quantenzitrone
18dc8a95fb
this shouldn't create any rebuilds
the following script was used to generate this:
```fish
#!/usr/bin/env fish
# nix shell .#nixfmt nixpkgs#{nixf-diagnose,ripgrep,sd}
set base (git rev-parse HEAD)
set scope pkgs/by-name
set builder buildPythonApplication
set files (rg --files-with-matches -F "$builder rec {" $scope | sort -u)
for file in $files
echo $file
sd -F "$builder rec {" "$builder (finalAttrs: {" $file
# version
sd -F 'version}' 'finalAttrs.version}' $file
sd -F '${version' '${finalAttrs.version' $file
sd -F '= version' '= finalAttrs.version' $file
sd -F 'inherit version;' 'inherit (finalAttrs) version;' $file
sd -F ' + version;' ' + finalAttrs.version;' $file
sd 'replaceStrings (.*) version' 'replaceStrings $1 finalAttrs.version' $file
sd -F 'splitVersion version' 'splitVersion finalAttrs.version' $file
sd -F 'versionAtLeast version' 'versionAtLeast finalAttrs.version' $file
sd 'versions\.([a-z]+) version' 'versions.$1 finalAttrs.version' $file
# src
sd -F 'src}' 'finalAttrs.src}' $file
sd -F '${src' '${finalAttrs.src' $file
sd -F '= src' '= finalAttrs.src' $file
sd -F 'inherit src;' 'inherit (finalAttrs) src;' $file
sd -F 'inherit (src' 'inherit (finalAttrs.src' $file
# meta
sd -F '${meta' '${finalAttrs.meta' $file
sd -F '= meta' '= finalAttrs.meta' $file
sd -F 'inherit (meta' 'inherit (finalAttrs.meta' $file
# pname (restored afterwards)
sd -F 'pname}' 'finalAttrs.pname}' $file
sd -F '${pname' '${finalAttrs.pname' $file
sd -F '= pname' '= finalAttrs.pname' $file
# combinations
sd -F 'inherit version src;' 'inherit (finalAttrs) version src;' $file
sd -F 'inherit src version;' 'inherit (finalAttrs) src version;' $file
sd -F 'inherit version pname;' 'inherit (finalAttrs) version pname;' $file
sd -F 'inherit pname version;' 'inherit (finalAttrs) pname version;' $file
sd -F 'inherit pname src version;' 'inherit (finalAttrs) pname src version;' $file
sd -F 'inherit pname version src;' 'inherit (finalAttrs) pname version src;' $file
sd -F 'inherit src pname version;' 'inherit (finalAttrs) src pname version;' $file
sd -F 'inherit src version pname;' 'inherit (finalAttrs) src version pname;' $file
sd -F 'inherit version pname src;' 'inherit (finalAttrs) version pname src;' $file
sd -F 'inherit version src pname;' 'inherit (finalAttrs) version src pname;' $file
# other
sd -F 'makeLibraryPath buildInputs' 'makeLibraryPath finalAttrs.buildInputs' $file
sd -F 'nativeBuildInputs}' 'finalAttrs.nativeBuildInputs}' $file
sd -F 'buildInputs}' 'finalAttrs.buildInputs}' $file
sd -F 'propagatedBuildInputs}' 'finalAttrs.propagatedBuildInputs}' $file
sd -F 'desktopItem}' 'finalAttrs.desktopItem}' $file
sd -F 'runtimeLibs}' 'finalAttrs.runtimeLibs}' $file
sd -F 'makePythonPath dependencies' 'makePythonPath finalAttrs.dependencies' $file
sd -F 'makePythonPath propagatedBuildInputs' 'makePythonPath finalAttrs.propagatedBuildInputs' $file
sd -F 'libPath}' 'finalAttrs.libPath}' $file
sd -F 'runtimeDependencies}' 'finalAttrs.runtimeDependencies}' $file
sd -F 'runtimeDeps}' 'finalAttrs.runtimeDeps}' $file
sd -F 'nativeRuntimeInputs}' 'finalAttrs.nativeRuntimeInputs}' $file
sd -F '(!doCheck)' '(!finalAttrs.doCheck)' $file
sd -F 'optional doCheck' 'optional finalAttrs.doCheck' $file
sd -F 'optionals doCheck' 'optionals finalAttrs.doCheck' $file
sd -F '++ runtimeDependencies' '++ finalAttrs.runtimeDependencies' $file
# close finalAttrs lambda
echo ')' >>$file
# catch some errors early
if ! nixfmt $file
git restore $file
continue
end
if ! nixf-diagnose -i sema-primop-overridden $file
git restore $file
continue
end
end
set torestore (rg -F .finalAttrs --files-with-matches $scope)
if test (count $torestore) -gt 0
git restore $torestore
end
set torestore (rg -F finalAttrs.pname --files-with-matches $scope)
if test (count $torestore) -gt 0
git restore $torestore
end
# commit for faster eval times
git add pkgs
git commit --no-gpg-sign -m temp
set torestore
for file in $files
# file hasn't changed
if git diff --quiet $base $file
continue
end
# try to eval the package to definitely catch all errors
echo $file
set pname (string split / $file -f 4)
if ! nix eval .#$pname
set torestore $torestore $file
end
end
# restore files that don't eval
git reset --soft $base
git restore --staged .
if test (count $torestore) -gt 0
git restore $torestore
end
```
after that some manual cleanup was done:
- restoring files that cause changes in the number of lines
- restoring files that cause rebuilds
- restoring files that cause merge conflicts with staging
66 lines
1.6 KiB
Nix
66 lines
1.6 KiB
Nix
{
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lib,
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python3Packages,
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fetchFromGitHub,
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addBinToPathHook,
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}:
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python3Packages.buildPythonApplication (finalAttrs: {
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pname = "deeptools";
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version = "3.5.6";
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pyproject = true;
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src = fetchFromGitHub {
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owner = "deeptools";
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repo = "deepTools";
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tag = finalAttrs.version;
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hash = "sha256-dxXlOvOjF4KSc5YO+1A5hlp95sfeyPSbmp93tihm7Vo=";
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};
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build-system = with python3Packages; [
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setuptools
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];
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dependencies = with python3Packages; [
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numpy
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scipy
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matplotlib
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pysam
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numpydoc
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pybigwig
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py2bit
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plotly
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deeptoolsintervals
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];
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nativeCheckInputs = with python3Packages; [
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pytestCheckHook
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addBinToPathHook
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];
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disabledTestPaths = [
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# tests trip on `len(sys.argv) == 1`
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"deeptools/test/test_bigwigAverage.py"
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"deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py"
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"deeptools/test/test_heatmapper.py"
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"deeptools/test/test_multiBamSummary.py"
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];
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meta = {
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homepage = "https://deeptools.readthedocs.io/en/develop";
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description = "Tools for exploring deep DNA sequencing data";
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longDescription = ''
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deepTools contains useful modules to process the mapped reads data for multiple
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quality checks, creating normalized coverage files in standard bedGraph and bigWig
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file formats, that allow comparison between different files (for example, treatment and control).
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Finally, using such normalized and standardized files, deepTools can create many
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publication-ready visualizations to identify enrichments and for functional
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annotations of the genome.
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'';
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license = with lib.licenses; [
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mit
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bsd3
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];
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};
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})
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