CI: Use mamba-org/provision-with-micromamba to setup micromamba

.github/ISSUE_TEMPLATE/bump_gmt_checklist.md

@@ -17,11 +17,12 @@ 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_docs.yml`
+  - [ ] Update `.github/workflows/ci_doctests.yaml`
   - [ ] 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
 
@@ -32,5 +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)

.github/workflows/cache_data.yaml

@@ -3,7 +3,7 @@ name: Cache data
 
 on:
   # Uncomment the 'pull_request' line below to manually re-cache data artifacts
-  # pull_request:
+  pull_request:
   # Schedule runs on 12 noon every Sunday
   schedule:
     - cron: '0 12 * * 0'
@@ -24,23 +24,20 @@ 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
           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

.github/workflows/ci_docs.yml

@@ -18,12 +18,11 @@ 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:
@@ -53,30 +52,18 @@ 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 }}
-          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
+          environment-file: "ci/requirements/docs.yml"
+          cache-downloads: true
+          cache-env: true
+          extra-specs: |
+            python=3.11
 
       # Show installed pkg information for postmortem diagnostic
       - name: List installed packages
-        run: mamba list
+        run: micromamba list
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub

.github/workflows/ci_doctests.yaml

@@ -5,7 +5,7 @@ name: Doctests
 on:
   # push:
   #   branches: [ main ]
-  # pull_request:
+  pull_request:
   # Schedule weekly tests on Sunday
   schedule:
     - cron: '0 0 * * 0'
@@ -37,32 +37,17 @@ 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'
-          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
+          environment-file: "ci/requirements/doctests.yml"
+          extra-specs: |
+            python=3.11
+            gmt=6.4.0
 
       # Show installed pkg information for postmortem diagnostic
       - name: List installed packages
-        run: mamba list
+        run: micromamba list
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub

.github/workflows/ci_tests.yaml

@@ -44,10 +44,11 @@ jobs:
         include:
           - python-version: '3.9'
             numpy-version: '1.21'
-            optional-packages: ''
+            environment-file: 'ci/requirements/tests.yml'
           - python-version: '3.11'
             numpy-version: '1.24'
-            optional-packages: 'contextily geopandas ipython rioxarray'
+            environment-file: 'ci/requirements/tests_with_optional_dependencies.yml'
+
     timeout-minutes: 30
     defaults:
       run:
@@ -73,32 +74,20 @@ 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: ${{ matrix.python-version }}
-          channels: conda-forge,nodefaults
-          channel-priority: strict
-          miniforge-version: latest
-          miniforge-variant: Mambaforge
-          mamba-version: "*"
-          run-post: false
-          use-mamba: true
-
-      # Install GMT and other required dependencies from conda-forge
-      - name: Install dependencies
-        run: |
-          mamba install gmt=6.4.0 numpy=${{ matrix.numpy-version }} \
-                        pandas xarray netCDF4 packaging \
-                        ${{ matrix.optional-packages }} \
-                        build dvc make 'pytest>=6.0' \
-                        pytest-cov pytest-doctestplus pytest-mpl sphinx-gallery
+          environment-file: ${{ matrix.environment-file }}
+          cache-downloads: true
+          cache-env: true
+          extra-specs: |
+            python=${{ matrix.python-version }}
+            numpy=${{ matrix.numpy-version }}
+            gmt=6.4.0
 
       # Show installed pkg information for postmortem diagnostic
       - name: List installed packages
-        run: mamba list
+        run: micromamba list
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub

.github/workflows/ci_tests_dev.yaml

@@ -6,7 +6,7 @@ on:
   # push:
   #   branches: [ main ]
   pull_request:
-    types: [ready_for_review]
+    # types: [ready_for_review]
     paths-ignore:
       - 'doc/**'
       - 'examples/**'
@@ -27,7 +27,6 @@ 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
@@ -79,32 +78,44 @@ 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: ${{ matrix.python-version }}
+          environment-name: pygmt
           channels: conda-forge,nodefaults
-          channel-priority: strict
-          miniforge-version: latest
-          miniforge-variant: Mambaforge
-          mamba-version: "*"
-          run-post: false
-          use-mamba: true
-
-      # Install dependencies from conda-forge
+          cache-downloads: true
+          cache-env: true
+          extra-specs: |
+            python=3.11
+            cmake
+            make
+            ninja
+            curl
+            fftw
+            ghostscript
+            hdf5
+            libblas
+            libcblas
+            libgdal
+            liblapack
+            libnetcdf
+            pcre
+            zlib
+            geopandas
+
+      # Install dependencies from PyPI
       - name: Install dependencies
         run: |
-          mamba install python=${{ 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'
@@ -128,7 +139,7 @@ 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

.github/workflows/ci_tests_legacy.yaml

@@ -5,7 +5,7 @@ name: GMT Legacy Tests
 on:
   # push:
   #   branches: [ main ]
-  # pull_request:
+  pull_request:
     # types: [ready_for_review]
     # paths-ignore:
     #  - 'doc/**'
@@ -25,7 +25,6 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9']
         os: [ubuntu-20.04, macOS-11, windows-2019]
         gmt_version: ['6.3']
     timeout-minutes: 30
@@ -47,32 +46,19 @@ 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: ${{ matrix.python-version }}
-          channels: conda-forge,nodefaults
-          channel-priority: strict
-          miniforge-version: latest
-          miniforge-variant: Mambaforge
-          mamba-version: "*"
-          run-post: false
-          use-mamba: true
-
-      # Install GMT and other required dependencies from conda-forge
-      - name: Install dependencies
-        run: |
-          mamba install gmt=${{ matrix.gmt_version }} numpy \
-                        pandas xarray netCDF4 packaging \
-                        contextily geopandas ipython rioxarray \
-                        build dvc make 'pytest>=6.0' \
-                        pytest-cov pytest-doctestplus pytest-mpl sphinx-gallery
+          environment-file: "ci/requirements/tests_legacy.yml"
+          cache-downloads: true
+          cache-env: true
+          extra-specs: |
+            python=3.9
+            gmt=${{ matrix.gmt_version }}
 
       # Show installed pkg information for postmortem diagnostic
       - name: List installed packages
-        run: mamba list
+        run: micromamba list
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub

ci/requirements/docs.yml

@@ -1,10 +1,9 @@
 name: pygmt
 channels:
     - conda-forge
-    - defaults
+    - nodefaults
 dependencies:
     # Required dependencies
-    - pip
     - gmt=6.4.0
     - numpy>=1.21
     - pandas
@@ -14,11 +13,12 @@ dependencies:
     # Optional dependencies
     - contextily
     - geopandas
+    - ipython
     - rioxarray
     # Development dependencies (general)
     - build
-    - ipython
     - make
+    - pip
     # Dev dependencies (building documentation)
     - myst-parser
     - sphinx