Version 0.2.0

.github/workflows/publish_docs.yml

@@ -0,0 +1,50 @@
+name: Publish docs
+
+on:
+  release:
+    types:
+      - created
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.9']
+        include:
+          - os: ubuntu-20.04
+            label: linux-64
+            prefix: /usr/share/miniconda3/envs/
+
+    name: ${{ matrix.label }}-py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v1
+
+      - name: Install Dependencies
+        shell: bash -l {0}
+        run: |
+          pip install cookiecutter mkdocs mkdocs-material mike
+
+      # extract the first two digits from the release note
+      - name: Set release notes tag
+        run: |
+          export RELEASE_TAG_VERSION=${{ github.event.release.tag_name }}
+          echo "RELEASE_TAG_VERSION=${RELEASE_TAG_VERSION%.*}">> $GITHUB_ENV
+
+      - name: Echo release notes tag
+        run: |
+          echo "${RELEASE_TAG_VERSION}"
+
+      - name: Build docs website
+        shell: bash -l {0}
+        run: |
+          git config user.name ci-bot
+          git config user.email [email protected]
+          mike deploy --push --rebase --update-aliases ${RELEASE_TAG_VERSION} latest

.github/workflows/test_suite.yml

@@ -0,0 +1,195 @@
+name: Test Suite
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+
+  pull_request:
+    types:
+      - opened
+      - reopened
+      - synchronize
+
+env:
+  CACHE_NUMBER: 3  # increase to reset cache manually
+  CONDA_ENV_FILE: 'env.yaml'
+  CONDA_ENV_NAME: 'project-test'
+  COOKIECUTTER_PROJECT_NAME: 'project-test'
+
+jobs:
+  build:
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.8', '3.9']
+        include:
+          - os: ubuntu-20.04
+            label: linux-64
+            prefix: /usr/share/miniconda3/envs/
+
+#           - os: macos-latest
+#             label: osx-64
+#             prefix: /Users/runner/miniconda3/envs/$CONDA_ENV_NAME
+
+#           - os: windows-latest
+#             label: win-64
+#             prefix: C:\Miniconda3\envs\$CONDA_ENV_NAME
+
+    name: ${{ matrix.label }}-py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Parametrize conda env name
+        run: echo "PY_CONDA_ENV_NAME=${{ env.CONDA_ENV_NAME }}-${{ matrix.python-version }}" >> $GITHUB_ENV
+      - name: echo conda env name
+        run: echo ${{ env.PY_CONDA_ENV_NAME }}
+
+      - name: Parametrize conda prefix
+        run: echo "PY_PREFIX=${{ matrix.prefix }}${{ env.PY_CONDA_ENV_NAME }}" >> $GITHUB_ENV
+      - name: echo conda prefix
+        run: echo ${{ env.PY_PREFIX }}
+
+      - name: Define generated project files paths
+        run: |
+          echo "PROJECT_SETUPCFG_FILE=${{ env.COOKIECUTTER_PROJECT_NAME }}/setup.cfg" >> $GITHUB_ENV
+          echo "PROJECT_CONDAENV_FILE=${{ env.COOKIECUTTER_PROJECT_NAME }}/${{ env.CONDA_ENV_FILE }}" >> $GITHUB_ENV
+          echo "PROJECT_PRECOMMIT_FILE=${{ env.COOKIECUTTER_PROJECT_NAME }}/.pre-commit-config.yaml" >> $GITHUB_ENV
+
+      - uses: actions/checkout@v2
+
+      # COOKIECUTTER GENERATION
+      - name: Set up Python
+        uses: actions/setup-python@v1
+
+      - name: Install Dependencies
+        shell: bash -l {0}
+        run: |
+          pip install cookiecutter
+
+      - name: Generate Repo
+        shell: bash -l {0}
+        run: |
+          echo -e 'n\nn\nn\n' | cookiecutter . --no-input project_name=${{ env.COOKIECUTTER_PROJECT_NAME }}
+
+      - name: Init git into generated repo
+        shell: bash -l {0}
+        run: |
+          git config --global user.name ci-bot
+          git config --global user.email [email protected]
+          git init
+          git add --all
+          git commit -m "Initial commit"
+        working-directory: ${{ env.COOKIECUTTER_PROJECT_NAME }}
+
+      - name: Define cache key postfix
+        run: |
+          echo "CACHE_KEY_POSTFIX=${{ matrix.label }}-${{ matrix.python-version }}-${{ env.CACHE_NUMBER }}-${{ env.PY_CONDA_ENV_NAME }}-${{ hashFiles(env.PROJECT_CONDAENV_FILE) }}-${{ hashFiles(env.PROJECT_SETUPCFG_FILE) }}" >> $GITHUB_ENV
+
+      - name: Echo cache keys
+        run: |
+          echo ${{ env.PROJECT_SETUPCFG_FILE }}
+          echo ${{ env.PROJECT_CONDAENV_FILE }}
+          echo ${{ env.PROJECT_PRECOMMIT_FILE }}
+          echo ${{ env.CACHE_KEY_POSTFIX }}
+
+      # GENERATED PROJECT CI/CD
+
+      # Remove the python version pin from the env.yml which could be inconsistent
+      - name: Remove explicit python version from the environment
+        shell: bash -l {0}
+        run: |
+          sed -Ei '/^\s*-?\s*python\s*([#=].*)?$/d' ${{ env.CONDA_ENV_FILE }}
+          cat  ${{ env.CONDA_ENV_FILE }}
+        working-directory: ${{ env.COOKIECUTTER_PROJECT_NAME }}
+
+      - name: Setup Mambaforge
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+            miniforge-variant: Mambaforge
+            miniforge-version: latest
+            activate-environment: ${{ env.PY_CONDA_ENV_NAME }}
+            python-version: ${{ matrix.python-version }}
+            use-mamba: true
+
+      - uses: actions/cache@v2
+        name: Conda cache
+        with:
+          path: ${{ env.PY_PREFIX }}
+          key: conda-${{ env.CACHE_KEY_POSTFIX }}
+        id: conda_cache
+
+      - uses: actions/cache@v2
+        name: Pip cache
+        with:
+          path: ~/.cache/pip
+          key: pip-${{ env.CACHE_KEY_POSTFIX }}
+
+      - uses: actions/cache@v2
+        name: Pre-commit cache
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ hashFiles(env.PROJECT_PRECOMMIT_FILE) }}-conda-${{ env.CACHE_KEY_POSTFIX }}
+
+      # Ensure the hack for the python version worked
+      - name: Ensure we have the right Python
+        shell: bash -l {0}
+        run: |
+          echo "Installed Python: $(python --version)"
+          echo "Expected: ${{ matrix.python-version }}"
+          python --version | grep "Python ${{ matrix.python-version }}"
+        working-directory: ${{ env.COOKIECUTTER_PROJECT_NAME }}
+
+      # https://stackoverflow.com/questions/70520120/attributeerror-module-setuptools-distutils-has-no-attribute-version
+      # https://github.com/pytorch/pytorch/pull/69904
+      - name: Downgrade setuptools due to a but in PyTorch 1.10.1
+        shell: bash -l {0}
+        run: |
+          pip install setuptools==59.5.0 --upgrade
+        working-directory: ${{ env.COOKIECUTTER_PROJECT_NAME }}
+
+      - name: Update conda environment
+        run: mamba env update -n ${{ env.PY_CONDA_ENV_NAME }} -f ${{ env.CONDA_ENV_FILE }}
+        if: steps.conda_cache.outputs.cache-hit != 'true'
+        working-directory: ${{ env.COOKIECUTTER_PROJECT_NAME }}
+
+      # Update pip env whether or not there was a conda cache hit
+      - name: Update pip environment
+        shell: bash -l {0}
+        run: pip install -e ".[dev]"
+        if: steps.conda_cache.outputs.cache-hit == 'true'
+        working-directory: ${{ env.COOKIECUTTER_PROJECT_NAME }}
+
+      - run: pip3 list
+        shell: bash -l {0}
+        working-directory: ${{ env.COOKIECUTTER_PROJECT_NAME }}
+
+      - run: mamba info
+        working-directory: ${{ env.COOKIECUTTER_PROJECT_NAME }}
+
+      - run: mamba list
+        working-directory: ${{ env.COOKIECUTTER_PROJECT_NAME }}
+
+      # Ensure the hack for the python version worked
+      - name: Ensure we have the right Python
+        shell: bash -l {0}
+        run: |
+          echo "Installed Python: $(python --version)"
+          echo "Expected: ${{ matrix.python-version }}"
+          python --version | grep "Python ${{ matrix.python-version }}"
+        working-directory: ${{ env.COOKIECUTTER_PROJECT_NAME }}
+
+      - name: Run pre-commits
+        shell: bash -l {0}
+        run: |
+          pre-commit install
+          pre-commit run -v --all-files --show-diff-on-failure
+        working-directory: ${{ env.COOKIECUTTER_PROJECT_NAME }}
+
+      - name: Test with pytest
+        shell: bash -l {0}
+        run: |
+          pytest -v
+        working-directory: ${{ env.COOKIECUTTER_PROJECT_NAME }}

.gitignore

@@ -1,3 +1,9 @@
+wandb
+multirun.yaml
+storage
+
+# ignore the _version.py file
+_version.py
 
 # .gitignore defaults for python and pycharm
 .idea