Merge branch 'master' of https://github.com/underworldcode/stripy

.github/workflows/build_deploy_jbdoc.yml

@@ -3,7 +3,7 @@ name: API docs / jupyterbook
 # We should trigger this from an upload event 
 
 on:
-  push:
+  push:   # We publish the beta docs as well
     branches: 
       - master 
       - dev
@@ -31,7 +31,6 @@ jobs:
           path: |
             ~/conda_pkgs_dir
             ~/.cache/pip
-            /usr/share/miniconda3/envs/jupyter-book
             ~/stripy/jupyterbook/_build
             
           key: macos-jbdoc-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('.github/workflows/resources/conda_jb_docs_environment.yml') }}
@@ -52,7 +51,7 @@ jobs:
           VERSION=`python setup.py --version`
           echo "VERSION=$(echo $VERSION)" >> $GITHUB_ENV
           cd jupyterbook
-          jupyter-book build .
+          ./build-book.sh 
 
       # Note deploy key needs the ----BEGIN ... KEY---- lines too
 

.github/workflows/build_deploy_pdoc.yml

@@ -3,8 +3,9 @@ name: API docs / pdoc3
 # We should trigger this from an upload event 
 
 on:
-  push:
-    branches: [master]
+  push:       # This is not really a great idea 
+    branches:
+      - master
 
   workflow_run:
     workflows: ["Conda Deployment"]

.github/workflows/conda_deploy.yml

@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.7", "3.8"]
+        python-version: ["3.7", "3.8", "3.9"]
     steps:
       - uses: actions/checkout@v2
 

.github/workflows/python_pip_build_test.yml

@@ -18,50 +18,54 @@ jobs:
       fail-fast: false
       matrix:
         os: [ 'macos-latest', 'ubuntu-latest', 'windows-latest']
-        python-version: ['2.7', '3.7', '3.8']
+        python-version: ['2.7', '3.7', '3.8', '3.9']
         exclude:
           - os: 'windows-latest'
             python-version: 2.7
           - os: 'windows-latest'
             python-version: 3.8
+          - os: 'windows-latest'
+            python-version: 3.9
 
     runs-on: ${{ matrix.os }}
 
     steps:
       - name: Checkout  
         uses: actions/checkout@v2
 
-      - name: Set up Python
-        uses: actions/setup-python@v1
+      - name: Cache conda
+        uses: actions/cache@v1
+        env:
+        # Increase this value to reset cache if etc/example-environment.yml has not changed
+          CACHE_NUMBER: 1
         with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install gfortran (ubuntu)
-        if: matrix.os == 'ubuntu-latest' 
-        run: |
-          sudo apt-get install -y gfortran
+          path: |
+            ~/conda_pkgs_dir
+            ~/.cache/pip
+            ~/stripy/jupyterbook/_build
+            
+          key: macos-test-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('.github/workflows/resources/conda_test_environment.yml') }}
 
-      - name: Install gfortran (macos)
-        if: matrix.os == 'macos-latest' 
-        run: |
-          brew cask install gfortran
-
-      - name: Install Python dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install numpy 
-          pip install scipy 
-          pip install Cython
-          
+      - name: Miniconda + Cache
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+            miniconda-version: "latest"
+            auto-update-conda: true
+            environment-file: .github/workflows/resources/conda_test_environment.yml
+            activate-environment: conda-test
+            python-version: 3.7
+            use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+
       - name: Install (self)
+        shell: bash -l {0}
         run: |
-          pip install -e . 
-          
+          pip install -e .      
+
       - name: Test with pytest
+        shell: bash -l {0}
         run: |
           python -c 'import stripy;'
           pip install pytest
           pytest
-
-
-        
+ 
+

.github/workflows/python_pypi_upload_macos_wheel.yml

@@ -3,10 +3,13 @@ name: PYPI wheels macos
 on: 
   release:
     types: [created, edited]
+
   # push:
   #   branches:
   #     - dev
 
+  workflow_dispatch:
+
 
 jobs:
   deploy_to_pypi:
@@ -16,38 +19,56 @@ jobs:
       fail-fast: false
       matrix:
         os: [ 'macos-latest']
-        python-version: ['2.7', '3.7', '3.8']
+        python-version: ['2.7', '3.7', '3.8', '3.9']
 
     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 gfortran (macos)
-      run: |
-        brew cask install gfortran
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-        pip install numpy
-        pip install scipy
-        pip install Cython
-        pip install delocate
-        
-    - name: Build the wheel
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-
-      run: |
- 
-        python setup.py bdist_wheel 
-        delocate-wheel -d -w fixed_wheels dist/*whl
-        twine upload fixed_wheels/*whl  --skip-existing
+      - name: Checkout  
+        uses: actions/checkout@v2
+
+      - name: Cache conda
+        uses: actions/cache@v1
+        env:
+        # Increase this value to reset cache if etc/example-environment.yml has not changed
+          CACHE_NUMBER: 1
+        with:
+          path: |
+            ~/conda_pkgs_dir
+            ~/.cache/pip
+            ~/stripy/jupyterbook/_build
+            
+          key: macos-test-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('.github/workflows/resources/conda_test_environment.yml') }}
+
+      - name: Miniconda + Cache
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+            miniconda-version: "latest"
+            auto-update-conda: true
+            environment-file: .github/workflows/resources/conda_test_environment.yml
+            activate-environment: conda-test
+            python-version: 3.7
+            use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+
+      - name: Install (self)
+        shell: bash -l {0}
+        run: |
+          pip install -e .      
+
+      - name: Test with pytest
+        shell: bash -l {0}
+        run: |
+          pip install setuptools wheel twine
+          pip install delocate
+  
+
+      - name: Build the wheel
+        shell: bash -l {0}
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+
+        run: |
+          python setup.py bdist_wheel 
+          delocate-wheel -d -w fixed_wheels dist/*whl
+          twine upload fixed_wheels/*whl  --skip-existing

.github/workflows/python_pypi_upload_mlinux_wheel.yml

@@ -25,7 +25,7 @@ jobs:
     - 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'
+        python-versions: 'cp27-cp27m cp36-cp36m cp37-cp37m cp38-cp38 cp39-39'
         build-requirements: 'cython numpy scipy'
         system-packages: 'libgfortran'
         package-path: ''

.github/workflows/resources/conda_build_environment.yml

@@ -1,14 +1,13 @@
-# This is the environment needed to build stripy. As this will be cached, we can include any stripy dependencies
-# so they are not downloaded again - this should save a bit of time
+# This is the environment needed to build stripy. Note, the build is in a new
+# environment so all we need here is the tools to run the build in the first place
+# not all the stripy dependencies. 
 
 name: conda-build
 channels: 
   - conda-forge
 dependencies:
-  - compilers
-  - pytest
-  - numpy>=1.16.0
-  - scipy>=1.0.0
+  # numpy is needed for some of the setup tools 
+  - numpy
   - conda-build 
   - conda-verify
   - anaconda-client

.github/workflows/resources/conda_jb_docs_environment.yml

@@ -5,7 +5,7 @@ channels:
   - conda-forge
   - geo-down-under
 dependencies:
-  - geo-down-under::stripy==2.0.5b2
+  - geo-down-under::stripy==2.0.5b2  # this only works after the upload, of course
   - geo-down-under::litho1pt0
   - matplotlib
   - pyproj
@@ -14,10 +14,9 @@ dependencies:
   - netcdf4
   - cartopy
   - xarray
-  - xvfbwrapper
+  - k3d
   - pip 
 
   - pip:
     - jupyter-book
-    - lavavu
 

.github/workflows/resources/conda_test_environment.yml

@@ -0,0 +1,14 @@
+# This is the environment needed to build stripy for pip
+
+name: conda-test
+channels: 
+  - conda-forge
+dependencies:
+  # numpy is needed for some of the setup tools 
+  - compilers
+  - numpy
+  - scipy
+  - cython
+  - pip 
+
+

.gitignore

@@ -47,3 +47,7 @@ litho1pt0-src/litho1pt0/Notebooks/litho1pt0/Data/ETOPO1_Ice_g_geotiff.tif.zip
 /.spyproject/
 
 fixed_wheels/stripy-1.2.2-cp37-cp37m-macosx_10_9_x86_64.whl
+
+# macos
+
+.DS_Store