GitHub Actions (#1806)

* Use pytest-xdist, avoid setup.py test and update CircleCI config * Try to use codacy coverage orb * Remove test alias * Require minimal version of pytest-cov * Require minimum version of pytest-flake8 * added extra requirement for conda build memory * added actions workflows * added conda build workflow * comment out julis symlink for now * use 2020 pip solver * gaahhh * force ncurses to be from conda forge * wrong OS for ncurses fixed * removed py 38 from OSX conda install * try to install R and Julia first * force ncurses from conda forge * removed channel activation and forcing ncurses * force and keep ancurses from conda forge * force ncurses via uninstall * gave up installing full package and revert to only python and ncl * remove tweaking ncurses * made the r-lint as install test to be skipped * removed py 3.8 for osx testing * removed py 3.8 for osx testing * removed py 3.8 for osx testing * removed requirement - weird - I thought I removed this ages ago * removed some comments Co-authored-by: Bouwe Andela <b.andela@esciencecenter.nl>
ESMValGroup · Sep 17, 2020 · 1125c36 · 1125c36
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diff --git a/.github/workflows/action-conda-build.yml b/.github/workflows/action-conda-build.yml
@@ -0,0 +1,48 @@
+name: Conda-build
+
+# runs on a push on master and at the end of every day
+on:
+  push:
+    branches:
+    - master
+    - github-actions2  # testing branch
+  schedule:
+    - cron: '0 0 * * *'
+
+jobs:
+  linux:
+    runs-on: "ubuntu-latest"  # use only Linux for conda build
+    strategy:
+      matrix:
+        python-version: [3.8]  # use only the latest for conda build
+      fail-fast: false
+    name: Linux Python ${{ matrix.python-version }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: goanpeca/setup-miniconda@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+          miniconda-version: "latest"
+          channels: conda-forge
+      - shell: bash -l {0}
+        run: mkdir -p condabuild_artifacts_python_${{ matrix.python-version }}
+      - shell: bash -l {0}
+        run: conda --version 2>&1 | tee condabuild_artifacts_python_${{ matrix.python-version }}/conda_version.txt
+      - shell: bash -l {0}
+        run: python -V 2>&1 | tee condabuild_artifacts_python_${{ matrix.python-version }}/python_version.txt
+      - shell: bash -l {0}
+        run: wget https://julialang-s3.julialang.org/bin/linux/x64/1.0/julia-1.0.3-linux-x86_64.tar.gz
+      - shell: bash -l {0}
+        run: tar xfz julia-*-linux-x86_64.tar.gz
+      #- shell: bash -l {0}
+      #  run: ln -s $(pwd)/julia-*/bin/julia /usr/bin/julia
+      - shell: bash -l {0}
+        run: conda install -y conda-build conda-verify 2>&1 | tee condabuild_artifacts_python_${{ matrix.python-version }}/install_conda_buildtools.txt
+      - shell: bash -l {0}
+        run: conda build package -c conda-forge -c esmvalgroup 2>&1 | tee condabuild_artifacts_python_${{ matrix.python-version }}/conda_build.txt
+      - name: Upload artifacts
+        if: ${{ always() }}  # upload artifacts even if fail
+        uses: actions/upload-artifact@v2
+        with:
+          name: Condabuild_python_${{ matrix.python-version }}
+          path: condabuild_artifacts_python_${{ matrix.python-version }}
diff --git a/.github/workflows/action-install-from-conda.yml b/.github/workflows/action-install-from-conda.yml
@@ -0,0 +1,94 @@
+name: Conda Base Install
+
+# runs on a push on master and at the end of every day
+on:
+  push:
+    branches:
+    - master
+    - github-actions2  # testing branch
+  schedule:
+    - cron: '0 0 * * *'
+
+jobs:
+  linux:
+    runs-on: "ubuntu-latest"
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+      # fail-fast set to False allows all other tests
+      # in the worflow to run regardless of any fail
+      fail-fast: false
+    name: Linux Python ${{ matrix.python-version }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: goanpeca/setup-miniconda@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+          miniconda-version: "latest"
+          channels: esmvalgroup,conda-forge
+      - shell: bash -l {0}
+        run: mkdir -p conda_install_linux_artifacts_python_${{ matrix.python-version }}
+      - shell: bash -l {0}
+        run: conda --version 2>&1 | tee conda_install_linux_artifacts_python_${{ matrix.python-version }}/conda_version.txt
+      - shell: bash -l {0}
+        run: which conda 2>&1 | tee conda_install_linux_artifacts_python_${{ matrix.python-version }}/conda_path.txt
+      - shell: bash -l {0}
+        run: python -V 2>&1 | tee conda_install_linux_artifacts_python_${{ matrix.python-version }}/python_version.txt
+      - shell: bash -l {0}
+        run: conda install esmvaltool 2>&1 | tee conda_install_linux_artifacts_python_${{ matrix.python-version }}/install.txt
+      - shell: bash -l {0}
+        run: esmvaltool --help
+      - shell: bash -l {0}
+        run: esmvaltool version 2>&1 | tee conda_install_linux_artifacts_python_${{ matrix.python-version }}/version.txt
+      - name: Upload artifacts
+        if: ${{ always() }}  # upload artifacts even if fail
+        uses: actions/upload-artifact@v2
+        with:
+          name: Conda_Install_Linux_python_${{ matrix.python-version }}
+          path: conda_install_linux_artifacts_python_${{ matrix.python-version }}
+
+  osx:
+    runs-on: "macos-latest"
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7]  # 3.8.5 not working as of 07-Sep-2020; serious issues at env solving
+      fail-fast: false
+    name: OSX Python ${{ matrix.python-version }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: goanpeca/setup-miniconda@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+          miniconda-version: "latest"
+          channels: esmvalgroup,conda-forge
+      - shell: bash -l {0}
+        run: mkdir -p conda_install_osx_artifacts_python_${{ matrix.python-version }}
+      - shell: bash -l {0}
+        run: conda --version 2>&1 | tee conda_install_osx_artifacts_python_${{ matrix.python-version }}/conda_version.txt
+      - shell: bash -l {0}
+        run: which conda 2>&1 | tee conda_install_osx_artifacts_python_${{ matrix.python-version }}/conda_path.txt
+      - shell: bash -l {0}
+        run: python -V 2>&1 | tee conda_install_osx_artifacts_python_${{ matrix.python-version }}/python_version.txt
+      # ncurses needs to be from conda-forge and not main channel
+      # for now it's turned off since we're not testing R/Julia installs
+      # - shell: bash -l {0}
+      #   run: conda uninstall -y ncurses
+      # - shell: bash -l {0}
+      #   run: conda list ncurses
+      # - shell: bash -l {0}
+      #   run: conda install -y conda-forge::ncurses
+      # - shell: bash -l {0}
+      #   run: conda list ncurses
+      - shell: bash -l {0}
+        #run: conda install esmvaltool --no-update-deps 2>&1 | tee conda_install_osx_artifacts_python_${{ matrix.python-version }}/install.txt
+        run: conda install esmvaltool-python esmvaltool-ncl 2>&1 | tee conda_install_osx_artifacts_python_${{ matrix.python-version }}/install.txt
+      - shell: bash -l {0}
+        run: esmvaltool --help
+      - shell: bash -l {0}
+        run: esmvaltool version 2>&1 | tee conda_install_osx_artifacts_python_${{ matrix.python-version }}/version.txt
+      - name: Upload artifacts
+        if: ${{ always() }}  # upload artifacts even if fail
+        uses: actions/upload-artifact@v2
+        with:
+          name: Conda_Install_OSX_python_${{ matrix.python-version }}
+          path: conda_install_osx_artifacts_python_${{ matrix.python-version }}
diff --git a/.github/workflows/action-install-from-source.yml b/.github/workflows/action-install-from-source.yml
@@ -0,0 +1,81 @@
+name: Source Install
+
+# runs on a push on master and at the end of every day
+on:
+  push:
+    branches:
+    - master
+    - github-actions2  # testing branch
+  schedule:
+    - cron: '0 0 * * *'
+
+jobs:
+  linux:
+    runs-on: "ubuntu-latest"
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+      fail-fast: false
+    name: Linux Python ${{ matrix.python-version }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: goanpeca/setup-miniconda@v1
+        with:
+          activate-environment: esmvaltool
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+          miniconda-version: "latest"
+          channels: conda-forge
+      - shell: bash -l {0}
+        run: mkdir -p source_install_linux_artifacts_python_${{ matrix.python-version }}
+      - shell: bash -l {0}
+        run: conda --version 2>&1 | tee source_install_linux_artifacts_python_${{ matrix.python-version }}/conda_version.txt
+      - shell: bash -l {0}
+        run: python -V 2>&1 | tee source_install_linux_artifacts_python_${{ matrix.python-version }}/python_version.txt
+      - shell: bash -l {0}
+        run: pip install -e .[develop] 2>&1 | tee source_install_linux_artifacts_python_${{ matrix.python-version }}/install.txt
+      - shell: bash -l {0}
+        run: esmvaltool --help
+      - shell: bash -l {0}
+        run: esmvaltool version 2>&1 | tee source_install_linux_artifacts_python_${{ matrix.python-version }}/version.txt
+      - name: Upload artifacts
+        if: ${{ always() }}  # upload artifacts even if fail
+        uses: actions/upload-artifact@v2
+        with:
+          name: Source_Install_Linux_python_${{ matrix.python-version }}
+          path: source_install_linux_artifacts_python_${{ matrix.python-version }}
+
+  osx:
+    runs-on: "macos-latest"
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7]  # 3.8.5 poses serious issues at env solving stage
+      fail-fast: false
+    name: OSX Python ${{ matrix.python-version }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: goanpeca/setup-miniconda@v1
+        with:
+          activate-environment: esmvaltool
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+          miniconda-version: "latest"
+          channels: conda-forge
+      - shell: bash -l {0}
+        run: mkdir -p source_install_osx_artifacts_python_${{ matrix.python-version }}
+      - shell: bash -l {0}
+        run: conda --version 2>&1 | tee source_install_osx_artifacts_python_${{ matrix.python-version }}/conda_version.txt
+      - shell: bash -l {0}
+        run: python -V 2>&1 | tee source_install_osx_artifacts_python_${{ matrix.python-version }}/python_version.txt
+      - shell: bash -l {0}
+        run: pip install -e .[develop] 2>&1 | tee source_install_osx_artifacts_python_${{ matrix.python-version }}/install.txt
+      - shell: bash -l {0}
+        run: esmvaltool --help
+      - shell: bash -l {0}
+        run: esmvaltool version 2>&1 | tee source_install_osx_artifacts_python_${{ matrix.python-version }}/version.txt
+      - name: Upload artifacts
+        if: ${{ always() }}  # upload artifacts even if fail
+        uses: actions/upload-artifact@v2
+        with:
+          name: Source_Install_OSX_python_${{ matrix.python-version }}
+          path: source_install_osx_artifacts_python_${{ matrix.python-version }}
diff --git a/.github/workflows/action-test.yml b/.github/workflows/action-test.yml
@@ -0,0 +1,89 @@
+name: Test
+
+# runs on a push on master and at the end of every day
+on:
+  push:
+    branches:
+    - master
+    - github-actions2  # testing branch
+  schedule:
+    - cron: '0 0 * * *'
+
+jobs:
+  linux:
+    runs-on: "ubuntu-latest"
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+      fail-fast: false
+    name: Linux Python ${{ matrix.python-version }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: goanpeca/setup-miniconda@v1
+        with:
+          activate-environment: esmvaltool
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+          miniconda-version: "latest"
+          channels: conda-forge
+      - shell: bash -l {0}
+        run: mkdir -p test_linux_artifacts_python_${{ matrix.python-version }}
+      - shell: bash -l {0}
+        run: conda --version 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/conda_version.txt
+      - shell: bash -l {0}
+        run: python -V 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/python_version.txt
+      - shell: bash -l {0}
+        run: pip install -e .[develop] 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/install.txt
+      - shell: bash -l {0}
+        run: esmvaltool install R
+      - shell: bash -l {0}
+        run: esmvaltool install Julia
+      - shell: bash -l {0}
+        run: pytest -n 2 -m "not installation" 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/test_report.txt
+      - name: Upload artifacts
+        if: ${{ always() }}  # upload artifacts even if fail
+        uses: actions/upload-artifact@v2
+        with:
+          name: Test_Linux_python_${{ matrix.python-version }}
+          path: test_linux_artifacts_python_${{ matrix.python-version }}
+
+  osx:
+    runs-on: "macos-latest"
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7]  # 3.8.5 poses serious issues with environment solving
+      fail-fast: false
+    name: OSX Python ${{ matrix.python-version }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: goanpeca/setup-miniconda@v1
+        with:
+          activate-environment: esmvaltool
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+          miniconda-version: "latest"
+          channels: conda-forge
+      - shell: bash -l {0}
+        run: mkdir -p test_osx_artifacts_python_${{ matrix.python-version }}
+      - shell: bash -l {0}
+        run: conda --version 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/conda_version.txt
+      - shell: bash -l {0}
+        run: python -V 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/python_version.txt
+      - shell: bash -l {0}
+        run: pip install -e .[develop] --use-feature=2020-resolver 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/install.txt
+      # ncurses needs to be from conda-forge and not main channel
+      # for now it's turned off since we're not testing R/Julia installs
+      # - shell: bash -l {0}
+      #   run: conda install -y conda-forge::ncurses 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/ncurses.txt
+      # - shell: bash -l {0}
+      #   run: esmvaltool install R
+      # - shell: bash -l {0}
+      #   run: esmvaltool install Julia
+      - shell: bash -l {0}
+        run: pytest -n 2 -m "not installation" 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/test_report.txt
+      - name: Upload artifacts
+        if: ${{ always() }}  # upload artifacts even if fail
+        uses: actions/upload-artifact@v2
+        with:
+          name: Test_OSX_python_${{ matrix.python-version }}
+          path: test_osx_artifacts_python_${{ matrix.python-version }}
diff --git a/tests/unit/test_lint.py b/tests/unit/test_lint.py
@@ -1,5 +1,6 @@
 """Lint tests."""
 import os
+import pytest
 import subprocess
 import textwrap
 from pathlib import Path
@@ -41,6 +42,7 @@ def test_nclcodestyle():
     assert success, "Your NCL code does not follow our formatting standards."
 
 
+@pytest.mark.installation
 def test_r_lint(monkeypatch):
     """Test R lint."""
     monkeypatch.setenv("LINTR_COMMENT_BOT", "FALSE")