From 8fb567c1c20db084f147e27ac14bb1e03c079f8c Mon Sep 17 00:00:00 2001
From: Alexis Praga <alexis@praga.dev>
Date: Thu, 9 Jan 2025 22:28:56 +0100
Subject: [PATCH] multiqc: init at 1.26.

Update the work of dflores to latest version and official tests. All test pass.
Spectra has been added as dependencies in a previous commit.
---
 pkgs/by-name/mu/multiqc/package.nix | 117 ++++++++++++++++++++++++++++
 1 file changed, 117 insertions(+)
 create mode 100644 pkgs/by-name/mu/multiqc/package.nix

diff --git a/pkgs/by-name/mu/multiqc/package.nix b/pkgs/by-name/mu/multiqc/package.nix
new file mode 100644
index 000000000000..be3f8ad6ea86
--- /dev/null
+++ b/pkgs/by-name/mu/multiqc/package.nix
@@ -0,0 +1,117 @@
+{
+  lib,
+  python3Packages,
+  fetchFromGitHub,
+  procps,
+  stdenv,
+  versionCheckHook,
+}:
+
+python3Packages.buildPythonApplication rec {
+  pname = "multiqc";
+  version = "1.26";
+
+  # Two data sources. One for the code, another for the test data
+  srcs = [
+    (fetchFromGitHub {
+      name = "multiqc";
+      owner = "MultiQC";
+      repo = "MultiQC";
+      tag = "v${version}";
+      hash = "sha256-MPAw6gG/3LzdskkDXOTDEM1NpG0sH9GvklYFQ1ZXWIs=";
+    })
+    (fetchFromGitHub {
+      owner = "MultiQC";
+      repo = "test-data";
+      rev = "67435083a8bfa228dca3dda7d835facef15fc2c7";
+      hash = "sha256-oYmPIJSy6dOKPcMr3B4foGoWcerA29x0XeGoU4dSYsA=";
+      name = "test-data";
+    })
+  ];
+
+  sourceRoot = "multiqc";
+
+  dependencies = with python3Packages; [
+    click
+    humanize
+    importlib-metadata
+    jinja2
+    kaleido
+    markdown
+    natsort
+    numpy
+    packaging
+    requests
+    pillow
+    plotly
+    pyyaml
+    rich
+    rich-click
+    coloredlogs
+    spectra
+    pydantic
+    typeguard
+    tqdm
+  ];
+
+  optional-dependencies = {
+    dev = with python3Packages; [
+      pre-commit-hooks
+      pdoc3
+      pytest
+      pytest-cov-stub
+      pytest-xdist
+      syrupy
+      pygithub
+      mypy
+      types-pyyaml
+      types-tqdm
+      types-requests
+      types-markdown
+      types-beautifulsoup4
+      types-pillow
+    ];
+  };
+
+  # Some tests run subprocess.run() with "multiqc"
+  preCheck = ''
+    chmod -R u+w ../test-data
+    ln -s ../test-data .
+    export PATH=$out/bin:$PATH
+  '';
+
+  # Some tests run subprocess.run() with "ps"
+  nativeCheckInputs = with python3Packages; [
+    procps
+    pytest-cov
+    pytest-xdist
+    pytestCheckHook
+    syrupy
+    pygithub
+    versionCheckHook
+  ];
+
+  versionCheckProgramArg = [ "--version" ];
+
+  disabledTests =
+    # On darwin, kaleido fails to starts
+    lib.optionals (stdenv.hostPlatform.isDarwin) [
+      "test_flat_plot"
+    ];
+
+  meta = {
+    description = "Aggregates bioinformatics results from multiple samples into a unified report";
+    longDescription = ''
+      MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
+
+      Reports are generated by scanning given directories for recognised log files. These are parsed and a single HTML report is generated summarising the statistics for all logs found. MultiQC reports can describe multiple analysis steps and large numbers of samples within a single plot, and multiple analysis tools making it ideal for routine fast quality control.
+    '';
+    homepage = "https://multiqc.info";
+    changelog = "https://github.com/MultiQC/MultiQC/releases/tag/v${version}/";
+    license = [ lib.licenses.gpl3Plus ];
+    maintainers = [ lib.maintainers.apraga ];
+    mainProgram = "multiqc";
+    platforms = lib.platforms.unix;
+  };
+
+}