pyrox.dev
multiqc: 1.29 -> 1.30 (#433130)
authored by Peder Bergebakken Sundt and committed by GitHub 2cb26015 b1625a5a
+43
-28
pkgs/by-name/mu/multiqc/package.nix
+43
-28
pkgs/by-name/mu/multiqc/package.nix
···
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addBinToPathHook,
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}:
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-
let
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test-data = fetchFromGitHub {
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name = "test-data";
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owner = "MultiQC";
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repo = "test-data";
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rev = "d775b73c106d48726653f2fd02e473b7acbd93d8";
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hash = "sha256-uxBpMx22gWJmnbF9tVuVIdYdiqUh7n51swzu5hnfZQ0=";
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};
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in
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python3Packages.buildPythonApplication rec {
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pname = "multiqc";
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version = "1.29";
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pyproject = true;
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src = fetchFromGitHub {
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name = "multiqc";
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owner = "MultiQC";
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repo = "MultiQC";
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tag = "v${version}";
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hash = "sha256-KKLdDNf889lEbCyNpJFZoE8rNO50CRzNP4hKpKHRAcE=";
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};
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# Multiqc cannot remove temporary directories in some case.
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# Default is 10 retries, lower it to 2
···
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--replace-fail \
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"max_retries: int = 10," \
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"max_retries: int = 2,"
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'';
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build-system = with python3Packages; [ setuptools ];
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dependencies = with python3Packages; [
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boto3
···
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jinja2
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kaleido
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markdown
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numpy
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packaging
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requests
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pillow
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plotly
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pyyaml
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rich
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rich-click
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coloredlogs
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spectra
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pydantic
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typeguard
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tqdm
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python-dotenv
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natsort
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tiktoken
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jsonschema
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-
polars
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pyarrow
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];
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optional-dependencies = {
···
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];
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};
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preCheck = ''
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ln -s ${test-data} ./test-data
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'';
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nativeCheckInputs =
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(with python3Packages; [
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pytest-xdist
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pytestCheckHook
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-
])
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++ [
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addBinToPathHook # Some tests run subprocess.run() with "multiqc"
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-
procps # Some tests run subprocess.run() with "ps"
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versionCheckHook
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];
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versionCheckProgramArg = "--version";
···
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addBinToPathHook,
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}:
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python3Packages.buildPythonApplication rec {
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pname = "multiqc";
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version = "1.30";
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pyproject = true;
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# Two data sources. One for the code, another for the test data
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srcs = [
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(fetchFromGitHub {
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name = "multiqc";
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owner = "MultiQC";
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+
repo = "MultiQC";
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+
tag = "v${version}";
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hash = "sha256-TR5YFoWj97gpsykIzc1lqtYVePsVLRIT0HXw+VPJ7o4=";
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})
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(fetchFromGitHub {
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owner = "MultiQC";
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+
repo = "test-data";
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+
rev = "cc9f853e7892eb537e91505e0e847ff63669138d";
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hash = "sha256-/MiNnPayG6wpF2S09ENYTlEBF7Km4aH1RjdGOfMgZcA=";
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name = "test-data";
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})
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];
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# Multiqc cannot remove temporary directories in some case.
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# Default is 10 retries, lower it to 2
···
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--replace-fail \
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"max_retries: int = 10," \
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"max_retries: int = 2,"
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substituteInPlace pyproject.toml \
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--replace 'polars-lts-cpu' 'polars'
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'';
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sourceRoot = "multiqc";
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+
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nativeBuildInputs = with python3Packages; [
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+
setuptools
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+
wheel
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];
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dependencies = with python3Packages; [
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boto3
···
57
jinja2
58
kaleido
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markdown
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+
natsort
61
numpy
62
packaging
63
requests
64
+
polars
65
pillow
66
plotly
67
+
pyarrow
68
pyyaml
69
rich
70
rich-click
71
coloredlogs
72
spectra
73
pydantic
74
+
tiktoken
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typeguard
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tqdm
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python-dotenv
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jsonschema
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];
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optional-dependencies = {
···
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];
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};
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+
# Some tests run subprocess.run() with "multiqc"
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preCheck = ''
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chmod -R u+w ../test-data
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ln -s ../test-data .
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'';
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+
# Some tests run subprocess.run() with "ps"
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nativeCheckInputs =
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+
with python3Packages;
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[
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+
pytest-cov-stub
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pytest-xdist
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pytestCheckHook
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+
syrupy
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+
pygithub
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versionCheckHook
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+
]
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+
++ [
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+
procps
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addBinToPathHook
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];
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versionCheckProgramArg = "--version";