Merge pull request #125 from jdenholm/dev

v0.11.0

.github/workflows/code-quality.yml

@@ -6,41 +6,52 @@ on:
   pull_request:
     branches: [ dev ]
 
-jobs:
-  build-linux:
-    runs-on: ubuntu-latest
 
+
+
+jobs:
+  code-quality:
+    name: Code quality (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      max-parallel: 3
+      matrix:
+        os: ["macos-latest"]
+        python-version: ["3.9", "3.10", "3.11"]
     steps:
-    - uses: actions/checkout@v3
-    - 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: Install dependencies
-      run: |
-        conda env update --file requirements-dev.conda.yaml --name base
-
-    - name: Print python version
-      run: |
-        python --version
-
-    - name: Lint with Pylint
-      run: |
-        pylint $(git ls-files src/) --disable=duplicate-code
-
-    - name: Lint with Mypy
-      run: |
-        mypy $(git ls-files src/)
-
-    - name: Lint with Pydocstyle
-      run: |
-        pydocstyle --convention=numpy $(git ls-files src/)
-
-    - name: Test with Pytest
-      run: |
-        pytest tests/
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: torch-tools
+          auto-update-conda: true
+          environment-file: requirements-dev.conda.yaml
+          auto-activate-base: false
+          python-version: ${{ matrix.python-version }}
+          channels: anaconda, conda-forge, defaults
+
+      - name: env list
+        shell: bash -l {0}
+        run: |
+          conda list
+
+      - name: Lint with Pylint
+        shell: bash -l {0}
+        run: |
+          python -m pylint $(git ls-files src/) --disable=duplicate-code
+
+      - name: Lint with Mypy
+        shell: bash -l {0}
+        run: |
+          python -m mypy $(git ls-files src/)
+
+      - name: Lint with Pydocstyle
+        shell: bash -l {0}
+        run: |
+          python -m pydocstyle --convention=numpy $(git ls-files src/)
+
+      - name: Test with Pytest
+        shell: bash -l {0}
+        run: |
+          python -m pytest tests/

.github/workflows/doc-update.yml

@@ -6,34 +6,34 @@ on:
       - main
 
 jobs:
-  build:
-
+  code-quality:
+    name: Publish docs (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
     strategy:
+      fail-fast: false
+      max-parallel: 3
       matrix:
-        python_version: ["3.10"]
         os: ["ubuntu-latest"]
-
-    name: ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
+        python-version: ["3.10"]
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python_version }}
-    - 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
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: torch-tools
+          auto-update-conda: true
+          environment-file: requirements-dev.conda.yaml
+          auto-activate-base: false
+          python-version: ${{ matrix.python-version }}
+          channels: anaconda, conda-forge, defaults
 
-    - name: Create conda env
-      run: |
-        conda env update --file requirements-dev.conda.yaml --name base
 
-    - name: Print python version
-      run: |
-        python --version
+      - name: Print python version
+        shell: bash -l {0}
+        run: |
+          python --version
 
-    - name: Update docs
-      run : |
-        ./.build_docs.sh
+      - name: Update docs
+        shell: bash -l {0}
+        run: |
+          ./.build_docs.sh

.github/workflows/torch-tools-install.yml

@@ -4,36 +4,61 @@ on:
     branches: [ dev ]
   pull_request:
     branches: [ dev ]
-jobs:
-  build:
 
+jobs:
+  install-package:
+    name: (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        python_version: ["3.10"]
-        os: ["ubuntu-latest", "macos-latest"]
-
-    name: ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.9", "3.10", "3.11"]
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python_version }}
-
-    - 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: Install dependencies
-      run: |
-        conda install "python>=3.9.10" --name base
-
-    - name: Print python version
-      run: |
-        python --version
-
-    - name: Install TorchTools
-      run : |
-        pip install .
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          auto-activate-base: true
+          python-version: ${{ matrix.python-version }}
+          channels: anaconda, conda-forge, defaults
+      - name: Install Python with conda
+        run: |
+          conda install python=${{ matrix.python-version }} --name base
+
+      - uses: actions/checkout@v4
+      - name: Install TorchTools
+        run : |
+          pip install .
+
+# jobs:
+#   build:
+
+#     strategy:
+#       matrix:
+#         python_version: ["3.10"]
+#         os: ["ubuntu-latest", "macos-latest"]
+
+#     name: ${{ matrix.os }}
+#     runs-on: ${{ matrix.os }}
+#     steps:
+#     - uses: actions/checkout@v3
+#     - name: Set up Python
+#       uses: actions/setup-python@v2
+#       with:
+#         python-version: ${{ matrix.python_version }}
+
+#     - name: Add conda to system path
+#       run: |
+#         echo $CONDA/bin >> $GITHUB_PATH
+
+#     - name: Install dependencies
+#       run: |
+#         conda install "python>=3.9.10" --name base
+
+#     - name: Print python version
+#       run: |
+#         python --version
+
+#     - name: Install TorchTools
+#       run : |
+#         pip install .

CHANGELOG.md

@@ -1,3 +1,9 @@
+## Version 0.11.0
+  - Made changes to ``VAE2d``:
+    - Added the option to have the mean and variance nets be CNNs, rather than MLPs.
+    - Started returning the KL divergence during training and validation.
+    - Added extra tests accordingly.
+
 ## Version 0.10.3
   - Added the option to freeze the encoder in the forward pass of ``SimpleConvNet2d``.