Conditional standard deviations of the random effects

.github/workflows/Build.yml

@@ -1,20 +1,30 @@
-name: Build (& Test)
+name: Build and Deploy
 on:
   workflow_dispatch:
     inputs:
-      debug_enabled:
-        description: 'Run workflow with ssh debugging'
+      upload_anaconda:
+        description: 'Upload build to anaconda'
+        required: false
+        default: 'skip'
+        type: choice
+        options:
+          - 'pre-release'
+          - 'main'
+          - 'skip'
+      upload_pypi:
+        description: 'Upload build to pypi'
         required: false
         default: false
-  release:
-    types: [published]
-
-  schedule:
-    - cron: '0 0 * * 0'
+        type: boolean
+      deploy_docs:
+        description: 'Deploy docs to github pages'
+        required: false
+        default: false
+        type: boolean
 
 env:
   PACKAGE_NAME: pymer4
-  DEPLOY_PY_VER: 3.8  # only this job deploys docs, anaconda.org, pypi
+  DEPLOY_PY_VER: 3.8  # only this job runner deploys docs and pypi package
   DEPLOY_OS: ubuntu-latest
   CONDA_BLD_PATH: /tmp/ci_conda_bld
 
@@ -29,18 +39,11 @@ jobs:
     runs-on: ${{ matrix.os }}
     continue-on-error: ${{ matrix.experimental }}
     strategy:
-      fail-fast: false
+      fail-fast: true
       matrix:
-        py_ver: [3.8, 3.9]
+        py_ver: [3.8, 3.9, '3.10', 3.11]
         os: [ubuntu-latest, macos-latest]
-        experimental: [false]
-        include:
-          - py_ver: 3.7
-            os: macos-latest
-            experimental: true
-          - py_ver: 3.7
-            os: ubuntu-latest
-            experimental: false
+        experimental: [true]
 
     outputs:
       # tarballs are py3X job-specific
@@ -89,12 +92,11 @@ jobs:
           conda config --show | grep bld_path
           conda info
           conda-build ./conda/ --python=$PY_VER -c https://conda.anaconda.org/conda-forge/ --verify
-          tarball=$(conda build --python=$PY_VER conda --output | tail -1)
+          tarball=$(conda-build --python=$PY_VER conda --output | tail -1)
+          echo "conda build tarball" $tarball
           if [[ $OS == "Linux" ]]; then \
               conda convert -p win-64 -o $CONDA_BLD_PATH $tarball; \
           fi
-          echo "conda build tarball" $tarball
-          echo "::set-output name=conda-tarball::$tarball"
           echo "{conda-tarball}={$tarball}" >> $GITHUB_OUTPUT
 
       # ------------------------------------------------------------
@@ -107,6 +109,7 @@ jobs:
         run: |
           conda create -n env_$PY_VER python=$PY_VER $PACKAGE_NAME -c $CONDA_BLD_PATH -c conda-forge -c defaults
           conda activate env_$PY_VER
+          conda info | grep active
           pip install -r requirements-dev.txt
           python -c "from pymer4.test_install import test_install; test_install()"
 
@@ -116,6 +119,8 @@ jobs:
           PY_VER: ${{ matrix.py_ver }}
         run: |
           conda activate env_$PY_VER
+          conda info | grep active
+          black --version
           black --check --verbose .
           pytest pymer4/tests
 
@@ -127,60 +132,63 @@ jobs:
         if: ${{ matrix.py_ver == env.DEPLOY_PY_VER && matrix.os == env.DEPLOY_OS }}
         run: |
           conda activate env_$PY_VER
+          conda info | grep active
           conda install sphinx sphinx_bootstrap_theme sphinx-gallery -c conda-forge
           cd docs && make clean && make html
           touch _build/html/.nojekyll
 
-      # 5b. Deploy docs (only for 3.8 which handles deployment)
-      # Only runs when a PR is merged into master or there's a direct push to master
+      # 5b. Deploy docs
+      # Only runs on the 3.8 runner when there's a release
       - name: Deploy docs
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        if: ${{ (matrix.py_ver == env.DEPLOY_PY_VER && matrix.os == env.DEPLOY_OS) && ((github.event_name == 'push' && github.ref == 'refs/heads/master') || (github.event.pull_request.merged && github.base_ref == 'master' && github.head_ref == 'dev')) }}
+        if: ${{ (matrix.py_ver == env.DEPLOY_PY_VER && matrix.os == env.DEPLOY_OS) && (github.event_name == 'release' || inputs.deploy_docs)}}
         uses: crazy-max/ghaction-github-pages@v2
         with:
           target_branch: gh-pages
           build_dir: docs/_build/html
 
-      # 6. Build package for PyPi (only for 3.8 linux which handles deployment)
+      # 6. Build package for PyPi
+      # Only runs on the 3.8 runner
       - name: Build for Pypi
+        env:
+          PY_VER: ${{ matrix.py_ver }}
         if: ${{ matrix.py_ver == env.DEPLOY_PY_VER && matrix.os == env.DEPLOY_OS }}
         run: |
           conda activate env_$PY_VER
+          conda info | grep active
           pip install build
           python -m build --sdist --wheel --outdir dist/
 
       # 7. Deploy package to Pypi 
-      # Only runs when a manual github release is created
+      # Only runs on the 3.8 runner when there's a release
       - name: PyPi deploy
-        if: ${{ matrix.py_ver == env.DEPLOY_PY_VER && matrix.os == env.DEPLOY_OS && github.event_name == 'release'}}
+        if: ${{ (matrix.py_ver == env.DEPLOY_PY_VER && matrix.os == env.DEPLOY_OS) && (github.event_name == 'release' || inputs.upload_pypi)}}
         uses: pypa/gh-action-pypi-publish@master
         with:
           password: ${{ secrets.PYPI_API_TOKEN }}
 
-      # 8a. Deploy package to main conda channel but each OS uploads their own and linux uploads for linux and windows
-      # Only runs when a manual github release is created
+      # 8a. Deploy package to main conda main channel
+      # Runs when a github release is created, but can also be triggered manually
       - name: Conda main deploy 
-        if: ${{ github.event_name == 'release' }}
+        if: ${{ (github.event_name == 'release') || (inputs.upload_anaconda == 'main') }}
         env:
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
         run: |
           echo 'Conda release on main channel'
+          conda install anaconda-client
           anaconda -t "$ANACONDA_TOKEN" upload $CONDA_BLD_PATH/**/${PACKAGE_NAME}*.tar.bz2 -l "main"
 
       # OR -----
 
-      # 8b. Deploy package to pre-release conda channel (only for 3.8 which handles deployment) but each OS uploads their own and linux uploads for linux and windows
-      # Only runs when a PR is merged into master or there's a direct push to master
+      # 8b. Deploy package to pre-release conda channel 
+      # Only runs when triggered manually
       - name: Conda pre-release deploy
-        if: ${{ ((github.event_name == 'push' && github.ref == 'refs/heads/master') || (github.event.pull_request.merged && github.base_ref == 'master' && github.head_ref == 'dev')) }}
+        if: ${{ inputs.upload_anaconda == 'pre-release' }}
         env:
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
         run: |
           echo 'Conda release on pre-release channel'
+          conda install anaconda-client
           anaconda -t "$ANACONDA_TOKEN" upload $CONDA_BLD_PATH/**/${PACKAGE_NAME}*.tar.bz2 -l "pre-release"
-
-      # N. Optionall debug via ssh if workflow is run manually with debug_enabled = true
-      - name: Setup SSH session
-        if: ${{ github.event_name == 'workflow_dispatch' && github.events.inputs.debug_enabled }}
-        uses: mxschmitt/action-tmate@v3
+

.github/workflows/Build_noarch.yml

@@ -0,0 +1,137 @@
+name: Build and Deploy noarch
+on:
+  workflow_dispatch:
+    inputs:
+      upload_anaconda:
+        description: 'Upload build to anaconda'
+        required: false
+        default: 'skip'
+        type: choice
+        options:
+          - 'pre-release'
+          - 'main'
+          - 'skip'
+
+env:
+  PACKAGE_NAME: pymer4
+  DEPLOY_PY_VER: 3.8  # only this job runner deploys docs and pypi package
+  DEPLOY_OS: ubuntu-latest
+  CONDA_BLD_PATH: /tmp/ci_conda_bld
+
+defaults:
+  run:
+    # login shell to source the conda hook in .bash_profile
+    shell:
+      bash -l {0}
+
+jobs:
+  ci:
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.experimental }}
+    strategy:
+      fail-fast: true
+      matrix:
+        py_ver: [3.9]
+        os: [ubuntu-latest]
+        experimental: [true]
+
+    outputs:
+      # tarballs are py3X job-specific
+      conda-tarball: ${{ steps.conda-bld.outputs.conda-tarball }}
+
+    steps:
+
+      # ------------------------------------------------------------
+      # 0. Print some basic github action info
+      - name: diagnostic info
+        run: |
+          echo "OS: ${{ matrix.os }}" 
+          echo "Python: ${{ matrix.py_ver }}" 
+          echo "Conda build path: $CONDA_BLD_PATH"
+          echo "Deploy OS: $DEPLOY_OS"
+          echo "Deploy Python: $DEPLOY_PY_VER"
+          echo "GA event name: ${{ github.event_name }}"
+          echo "GA ref: ${{ github.ref }}"
+
+      # ------------------------------------------------------------
+      # Step up miniconda
+      - name: Download Miniconda
+        uses: conda-incubator/setup-miniconda@059455a698430d8b68fa317268fa2e3da3492a98
+        with:
+          miniconda-version: "latest"
+          python-version: ${{ matrix.py_ver }}
+
+      # ------------------------------------------------------------
+      # Get code
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      # ------------------------------------------------------------
+      # Setup conda build environment and build package
+      # env defined here are just for convenience when writing bash commands
+      - name: Setup and build package
+        env:
+          OS: ${{ runner.os }}   
+          PY_VER: ${{ matrix.py_ver }}
+        run: |
+          conda config --set always_yes yes --set changeps1 no
+          conda config --set bld_path $CONDA_BLD_PATH
+          conda install -n base -q conda-build
+          conda deactivate
+          echo "# ----------------BUILDING---------------------------------"
+          conda config --show | grep bld_path
+          conda info
+          conda-build ./conda_noarch -c https://conda.anaconda.org/conda-forge --verify
+          tarball=$(conda-build ./conda_noarch --output | tail -1)
+          echo "conda build tarball" $tarball
+          echo "{conda-tarball}={$tarball}" >> $GITHUB_OUTPUT
+
+      # ------------------------------------------------------------
+      # Create new conda env and install package locally
+      # Test installation worked
+      # Get black and pytest from pip because black version on conda lags behind
+      - name: Test installation 
+        env:
+          PY_VER: ${{ matrix.py_ver }}
+        run: |
+          conda create -n env_$PY_VER python=$PY_VER $PACKAGE_NAME -c $CONDA_BLD_PATH -c conda-forge -c defaults
+          conda activate env_$PY_VER
+          conda info | grep active
+          pip install -r requirements-dev.txt
+          python -c "from pymer4.test_install import test_install; test_install()"
+
+      # 4. Run code tests
+      - name: Run Test Suite
+        env:
+          PY_VER: ${{ matrix.py_ver }}
+        run: |
+          conda activate env_$PY_VER
+          conda info | grep active
+          black --version
+          black --check --verbose .
+          pytest pymer4/tests
+
+      # 8a. Deploy package to main conda main channel
+      # Runs when a github release is created, but can also be triggered manually
+      - name: Conda main deploy 
+        if: ${{ (github.event_name == 'release') || (inputs.upload_anaconda == 'main') }}
+        env:
+          ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+        run: |
+          echo 'Conda release on main channel'
+          conda install anaconda-client
+          anaconda -t "$ANACONDA_TOKEN" upload $CONDA_BLD_PATH/**/${PACKAGE_NAME}*.tar.bz2 -l "main"
+
+      # OR -----
+
+      # 8b. Deploy package to pre-release conda channel 
+      # Only runs when triggered manually
+      - name: Conda pre-release deploy
+        if: ${{ inputs.upload_anaconda == 'pre-release' }}
+        env:
+          ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+        run: |
+          echo 'Conda release on pre-release channel'
+          conda install anaconda-client
+          anaconda -t "$ANACONDA_TOKEN" upload $CONDA_BLD_PATH/**/${PACKAGE_NAME}*.tar.bz2 -l "pre-release"
+

.github/workflows/Docs.yml

@@ -0,0 +1,71 @@
+name: Manual Deploy Docs
+on: 
+  workflow_dispatch:
+
+env:
+  PACKAGE_NAME: pymer4
+  DEPLOY_PY_VER: 3.8  # only this job deploys docs, anaconda.org, pypi
+  DEPLOY_OS: ubuntu-latest
+  CONDA_BLD_PATH: /tmp/ci_conda_bld
+
+defaults:
+  run:
+    # login shell to source the conda hook in .bash_profile
+    shell:
+      bash -l {0}
+
+jobs:
+  ci:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        py_ver: [3.8]
+        os: [ubuntu-latest]
+
+    steps:
+
+      # ------------------------------------------------------------
+      # Step up miniconda
+      - name: Download Miniconda
+        uses: conda-incubator/setup-miniconda@059455a698430d8b68fa317268fa2e3da3492a98
+        with:
+          miniconda-version: "latest"
+
+      # ------------------------------------------------------------
+      # Get code
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+
+      # ------------------------------------------------------------
+      # Setup conda build environment and build package
+      # env defined here are just for convenience when writing bash commands
+      - name: Install package
+        env:
+          PY_VER: ${{ matrix.py_ver }}
+        run: |
+          conda config --set always_yes yes --set changeps1 no
+          conda create -n pkg_test -c conda-forge python=$PY_VER 'r-lmerTest' 'r-emmeans' 'rpy2'
+
+          conda activate pkg_test
+          pip install -r requirements-dev.txt
+          pip install .
+
+      # ------------------------------------------------------------
+      # Build docs
+      - name: Build Docs
+        run: |
+          conda activate pkg_test
+          python -c "from pymer4.test_install import test_install; test_install()"
+          cd docs && make clean && make html
+          touch _build/html/.nojekyll
+
+      # Deploy docs
+      - name: Deploy docs
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        uses: crazy-max/ghaction-github-pages@v2
+        with:
+          target_branch: gh-pages
+          build_dir: docs/_build/html