Merge branch 'main' into optional-context

Author: seisman

.github/workflows/cache_data.yaml

@@ -46,7 +46,7 @@ jobs:
       - name: Install the package
         run: |
           python -m build --sdist
-          pip install dist/*
+          python -m pip install dist/*
 
       # Download remote files
       - name: Download remote data

.github/workflows/ci_docs.yml

@@ -100,7 +100,7 @@ jobs:
       - name: Install the package
         run: |
           python -m build --sdist
-          pip install dist/*
+          python -m pip install dist/*
 
       # Build the documentation
       - name: Build the documentation

.github/workflows/ci_doctests.yaml

@@ -0,0 +1,91 @@
+# This workflow installs PyGMT and runs all doctests
+
+name: Doctests
+
+on:
+  # push:
+  #   branches: [ main ]
+  # pull_request:
+  # Schedule weekly tests on Sunday
+  schedule:
+    - cron: '0 0 * * 0'
+
+jobs:
+  test:
+    name: ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macOS-latest, windows-latest]
+    timeout-minutes: 30
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      # Cancel previous runs that are not completed
+      - name: Cancel Previous Runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+
+      # Checkout current git repository
+      - name: Checkout
+        uses: actions/[email protected]
+        with:
+          # fetch all history so that setuptools-scm works
+          fetch-depth: 0
+
+      # Install Mambaforge with conda-forge dependencies
+      - name: Setup Mambaforge
+        uses: conda-incubator/[email protected]
+        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
+
+      # Show installed pkg information for postmortem diagnostic
+      - name: List installed packages
+        run: mamba list
+
+      # Download cached remote files (artifacts) from GitHub
+      - name: Download remote data from GitHub
+        uses: dawidd6/[email protected]
+        with:
+          workflow: cache_data.yaml
+          workflow_conclusion: success
+          name: gmt-cache
+          path: .gmt
+
+      # Move downloaded files to ~/.gmt directory and list them
+      - name: Move and list downloaded remote files
+        run: |
+          mkdir -p ~/.gmt
+          mv .gmt/* ~/.gmt
+          # Change modification times of the two files, so GMT won't refresh it
+          touch ~/.gmt/server/gmt_data_server.txt ~/.gmt/server/gmt_hash_server.txt
+          ls -lhR ~/.gmt
+
+      # Install the package that we want to test
+      - name: Install the package
+        run: make install
+
+      # Run the doctests
+      - name: Run doctests
+        run: make doctest PYTEST_EXTRA="-r P"

.github/workflows/ci_tests.yaml

@@ -130,14 +130,8 @@ jobs:
 
       # Run the regular tests
       - name: Run tests
-        if: ${{ !endsWith(github.event.schedule, '3') }}
         run: make test PYTEST_EXTRA="-r P"
 
-      # Run full tests including doctests on Wednesday
-      - name: Run full tests
-        if: github.event_name == 'schedule' && endsWith(github.event.schedule, '3')
-        run: make fulltest PYTEST_EXTRA="-r P"
-
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
         uses: actions/upload-artifact@v3
@@ -148,7 +142,7 @@ jobs:
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/[email protected].1
+        uses: codecov/[email protected].2
         with:
           file: ./coverage.xml # optional
           env_vars: OS,PYTHON,NUMPY

.github/workflows/ci_tests_dev.yaml

@@ -71,7 +71,7 @@ jobs:
           fetch-depth: 0
 
       - name: Show job URL
-        uses: peter-evans/create-or-update-comment@v2.1.1
+        uses: peter-evans/create-or-update-comment@v3.0.0
         if: github.event_name == 'repository_dispatch' && (matrix.os == 'ubuntu-latest')
         with:
           token: ${{ steps.generate-token.outputs.token }}
@@ -99,7 +99,7 @@ jobs:
           mamba install python=${{ matrix.python-version }} \
                         ninja cmake libblas libcblas liblapack fftw libgdal \
                         geopandas ghostscript libnetcdf hdf5 zlib curl pcre make
-          pip install --pre --prefer-binary \
+          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 \

.github/workflows/dvc-diff.yml

@@ -102,14 +102,14 @@ jobs:
 
     - name: Create comment with image diff report
       if: steps.fc.outputs.comment-id == ''
-      uses: peter-evans/create-or-update-comment@v2.1.1
+      uses: peter-evans/create-or-update-comment@v3.0.0
       with:
         issue-number: ${{ github.event.pull_request.number }}
         body: ${{ steps.image-diff.outputs.report }}
 
     - name: Update comment with new image diff report
       if: steps.fc.outputs.comment-id != ''
-      uses: peter-evans/create-or-update-comment@v2.1.1
+      uses: peter-evans/create-or-update-comment@v3.0.0
       with:
         comment-id: ${{ steps.fc.outputs.comment-id }}
         body: ${{ steps.image-diff.outputs.report }}

.github/workflows/format-command.yml

@@ -28,7 +28,7 @@ jobs:
       # Install formatting tools
       - name: Install formatting tools
         run: |
-          pip install black blackdoc docformatter==1.5.1 flakeheaven isort
+          python -m pip install black blackdoc docformatter==1.5.1 flakeheaven isort
           sudo apt-get install dos2unix
 
       # Run "make format" and commit the change to the PR branch
@@ -45,7 +45,7 @@ jobs:
           fi
 
       - name: Add reaction
-        uses: peter-evans/create-or-update-comment@v2.1.1
+        uses: peter-evans/create-or-update-comment@v3.0.0
         with:
           token: ${{ steps.generate-token.outputs.token }}
           repository: ${{ github.event.client_payload.github.payload.repository.full_name }}

.github/workflows/style_checks.yaml

@@ -26,7 +26,7 @@ jobs:
 
       - name: Install packages
         run: |
-          pip install black blackdoc docformatter==1.5.1 flakeheaven pylint isort
+          python -m pip install black blackdoc docformatter==1.5.1 flakeheaven pylint isort
           sudo apt-get install dos2unix
 
       - name: Formatting check (black, blackdoc, docformatter, flakeheaven and isort)

Makefile

@@ -23,7 +23,7 @@ help:
 	@echo ""
 
 install:
-	pip install --no-deps -e .
+	python -m pip install --no-deps -e .
 
 package:
 	python -m build

doc/contributing.md

@@ -227,7 +227,7 @@ To install the current source code into your testing environment, run:
 
 ```bash
 make install  # on Linux/macOS
-pip install --no-deps -e .  # on Windows
+python -m pip install --no-deps -e .  # on Windows
 ```
 
 This installs your project in *editable* mode, meaning that changes made to the source

doc/install.rst

@@ -218,17 +218,17 @@ Using pip
 This installs the latest stable release from
 `PyPI <https://pypi.org/project/pygmt>`__::
 
-    pip install pygmt
+    python -m pip install pygmt
 
 .. tip::
 
-   You can also run ``pip install pygmt[all]`` to install pygmt with
+   You can also run ``python -m pip install pygmt[all]`` to install pygmt with
    all of its optional dependencies.
 
 Alternatively, you can install the latest development version from
 `TestPyPI <https://test.pypi.org/project/pygmt>`__::
 
-    pip install --pre --extra-index-url https://test.pypi.org/simple/ pygmt
+    python -m pip install --pre --extra-index-url https://test.pypi.org/simple/ pygmt
 
 To upgrade the installed stable release or development version to be the latest
 one, just add ``--upgrade`` to the corresponding command above.

doc/maintenance.md

@@ -79,8 +79,7 @@ There are 11 configuration files located in `.github/workflows`:
 2. `ci_tests.yaml` (Tests on Linux/macOS/Windows)
 
    This is run on every commit to the *main* and pull request branches.
-   It is also scheduled to run regular tests daily and run full tests
-   (including doctests) on Wednesday on the *main* branch.
+   It is also scheduled to run regular tests daily on the *main* branch.
    In draft pull requests, only two jobs on Linux are triggered to save on
    Continuous Integration resources:
 
@@ -93,7 +92,12 @@ There are 11 configuration files located in `.github/workflows`:
    via the [Codecov GitHub Action](https://github.com/codecov/codecov-action).
    More codecov related configurations are stored in `.github/codecov.yml`.
 
-3. `ci_docs.yml` (Build documentation on Linux/macOS/Windows)
+3. `ci_doctests.yaml` (Doctests on Linux/macOS/Windows)
+
+    This workflow is scheduled to run all doctests every Sunday on the *main*
+    branch.
+
+4. `ci_docs.yml` (Build documentation on Linux/macOS/Windows)
 
    This is run on every commit to the *main* and pull request branches.
    In draft pull requests, only the job on Linux is triggered to save on
@@ -106,47 +110,47 @@ There are 11 configuration files located in `.github/workflows`:
      from the *main* branch onto the `dev` folder of the *gh-pages* branch.
    * Updating the `latest` documentation link to the new release.
 
-4. `ci_tests_dev.yaml` (GMT Dev Tests on Linux/macOS/Windows).
+5. `ci_tests_dev.yaml` (GMT Dev Tests on Linux/macOS/Windows).
 
    This is triggered when a PR is marked as "ready for review", or using the
    slash command `/test-gmt-dev`. It is also scheduled to run on Monday,
    Wednesday and Friday on the *main* branch.
 
-5. `cache_data.yaml` (Caches GMT remote data files needed for GitHub Actions CI)
+6. `cache_data.yaml` (Caches GMT remote data files needed for GitHub Actions CI)
 
    This is scheduled to run every Sunday at 12:00 (UTC).
    If new remote files are needed urgently, maintainers can manually uncomment
    the 'pull_request:' line in that `cache_data.yaml` file to refresh the cache.
 
-6. `publish-to-pypi.yml` (Publish wheels to TestPyPI and PyPI)
+7. `publish-to-pypi.yml` (Publish wheels to TestPyPI and PyPI)
 
    This workflow is ran to publish wheels to TestPyPI (for testing only) and
    PyPI. Archives will be pushed to TestPyPI on every commit to the *main*
    branch and tagged releases, and to PyPI for tagged releases only. Note that
    authentication to TestPyPI/PyPI is done via OpenID Connect, see also
    https://github.com/pypa/gh-action-pypi-publish/tree/release/v1#publishing-with-openid-connect
 
-7. `release-drafter.yml` (Drafts the next release notes)
+8. `release-drafter.yml` (Drafts the next release notes)
 
     This workflow is run to update the next releases notes as pull requests are
-    merged into the main branch.
+    merged into the *main* branch.
 
-8. `check-links.yml` (Check links in the repository and website)
+9. `check-links.yml` (Check links in the repository and website)
 
    This workflow is run weekly to check all external links in plaintext and
    HTML files. It will create an issue if broken links are found.
 
-9. `format-command.yml` (Format the codes using slash command)
+10. `format-command.yml` (Format the codes using slash command)
 
    This workflow is triggered in a PR if the slash command `/format` is used.
 
-10. `dvc-diff.yml` (Report changes to test images on dvc remote)
+11. `dvc-diff.yml` (Report changes to test images on dvc remote)
 
     This workflow is triggered in a PR when any *.png.dvc files have been added,
     modified, or deleted. A GitHub comment will be published that contains a summary
     table of the images that have changed along with a visual report.
 
-11. `release-baseline-images.yml` (Upload the ZIP archive of baseline images as a release asset)
+12. `release-baseline-images.yml` (Upload the ZIP archive of baseline images as a release asset)
 
     This workflow is run to upload the ZIP archive of baseline images as a release
     asset when a release is published.

pygmt/__init__.py

@@ -165,6 +165,8 @@ def _get_ghostscript_version():
         "packaging",
         "contextily",
         "geopandas",
+        "IPython",
+        "rioxarray",
     ]
 
     print("PyGMT information:", file=file)

pygmt/datasets/tile_map.py

@@ -87,7 +87,7 @@ def load_tile_map(region, zoom="auto", source=None, lonlat=True, wait=0, max_ret
     ImportError
         If ``contextily`` is not installed or can't be imported. Follow
         :doc:`install instructions for contextily <contextily:index>`, (e.g.
-        via ``pip install contextily``) before using this function.
+        via ``python -m pip install contextily``) before using this function.
 
     Examples
     --------
@@ -111,7 +111,7 @@ def load_tile_map(region, zoom="auto", source=None, lonlat=True, wait=0, max_ret
     if contextily is None:
         raise ImportError(
             "Package `contextily` is required to be installed to use this function. "
-            "Please use `pip install contextily` or "
+            "Please use `python -m pip install contextily` or "
             "`mamba install -c conda-forge contextily` "
             "to install the package."
         )

pygmt/src/tilemap.py

@@ -115,14 +115,15 @@ def tilemap(
     ImportError
         If ``rioxarray`` is not installed. Follow
         :doc:`install instructions for rioxarray <rioxarray:installation>`,
-        (e.g. via ``pip install rioxarray``) before using this function.
+        (e.g. via ``python -m pip install rioxarray``) before using this
+        function.
     """
     kwargs = self._preprocess(**kwargs)  # pylint: disable=protected-access
 
     if rioxarray is None:
         raise ImportError(
             "Package `rioxarray` is required to be installed to use this function. "
-            "Please use `pip install rioxarray` or "
+            "Please use `python -m pip install rioxarray` or "
             "`mamba install -c conda-forge rioxarray` "
             "to install the package."
         )