Merge branch 'main' into update-common-strings

Author: Meghan Jones

.github/workflows/cache_data.yaml

@@ -24,17 +24,21 @@ jobs:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
 
-      # Setup Miniconda
-      - name: Setup Miniconda
+      # Install Mambaforge with conda-forge dependencies
+      - name: Setup Mambaforge
         uses: conda-incubator/setup-miniconda@v2.1.1
         with:
-          channels: conda-forge
-          miniconda-version: "latest"
+          channels: conda-forge,nodefaults
+          channel-priority: strict
+          miniforge-version: latest
+          miniforge-variant: Mambaforge
+          mamba-version: "*"
+          use-mamba: true
 
       # Install GMT and other required dependencies from conda-forge
       - name: Install dependencies
         run: |
-          conda install gmt=6.2.0 \
+          mamba install gmt=6.2.0 \
                         numpy pandas xarray netCDF4 packaging matplotlib
 
       # Install the package that we want to test

.github/workflows/ci_docs.yml

@@ -54,25 +54,29 @@ jobs:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
 
-      # Setup Miniconda
-      - name: Setup Miniconda
+      # Install Mambaforge with conda-forge dependencies
+      - name: Setup Mambaforge
         uses: conda-incubator/setup-miniconda@v2.1.1
         with:
           activate-environment: pygmt
           python-version: ${{ matrix.python-version }}
-          channels: conda-forge
-          miniconda-version: "latest"
+          channels: conda-forge,nodefaults
+          channel-priority: strict
+          miniforge-version: latest
+          miniforge-variant: Mambaforge
+          mamba-version: "*"
+          use-mamba: true
 
       # Install GMT and other required dependencies from conda-forge
       - name: Install dependencies
         run: |
-          conda install gmt=6.2.0 numpy pandas xarray netCDF4 packaging \
+          mamba install gmt=6.2.0 numpy pandas xarray netCDF4 packaging \
                         ipython make myst-parser geopandas \
                         sphinx sphinx-copybutton sphinx-gallery sphinx_rtd_theme
 
       # Show installed pkg information for postmortem diagnostic
       - name: List installed packages
-        run: conda list
+        run: mamba list
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub

.github/workflows/ci_tests.yaml

@@ -77,28 +77,32 @@ jobs:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
 
-      # Setup Miniconda
-      - name: Setup Miniconda
+      # Install Mambaforge with conda-forge dependencies
+      - name: Setup Mambaforge
         uses: conda-incubator/setup-miniconda@v2.1.1
         with:
           activate-environment: pygmt
           python-version: ${{ matrix.python-version }}
-          channels: conda-forge
-          miniconda-version: "latest"
+          channels: conda-forge,nodefaults
+          channel-priority: strict
+          miniforge-version: latest
+          miniforge-variant: Mambaforge
+          mamba-version: "*"
+          use-mamba: true
 
       # Install GMT and other required dependencies from conda-forge
       - name: Install dependencies
         run: |
-          conda install gmt=6.2.0 numpy=${{ matrix.numpy-version }} \
+          mamba install gmt=6.2.0 numpy=${{ matrix.numpy-version }} \
                         pandas xarray netCDF4 packaging \
                         ${{ matrix.optional-packages }} \
-                        codecov coverage[toml] dvc ipython make \
+                        coverage[toml] dvc ipython make \
                         pytest-cov pytest-mpl pytest>=6.0 \
                         sphinx-gallery
 
       # Show installed pkg information for postmortem diagnostic
       - name: List installed packages
-        run: conda list
+        run: mamba list
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub

.github/workflows/ci_tests_dev.yaml

@@ -71,19 +71,23 @@ jobs:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
 
-      # Setup Miniconda
-      - name: Setup Miniconda
+      # Install Mambaforge with conda-forge dependencies
+      - name: Setup Mambaforge
         uses: conda-incubator/setup-miniconda@v2.1.1
         with:
           activate-environment: pygmt
           python-version: ${{ matrix.python-version }}
-          channels: conda-forge
-          miniconda-version: "latest"
+          channels: conda-forge,nodefaults
+          channel-priority: strict
+          miniforge-version: latest
+          miniforge-variant: Mambaforge
+          mamba-version: "*"
+          use-mamba: true
 
       # Install dependencies from conda-forge
       - name: Install dependencies
         run: |
-          conda install ninja cmake libblas libcblas liblapack fftw gdal geopandas \
+          mamba install ninja cmake libblas libcblas liblapack fftw gdal geopandas \
                         ghostscript libnetcdf hdf5 zlib curl pcre make dvc
           pip install --pre numpy pandas xarray netCDF4 packaging \
                             ipython pytest-cov pytest-mpl pytest>=6.0 sphinx-gallery \
@@ -98,7 +102,7 @@ jobs:
         if: runner.os != 'Windows'
 
       - name: Install GMT dev version from conda-forge (Windows)
-        run: conda install -c conda-forge/label/dev gmt
+        run: mamba install -c conda-forge/label/dev gmt=6.3
         if: runner.os == 'Windows'
 
       # Download cached remote files (artifacts) from GitHub

README.rst

@@ -16,9 +16,9 @@ PyGMT
 .. image:: https://github.com/GenericMappingTools/pygmt/workflows/GMT%20Dev%20Tests/badge.svg
     :alt: GitHub Actions GMT Dev Tests status
     :target: https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_tests_dev.yaml
-.. image:: https://img.shields.io/codecov/c/github/GenericMappingTools/pygmt/main.svg?style=flat-square
+.. image:: https://codecov.io/gh/GenericMappingTools/pygmt/branch/main/graph/badge.svg?token=78Fu4EWstx
     :alt: Test coverage status
-    :target: https://codecov.io/gh/GenericMappingTools/pygmt
+    :target: https://app.codecov.io/gh/GenericMappingTools/pygmt
 .. image:: https://img.shields.io/pypi/pyversions/pygmt.svg?style=flat-square
     :alt: Compatible Python versions.
     :target: https://pypi.python.org/pypi/pygmt

doc/maintenance.md

@@ -87,6 +87,11 @@ There are 11 configuration files located in `.github/workflows`:
      Python/NumPy versions
    - Latest Python/NumPy versions + optional packages (e.g. GeoPandas)
 
+   This workflow is also responsible for uploading test coverage reports stored
+   in `.coverage.xml` to https://app.codecov.io/gh/GenericMappingTools/pygmt
+   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)
 
    This is run on every commit to the *main* and Pull Request branches.

environment.yml

@@ -16,7 +16,6 @@ dependencies:
     # Development dependencies
     - black
     - blackdoc
-    - codecov
     - coverage[toml]
     - docformatter
     - dvc

pygmt/tests/test_io.py

@@ -0,0 +1,34 @@
+"""
+Tests for input/output (I/O) utilities.
+"""
+import numpy as np
+import pytest
+import xarray as xr
+from pygmt.helpers import GMTTempFile
+from pygmt.io import load_dataarray
+
+
+def test_io_load_dataarray():
+    """
+    Check that load_dataarray works to read a NetCDF grid with
+    GMTDataArrayAccessor information loaded.
+    """
+    with GMTTempFile(suffix=".nc") as tmpfile:
+        grid = xr.DataArray(
+            data=np.random.rand(2, 2), coords=[[0.1, 0.2], [0.3, 0.4]], dims=("x", "y")
+        )
+        grid.to_netcdf(tmpfile.name)
+        dataarray = load_dataarray(tmpfile.name)
+        assert dataarray.gmt.gtype == 0  # Cartesian grid
+        assert dataarray.gmt.registration == 1  # Pixel registration
+        # this would fail if we used xr.open_dataarray instead of
+        # load_dataarray
+        dataarray.to_netcdf(tmpfile.name)
+
+
+def test_io_load_dataarray_cache():
+    """
+    Check that load_dataarray fails when the cache argument is used.
+    """
+    with pytest.raises(TypeError):
+        _ = load_dataarray("somefile.nc", cache=True)