Merge pull request #45 from softwareunderground/t21-main

Part I of the T21 hackathon - versioning and autodeploy to PyPI/conda-forge

.github/workflows/docs.yml

@@ -0,0 +1,56 @@
+name: docs
+
+# Controls when the action will run.
+on:
+  # Triggers the workflow on push or pull request events but only for the master branch
+  push:
+    branches:
+        - main
+  release:
+      types:
+        - published
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  docs:
+
+    runs-on: ubuntu-latest
+
+    env:
+      DISPLAY: ':99.0'
+      PYVISTA_OFF_SCREEN: 'True'
+      ALLOW_PLOTTING: true
+      SHELLOPTS: 'errexit:pipefail'
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Setup Headless Display
+        run: |
+          sudo apt-get install libgl1-mesa-glx
+          sudo apt-get install -y xvfb
+          Xvfb :99 -screen 0 1024x768x24 > /dev/null 2>&1 &
+          sleep 3
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.8'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements_dev.txt
+          pip install -e .
+
+      - name: Generate Sphinx Docs
+        working-directory: docs/
+        run: make html
+
+      - name: Publish generated content to GitHub Pages
+        uses: tsunematsu21/[email protected]
+        with:
+          dir: docs/build/html
+          branch: gh-pages
+          token: ${{ secrets.ACCESS_TOKEN }}

.github/workflows/main.yml

@@ -1,64 +1,59 @@
-# This is a basic workflow to help you get started with Actions
+name: linux
 
-name: subsurface CI
-
-# Controls when the action will run. 
+# Controls when the action will run.
 on:
   # Triggers the workflow on push or pull request events but only for the master branch
   push:
     branches: [ main, mig_dev, main_candidate, t21-main ]
   pull_request:
     branches: [ main, t21-main ]
+  release:
+    types:
+      - published
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # This workflow contains a single job called "build"
   pytest:
-    runs-on: ubuntu-latest
-    env:
-      DISPLAY: ':99.0'
-      PYVISTA_OFF_SCREEN: 'True'
-      ALLOW_PLOTTING: true
-      SHELLOPTS: 'errexit:pipefail'
-    # The type of runner that the job will run on
 
-    steps:
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.8'
-
-    - uses: actions/checkout@v2
-    - name: Setup Headless Display
-      run: |
-        sudo apt-get install libgl1-mesa-glx
-        sudo apt-get install -y xvfb
-        Xvfb :99 -screen 0 1024x768x24 > /dev/null 2>&1 &
-        sleep 3
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt
-        pip install -r optional_requirements.txt
-
-    - name: Test with pytest
-      run: |
-        pip install pytest
-        pip install pytest-cov
-        pytest
-  docs:
-    runs-on: ubuntu-latest
+    name: ${{ matrix.case.os }} py${{ matrix.case.python-version }} ${{ matrix.case.name }}
+    runs-on: ${{ matrix.case.os }}-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu, ]  # macos, windows]  # Only Linux currently.
+        case:
+          - python-version: 3.8
+            name: basic
+            os: ubuntu
+          # - python-version: 3.9
+          #   name: basic
+          #   os: ubuntu
+
     env:
       DISPLAY: ':99.0'
       PYVISTA_OFF_SCREEN: 'True'
       ALLOW_PLOTTING: true
       SHELLOPTS: 'errexit:pipefail'
+      OS: ${{ matrix.case.os }}
+      PYTHON: ${{ matrix.case.python-version }}
 
     steps:
+
+      # Cancel any previous run of the test job; [pin v0.8.0 (2021-02-13)]
+      - name: Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@3d86a7cc43670094ac248017207be0295edbc31d
+        with:
+          access_token: ${{ github.token }}
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.case.python-version }}
+
       - uses: actions/checkout@v2
       - name: Setup Headless Display
         run: |
@@ -67,24 +62,85 @@ jobs:
           Xvfb :99 -screen 0 1024x768x24 > /dev/null 2>&1 &
           sleep 3
 
-      - name: Set up Python
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements_dev.txt
+
+      - name: Test with pytest
+        run: pytest --cov=subsurface
+
+  # # # # DEPLOY # # #
+  deploy:
+    needs: pytest
+    name: Deploy to PyPI
+    runs-on: ubuntu-latest
+    # Only from the origin repository, not forks; only main and tags.
+    if: github.repository_owner == 'softwareunderground' && (github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/'))
+
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE
+      - name: Checkout
+        uses: actions/checkout@v2
+        with:
+          # Need to fetch more than the last commit so that setuptools_scm can
+          # create the correct version string. If the number of commits since
+          # the last release is greater than this, the version will still be
+          # wrong. Increase if necessary.
+          fetch-depth: 100
+          # The GitHub token is preserved by default but this job doesn't need
+          # to be able to push to GitHub.
+          persist-credentials: false
+
+      # Need the tags so that setuptools_scm can form a valid version number
+      - name: Fetch git tags
+        run: git fetch origin 'refs/tags/*:refs/tags/*'
+
+      - name: Setup Python
         uses: actions/setup-python@v2
         with:
-          python-version: '3.8'
+          python-version: "3.8"
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
+          pip install wheel setuptools_scm
           pip install -r requirements.txt
-          pip install -r optional_requirements.txt
-          pip install -r dev_requirements.txt
-          pip install -e .
-      - name: Generate Sphinx Docs
-        working-directory: docs/
-        run: make html
-      - name: Publish generated content to GitHub Pages
-        uses: tsunematsu21/[email protected]
+
+      - name: Build source and wheel distributions
+        if: github.ref == 'refs/heads/main'
+        run: |
+          # Change setuptools-scm local_scheme to "no-local-version" so the
+          # local part of the version isn't included, making the version string
+          # compatible with Test PyPI.
+          sed --in-place "s/'root'/'local_scheme':'no-local-version','root'/g" setup.py
+
+      - name: Build source and wheel distributions
+        run: |
+          # Build source and wheel packages
+          python setup.py sdist
+          python setup.py bdist_wheel
+          echo ""
+          echo "Generated files:"
+          ls -lh dist/
+
+      - name: Publish to Test PyPI
+        if: success()
+        # Hash corresponds to v1.4.1
+        uses: pypa/gh-action-pypi-publish@54b39fb9371c0b3a6f9f14bb8a67394defc7a806
         with:
-          dir: docs/build/html
-          branch: gh-pages
-          token: ${{ secrets.ACCESS_TOKEN }}
+          user: __token__
+          password: ${{ secrets.TEST_PYPI_PASSWORD }}
+          repository_url: https://test.pypi.org/legacy/
+          # Allow existing releases on test PyPI without errors.
+          # NOT TO BE USED in PyPI!
+          skip_existing: true
 
+      - name: Publish to PyPI
+        # Only for releases
+        if: success() && github.event_name == 'release'
+        # Hash corresponds to v1.4.1
+        uses: pypa/gh-action-pypi-publish@54b39fb9371c0b3a6f9f14bb8a67394defc7a806
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

.gitignore

@@ -1,3 +1,5 @@
+subsurface/_version.py
+
 # vscode
 .vscode/*
 
@@ -116,4 +118,4 @@ venv.bak/
 !/docs/source/_templates/
 /data/
 
-.idea
+.idea

DevelopersGuide.md

@@ -1,24 +1,21 @@
-Before a release.
+NOTES
+-----
+
+TODO: Re-work and automate this. Steps that should be necessary:
+
+
+**Important.** Due to the use of ``setuptools_scm``, everything is by default
+added to the wheel on PyPI. Documents that should not be in a release have to
+be excluded by adding it to the ``MANIFEST.in``.
+
+
+Making a release
 ----------------
-# set version number in setup.py, also in the config file of the documentation and init of the package
-- [ ] setup.py
-- [ ] subsurface._version
-> Note: in the config for sphinx~ this is taken from subsurface._version
-
-Github release
---------------
-    # add new tag
-    $ git tag X.X -m "Add X.X tag for PyPI"
-    # push git tag
-    $ git push --tags origin master
-
-PyPi release
-------------
-    #  First create the dist
-    python3 setup.py sdist bdist_wheel
-
-    # Second upload the distributions
-    twine upload dist/*
+
+Create a release on GitHub. This will run the tests, and then automatically
+deploy it to PyPI, from where conda-forge will pick it up as well.
+If everything works fine it should be available from PyPI within minutes after
+the tests passed, and within an hour or two from conda-forge.
 
 
 ### Type of commits:

MANIFEST.in

@@ -0,0 +1,11 @@
+prune docs
+prune examples
+prune tests
+prune .github
+exclude CONTRIBUTING.md
+exclude DevelopersGuide.md
+exclude MANIFEST.in
+exclude requirements.txt
+exclude requirements_dev.txt
+exclude requirements_opt.txt
+exclude .gitignore

README.md

@@ -14,27 +14,33 @@ The difference between data levels is **not** which data they store but which da
 
 **Human**
 
-     \=================================/'  
-      \===============================/ ' \
-       \==========geo_format=========/ '   \    -> Additional context/meta information about the data
-        \===========================/'   '   \     
-         \=======geo_object========/   '    ' \   -> Elements that represent some 
-          \=======================/  '   '    /      geological concept. E.g: faults, seismic
-           \=====================/' '   ' ' /      
-            \======element======/' ' '  ' /   -> type of geometric object: PointSet,
-             \=================/' ' ' ' /      TriSurf, LineSet, Tetramesh
-              \=primary_struct/   ''  /    - > Set of arrays that define a geometric object: 
-               \=============/ ' '  /            e.g. *StructuredData* **UnstructuredData**
-                \============/''  /  
-                 \DF/Xarray/ ' '/ -> Label numpy.arrays
-                  \=======/'' /
-                   \array/' /   -> Memory allocation
-                    \===/ /
-                     \=//
-                      '
+
+      \‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾/\
+       \= = = = = = = = = = = = = = /. \     -> Additional context/meta information about the data
+        \= = = = geo_format= = = = /. . \
+         \= = = = = = = = = = = = /. . . \   -> Elements that represent some
+          \= = = geo_object= = = /. . . . \      geological concept. E.g: faults, seismic
+           \= = = = = = = = = = /. . . . ./
+            \= = element = = = /. . . . /    -> type of geometric object: PointSet,
+             \= = = = = = = = /. . . ./         TriSurf, LineSet, Tetramesh
+              \primary_struct/. . . /        -> Set of arrays that define a geometric object:
+               \= = = = = = /. . ./             e.g. *StructuredData* **UnstructuredData**
+                \DF/Xarray /. . /            -> Label numpy.arrays
+                 \= = = = /. ./
+                  \array /. /                -> Memory allocation
+                   \= = /./
+                    \= //
+                     \/
+
 
 **Computer**
 
+## Documentation (WIP)
+
+An early version of the documentation can be found here:
+
+https://softwareunderground.github.io/subsurface/
+
 ## Installation
 
 `pip install subsurface`
@@ -49,9 +55,9 @@ We are changing things. Help us figure it out!
 
 #### Original statement
 
-The goal of this project is to support other subsurface geoscience and 
-engineering projects with a set of classes for common subsurface data entities, 
-such as seismic and GPR datasets, log curves, and so on. The current plan is to 
+The goal of this project is to support other subsurface geoscience and
+engineering projects with a set of classes for common subsurface data entities,
+such as seismic and GPR datasets, log curves, and so on. The current plan is to
  use `xarray` under the hood, with `pint` for units support and `cartopy` for CRS and map support.
 
 It's early days, everything might change. Help us figure it out!