init

.devcontainer/dev.Dockerfile

@@ -0,0 +1,35 @@
+FROM docker.io/rockylinux:9
+
+ARG USERNAME=vscode
+ARG USER_UID=1000
+ARG USER_GID=$USER_UID
+ARG WORK_DIR=/workspace
+ENV HOME="/home/${USERNAME}"
+ENV PATH="$HOME/.local/bin:$PATH"
+
+RUN groupadd --gid $USER_GID $USERNAME \
+    && useradd -m -d $HOME \
+    --uid $USER_UID --gid $USER_GID $USERNAME
+
+ENV PYENV_ROOT="${HOME}/.pyenv"
+ENV PATH="${PYENV_ROOT}/shims:${PYENV_ROOT}/bin:${HOME}/.local/bin:${PATH}"
+
+COPY . /tmp/app
+
+WORKDIR /tmp/app
+
+RUN bash ./bin/deploy/prep.sh && bash ./bin/deploy/req.sh
+
+WORKDIR /
+
+RUN rm -rf /tmp/app
+
+RUN git config --global --add safe.directory $WORK_DIR
+
+RUN mkdir -p $WORK_DIR && \
+    chown $USERNAME:$USERNAME -R $WORK_DIR && \
+    chown $USERNAME:$USERNAME -R $HOME
+
+USER $USERNAME
+
+ENTRYPOINT ["/bin/sh", "/entrypoint.sh"]

.devcontainer/dev.docker-compose.yml

@@ -0,0 +1,23 @@
+version: '3'
+services:
+  dev:
+    user: vscode
+    build:
+      context: .
+      dockerfile: .devcontainer/dev.Dockerfile
+      args:
+      - USERNAME=vscode
+      - USER_UID=1000
+      - USER_GID=1000
+      - WORK_DIR=/workspace
+    volumes:
+    - .:/workspace
+    - ~/.gitconfig:/etc/gitconfig:ro
+    networks:
+    - bio
+
+
+networks:
+  bio:
+    name: bioindustry
+    external: true

.devcontainer/devcontainer.json

@@ -0,0 +1,47 @@
+{
+  "customizations": {
+    "vscode": {
+      "extensions": [
+        "njpwerner.autodocstring",
+        "formulahendry.code-runner",
+        "streetsidesoftware.code-spell-checker",
+        "kamikillerto.vscode-colorize",
+        "ms-azuretools.vscode-docker",
+        "donjayamanne.githistory",
+        "eamodio.gitlens",
+        "oderwat.indent-rainbow",
+        "yzhang.markdown-all-in-one",
+        "christian-kohler.path-intellisense",
+        "ms-python.vscode-pylance",
+        "ms-python.python",
+        "ChristianDein.python-radon",
+        "foxundermoon.shell-format",
+        "ms-vscode.test-adapter-converter",
+        "hbenl.vscode-test-explorer",
+        "Gruntfuggly.todo-tree",
+        "uctakeoff.vscode-counter",
+        "DotJoshJohnson.xml",
+        "aaron-bond.better-comments",
+        "KevinRose.vsc-python-indent",
+        "tamasfe.even-better-toml"
+      ]
+    }
+  },
+  "dockerComposeFile": [
+    "../docker-compose.yml",
+    "dev.docker-compose.yml"
+  ],
+  "mounts": [
+    "source=${localEnv:HOME}/tech/git/.authentication,target=/workspace/.authentication,type=bind,consistency=cached"
+  ],
+  "name": "microbial_strain_data_model",
+  "postAttachCommand": "make dev",
+  "remoteUser": "vscode",
+  "runServices": [
+    "dev"
+  ],
+  "service": "dev",
+  "shutdownAction": "stopCompose",
+  "updateRemoteUserUID": true,
+  "workspaceFolder": "/workspace"
+}

.dockerignore

@@ -0,0 +1,16 @@
+*
+
+!/bin
+!/src
+!/configs
+
+!Makefile
+!poetry.lock
+!pyproject.toml
+
+!README.md
+!LICENSE
+
+**/__pycache__
+**/*.py[cod]
+**/*$py.class

.github/workflows/main.yml

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+name: main
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  mac_win_test:
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.11']
+        os: [windows-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+    - uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install tox
+    - name: tox test
+      run: |
+        tox -e py
+  lin_lint:
+    env:
+      PY_DIR: pyenv
+      CU_HOME: /home/custom
+    strategy:
+      fail-fast: false
+    runs-on: ubuntu-latest
+    steps:
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.11'
+    - name: Install dependencies
+      run: |
+        sudo mkdir -p $CU_HOME && sudo chown runner -R $CU_HOME
+        sudo apt install -y libedit-dev curl make git-lfs
+        curl https://pyenv.run | PYENV_ROOT=$CU_HOME/$PY_DIR bash
+        echo "$CU_HOME/$PY_DIR/bin" >> $GITHUB_PATH
+        echo "$CU_HOME/$PY_DIR/shims" >> $GITHUB_PATH
+    - name: Checkout
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+    - name: lint and test
+      run: |
+        make dev
+        make runChecks

.github/workflows/mkdocs.yml

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+name: Deploy static documentation to Pages
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
+jobs:
+  build:
+    env:
+      PY_DIR: pyenv
+      CU_HOME: /home/custom
+    runs-on: ubuntu-latest
+    steps:
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.11'
+    - name: Install dependencies
+      run: |
+        sudo mkdir -p $CU_HOME && sudo chown runner -R $CU_HOME
+        sudo apt install -y libedit-dev curl make git-lfs
+        curl https://pyenv.run | PYENV_ROOT=$CU_HOME/$PY_DIR bash
+        echo "$CU_HOME/$PY_DIR/bin" >> $GITHUB_PATH
+        echo "$CU_HOME/$PY_DIR/shims" >> $GITHUB_PATH
+    - name: Checkout
+      uses: actions/checkout@v3
+    - name: Setup Pages
+      uses: actions/configure-pages@v3
+    - name: Create documentation html
+      run: |
+        make docs
+        make runDocs
+    - name: Upload artifact
+      uses: actions/upload-pages-artifact@v1
+      with:
+        path: ./public
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+    - name: Deploy to GitHub Pages
+      id: deployment
+      uses: actions/deploy-pages@v2