LewisResearchGroup · sorenwacker · Mar 2, 2026 · Oct 31, 2022 · Oct 31, 2022 · Oct 31, 2022
diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,21 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
diff --git a/docs/_templates/layout.html b/docs/_templates/layout.html
@@ -0,0 +1,14 @@
+{% extends "!layout.html" %}
+
+{% block footer %}
+  {{ super() }}
+  <!-- Google tag (gtag.js) -->
+  <script async src="https://www.googletagmanager.com/gtag/js?id=G-9RJ7Z0BG5W"></script>
+  <script>
+    window.dataLayer = window.dataLayer || [];
+    function gtag(){dataLayer.push(arguments);}
+    gtag('js', new Date());
+
+    gtag('config', 'G-9RJ7Z0BG5W');
+  </script>
+{% endblock %}
diff --git a/docs/conf.py b/docs/conf.py
@@ -0,0 +1,104 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+import sphinx_rtd_theme
+
+sys.path.insert(0, os.path.abspath(".."))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "ms-mint"
+copyright = "2022, Soren Wacker"
+author = "Soren Wacker"
+
+# The full version, including alpha/beta/rc tags
+release = "0.1.6"
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+# extensions = [
+#    "sphinx.ext.autodoc",
+#    "sphinx.ext.githubpages",
+# ]
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.githubpages",
+    "sphinx.ext.napoleon",
+    "myst_parser",
+]
+
+# Napoleon settings
+napoleon_google_docstring = True
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = True
+napoleon_include_private_with_doc = True
+napoleon_include_special_with_doc = True
+napoleon_use_admonition_for_examples = False
+napoleon_use_admonition_for_notes = False
+napoleon_use_admonition_for_references = False
+napoleon_use_ivar = False
+napoleon_use_param = True
+napoleon_use_rtype = True
+
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = [
+    "_build",
+    "Thumbs.db",
+    ".DS_Store",
+    "versioneer.py",
+    "setup.py",
+    "ms_mint/filelock.py",
+    "notebooks",
+    "**.ipynb_checkpoints",
+]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+
+html_theme = "sphinx_rtd_theme"
+# html_theme = "alabaster"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+
+source_suffix = [".rst"]
+
+html_baseurl = "https://lewisresearchgroup.github.io/ms-mint"
+
+requirements_path = "docs/requirements.txt"
diff --git a/docs/index.rst b/docs/index.rst
@@ -0,0 +1,22 @@
+.. ms-mint documentation master file, created by
+   sphinx-quickstart on Tue May 24 19:54:56 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to ms-mint's documentation!
+===================================
+
+.. toctree::
+   :maxdepth: 4
+   :caption: Contents:
+
+   readme
+   modules   
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/make.bat b/docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/docs/modules.rst b/docs/modules.rst
@@ -0,0 +1,7 @@
+ms_mint
+=======
+
+.. toctree::
+   :maxdepth: 4
+
+   ms_mint
diff --git a/docs/ms_mint.rst b/docs/ms_mint.rst
@@ -0,0 +1,125 @@
+ms_mint package
+================
+
+Submodules
+----------
+
+ms_mint.Mint module
+--------------------
+
+.. automodule:: ms_mint.Mint
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ms_mint.Chromatogram module
+----------------------------
+
+.. automodule:: ms_mint.Chromatogram
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ms_mint.filelock module
+------------------------
+
+.. automodule:: ms_mint.filelock
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ms_mint.filters module
+----------------------
+
+.. automodule:: ms_mint.filters
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ms_mint.io module
+------------------
+
+.. automodule:: ms_mint.io
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ms_mint.matplotlib_tools module
+---------------------------------
+
+.. automodule:: ms_mint.matplotlib_tools
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ms_mint.notebook module
+------------------------
+
+.. automodule:: ms_mint.notebook
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ms_mint.pca module
+-------------------
+
+.. automodule:: ms_mint.pca
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ms_mint.plotly_tools module
+-----------------------------
+
+.. automodule:: ms_mint.plotly_tools
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ms_mint.plotting module
+------------------------
+
+.. automodule:: ms_mint.plotting
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ms_mint.processing module
+--------------------------
+
+.. automodule:: ms_mint.processing
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ms_mint.standards module
+-------------------------
+
+.. automodule:: ms_mint.standards
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ms_mint.targets module
+-----------------------
+
+.. automodule:: ms_mint.targets
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ms_mint.tools module
+---------------------
+
+.. automodule:: ms_mint.tools
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: ms_mint
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/readme.rst b/docs/readme.rst
@@ -0,0 +1,2 @@
+.. include:: ../README.md
+   :parser: myst_parser.sphinx_
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -0,0 +1,4 @@
+sphinx-rtd-theme
+sphinx-materialdesign-theme
+myst-parser
+..
diff --git a/images/hierarchical-clustering.png b/images/hierarchical-clustering.png
diff --git a/images/peak-shapes.png b/images/peak-shapes.png
diff --git a/images/results-example.png b/images/results-example.png
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -0,0 +1,4 @@
+setuptools_scm
+pytest
+pytest-cov
+coverage-badge
diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,32 @@
+pytest
+six
+jsonschema
+entrypoints
+pygments
+pexpect
+decorator
+pillow
+lxml
+pandas>=2
+matplotlib
+seaborn
+pyteomics
+scikit-learn
+molmass
+pymzml
+plotly
+colorlover
+tqdm
+ipywidgets
+openpyxl
+pyarrow
+tables
+h5py
+ipyfilechooser
+hdf5plugin
+nbformat>=4.2.0 
+sphinx
+sphinx-rtd-theme
+myst-parser
+psims
+numpy<2.0.0
diff --git a/tests/test__notebook.py b/tests/test__notebook.py
@@ -0,0 +1,17 @@
+from ms_mint.notebook import Mint
+
+mint = Mint(verbose=True)
+
+
+class TestClass:
+    def test__mint_n_files(self):
+        ms_files = [
+            "tests/data/ms_files/fileA.mzXML",
+            "tests/data/ms_files/fileB.mzxml",
+            "tests/data/ms_files/fileC.mzML",
+            "tests/data/ms_files/fileD.mzml",
+        ]
+        mint.ms_files = ms_files
+        result = mint.n_files
+        expect = len(ms_files)
+        assert result == expect, f"Expected ({expect}) != result ({result})"
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		.. include:: ../README.md
		:parser: myst_parser.sphinx_