CI: Use mamba-org/provision-with-micromamba to setup micromamba (#2435)

seisman · weiji14 · web-flow · commit 5d2d8ba69c09 · 2023-04-24T07:43:21.000+08:00
Co-authored-by: Wei Ji &lt;23487320+weiji14@users.noreply.github.com&gt;
diff --git a/.github/ISSUE_TEMPLATE/bump_gmt_checklist.md b/.github/ISSUE_TEMPLATE/bump_gmt_checklist.md
@@ -17,11 +17,13 @@ assignees: ''
 **To-Do for bumping the GMT version in CI**:
 
 - [ ] Bump the GMT version in CI (1 PR)
+  - [ ] Update `environment.yml`
+  - [ ] Update `ci/requirements/docs.yml`
   - [ ] Update `.github/workflows/cache_data.yaml`
+  - [ ] Update `.github/workflows/ci_doctests.yaml`
   - [ ] Update `.github/workflows/ci_docs.yml`
   - [ ] Update `.github/workflows/ci_tests.yaml`
-  - [ ] Update `ci/requirements/docs.yml`
-  - [ ] Update `environment.yml`
+  - [ ] Add the legacy GMT version to `.github/workflows/ci_tests_legacy.yaml`
 - [ ] Fix failing tests (1 or more PRs)
 - [ ] Fix [xfail](https://docs.pytest.org/en/stable/skipping.html#xfail-mark-test-functions-as-expected-to-fail) pytest markers on tests that are now xpass
 
@@ -31,5 +33,6 @@ assignees: ''
   - [ ] Update `required_version` in `pygmt/clib/session.py`
   - [ ] Update `test_get_default` in `pygmt/tests/test_clib.py`
   - [ ] Update compatibility table in `README.rst`
+  - [ ] Remove unsupported GMT version from `.github/workflows/ci_tests_legacy.yaml`
 - [ ] Remove [xfail](https://docs.pytest.org/en/stable/skipping.html#xfail-mark-test-functions-as-expected-to-fail) pytest markers on tests that are now xpass
 - [ ] Update deprecated syntax in source code and examples based on the [GMT Changelog](https://docs.generic-mapping-tools.org/latest/changes.html)
diff --git a/.github/workflows/cache_data.yaml b/.github/workflows/cache_data.yaml
@@ -33,23 +33,21 @@ jobs:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
 
-      # Install Mambaforge with conda-forge dependencies
-      - name: Setup Mambaforge
-        uses: conda-incubator/setup-miniconda@v2.2.0
+      - name: Setup Micromamba
+        uses: mamba-org/provision-with-micromamba@v15
         with:
+          environment-name: pygmt
+          environment-file: false
           channels: conda-forge,nodefaults
-          channel-priority: strict
-          miniforge-version: latest
-          miniforge-variant: Mambaforge
-          mamba-version: "*"
-          run-post: false
-          use-mamba: true
-
-      # Install GMT and other required dependencies from conda-forge
-      - name: Install dependencies
-        run: |
-          mamba install gmt=6.4.0 numpy pandas xarray netCDF4 packaging \
-                        build
+          extra-specs: |
+            python=3.11
+            gmt=6.4.0
+            numpy
+            pandas
+            xarray
+            netCDF4
+            packaging
+            build
 
       # Install the package that we want to test
       - name: Install the package
diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml
@@ -31,12 +31,11 @@ on:
 
 jobs:
   docs:
-    name: ${{ matrix.os }} - Python ${{ matrix.python-version }}
+    name: ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.11']
         os: [ubuntu-latest, macOS-latest, windows-latest]
         # Is it a draft Pull Request (true or false)?
         isDraft:
@@ -66,30 +65,35 @@ jobs:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
 
-      # Install Mambaforge with conda-forge dependencies
-      - name: Setup Mambaforge
-        uses: conda-incubator/setup-miniconda@v2.2.0
+      - name: Setup Micromamba
+        uses: mamba-org/provision-with-micromamba@v15
         with:
-          activate-environment: pygmt
-          python-version: ${{ matrix.python-version }}
+          environment-name: pygmt
+          environment-file: false
           channels: conda-forge,nodefaults
-          channel-priority: strict
-          miniforge-version: latest
-          miniforge-variant: Mambaforge
-          mamba-version: "*"
-          run-post: false
-          use-mamba: true
-
-      # Install GMT and other required dependencies from conda-forge
-      - name: Install dependencies
-        run: |
-          mamba install gmt=6.4.0 numpy pandas xarray netCDF4 packaging \
-                        build ipython make myst-parser contextily geopandas rioxarray \
-                        sphinx sphinx-copybutton sphinx-design sphinx-gallery sphinx_rtd_theme
-
-      # Show installed pkg information for postmortem diagnostic
-      - name: List installed packages
-        run: mamba list
+          cache-downloads: true
+          cache-env: true
+          extra-specs: |
+            python=3.11
+            gmt=6.4.0
+            numpy
+            pandas
+            xarray
+            netCDF4
+            packaging
+            contextily
+            geopandas
+            ipython
+            rioxarray
+            build
+            make
+            pip
+            myst-parser
+            sphinx
+            sphinx-copybutton
+            sphinx-design
+            sphinx-gallery
+            sphinx_rtd_theme
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
diff --git a/.github/workflows/ci_doctests.yaml b/.github/workflows/ci_doctests.yaml
@@ -40,32 +40,31 @@ jobs:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
 
-      # Install Mambaforge with conda-forge dependencies
-      - name: Setup Mambaforge
-        uses: conda-incubator/setup-miniconda@v2.2.0
+      - name: Setup Micromamba
+        uses: mamba-org/provision-with-micromamba@v15
         with:
-          activate-environment: pygmt
-          python-version: '3.11'
+          environment-name: pygmt
+          environment-file: false
           channels: conda-forge,nodefaults
-          channel-priority: strict
-          miniforge-version: latest
-          miniforge-variant: Mambaforge
-          mamba-version: "*"
-          run-post: false
-          use-mamba: true
-
-      # Install GMT and other required dependencies from conda-forge
-      - name: Install dependencies
-        run: |
-          mamba install gmt=6.4.0 numpy \
-                        pandas xarray netCDF4 packaging \
-                        build make 'pytest>=6.0' \
-                        pytest-cov pytest-doctestplus pytest-mpl sphinx-gallery \
-                        contextily geopandas ipython rioxarray
-
-      # Show installed pkg information for postmortem diagnostic
-      - name: List installed packages
-        run: mamba list
+          extra-specs: |
+            python=3.11
+            gmt=6.4.0
+            numpy
+            pandas
+            xarray
+            netCDF4
+            packaging
+            contextily
+            geopandas
+            ipython
+            rioxarray
+            build
+            make
+            pip
+            pytest
+            pytest-doctestplus
+            pytest-mpl
+            sphinx-gallery
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
diff --git a/.github/workflows/ci_tests.yaml b/.github/workflows/ci_tests.yaml
@@ -67,7 +67,12 @@ jobs:
             optional-packages: ''
           - python-version: '3.11'
             numpy-version: '1.24'
-            optional-packages: 'contextily geopandas ipython rioxarray'
+            optional-packages: |
+              contextily
+              geopandas
+              ipython
+              rioxarray
+
     timeout-minutes: 30
     defaults:
       run:
@@ -93,32 +98,32 @@ jobs:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
 
-      # Install Mambaforge with conda-forge dependencies
-      - name: Setup Mambaforge
-        uses: conda-incubator/setup-miniconda@v2.2.0
+      - name: Setup Micromamba
+        uses: mamba-org/provision-with-micromamba@v15
         with:
-          activate-environment: pygmt
-          python-version: ${{ matrix.python-version }}
+          environment-name: pygmt
+          environment-file: false
           channels: conda-forge,nodefaults
-          channel-priority: strict
-          miniforge-version: latest
-          miniforge-variant: Mambaforge
-          mamba-version: "*"
-          run-post: false
-          use-mamba: true
-
-      # Install GMT and other required dependencies from conda-forge
-      - name: Install dependencies
-        run: |
-          mamba install gmt=6.4.0 numpy=${{ matrix.numpy-version }} \
-                        pandas xarray netCDF4 packaging \
-                        ${{ matrix.optional-packages }} \
-                        build dvc make 'pytest>=6.0' \
-                        pytest-cov pytest-doctestplus pytest-mpl sphinx-gallery
-
-      # Show installed pkg information for postmortem diagnostic
-      - name: List installed packages
-        run: mamba list
+          cache-downloads: true
+          cache-env: true
+          extra-specs: |
+            python=${{ matrix.python-version }}
+            gmt=6.4.0
+            numpy=${{ matrix.numpy-version }}
+            pandas
+            xarray
+            netCDF4
+            packaging
+            ${{ matrix.optional-packages }}
+            build
+            dvc
+            make
+            pip
+            pytest
+            pytest-cov
+            pytest-doctestplus
+            pytest-mpl
+            sphinx-gallery
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
diff --git a/.github/workflows/ci_tests_dev.yaml b/.github/workflows/ci_tests_dev.yaml
@@ -38,7 +38,6 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.11']
         os: [ubuntu-22.04, macOS-12, windows-2022]
         gmt_git_ref: [master]
     timeout-minutes: 30
@@ -90,32 +89,45 @@ jobs:
           comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
           body: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}
 
-      # Install Mambaforge with conda-forge dependencies
-      - name: Setup Mambaforge
-        uses: conda-incubator/setup-miniconda@v2.2.0
+      - name: Setup Micromamba
+        uses: mamba-org/provision-with-micromamba@v15
         with:
-          activate-environment: pygmt
-          # python-version: ${{ matrix.python-version }}
+          environment-name: pygmt
+          environment-file: false
           channels: conda-forge,nodefaults
-          channel-priority: strict
-          miniforge-version: latest
-          miniforge-variant: Mambaforge
-          mamba-version: "*"
-          run-post: false
-          use-mamba: true
-
-      # Install dependencies from conda-forge
+          cache-downloads: true
+          cache-env: true
+          extra-specs: |
+            python=3.11
+            cmake
+            make
+            ninja
+            curl
+            fftw
+            ghostscript
+            hdf5
+            libblas
+            libcblas
+            libgdal
+            liblapack
+            libnetcdf
+            pcre
+            zlib
+            geopandas
+
+      # Install dependencies from PyPI
       - name: Install dependencies
         run: |
-          mamba install python=${{ matrix.python-version }} \
-                        ninja cmake libblas libcblas liblapack fftw libgdal \
-                        geopandas ghostscript libnetcdf hdf5 zlib curl pcre make
           python -m pip install --pre --prefer-binary \
                         numpy pandas xarray netCDF4 packaging \
                         build contextily dvc ipython rioxarray \
                         'pytest>=6.0' pytest-cov pytest-doctestplus pytest-mpl \
                         sphinx-gallery
 
+      # Show installed pkg information for postmortem diagnostic
+      - name: List installed packages
+        run: micromamba list
+
       # Pull baseline image data from dvc remote (DAGsHub)
       - name: Pull baseline image data from dvc remote
         if: github.event_name == 'schedule'
@@ -139,7 +151,7 @@ jobs:
         if: runner.os != 'Windows'
 
       - name: Install GMT dev version from conda-forge (Windows)
-        run: mamba install -c conda-forge/label/dev gmt
+        run: micromamba install -c conda-forge/label/dev gmt
         if: runner.os == 'Windows'
 
       # Download cached remote files (artifacts) from GitHub
diff --git a/.github/workflows/ci_tests_legacy.yaml b/.github/workflows/ci_tests_legacy.yaml
