Merge pull request #20 from quanted/dev

Updates to paper bib and gh action workflows
quanted · Dec 9, 2024 · b2f7cc7 · b2f7cc7
2 parents f314260 + 08c5a68
commit b2f7cc7
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diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -4,9 +4,6 @@ on:
   push:
     branches:
       - main
-  pull_request:
-    branches:
-      - main
   workflow_dispatch:
 
 permissions:

diff --git a/.github/workflows/package-publish.yml b/.github/workflows/package-publish.yml
@@ -1,26 +1,30 @@
-name: Build and Publish Wheel
+name: Build and Publish Python Packages
 
 on:
 #  release:
 #    types: [published]
-  push:
+  push:   # Only for testing while publish-to-pypi is commented out
     branches:
       - main
 
+env:
+  MACOSX_DEPLOYMENT_TARGET: "10.12"
+  CIBW_BUILD: "cp310-* cp311-* cp312-*"
+
 jobs:
   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"]
+        os: [ubuntu-latest, windows-latest, macos-13, macos-latest]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python_version }}
+          python-version: "3.12"
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.22.0
       - name: Install setuptools
         run: |
             python -m pip install --upgrade pip
@@ -29,46 +33,44 @@ jobs:
             rustc --version
             python -m pip install build setuptools setuptools-rust
       - name: Build wheels
-        run:
-            python -m build --outdir py_dist
-      - name: Store the distribution packages
+        run: python -m cibuildwheel --output-dir py_dist
+      - name: Store the compiled packages
         uses: actions/upload-artifact@v4
         with:
-          name: esat-wheels-${{ matrix.os }}-py${{matrix.python_version}}
+          name: esat-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: py_dist/
 
-  build_windows_wheel:
-    name: Build wheels on windows-latest
-    runs-on: windows-latest
-    strategy:
-      matrix:
-        python_version: [ "3.10", "3.11", "3.12" ]
+  publish-to-testpypi:
+    name: Publish Python 🐍 distribution 📦 to TestPyPI
+    needs:
+      - build_wheels
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/esat
+    permissions:
+      id-token: write
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python_version }}
-      - name: Install setuptools
-        run: |
-          python -m pip install --upgrade pip
-          curl https://sh.rustup.rs -sSf | sh -s -- -y --default-toolchain=stable
-          echo "${HOME}/.cargo/bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
-          python -m pip install build setuptools setuptools-rust
-      - name: Build wheels
-        run: python -m build --outdir py_dist
-      - name: Store the distribution packages
-        uses: actions/upload-artifact@v4
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
         with:
-          name: esat-wheels-${{ matrix.os }}-py${{matrix.python_version}}
+          pattern: esat-wheels-*
+          merge-multiple: true
           path: py_dist/
+      - name: Publish distribution 📦 to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: py_dist/
+          skip-existing: true
+          repository-url: https://test.pypi.org/legacy/
 
 #  publish-to-pypi:
 #    name: >-
 #      Publish Python 🐍 distribution 📦 to PyPI
 #    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
 #    needs:
 #      - build_wheels
-#      - build_windows_wheel
+#      - publish-to-testpypi
 #    runs-on: ubuntu-latest
 #    environment:
 #      name: pypi
@@ -79,11 +81,16 @@ jobs:
 #      - name: Download all the dists
 #        uses: actions/download-artifact@v4
 #        with:
-#          name: python-package-distributions
+#          pattern: esat-wheels-*
+#          merge-multiple: true
 #          path: py_dist/
 #      - name: Publish distribution 📦 to PyPI
 #        uses: pypa/gh-action-pypi-publish@release/v1
-#
+#        with:
+#          packages-dir: py_dist/
+
+# Currently not intending on using automated github-release as the primary trigger for pypi publishing is by creating
+# a new github version release. This is done manually by the developer.
 #  github-release:
 #    name: >-
 #      Sign the Python 🐍 distribution 📦 with Sigstore
@@ -126,31 +133,3 @@ jobs:
 #          gh release upload
 #          '${{ github.ref_name }}' py_dist/**
 #          --repo '${{ github.repository }}'
-
-
-  publish-to-testpypi:
-    name: Publish Python 🐍 distribution 📦 to TestPyPI
-    needs:
-      - build_wheels
-      - build_windows_wheel
-    runs-on: ubuntu-latest
-
-    environment:
-      name: testpypi
-      url: https://test.pypi.org/p/esat
-
-    permissions:
-      id-token: write  # IMPORTANT: mandatory for trusted publishing
-
-    steps:
-      - name: Download all the dists
-        uses: actions/download-artifact@v4
-        with:
-          pattern: esat-wheels-*
-          merge-multiple: true
-          path: py_dist/
-      - name: Publish distribution 📦 to TestPyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          packages-dir: py_dist/
-          repository-url: https://test.pypi.org/legacy/
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -1,59 +1,90 @@
-name: Build and Publish Wheel
+name: Build and Publish Artifacts
 
 on:
   push:
     branches:
-      - main
+      - dev
+
+env:
+  MACOSX_DEPLOYMENT_TARGET: "10.12"
+  CIBW_BUILD: "cp310-* cp311-* cp312-*"
 
 jobs:
   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"]
+        os: [ ubuntu-latest, windows-latest, macos-13, macos-latest ]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         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
-        run:
-            python -m build --outdir wheelhouse
-      - uses: actions/upload-artifact@v4
-        with:
-          name: esat-wheels-${{ matrix.os }}-py${{matrix.python_version}}
-          path: ./wheelhouse/*.whl
-
-  build_windows_wheel:
-    name: Build wheels on windows-latest
-    runs-on: windows-latest
-    strategy:
-      matrix:
-        python_version: [ "3.10", "3.11", "3.12" ]
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python_version }}
+          python-version: "3.12"
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.22.0
       - name: Install setuptools
         run: |
           python -m pip install --upgrade pip
           curl https://sh.rustup.rs -sSf | sh -s -- -y --default-toolchain=stable
-          echo "${HOME}/.cargo/bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
+          echo "PATH=${PATH}:${HOME}/.cargo/bin" >> "$GITHUB_ENV"
+          rustc --version
           python -m pip install build setuptools setuptools-rust
       - name: Build wheels
-        run: python -m build --outdir wheelhouse
+        run: python -m cibuildwheel --output-dir wheelhouse
       - uses: actions/upload-artifact@v4
         with:
-          name: esat-wheels-windows-py${{matrix.python_version}}
+          name: esat-wheels-${{ 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:
+#      - uses: actions/checkout@v4
+#      - uses: actions/setup-python@v5
+#        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
+#        run:
+#            python -m build --outdir wheelhouse
+#      - uses: actions/upload-artifact@v4
+#        with:
+#          name: esat-wheels-${{ matrix.os }}-py${{matrix.python_version}}
+#          path: ./wheelhouse/*.whl
+#
+#  build_windows_wheel:
+#    name: Build wheels on windows-latest
+#    runs-on: windows-latest
+#    strategy:
+#      matrix:
+#        python_version: [ "3.10", "3.11", "3.12" ]
+#    steps:
+#      - uses: actions/checkout@v4
+#      - uses: actions/setup-python@v5
+#        with:
+#          python-version: ${{ matrix.python_version }}
+#      - name: Install setuptools
+#        run: |
+#          python -m pip install --upgrade pip
+#          curl https://sh.rustup.rs -sSf | sh -s -- -y --default-toolchain=stable
+#          echo "${HOME}/.cargo/bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
+#          python -m pip install build setuptools setuptools-rust
+#      - name: Build wheels
+#        run: python -m build --outdir wheelhouse
+#      - uses: actions/upload-artifact@v4
+#        with:
+#          name: esat-wheels-windows-py${{matrix.python_version}}
+#          path: ./wheelhouse/*.whl
diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 # Environmental Source Apportionment Toolkit (ESAT)
-Last Update: 08-15-2024
+Last Update: 12-09-2024
 
 ## Table of Contents
  - [Description](#description)
@@ -38,24 +38,25 @@ ESAT supports python version 3.10, 3.11, and 3.12. As the python package contain
 specific versions, supporting Mac Intel, Mac M1+, Linux, and Windows.
 
 ### Documentation
-The Python API and CLI documentation can be found at the Github ESAT IO site: [https://quanted.github.io/esat/](https://quanted.github.io/esat/)
+The Python API and CLI documentation can be found at the GitHub ESAT IO site: [https://quanted.github.io/esat/](https://quanted.github.io/esat/)
 
 ### Installation
 The ESAT python package contains all compiled code and required dependencies and can be installed using pip
 ```bash
-pip install esat-VERSION-OS.whl
+pip install esat
 ```
-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.
+which will install the latest version that supports and is available for your python version and OS.
 
-The latest version of the ESAT python package can be found on the github actions page, for users who are signed into github, 
+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.
+download in the 'Artifacts' section of the completed workflow. There wheel files can be found for specific versions
+of python and supported operating systems. 
 
-When the package becomes available on pypi, the package will be able to be installed with 
+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 
 ```bash
-pip install esat
+pip install <wheel file name>
 ```
 The esat python package is recommended to be installed in its own dedicated python virtual environment or conda environment.
 

diff --git a/eval/factor_comparison.py b/eval/factor_comparison.py
@@ -450,3 +450,41 @@ def combine_factors(self, factors, model_correlation, model_contributions, facto
         r_avg_3 = np.mean(r_values_3)
         return factors, r_avg, r_values, r_avg_2, r_values_2, r_avg_3, r_values_3
 
+# class FactorCompareV2:
+#     """
+#
+#     Parameters
+#     ----------
+#     base_model : BaseModel
+#         The base model to compare against.
+#     models : list
+#         A list of models to compare against the base model.
+#     method : str
+#         Correlation method to use
+#     """
+#     def __init__(self, base_model, models, method: str = "all"):
+#         self.base_model = base_model
+#         self.models = models
+#         self.method = method
+#         self.base_factors = base_model.factors
+#         self.base_features = base_model.features
+#
+#         self.model_results = {}
+#
+#         self.factor_map = None
+#
+#     def compare(self, verbose: bool = True):
+#         """
+#
+#         Parameters
+#         ----------
+#         verbose
+#
+#         Returns
+#         -------
+#
+#         """
+#         base_mean_W = np.mean(self.base_model.W, axis=0)[0]
+#         base_mass_matrix = (base_mean_W*self.base_model.H)/np.sum(base_mean_W*self.base_model.H)
+
+