From 68db17766bcc45af4187a1e7b6e082e7e7bbf89c Mon Sep 17 00:00:00 2001
From: lmoresi <>
Date: Wed, 18 Mar 2020 21:35:14 +1100
Subject: [PATCH] Copy in the quagmire workflows

---
 .github/workflows/build_deploy_pdoc.yml       | 48 +++++++++++
 .github/workflows/python_conda_build_test.yml | 52 ++++++++++++
 .github/workflows/python_conda_upload.yml     | 83 +++++++++++++++++++
 .../workflows/python_deploy_release_pypi.yml  | 39 +++++++++
 .../python_pypi_upload_macos_wheel.yml        | 51 ++++++++++++
 .../python_pypi_upload_mlinux_wheel.yml       | 41 +++++++++
 .../workflows/python_pypi_upload_source.yml   | 37 +++++++++
 .../python_pypi_upload_windows_wheel.yml      | 43 ++++++++++
 8 files changed, 394 insertions(+)
 create mode 100644 .github/workflows/build_deploy_pdoc.yml
 create mode 100644 .github/workflows/python_conda_build_test.yml
 create mode 100644 .github/workflows/python_conda_upload.yml
 create mode 100644 .github/workflows/python_deploy_release_pypi.yml
 create mode 100644 .github/workflows/python_pypi_upload_macos_wheel.yml
 create mode 100644 .github/workflows/python_pypi_upload_mlinux_wheel.yml
 create mode 100644 .github/workflows/python_pypi_upload_source.yml
 create mode 100644 .github/workflows/python_pypi_upload_windows_wheel.yml

diff --git a/.github/workflows/build_deploy_pdoc.yml b/.github/workflows/build_deploy_pdoc.yml
new file mode 100644
index 0000000..cc1710e
--- /dev/null
+++ b/.github/workflows/build_deploy_pdoc.yml
@@ -0,0 +1,48 @@
+name: Deploy docs to gh-pages
+
+on:
+  push:
+    branches: [none]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+  
+      - name: Set up Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: '3.x'    
+
+        # This is needed because we install stripy for litho1pt0 build for documentation
+      - name: Install gfortran 
+        run: |
+          sudo apt-get install -y gfortran
+
+      - name: Install petsc 
+        run:  echo ""
+         
+        # The numpy etc are needed because we install stripy for litho1pt0 build for documentation
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install numpy 
+          pip install scipy 
+          pip install Cython
+          pip install sympy
+          pip install pint
+          pip install stripy
+          pip install pdoc3
+   
+      - name: Build docs with pdoc
+        run: | 
+          mkdir -p docs
+          pdoc --config latex_math=True --html -o docs --force quagmire 
+
+      # Note deploy key needs the ----BEGIN ... KEY---- lines too
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          deploy_key: ${{ secrets.GH_PAGES_DEPLOY_PR_KEY }}
+          publish_dir: docs/quagmire
\ No newline at end of file
diff --git a/.github/workflows/python_conda_build_test.yml b/.github/workflows/python_conda_build_test.yml
new file mode 100644
index 0000000..a39b2cf
--- /dev/null
+++ b/.github/workflows/python_conda_build_test.yml
@@ -0,0 +1,52 @@
+## Workflow to build dependencies with conda / install locally with pip
+name: conda + pip
+
+on: 
+  push
+
+jobs:
+  build_and_test: 
+    name: Build test (${{matrix.os}}, py ${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ 'macos-latest', 'ubuntu-latest' ]
+        python-version: [  '3.7' ]
+      
+        # exclude: 
+        # - os: ubuntu-latest
+        #   python-version: '2.7'
+        # - os: macos-latest
+        #   python-version: '2.7'
+
+    steps:
+
+      - uses: actions/checkout@v2
+      - uses: goanpeca/setup-miniconda@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies with conda
+        shell: bash -l {0}
+        run: |
+          conda install pip 
+          conda install -c conda-forge compilers numpy scipy sympy
+          conda install -c conda-forge petsc4py petsc mpi4py h5py
+          conda install -c conda-forge pint 
+          conda install -c underworldcode stripy 
+          conda install pytest
+
+      - name: Install (self)
+        shell: bash -l {0}
+        run: |
+          python --version 
+          pip install -e . 
+          
+      - name: Test with pytest
+        shell: bash -l {0}
+        run: |
+          pytest
+
+
+          
diff --git a/.github/workflows/python_conda_upload.yml b/.github/workflows/python_conda_upload.yml
new file mode 100644
index 0000000..86b754a
--- /dev/null
+++ b/.github/workflows/python_conda_upload.yml
@@ -0,0 +1,83 @@
+name: conda -c underworldcode 
+
+on: 
+  release:
+    types: [created, edited]
+  push:
+    branches:
+      - dev
+
+# Limited to ubuntu and macos because of petsc / petsc4py
+# py27 seems problematic in stripy builds
+
+jobs:
+  catch_and_release: 
+    name: ${{matrix.os}} build and test on py (${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [  'ubuntu-latest', 'macos-latest']
+        python-version: [ '3.7']
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: goanpeca/setup-miniconda@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Conda info
+        shell: bash -l {0}
+        run: conda info
+
+      - name: Install dependencies with conda
+        shell: bash -l {0}
+        run: |
+          conda install conda-build anaconda-client 
+          conda install -c conda-forge compilers numpy scipy sympy
+          conda install -c conda-forge petsc4py petsc mpi4py h5py
+          conda install -c conda-forge pint 
+          conda install -c underworldcode stripy 
+          conda install pytest
+
+          conda config --add channels underworldcode
+          conda config --add channels conda-forge
+
+
+      - name: Reinvent the wheel / upload (UBUNTU)
+        if: matrix.os == 'ubuntu-latest' 
+
+        env:
+          ANACONDA_USERNAME: ${{ secrets.ANACONDA_USERNAME}}
+          ANACONDA_PASSWORD: ${{ secrets.ANACONDA_PASSWORD}}
+
+        shell: bash -l {0}
+        run: |
+          # Conda version
+
+          anaconda logout
+          printf Y | anaconda login --username $ANACONDA_USERNAME --password $ANACONDA_PASSWORD --hostname quagy-virtual-${{ matrix.os}}-${{ matrix.python-version }}
+          python setup.py bdist_conda   # this will upload to lmoresi in the first instance ... 
+          anaconda upload -u underworldcode --skip-existing /usr/share/miniconda/envs/test/conda-bld/*/*.tar.bz2 
+          anaconda logout
+
+          
+      - name: Reinvent the wheel / upload (MACOS)
+        if: matrix.os == 'macos-latest' 
+
+        env:
+          ANACONDA_USERNAME: ${{ secrets.ANACONDA_USERNAME}}
+          ANACONDA_PASSWORD: ${{ secrets.ANACONDA_PASSWORD}}
+
+        shell: bash -l {0}
+        run: |
+          # Conda version
+
+          anaconda logout
+          printf Y | anaconda login --username $ANACONDA_USERNAME --password $ANACONDA_PASSWORD --hostname quagy-virtual-${{ matrix.os}}-${{ matrix.python-version }}
+          python setup.py bdist_conda   # this will upload to lmoresi in the first instance ... 
+          anaconda upload -u underworldcode --skip-existing /usr/local/miniconda/envs/test/conda-bld/*/*.tar.bz2 
+          anaconda logout
+
+         
+
+
diff --git a/.github/workflows/python_deploy_release_pypi.yml b/.github/workflows/python_deploy_release_pypi.yml
new file mode 100644
index 0000000..68c7899
--- /dev/null
+++ b/.github/workflows/python_deploy_release_pypi.yml
@@ -0,0 +1,39 @@
+name: Upload Python Package to PYPI
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: '3.x'
+
+    - name: Install gfortran
+      run: |
+        sudo apt-get install -y gfortran
+
+    - name: Install dependencies
+      run: |
+         python -m pip install --upgrade pip
+          pip install numpy 
+          pip install scipy 
+          pip install Cython
+          pip install sympy
+          pip install pint
+          pip install stripy
+          pip install pdoc3
+        
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*
diff --git a/.github/workflows/python_pypi_upload_macos_wheel.yml b/.github/workflows/python_pypi_upload_macos_wheel.yml
new file mode 100644
index 0000000..8a2b48d
--- /dev/null
+++ b/.github/workflows/python_pypi_upload_macos_wheel.yml
@@ -0,0 +1,51 @@
+name: PYPI wheels macos
+
+on: 
+  release:
+    types: [created, edited]
+
+
+jobs:
+  deploy_to_pypi:
+    name: ${{matrix.os}} build and deploy on pypi (${{ matrix.python-version }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ 'macos-latest']
+        python-version: ['2.7', '3.7', '3.8']
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: goanpeca/setup-miniconda@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Conda info
+        shell: bash -l {0}
+        run: conda info
+
+      - name: Install dependencies with conda
+        shell: bash -l {0}
+        run: |
+          conda install pip 
+          conda install -c conda-forge compilers numpy scipy sympy
+          conda install -c conda-forge petsc4py petsc mpi4py h5py
+          conda install -c conda-forge pint 
+          conda install -c underworldcode stripy 
+          conda install pytest
+    
+      - name: Build the wheel
+        shell: bash -l {0}
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+  
+        run: |
+          pip install setuptools wheel twine
+          pip install delocate
+
+          python setup.py bdist_wheel 
+          delocate-wheel -d -w fixed_wheels dist/*whl
+          twine upload fixed_wheels/*whl  --skip-existing
\ No newline at end of file
diff --git a/.github/workflows/python_pypi_upload_mlinux_wheel.yml b/.github/workflows/python_pypi_upload_mlinux_wheel.yml
new file mode 100644
index 0000000..371cefd
--- /dev/null
+++ b/.github/workflows/python_pypi_upload_mlinux_wheel.yml
@@ -0,0 +1,41 @@
+name: PYPI wheels manylinux
+
+on:
+  release:
+    types: [created, edited]
+
+jobs:
+  deploy_to_pypi:
+    name:  build and deploy manylinux on pypi 
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    
+    # Not sure how to fix this ... petsc from system packages ? 
+
+    - name: Build manylinux Python wheels
+      uses: RalfG/python-wheels-manylinux-build@v0.2.2-manylinux2010_x86_64
+      with:
+        python-versions: 'cp27-cp27m cp36-cp36m cp37-cp37m cp38-cp38'
+        build-requirements: 'cython numpy scipy'
+        system-packages: 'libgfortran'
+        package-path: ''
+        pip-wheel-args: '--no-deps'
+        
+    - name: Build the wheel
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+ 
+      run: |
+        twine upload wheelhouse/*-manylinux*.whl --skip-existing
\ No newline at end of file
diff --git a/.github/workflows/python_pypi_upload_source.yml b/.github/workflows/python_pypi_upload_source.yml
new file mode 100644
index 0000000..cc1d231
--- /dev/null
+++ b/.github/workflows/python_pypi_upload_source.yml
@@ -0,0 +1,37 @@
+name: PYPI source
+
+on:
+  release:
+    types: [created, edited]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: '3.x'
+
+    - name: Install gfortran
+      run: |
+        sudo apt-get install -y gfortran
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install numpy
+        pip install scipy
+        pip install Cython
+        
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        pip install setuptools wheel twine
+        python setup.py sdist
+        twine upload dist/*
diff --git a/.github/workflows/python_pypi_upload_windows_wheel.yml b/.github/workflows/python_pypi_upload_windows_wheel.yml
new file mode 100644
index 0000000..2f84f6a
--- /dev/null
+++ b/.github/workflows/python_pypi_upload_windows_wheel.yml
@@ -0,0 +1,43 @@
+name: PYPI wheels windows
+
+on:
+  release:
+    types: [created, edited]
+
+
+jobs:
+  deploy_to_pypi:
+    name: ${{matrix.os}} build and deploy on pypi (${{ matrix.python-version }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ 'windows-latest']
+        python-version: ['3.6', '3.7']
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install numpy
+        pip install scipy
+        pip install Cython
+        
+    - name: Build the wheel
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+
+      run: |
+        pip install setuptools wheel twine
+        python setup.py bdist_wheel
+        twine upload dist/*  --skip-existing