Update main to 2025.0.2

.github/workflows/documentation.yml

@@ -26,12 +26,12 @@ jobs:
           pip install --find-links dist esat
           sphinx-apidoc -o docs esat
           sphinx-apidoc -o docs eval
-          sphinx-build . _build
+          sphinx-build -b html . docs/_build/html
       - name: Deploy to GitHub Pages
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
         with:
           publish_branch: gh-pages
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: _build
+          publish_dir: docs/_build/html
           force_orphan: true

.github/workflows/python-package.yml

@@ -10,40 +10,11 @@ env:
   CIBW_BUILD: "cp310-* cp311-* cp312-*"
 
 jobs:
-#  build_wheels:
-#    name: Build wheels on ${{ matrix.os }}
-#    runs-on: ${{ matrix.os }}
-#    strategy:
-#      matrix:
-#        os: [ ubuntu-latest, windows-latest, macos-13, macos-latest ]
-#    steps:
-#      - uses: actions/checkout@v4
-#      - uses: actions/setup-python@v5
-#        with:
-#          python-version: "3.12"
-#      - name: Install cibuildwheel
-#        run: python -m pip install cibuildwheel==2.23.3
-#      - name: Install setuptools
-#        shell: bash
-#        run: |
-#          python -m pip install --upgrade pip
-#          curl https://sh.rustup.rs -sSf | sh -s -- -y --default-toolchain=stable
-#          echo "PATH=${PATH}:${HOME}/.cargo/bin" >> $GITHUB_ENV
-#          rustc --version
-#          python -m pip install build setuptools setuptools-rust
-#      - name: Build wheels
-#        run: python -m cibuildwheel --output-dir wheelhouse
-#      - uses: actions/upload-artifact@v4
-#        with:
-#          name: esat-wheels-${{ matrix.os }}-py${{matrix.python_version}}
-#          path: ./wheelhouse/*.whl
-
   build_wheels:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # macos-13 is an intel runner, macos-14 is apple silicon
         os: [ubuntu-latest, macos-13, macos-14]
         python_version: ["3.10", "3.11", "3.12"]
     steps:
@@ -52,23 +23,28 @@ jobs:
         with:
           python-version: ${{ matrix.python_version }}
       - name: Install setuptools
-        run: |
-            python -m pip install --upgrade pip
-            curl https://sh.rustup.rs -sSf | sh -s -- -y --default-toolchain=stable
-            echo "PATH=${PATH}:${HOME}/.cargo/bin" >> "$GITHUB_ENV"
-            rustc --version
-            python -m pip install build setuptools setuptools-rust
-      - name: Build wheels with cibuildwheel
         run: |
           python -m pip install --upgrade pip
+          curl https://sh.rustup.rs -sSf | sh -s -- -y --default-toolchain=stable
+          echo "PATH=${PATH}:${HOME}/.cargo/bin" >> "$GITHUB_ENV"
+          rustc --version
+          python -m pip install build setuptools setuptools-rust
+      - name: Build CPU wheels with cibuildwheel
+        run: |
           python -m pip install cibuildwheel==2.22.0
           python -m cibuildwheel --output-dir wheelhouse
-#      - name: Build wheels
-#        run:
-#            python -m build --outdir wheelhouse
       - uses: actions/upload-artifact@v4
         with:
-          name: esat-wheels-${{ matrix.os }}-py${{matrix.python_version}}
+          name: esat-wheels-cpu-${{ matrix.os }}-py${{ matrix.python_version }}
+          path: ./wheelhouse/*.whl
+      - name: Build GPU wheels with cibuildwheel
+        run: |
+          rm -rf wheelhouse
+          python -m pip install cibuildwheel==2.22.0
+          python -m cibuildwheel --output-dir wheelhouse
+      - uses: actions/upload-artifact@v4
+        with:
+          name: esat-wheels-gpu-${{ matrix.os }}-py${{ matrix.python_version }}
           path: ./wheelhouse/*.whl
 
   build_windows_wheel:
@@ -89,14 +65,20 @@ jobs:
           rustup target add aarch64-pc-windows-msvc i686-pc-windows-msvc x86_64-pc-windows-msvc
           echo "${HOME}/.cargo/bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
           python -m pip install build setuptools setuptools-rust
-      - name: Build wheels with cibuildwheel
+      - name: Build CPU wheels with cibuildwheel
         run: |
-          python -m pip install --upgrade pip
           python -m pip install cibuildwheel==2.22.0
           python -m cibuildwheel --output-dir wheelhouse
-#      - name: Build wheels
-#        run: python -m build --outdir wheelhouse
       - uses: actions/upload-artifact@v4
         with:
-          name: esat-wheels-windows-py${{matrix.python_version}}
+          name: esat-wheels-cpu-windows-py${{ matrix.python_version }}
           path: ./wheelhouse/*.whl
+      - name: Build GPU wheels with cibuildwheel
+        run: |
+          Remove-Item -Recurse -Force wheelhouse
+          python -m pip install cibuildwheel==2.22.0
+          python -m cibuildwheel --output-dir wheelhouse
+      - uses: actions/upload-artifact@v4
+        with:
+          name: esat-wheels-gpu-windows-py${{ matrix.python_version }}
+          path: ./wheelhouse/*.whl

.gitignore

@@ -30,6 +30,7 @@ docs/_downloads/
 docs/_sources/
 docs/_static/
 docs/html/
+build/
 
 notebooks/.ipynb_checkpoints/
 notebooks/old/.ipynb_checkpoints/
@@ -38,4 +39,4 @@ notebooks/old/.ipynb_checkpoints/
 *.dat
 profile.html
 profile.json
-data/test_output/
+data/test_output/

Cargo.toml

@@ -14,13 +14,15 @@ path = "rust/lib.rs"
 crate-type = ["cdylib"]
 
 [dependencies]
-numpy = "0.20.0"
-nalgebra = {version="0.32.4", features = ["rayon"]}
-ndarray = "0.15.6"
-rayon = "1.9.0"
-pyo3 = "0.20.3"
-indicatif = "0.17"
-console = "0.15.8"
+numpy = "0.25.0"
+nalgebra = "0.33.2"
+ndarray = "0.16.1"
+pyo3 = { version = "0.25.1", features = ["extension-module"] }
+indicatif = "0.18.0"
+console = "0.16.0"
+# GPU support
+candle-core = "0.9.1"
+#candle-core = { version = "0.9.1", features = ["cuda"] }
 
 [features]
 extension-module = ["pyo3/extension-module", "pyo3/generate-import-lib"]
@@ -33,3 +35,5 @@ debug = false
 [profile.release]
 opt-level = 3
 debug = false
+
+

doc-requirements.txt

@@ -7,6 +7,7 @@ plotly==6.0.1
 psutil==7.0.0
 scipy==1.15.2
 sphinx==8.2.3
+sphinx-book-theme==1.1.4
 sphinx-click==6.0.0
 sphinx-rtd-theme==3.0.2
 tabulate==0.9.0

docs/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 08826985b7a8d85c7fec8fc3270a1630
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: f688b6899233aa9a295b9d35a66d85ad
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/html/README.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Environmental Source Apportionment Toolkit (ESAT) &#8212; Environmental Source Apportionment Toolkit (ESAT) 2024.0.2 documentation</title>
+    <title>Environmental Source Apportionment Toolkit (ESAT) &#8212; Environmental Source Apportionment Toolkit (ESAT) 2025.0.2 documentation</title>
 
 
 
@@ -28,16 +28,16 @@
 <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.2/webfonts/fa-brands-400.woff2" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2" />
 
-    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" />
-    <link rel="stylesheet" type="text/css" href="_static/styles/sphinx-book-theme.css?v=a3416100" />
+    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=8f2a1f02" />
+    <link rel="stylesheet" type="text/css" href="_static/styles/sphinx-book-theme.css?v=eba8b062" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
   <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=dfe6caa3a7d634c4db9b" />
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=1300d73e"></script>
-    <script src="_static/doctools.js?v=9a2dae69"></script>
+    <script src="_static/documentation_options.js?v=b7785327"></script>
+    <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'README';</script>
@@ -324,7 +324,7 @@ <h2> Contents </h2>
 
   <section id="environmental-source-apportionment-toolkit-esat">
 <h1>Environmental Source Apportionment Toolkit (ESAT)<a class="headerlink" href="#environmental-source-apportionment-toolkit-esat" title="Link to this heading">#</a></h1>
-<p>Last Update: 08-15-2024</p>
+<p>Last Update: 04-16-2025</p>
 <section id="table-of-contents">
 <h2>Table of Contents<a class="headerlink" href="#table-of-contents" title="Link to this heading">#</a></h2>
 <ul class="simple">
@@ -367,26 +367,32 @@ <h2>Description<a class="headerlink" href="#description" title="Link to this hea
 factorization (NMF), both of which have been written in Rust and contained within the python package. A collection of
 data processing and visualization features are included for data and model analytics. The ESAT package includes a
 synthetic data generator and comparison tools to evaluate ESAT model outputs.</p>
+<p>The ESAT python package has been published with the Journal of Open Source Software (JOSS):</p>
+<p><a class="reference external" href="https://doi.org/10.21105/joss.07316"><img alt="DOI" src="https://joss.theoj.org/papers/10.21105/joss.07316/status.svg" /></a></p>
 </section>
 <section id="quick-start">
 <h2>Quick Start<a class="headerlink" href="#quick-start" title="Link to this heading">#</a></h2>
 <p>ESAT supports python version 3.10, 3.11, and 3.12. As the python package contains compiled code there are OS and python
 specific versions, supporting Mac Intel, Mac M1+, Linux, and Windows.</p>
 <section id="documentation">
 <h3>Documentation<a class="headerlink" href="#documentation" title="Link to this heading">#</a></h3>
-<p>The Python API and CLI documentation can be found at the Github ESAT IO site: <a class="reference external" href="https://quanted.github.io/esat/">https://quanted.github.io/esat/</a></p>
+<p>The Python API and CLI documentation can be found at the GitHub ESAT IO site: <a class="reference external" href="https://quanted.github.io/esat/">https://quanted.github.io/esat/</a></p>
 </section>
 <section id="installation">
 <h3>Installation<a class="headerlink" href="#installation" title="Link to this heading">#</a></h3>
 <p>The ESAT python package contains all compiled code and required dependencies and can be installed using pip</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>esat-VERSION-OS.whl
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>esat
 </pre></div>
 </div>
-<p>where the <i>VERSION</i> is the code version, such as <i>2024.1.0</i>, and <i>OS</i> is operating system targeted
-compiled version, such as <i>cp312-cp312-win_amd64</i>. If an error message appears during installation stating that the
-package is not supported check that the correct OS and python version are being installed for that system.</p>
-<p>When the package becomes available on pypi, the package will be able to be installed with</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>esat
+<p>which will install the latest version that supports and is available for your python version and OS.</p>
+<p>Development versions of ESAT can be found on the GitHub actions page, for logged-in users,
+under the ‘Build and Publish Wheel’ workflow. The latest version of the package will be available as an artifact for
+download in the ‘Artifacts’ section of the completed workflow. There wheel files can be found for specific versions
+of python and supported operating systems.</p>
+<p>If an error message appears during installation stating that the
+package is not supported check that the correct OS and python version are being installed for that system. The python
+wheels can be installed directly using</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>&lt;wheel<span class="w"> </span>file<span class="w"> </span>name&gt;
 </pre></div>
 </div>
 <p>The esat python package is recommended to be installed in its own dedicated python virtual environment or conda environment.</p>
@@ -619,7 +625,7 @@ <h2>Disclaimer<a class="headerlink" href="#disclaimer" title="Link to this headi
 
   <p class="copyright">
 
-      © Copyright 2024, EPA.
+      © Copyright 2025, EPA.
       <br/>
 
   </p>

docs/html/docs/cli.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Command Line Interface &#8212; Environmental Source Apportionment Toolkit (ESAT) 2024.0.2 documentation</title>
+    <title>Command Line Interface &#8212; Environmental Source Apportionment Toolkit (ESAT) 2025.0.2 documentation</title>
 
 
 
@@ -28,16 +28,16 @@
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.2/webfonts/fa-brands-400.woff2" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2" />
 
-    <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
-    <link rel="stylesheet" type="text/css" href="../_static/styles/sphinx-book-theme.css?v=a3416100" />
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=8f2a1f02" />
+    <link rel="stylesheet" type="text/css" href="../_static/styles/sphinx-book-theme.css?v=eba8b062" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
   <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=dfe6caa3a7d634c4db9b" />
 <link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="../_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="../_static/documentation_options.js?v=1300d73e"></script>
-    <script src="../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../_static/documentation_options.js?v=b7785327"></script>
+    <script src="../_static/doctools.js?v=9bcbadda"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'docs/cli';</script>
@@ -131,7 +131,7 @@
 
 
 
-    <p class="title logo__title">Environmental Source Apportionment Toolkit (ESAT) 2024.0.2 documentation</p>
+    <p class="title logo__title">Environmental Source Apportionment Toolkit (ESAT) 2025.0.2 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item">
@@ -629,7 +629,7 @@ <h4>plot-q<a class="headerlink" href="#esat-analysis-constrained-plot-q" title="
 <dd><p>Plot the loss value for qtype: True, Robust, Aux</p>
 <dl class="field-list simple">
 <dt class="field-odd">Default<span class="colon">:</span></dt>
-<dd class="field-odd"><p><code class="docutils literal notranslate"><span class="pre">Aux</span></code></p>
+<dd class="field-odd"><p><code class="docutils literal notranslate"><span class="pre">'Aux'</span></code></p>
 </dd>
 </dl>
 </dd></dl>
@@ -1618,7 +1618,7 @@ <h4>setup<a class="headerlink" href="#esat-simulator-setup" title="Link to this
 
   <p class="copyright">
 
-      © Copyright 2024, EPA.
+      © Copyright 2025, EPA.
       <br/>
 
   </p>

docs/html/docs/esat.cli.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>esat.cli package &#8212; Environmental Source Apportionment Toolkit (ESAT) 2024.0.2 documentation</title>
+    <title>esat.cli package &#8212; Environmental Source Apportionment Toolkit (ESAT) 2025.0.2 documentation</title>
 
 
 
@@ -28,16 +28,16 @@
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.2/webfonts/fa-brands-400.woff2" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2" />
 
-    <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
-    <link rel="stylesheet" type="text/css" href="../_static/styles/sphinx-book-theme.css?v=a3416100" />
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=8f2a1f02" />
+    <link rel="stylesheet" type="text/css" href="../_static/styles/sphinx-book-theme.css?v=eba8b062" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
   <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=dfe6caa3a7d634c4db9b" />
 <link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="../_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="../_static/documentation_options.js?v=1300d73e"></script>
-    <script src="../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../_static/documentation_options.js?v=b7785327"></script>
+    <script src="../_static/doctools.js?v=9bcbadda"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'docs/esat.cli';</script>
@@ -132,7 +132,7 @@
 
 
 
-    <p class="title logo__title">Environmental Source Apportionment Toolkit (ESAT) 2024.0.2 documentation</p>
+    <p class="title logo__title">Environmental Source Apportionment Toolkit (ESAT) 2025.0.2 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item">
@@ -469,7 +469,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
   <p class="copyright">
 
-      © Copyright 2024, EPA.
+      © Copyright 2025, EPA.
       <br/>
 
   </p>