Merge pull request #44 from corriporai/develop

BLD: Change from Travis CI to Github CI and ENH: Support to Heart Training Zones metrics  #38 #12

.coveragerc

@@ -1,6 +1,7 @@
 # .coveragerc to control coverage.py
 [run]
 source = runpandas
+relative_files = True
 branch = True
 include = */runpandas/*
 omit =

.github/workflows/build.yml

@@ -0,0 +1,124 @@
+name: Build
+
+on:
+  push:
+    branches:
+     - master
+     - develop
+  pull_request:
+    branches: [master]
+
+jobs:
+  Linting:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - uses: pre-commit/[email protected]
+
+  Test:
+    needs: Linting
+    name: ${{ matrix.os }}, ${{ matrix.env }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        include:
+          - env: "PANDAS=0.24 NUMPY=1.16 PYTHON=3.6"
+            os: ubuntu-latest
+            PANDAS: '0.24'
+            NUMPY: '1.16'
+            python-version: '3.6'
+          - env: "PANDAS=0.25 NUMPY=1.17 PYTHON=3.7 DOCBUILD=true"
+            os: ubuntu-latest
+            PANDAS: '0.25'
+            NUMPY: '1.17'
+            python-version: '3.7'
+          - env: "PANDAS=0.25 NUMPY=1.18 PYTHON=3.7"
+            os: ubuntu-latest
+            PANDAS: '0.25'
+            NUMPY: '1.18'
+            python-version: '3.7'
+          - env: "PANDAS=1 NUMPY=1.18 PYTHON=3.8"
+            os: ubuntu-latest
+            PANDAS: '1'
+            NUMPY: '1.18'
+            python-version: '3.8'
+          - env: "PANDAS=1 NUMPY=1.19 PYTHON=3.8"
+            os: ubuntu-latest
+            PANDAS: '1'
+            NUMPY: '1.19'
+            python-version: '3.8'
+          - env: "PANDAS=MASTER NUMPY=1.18 PYTHON=3.7"
+            os: ubuntu-latest
+            PANDAS: 'MASTER'
+            NUMPY: '1.18'
+            python-version: '3.7'
+          - env: "PANDAS=1 NUMPY=1.18 PYTHON=3.8"
+            os: macos-latest
+            PANDAS: '1'
+            NUMPY: '1.18'
+            python-version: '3.8'
+          - env: "PANDAS=1 NUMPY=1.18 PYTHON=3.8"
+            os: windows-latest
+            PANDAS: '1'
+            NUMPY: '1.18'
+            python-version: '3.8'
+          - env: "PANDAS=1 NUMPY=1.18 PYTHON=3.7"
+            os: macos-latest
+            PANDAS: '1'
+            NUMPY: '1.18'
+            python-version: '3.7'
+          - env: "PANDAS=1 NUMPY=1.18 PYTHON=3.7"
+            os: windows-latest
+            PANDAS: '1'
+            NUMPY: '1.18'
+            python-version: '3.7'
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Setup Environment
+        shell: bash
+        run: |
+          source ci/pypi-installer.sh;
+          pip install -e .
+          pip install -r requirements-dev.txt
+          python -V
+          pip list
+          python -c "import runpandas; runpandas.__version__;"
+        env:
+          PANDAS: ${{ matrix.PANDAS }}
+          NUMPY: ${{ matrix.NUMPY }}
+
+      - name: Test with Pytest
+        shell: bash
+        run: |
+          source ci/pypi-installer.sh;
+          pytest -v -s -r xX -m stable --cov-config .coveragerc --cov=runpandas --cov-report xml:/tmp/cov-runpandas.xml --junitxml=/tmp/runpandas.xml
+        env:
+          PANDAS: ${{ matrix.PANDAS }}
+          NUMPY: ${{ matrix.NUMPY }}
+
+      - uses: codecov/codecov-action@v1
+        if: startsWith(matrix.os, 'ubuntu')
+
+      - name: Coveralls
+        if: startsWith(matrix.os, 'ubuntu')
+        uses: AndreMiras/coveralls-python-action@develop
+        with:
+          parallel: true
+          flag-name: Unit Test
+
+  coveralls_finish:
+    needs: Test
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      uses: AndreMiras/coveralls-python-action@develop
+      with:
+        parallel-finished: true

.github/workflows/readthedocs.py

@@ -0,0 +1,78 @@
+"""
+Trigger ReadTheDocs documentation build and check response for confirmation
+"""
+
+import os
+import time
+import requests
+
+URL = 'https://readthedocs.org/api/v3/projects/runpandas'
+TOKEN = os.getenv('READTHEDOCS_TOKEN')
+HEADERS = {
+    'Authorization': f'Token {TOKEN}',
+    'Content-Length': '0',
+    }
+
+
+def build_status(build_id: str) -> str:
+    """
+    Use ReadTheDocs API to check build status until either failed or succeeds. The function checks the status in 30s
+    intervals. Stop process after max. 3min.
+
+    Response field state - code can have the following values: triggered, cloning, installing, building, finished and
+    failed (check TBD)
+    """
+
+    max_min = 3
+    status = 'triggered'
+
+    i = 0
+    while True:
+        i += 1
+        time.sleep(30)
+
+        response = requests.get(f'{URL}/builds/{build_id}/', headers=HEADERS)
+        response = response.json()
+
+        if response['success'] is True:
+            status = 'finished'
+            break
+        elif response['success'] is False:
+            status = 'failed'
+            break
+
+        if i == 2*max_min:
+            break
+
+    return status
+
+
+def main():
+    response = requests.post(f'{URL}/versions/latest/builds/', headers=HEADERS)
+    response = response.json()
+
+    if response['triggered']:
+        print('ReadTheDocs build successfully triggered.')
+        print(f"Build id: {response['build']['id']}")
+        print(f"Branch: {response['version']['identifier']}")
+        print(f"Version: {response['build']['version']}")
+
+        build_id = response['build']['id']
+        status = build_status(build_id)
+
+        if status == 'finished':
+            print('ReadTheDocs build successfully finished.')
+            return 0
+        if status == 'triggered':
+            print('ReadTheDocs build still ongoing... Please check manually.')
+            return 0
+        if status == 'failed':
+            print('ReadTheDocs build failed.')
+            return 1
+    else:
+        print('ReadTheDocs build triggering failed.')
+        return 1
+
+
+if __name__ == '__main__':
+    main()

.github/workflows/readthedocs.yml

@@ -0,0 +1,52 @@
+# Build documentation of ReadTheDocs
+
+name: Document on ReadTheDocs
+# TODO: Check running criteria for script
+on:
+  push:
+    branches:
+      - master
+      - develop
+
+jobs:
+  document:
+    name: Documentation build on ReadTheDocs
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@master
+
+      - name: Setup Python 3.7
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+          PANDAS: "0.25"
+          NUMPY: "1.17"
+
+      - name: Install required packages
+        run: |
+             source ci/pypi-installer.sh;
+             pip install -e .
+             pip install -r requirements-dev.txt
+             pip install -r docs/requirements.txt
+             pip install requests
+             pip list
+             python -c "import runpandas; runpandas.__version__;"
+        env:
+          PANDAS: "0.25"
+          NUMPY: "1.17"
+
+      - name: setup pandoc
+        uses: r-lib/actions/setup-pandoc@v1
+        with:
+          pandoc-version: '2.7.3' # The pandoc version to download (if necessary) and use.
+
+      - name: Trigger documentation build
+        run: |
+          set -e
+          cd docs
+          make html
+          cd ..
+          python .github/workflows/readthedocs.py
+        env:
+          READTHEDOCS_TOKEN: ${{ secrets.readthedocs_token }}

.pre-commit-config.yaml

@@ -1,11 +1,16 @@
+
+files: 'runpandas\/'
 repos:
 -   repo: https://github.com/python/black
     rev: stable
     hooks:
     -   id: black
-        language_version: python3.7
+        language_version: python3
 -   repo: https://gitlab.com/pycqa/flake8
-    rev: 3.7.7
+    rev: 3.8.3
     hooks:
     -   id: flake8
-        language: python_venv
+        language: python_venv
+
+
+

ci/pypi-installer.sh

@@ -1,17 +1,12 @@
 #!/usr/bin/env bash
 
-pip install pip --upgrade
+pip install pip --upgrade --user
 pip install numpy=="$NUMPY" lxml
 pip install -r requirements-dev.txt
 
 if [[ "$PANDAS" == "MASTER" ]]; then
   PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
-  pip install --pre --upgrade --timeout=60 -f "$PRE_WHEELS" pandas
+  pip install --pre --upgrade --timeout=60 -f "$PRE_WHEELS" pandas --user
 else
   pip install pandas=="$PANDAS"
-fi
-
-if [[ "$DOCBUILD" ]]; then
-  pip install doctr
-  pip install -r docs/requirements.txt
 fi