Nance-Lab-Brain-Image · nlsschim · Apr 21, 2025 · Apr 22, 2025 · Apr 22, 2025 · Apr 24, 2025
diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
@@ -7,20 +7,29 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 5
+    defaults:
+      run:
+      # Adding -l {0} helps ensure conda can be found properly.
+        shell: bash -l {0}
 
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python 3.10
       uses: actions/setup-python@v3
       with:
         python-version: '3.10'
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Setup Miniforge
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        miniforge-version: latest
+        python-version: ${{ matrix.python-version }}
+        environment-file: environment.yml
+        activate-environment: environment.yml
+        run-post: false
     - name: Install dependencies
       run: |
-        conda env update --file environment.yml --name base
+        python -m pip install flake8 pytest coverage pytest-cov
+        pip install .
     - name: Lint with flake8
       run: |
         conda install flake8
@@ -30,5 +39,9 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        conda install pytest
-        pytest
+        python -m pytest --cov=turmoric --cov-branch --cov-report=xml
+    - name: Upload coverage reports to Codecov
+      uses: codecov/[email protected]
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        slug: Nance-Lab/TURMorIC
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,11 @@
 *cache*
 *DS_Store*
-*egg-info*
+*egg-info/
+*.egg
+*.coverage
+.hypothesis/
+__pycache__/
+.vscode
+coverage.xml
+*.csv
+*.json
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,23 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version, and other tools you might need
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.13"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally, but recommended,
+# declare the Python requirements required to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+# python:
+#    install:
+#    - requirements: docs/requirements.txt
+
diff --git a/README.md b/README.md
@@ -27,7 +27,7 @@ This directory contains all of the source code for the functions of the TURMorIC
 # test Directory 
 This directory holds all of the test functions for each of the components. This includes functions to test if the image directory exists, cleaning the file and folder paths, adjusting contrast among other preprocessing steps.
 _________________________________________________________________
- ##Installation Instructions 
+## Installation Instructions 
 To get started with TURMERIC, follow these steps:
 
 Prerequisites:

diff --git a/docs/CHEME546_final_presentation.pptx b/docs/CHEME546_final_presentation.pptx
diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,20 @@
+# 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/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/modules.doctree b/docs/_build/doctrees/modules.doctree
diff --git a/docs/_build/doctrees/turmoric.doctree b/docs/_build/doctrees/turmoric.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: acbd4b40445a055688478a090e8bc54d
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html
@@ -0,0 +1,106 @@
+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Overview: module code &mdash; TURMorIC 0.0.1 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=b86133f3" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+
+
+      <script src="../_static/jquery.js?v=5d32c60e"></script>
+      <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+      <script src="../_static/documentation_options.js?v=d45e8c67"></script>
+      <script src="../_static/doctools.js?v=9bcbadda"></script>
+      <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+    <script src="../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+
+
+          <a href="../index.html" class="icon icon-home">
+            TURMorIC
+          </a>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../turmoric.html">turmoric package</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../index.html">TURMorIC</a>
+      </nav>
+
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">Overview: module code</li>
+      <li class="wy-breadcrumbs-aside">
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="turmoric/apply_thresholds.html">turmoric.apply_thresholds</a></li>
+<li><a href="turmoric/cell_analysis.html">turmoric.cell_analysis</a></li>
+<li><a href="turmoric/image_process.html">turmoric.image_process</a></li>
+<li><a href="turmoric/main.html">turmoric.main</a></li>
+<li><a href="turmoric/utils.html">turmoric.utils</a></li>
+<li><a href="turmoric/vampire_model.html">turmoric.vampire_model</a></li>
+</ul>
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2025, Nels Schimek, Colin Landis.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
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+</footer>
+        </div>
+      </div>
+    </section>
+  </div>
+  <script>
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script> 
+
+</body>
+</html>