From 77d19d14b4a09f27c2c05c07f17c9000b5e9621a Mon Sep 17 00:00:00 2001
From: Alexis Praga <alexis@praga.dev>
Date: Thu, 9 Jan 2025 22:26:53 +0100
Subject: [PATCH 1/2]  spectra: init at 0.0.11.

Dependency for multiqc
---
 .../python-modules/spectra/default.nix        | 49 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 51 insertions(+)
 create mode 100644 pkgs/development/python-modules/spectra/default.nix

diff --git a/pkgs/development/python-modules/spectra/default.nix b/pkgs/development/python-modules/spectra/default.nix
new file mode 100644
index 000000000000..f07c17a3bd16
--- /dev/null
+++ b/pkgs/development/python-modules/spectra/default.nix
@@ -0,0 +1,49 @@
+{
+  buildPythonPackage,
+  colormath,
+  fetchFromGitHub,
+  fetchpatch2,
+  lib,
+  pytestCheckHook,
+  setuptools,
+}:
+
+buildPythonPackage rec {
+  pname = "spectra";
+  version = "0.0.11";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "jsvine";
+    repo = "spectra";
+    tag = "v${version}";
+    hash = "sha256-4A2TWTxYqckJ3DX5cd2KN3KXcmO/lQdXmOEnGi76RsA=";
+  };
+
+  patches = [
+    # https://github.com/jsvine/spectra/pull/21
+    (fetchpatch2 {
+      name = "nose-to-pytest.patch";
+      url = "https://github.com/jsvine/spectra/commit/50037aba16dac4bf0fb7ffbd787d0e6b906e8a4b.patch";
+      hash = "sha256-cMoIbjRwcZjvhiIOcJR7NmIAOaqpr/e5eh9+sPGKqos=";
+      excludes = [ ".github/*" ];
+    })
+  ];
+
+  build-system = [
+    setuptools
+  ];
+
+  propagatedBuildInputs = [ colormath ];
+
+  nativeCheckInputs = [
+    pytestCheckHook
+  ];
+
+  meta = {
+    description = "Python library that makes color math, color scales, and color-space conversion easy";
+    homepage = "https://github.com/jsvine/spectra";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ apraga ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 8d3a99d79a72..c3364be62d90 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -15158,6 +15158,8 @@ self: super: with self; {
 
   speaklater3 = callPackage ../development/python-modules/speaklater3 { };
 
+  spectra = callPackage ../development/python-modules/spectra { };
+
   spectral-cube = callPackage ../development/python-modules/spectral-cube { };
 
   speechbrain = callPackage ../development/python-modules/speechbrain { };

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 2/2] 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;
+  };
+
+}