👷 CI overhaul (#7)

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+  - package-ecosystem: 'github-actions'
+    directory: '/'
+    schedule:
+      # Check for updates once a week
+      interval: 'weekly'

.github/workflows/ci.yaml

@@ -1,48 +1,57 @@
 name: CI
 on:
   push:
-    branches:
-      - "*"
   pull_request:
-    branches:
-      - "*"
+  workflow_dispatch: # allows you to trigger manually
 
 jobs:
+  pre-job:
+    runs-on: ubuntu-latest
+    outputs:
+      should_skip: ${{ steps.skip_check.outputs.should_skip }}
+    steps:
+      - id: skip_check
+        uses: fkirc/skip-duplicate-actions@master
+        with:
+          concurrent_skipping: 'same_content'
+          skip_after_successful_duplicate: 'false'
+          do_not_skip: '["workflow_dispatch", "schedule"]'
+          paths_ignore: '["**/docs/**"]'
   build:
-    name: Build (${{ matrix.python-version }}, ${{ matrix.os }})
-    runs-on: ${{ matrix.os }}
+    needs: pre-job
+    if: ${{ needs.pre-job.outputs.should_skip != 'true' }}
+    name: python-${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest"]
-        python-version: ["3.6", "3.7", "3.8"]
+        python-version: ['3.7', '3.8', '3.9']
     steps:
-      - uses: actions/checkout@v2
-      - name: Cache conda
-        uses: actions/cache@v1
-        env:
-          # Increase this value to reset cache if ci/environment.yml has not changed
-          CACHE_NUMBER: 0
+      - name: Cancel Previous Runs
+        uses: styfle/[email protected]
         with:
-          path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('ci/environment.yml') }}
-      - uses: goanpeca/setup-miniconda@v1
+          access_token: ${{ github.token }}
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
         with:
-          activate-environment: sandbox-devel # Defined in ci/environment.yml
+          channels: conda-forge,nodefaults
+          mamba-version: '*'
+          activate-environment: ecgtools-dev
           auto-update-conda: false
           python-version: ${{ matrix.python-version }}
           environment-file: ci/environment.yml
-          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+
       - name: Set up conda environment
-        shell: bash -l {0}
         run: |
           python -m pip install -e .
           conda list
 
       - name: Run Tests
-        shell: bash -l {0}
         run: |
-          pytest --cov=./ --cov-report=xml
+          python -m pytest --cov=./ --cov-report=xml --verbose
 
       - name: Upload code coverage to Codecov
         uses: codecov/codecov-action@v1
@@ -52,29 +61,3 @@ jobs:
           env_vars: OS,PYTHON
           name: codecov-umbrella
           fail_ci_if_error: false
-
-  docs-build:
-    name: Documentation build
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-      - name: set up Python 3.8
-        uses: actions/setup-python@v1
-        with:
-            python-version: 3.8
-
-      - name: Install package
-        run: |
-          sudo apt-get update && sudo apt-get install pandoc -y
-          python -m pip install --upgrade pip
-          python -m pip install -e .
-
-      - name: Install documentation dependencies
-        run: |
-          python -m pip install -r docs/requirements-docs.txt
-
-      - name: Build docs
-        run: |
-          cd docs
-          make html

.github/workflows/linting.yaml

@@ -1,62 +1,31 @@
-name: code-style
+name: linting
 
 on:
   push:
-    branches: "*"
   pull_request:
-    branches: master
-
-
+  workflow_dispatch:
 
 jobs:
-
-  lint-black:
-    name: black-formatter
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v1
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v1
-        with:
-          python-version: 3.8
-      - name: Install Black
-        run: |
-          python -m pip install black
-      - name: Black Code Formatter
-        run: |
-          black --check --line-length 100 --skip-string-normalization .
-
-  lint-flake8:
-    name: flake8
+  pre-job:
     runs-on: ubuntu-latest
+    outputs:
+      should_skip: ${{ steps.skip_check.outputs.should_skip }}
     steps:
-      - name: Checkout
-        uses: actions/checkout@v1
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v1
+      - id: skip_check
+        uses: fkirc/skip-duplicate-actions@master
         with:
-          python-version: 3.8
-      - name: Install Flake8
-        run: |
-          python -m pip install flake8
-      - name: Flake8 check
-        run: |
-          flake8 .
-
-  lint-isort:
-    name: isort
+          concurrent_skipping: 'same_content'
+          skip_after_successful_duplicate: 'false'
+          do_not_skip: '["workflow_dispatch", "schedule"]'
+  linting:
+    needs: pre-job
     runs-on: ubuntu-latest
+    if: ${{ needs.pre-job.outputs.should_skip != 'true' }}
     steps:
-      - name: Checkout
-        uses: actions/checkout@v1
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v1
+      - name: Cancel Previous Runs
+        uses: styfle/[email protected]
         with:
-          python-version: 3.8
-      - name: Install isort
-        run: |
-          python -m pip install isort
-      - name: isort check
-        run: |
-          isort --check-only .
+          access_token: ${{ github.token }}
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - uses: pre-commit/[email protected]

.github/workflows/pypi.yaml

@@ -1,26 +1,73 @@
-name: Upload Package to PyPI
+name: Upload ecgtools to PyPI
 
 on:
   release:
-    types: [created]
-
+    types:
+      - published
+  workflow_dispatch:
 jobs:
+  test-deploy:
+    if: github.repository == 'NCAR/ecgtools'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.x'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install setuptools setuptools-scm wheel twine check-manifest
+      - name: Build tarball and wheels
+        run: |
+          python setup.py sdist bdist_wheel
+          python -m pip wheel . -w dist --no-deps
+      - name: Test the artifacts
+        run: |
+          python -m twine check dist/*
+
+      - name: Publish package to TestPyPI
+        uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.TESTPYPI_PASSWORD }}
+          repository_url: https://test.pypi.org/legacy/
+          verbose: true
+
   deploy:
+    needs: test-deploy
+    if: startsWith(github.ref, 'refs/tags')
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v2
       - name: Set up Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v2
         with:
           python-version: '3.x'
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install setuptools setuptools-scm wheel twine
-      - name: Build and publish
-        env:
-          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+          python -m pip install setuptools setuptools-scm wheel twine check-manifest
+      - name: Build tarball and wheels
         run: |
           python setup.py sdist bdist_wheel
-          twine upload dist/*
+          python -m pip wheel . -w dist --no-deps
+      - name: Test the artifacts
+        run: |
+          python -m twine check dist/*
+
+      - name: Publish package to PyPI
+        uses: pypa/[email protected]
+        with:
+          user: ${{ secrets.PYPI_USERNAME }}
+          password: ${{ secrets.PYPI_PASSWORD }}
+          skip_existing: true
+          verbose: true
+
+      # - name: Publish package
+      #   env:
+      #     TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+      #     TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      #   run: |
+      #     python -m twine upload dist/* --skip-existing

.pre-commit-config.yaml

@@ -1,42 +1,50 @@
+exclude: schema/generic_schema.yaml
 repos:
-
-  -   repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v3.1.0
-      hooks:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.4.0
+    hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-docstring-first
+      - id: check-json
+      - id: check-yaml
       - id: double-quote-string-fixer
 
-  -   repo: https://github.com/ambv/black
-      rev: 19.10b0
-      hooks:
+  - repo: https://github.com/ambv/black
+    rev: 20.8b1
+    hooks:
       - id: black
-        args: ["--line-length", "100", "--skip-string-normalization"]
 
+  - repo: https://github.com/keewis/blackdoc
+    rev: v0.3.3
+    hooks:
+      - id: blackdoc
 
-  -   repo: https://gitlab.com/pycqa/flake8
-      rev: 3.8.3
-      hooks:
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.9.0
+    hooks:
       - id: flake8
 
-  -   repo: https://github.com/asottile/seed-isort-config
-      rev: v2.2.0
-      hooks:
+  - repo: https://github.com/asottile/seed-isort-config
+    rev: v2.2.0
+    hooks:
       - id: seed-isort-config
-  -   repo: https://github.com/pre-commit/mirrors-isort
-      rev: v5.1.4
-      hooks:
+  - repo: https://github.com/pre-commit/mirrors-isort
+    rev: v5.8.0
+    hooks:
       - id: isort
 
-  -   repo: https://github.com/deathbeds/prenotebook
-      rev: f5bdb72a400f1a56fe88109936c83aa12cc349fa
-      hooks:
-       - id: prenotebook
-         args:
-                [
-                "--keep-output",
-                "--keep-metadata",
-                "--keep-execution-count",
-                "--keep-empty",
-                ]
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v2.2.1
+    hooks:
+      - id: prettier
+
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 0.6.0
+    hooks:
+      - id: nbqa-black
+        additional_dependencies: [black==20.8b1]
+      - id: nbqa-pyupgrade
+        additional_dependencies: [pyupgrade==2.7.3]
+      - id: nbqa-isort
+        additional_dependencies: [isort==5.8.0]

.prettierrc.toml

@@ -0,0 +1,3 @@
+tabWidth = 2
+semi = false
+singleQuote = true

CONTRIBUTING.md

@@ -0,0 +1 @@
+# Contributing to ecgtools