Fix and clean CI configuration (#183)

* remove travis configuration * fix tox minimal * fix ubuntu dependecies install * remove codecov from minimal req * add assert to test_exception_pass test * add prerelase check * add download data step * change run branch on develop * fix if to check runner os instead of matrix.os * remove travis specific things * try if specyfic environ for azure pipelines work * another try of reference to deps * remove obsolete tox config file (azure specific) * tight prerelease check * correct numpy deprecation * clean float part two * fix deepsource warnings * add tox-gh-actions install
4DNucleome · Feb 2, 2021 · cd381a7 · cd381a7
1 parent 79222a1
commit cd381a7
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Showing 30 changed files with 260 additions and 215 deletions.
diff --git a/.azure-pipelines/tests.yaml b/.azure-pipelines/tests.yaml
@@ -6,7 +6,7 @@ steps:
       path: $(Build.SourcesDirectory)/test_data
   - script: pip install -r requirements/requirements_dev.txt
     displayName: "Install deps"
-  - script: tox -c tox-azure.ini -e py38-PyQt5
+  - script: tox -e py38-PyQt5-azure
     displayName: "Run Tox"
     env:
       CODECOV_TOKEN: $(codecov_token_secret)
diff --git a/.github/TEST_FAIL_TEMPLATE.md b/.github/TEST_FAIL_TEMPLATE.md
@@ -0,0 +1,12 @@
+---
+title: "{{ env.TITLE }}"
+labels: [bug]
+---
+The {{ workflow }} workflow failed on {{ date | date("YYYY-MM-DD HH:mm") }} UTC
+
+The most recent failing test was on {{ env.PLATFORM }} py{{ env.PYTHON }}
+with commit: {{ sha }}
+
+Full run: https://github.com/{{ payload.repository.full_name }}/actions/runs/{{ env.RUN_ID }}
+
+(This post will be updated if another test fails, as long as this issue remains open.)
diff --git a/.github/actions/run-test/action.yaml b/.github/actions/run-test/action.yaml
@@ -10,8 +10,17 @@ runs:
       python-version: ${{ matrix.python_version }}
 
   - name: Install ubuntu libraries
-    if: startsWith(matrix.os, 'ubuntu')
-    run: sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0
+    if: runner.os == 'Linux'
+    run: |
+      sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 \
+      libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 \
+      libxcb-xinput0 libxcb-xfixes0
+
+  - name: Install Windows OpenGL
+    if: runner.os == 'Windows'
+    run: |
+      git clone --depth 1 git://github.com/pyvista/gl-ci-helpers.git
+      powershell gl-ci-helpers/appveyor/install_opengl.ps1
 
   - name: Download test data
     uses: actions/download-artifact@v1

diff --git a/.github/workflows/test_prereleases.yml b/.github/workflows/test_prereleases.yml
@@ -0,0 +1,91 @@
+# An "early warning" cron job that will install dependencies
+# with `pip install --pre` periodically to test for breakage
+# (and open an issue if a test fails)
+name: --pre Test
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+  schedule:
+    - cron: '0 */12 * * *'  # every 12 hours
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  download_data:
+    name: Download test data
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@v1
+      - shell: bash
+        run: bash build_utils/download_data.sh
+      - name: Upload test data
+        uses: actions/upload-artifact@v1
+        with:
+          name: test_data
+          path: test_data
+
+
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python }} ${{ matrix.backend }} --pre
+    runs-on: ${{ matrix.platform }}
+    needs: download_data
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [windows-latest, macos-latest, ubuntu-latest]
+        python: [3.8]
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install Linux libraries
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 \
+            libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 \
+            libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0
+
+      - name: Install Windows OpenGL
+        if: runner.os == 'Windows'
+        run: |
+          git clone --depth 1 git://github.com/pyvista/gl-ci-helpers.git
+          powershell gl-ci-helpers/appveyor/install_opengl.ps1
+
+      - name: Download test data
+        uses: actions/download-artifact@v1
+        with:
+          name: test_data
+
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install setuptools tox tox-gh-actions
+
+      - name: Test with tox
+        # run tests using pip install --pre
+        run: tox -v --pre
+        env:
+          PLATFORM: ${{ matrix.platform }}
+          PYVISTA_OFF_SCREEN: True  # required for opengl on windows
+
+      # If something goes wrong, we can open an issue in the repo
+      - name: Report Failures
+        if: ${{ failure() }}
+        uses: JasonEtco/create-an-issue@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PLATFORM: ${{ matrix.platform }}
+          PYTHON: ${{ matrix.python }}
+          RUN_ID: ${{ github.run_id }}
+          TITLE: '[test-bot] pip install --pre is failing'
+        with:
+          filename: .github/TEST_FAIL_TEMPLATE.md
+          update_existing: true
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -17,7 +17,7 @@ jobs:
     steps:
       - uses: actions/checkout@v1
       - shell: bash
-        run: bash .travis/install2.sh
+        run: bash build_utils/download_data.sh
       - name: Upload test data
         uses: actions/upload-artifact@v1
         with:
@@ -50,7 +50,16 @@ jobs:
 
     - name: Install ubuntu libraries
       if: startsWith(matrix.os, 'ubuntu')
-      run: sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0
+      run: |
+        sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 \
+        libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 \
+        libxcb-xinput0 libxcb-xfixes0
+
+    - name: Install Windows OpenGL
+      if: runner.os == 'Windows'
+      run: |
+        git clone --depth 1 git://github.com/pyvista/gl-ci-helpers.git
+        powershell gl-ci-helpers/appveyor/install_opengl.ps1
 
     - name: Download test data
       uses: actions/download-artifact@v1
@@ -61,9 +70,9 @@ jobs:
 
     - name: Install dependencies
       run: |
-        python -m pip install -r requirements/requirements_dev.txt
+        python -m pip install -r requirements/requirements_dev.txt tox-gh-actions
     - name: Test PartSeg
-      run: tox -e ${{ matrix.toxenv }}
+      run: tox
 
 
   test_feature:
@@ -83,8 +92,17 @@ jobs:
           python-version: '3.7'
 
       - name: Install ubuntu libraries
-        if: startsWith(matrix.os, 'ubuntu')
-        run: sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 \
+          libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 \
+          libxcb-xinput0 libxcb-xfixes0
+
+      - name: Install Windows OpenGL
+        if: runner.os == 'Windows'
+        run: |
+          git clone --depth 1 git://github.com/pyvista/gl-ci-helpers.git
+          powershell gl-ci-helpers/appveyor/install_opengl.ps1
 
       - name: Download test data
         uses: actions/download-artifact@v1
@@ -95,7 +113,7 @@ jobs:
 
       - name: Install dependencies
         run: |
-          python -m pip install -r requirements/requirements_dev.txt
+          python -m pip install -r requirements/requirements_dev.txt tox-gh-actions
       - name: Test PartSeg
         run: tox -e  'py37-PyQt5,py37-PySide2'
 
@@ -110,10 +128,6 @@ jobs:
         with:
           python-version: '3.7'
 
-      - name: Install ubuntu libraries
-        if: startsWith(matrix.os, 'ubuntu')
-        run: sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0
-
       - name: Download test data
         uses: actions/download-artifact@v1
         with:
@@ -130,3 +144,34 @@ jobs:
         with:
           file: ./coverage.xml
           fail_ci_if_error: true
+
+
+  test_minimal:
+    name: Test PartSeg minimal
+    runs-on: ubuntu-latest
+    needs: download_data
+    steps:
+      - uses: actions/checkout@v1
+      - uses: actions/setup-python@v1
+        name: Install Python '3.6'
+        with:
+          python-version: '3.6'
+
+      - name: Install ubuntu libraries
+        run: |
+          sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 \
+          libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 \
+          libxcb-xinput0 libxcb-xfixes0
+
+      - name: Download test data
+        uses: actions/download-artifact@v1
+        with:
+          name: test_data
+      - name: create minimal req
+        run: python build_utils/create_minimal_req.py
+
+      - name: Install dependencies
+        run: |
+          python -m pip install -r requirements/requirements_dev.txt
+      - name: Test PartSeg
+        run: tox -e  'py36-PyQt5-minimal'
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -55,3 +55,4 @@ repos:
     rev: v0.11.0  # Use the ref you want to point at
     hooks:
     - id: markdownlint
+      exclude: vendored|__init__.py|examples|TEST_FAIL_TEMPLATE.md
diff --git a/.requires.yml b/.requires.yml
@@ -6,7 +6,3 @@ requirements:
   - docs/requirements.txt
   - setup.py
   - tox.ini
-  - path: tox-azure.ini
-    parser: python/tox
-  - path: tox-minimal.ini
-    parser: python/tox
diff --git a/.travis.yml b/.travis.yml
diff --git a/.travis/install.sh b/.travis/install.sh
diff --git a/Readme.md b/Readme.md
@@ -1,6 +1,5 @@
 # PartSeg
 
-[![Travis Build Status](https://travis-ci.com/4DNucleome/PartSeg.svg?branch=master)](https://travis-ci.com/4DNucleome/PartSeg)
 ![Tests](https://github.com/4DNucleome/PartSeg/workflows/Tests/badge.svg?branch=master)
 [![PyPI version](https://badge.fury.io/py/PartSeg.svg)](https://badge.fury.io/py/PartSeg)
 [![Documentation Status](https://readthedocs.org/projects/partseg/badge/?version=latest)](https://partseg.readthedocs.io/en/latest/?badge=latest)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -21,7 +21,7 @@ stages:
     - job: linux
       pool: {vmImage: 'Ubuntu-16.04'}
       steps:
-        - script: bash .travis/install2.sh
+        - script: bash build_utils/download_data.sh
           displayName: "download data"
         - task: UsePythonVersion@0
           inputs:

diff --git a/.travis/create_minimal_req.py → build_utils/create_minimal_req.py b/.travis/create_minimal_req.py → build_utils/create_minimal_req.py
diff --git a/.travis/install2.sh → build_utils/download_data.sh b/.travis/install2.sh → build_utils/download_data.sh
diff --git a/.travis/minimal-req.txt → build_utils/minimal-req.txt b/.travis/minimal-req.txt → build_utils/minimal-req.txt
@@ -1,6 +1,6 @@
 
-Cython==0.29.13
-PartSegData==0.9.4
+PartSegCore_compiled_backend==0.12.0a0
+PartSegData==0.10.0
 PyOpenGL-accelerate==3.1.5
 QtPy==1.7.0
 SimpleITK==1.1.0
@@ -17,13 +17,13 @@ openpyxl==2.4.9
 packaging==17.1
 pandas==0.22.0
 requests==2.18.0
-scipy==0.19.1
+scipy==1.2.0
 sentry_sdk==0.14.3
 six==1.11.0
 sympy==1.1.1
-tifffile==2019.7.26
+tifffile==2020.2.16
 xlrd==1.1.0
 xlsxwriter
 dataclasses==0.7 ;python_version < '3.7'
-typing-extensions==3.7 ;python_version < '3.8'
-PyQt5==5.12.3
+typing-extensions==3.7.4 ;python_version < '3.8'
+PyQt5!=5.15.0,==5.12.3