKGS_ALLOW_INSECURE=1
export NIXPKGS_ALLOW_BROKEN=1

git-wait restore .

test -s packages.json || ( set -x;
  time nix-env --extra-experimental-features no-url-literals --option system x86_64-linux -f ./. -qaP --json --meta --drv-path --out-path --show-trace --no-allow-import-from-derivation --arg config '{ allowAliases = false; }' > packages.json
)

list_attrpath_fname_col() {
    jq <packages.json 'to_entries[] | select(.value.meta.position==null|not) | "\(.key)\t\(.value.meta.position)"' -r |
        sed -e "s#\t$(realpath .)/#\t#" |
        sed -e 's#:\([0-9]*\)$#\t\1#' |
        grep . |
        grep -iv haskell |
        grep -iv /top-level/ |
        grep -iv chicken |
        grep pkgs/by-name/ |
        grep -iv build |
        grep -E '/(package|default)\.nix'
}

FLOCKDIR="$(mktemp -d)"
N_WORKERS=4
while read attrpath fname col; do
    grep -qE 'repo *= *("\$\{pname\}"|pname);' "$fname" || continue

    echo | (
        # mutex on fname
        flock --nonblock 200 || {
            >&2 echo "failed to aquire lock for $fname"
            exit 1
        }

        echo "$attrpath"
        data="$(nix eval --impure  --expr 'with import ./. {}; { inherit ('"$attrpath"') pname drvPath passthru meta; drvPath2='"$attrpath"'.src.drvPath; }' --json)" || exit
        test -n "$data" || exit
        pname="$(jq <<<"$data" .pname -r)"
        test -n "$pname" || exit

        (set -x
            sd -F '${pname}'  "$pname"         "$fname"
            sd -F ' = pname;' " = \"$pname\";" "$fname"
        )

        data2="$(nix eval --impure  --expr 'with import ./. {}; { inherit ('"$attrpath"') pname drvPath passthru meta; drvPath2='"$attrpath"'.src.drvPath; }' --json)"
        if [[ "$data" = "$data2" ]]; then
            (set -x; git-wait add "$fname")
        else
            (set -x; git-wait restore "$fname")
            exit
        fi

        (set -x
            sd -F ' rec {' ' {' "$fname"
        )

        data3="$(nix eval --impure  --expr 'with import ./. {}; { inherit ('"$attrpath"') pname drvPath passthru meta; drvPath2='"$attrpath"'.src.drvPath; }' --json 2>/dev/nul)"

        if [[ "$data" = "$data3" ]]; then
            (set -x; git-wait add "$fname")
        else
            (set -x; git-wait restore "$fname")
        fi

    ) 200>"$FLOCKDIR"/"$(sha256sum - <<<"$fname" | cut -d' ' -f1)".lock &

    while [[ $(jobs -p | wc -l) -ge $N_WORKERS ]]; do
        wait -n < <(jobs -p) || true
    done

done < <(list_attrpath_fname_col)

wait

git restore .

time nix-env --extra-experimental-features no-url-literals --option system x86_64-linux -f ./. -qaP --json --meta --drv-path --out-path --show-trace --no-allow-import-from-derivation --arg config '{ allowAliases = false; }' > packages2.json
```

`diff packages{,2}.json` is empty, indicating that no package nor src derivation has changed.
I checked and cherry-picked the changes using `GIT_DIFF_OPTS='-u15' git -c interactive.singleKey=true add --patch`
2025-03-11 23:55:31 +01:00
Peder Bergebakken Sundt
5aba99242e treewide: fix typos in comments
Made with

```shell
git restore .
fd '\.nix$' pkgs/ --type f -j1 -x bash -xc "$(cat <<"EOF"
    typos --no-check-filenames --write-changes "$1"
    git diff --exit-code "$1" && exit
    #( git diff "$1" | grep -qE "^\+ +[^# ]") && git restore "$1"
    count1="$( bat --language nix --diff --style changes "$1" --theme "Monokai Extended" --color always | aha --no-header | grep -E '^<span style="color:olive;">~</span> ' | wc -l )"
    count2="$( bat --language nix --diff --style changes "$1" --theme "Monokai Extended" --color always | aha --no-header | grep -E '^<span style="color:olive;">~</span> (<span style="color:#f8f8f2;"> *</span>)?<span style="color:#75715e;">.*</span>$' | wc -l )"
    [[ $count1 -ne $count2 ]] && git restore "$1"
EOF
)" -- {}
```

and filtered with `GIT_DIFF_OPTS='--unified=15' git -c interactive.singleKey=true add --patch`

I initially tried using the tree-sitter cli, python bindings and even ast-grep through various means, but this is what I ended up with.
2025-02-24 10:44:41 +01:00
Silvan Mosberger
4f0dadbf38 treewide: format all inactive Nix files
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 $NIXPKGS_PATH
2024-12-10 20:26:33 +01:00
nicoo
2641d97cbf pkgs/by-name: Convert hashes to SRI format
Reproduction script:
	# Bulk rewrite
	./maintainers/scripts/sha-to-sri.py pkgs/by-name
	# Revert some packages which will need manual intervention
	for n in amdvlk azure-cli cargo-profiler corefonts flatito fluxcd gist perf_data_converter protoc-gen-js solana-cli swt verible; do
		git checkout -- "pkgs/by-name/${n:0:2}/${n}"
	done
2024-09-15 11:24:31 +02:00
Alexis Praga
5db72db7fa hap-py: use rtgtools vcfeval as default core
For best results (quality and running time), the
authors advice to use RTGtools vcfeval as the
engine.

Depends on #230394
2024-04-07 21:05:23 +02:00
Alexis Praga
946f357e45 hap-py: init 0.3.15
New package for genetics : helps compared variants
called by a pipeline to a reference.

The only tests not passing are due to a difference
in float representation (same value but with
different number of digits after decimal).
2024-04-07 21:05:23 +02:00