Merge branch 'main' into grdhisteq

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 \
-                        ipython make myst-parser \
+          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

@@ -44,11 +44,11 @@ jobs:
           # - os: ubuntu-latest
           #   python-version: 3.7
           #   isDraft: true
-        # Pair Python 3.7 with NumPy 1.17 and Python 3.9 with NumPy 1.21
+        # Pair Python 3.7 with NumPy 1.18 and Python 3.9 with NumPy 1.21
         # Only install optional packages on Python 3.9/NumPy 1.21
         include:
           - python-version: 3.7
-            numpy-version: '1.17'
+            numpy-version: '1.18'
             optional-packages: ''
           - python-version: 3.9
             numpy-version: '1.21'
@@ -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
@@ -144,7 +148,7 @@ jobs:
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v2.0.2
+        uses: codecov/codecov-action@v2.1.0
         with:
           file: ./coverage.xml # optional
           env_vars: OS,PYTHON,NUMPY

.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

.github/workflows/dvc-diff.yml

@@ -22,7 +22,7 @@ jobs:
       uses: iterative/setup-dvc@v1.0.3
 
     - name: Setup continuous machine learning (CML)
-      uses: iterative/setup-cml@v1.0.3
+      uses: iterative/setup-cml@v1.1.0
 
     - name: Pull image data from cloud storage
       run: dvc pull --remote upstream
@@ -95,7 +95,7 @@ jobs:
         echo ::set-output name=report::$report
 
     - name: Find comment with image diff report
-      uses: peter-evans/find-comment@v1.2.0
+      uses: peter-evans/find-comment@v1.3.0
       id: fc
       with:
         issue-number: ${{ github.event.pull_request.number }}

Makefile

@@ -8,7 +8,7 @@ BLACK_FILES=$(PROJECT) setup.py doc/conf.py examples
 BLACKDOC_OPTIONS=--line-length 79
 DOCFORMATTER_FILES=$(PROJECT) setup.py doc/conf.py examples
 DOCFORMATTER_OPTIONS=--recursive --pre-summary-newline --make-summary-multi-line --wrap-summaries 79 --wrap-descriptions 79
-FLAKE8_FILES=$(PROJECT) setup.py doc/conf.py
+FLAKE8_FILES=$(PROJECT) setup.py doc/conf.py examples
 LINT_FILES=$(PROJECT) setup.py doc/conf.py
 
 help:

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
@@ -228,16 +228,21 @@ Compatibility with GMT/Python/NumPy versions
       - GMT
       - Python
       - Numpy
+    * - `v0.5.0 <https://github.com/GenericMappingTools/pygmt/milestone/8>`_ (upcoming release)
+      - `Dev Documentation <https://www.pygmt.org/dev>`_ (reflects `main branch <https://github.com/GenericMappingTools/pygmt>`_)
+      - >=6.2.0
+      - >=3.7
+      - >=1.18
     * - `v0.4.1 <https://github.com/GenericMappingTools/pygmt/releases/tag/v0.4.1>`_ (latest release)
       - `v0.4.1 Documentation <https://www.pygmt.org/v0.4.1>`_
       - >=6.2.0
       - >=3.7
-      - >=1.17.0
+      - >=1.17
     * - `v0.4.0 <https://github.com/GenericMappingTools/pygmt/releases/tag/v0.4.0>`_
       - `v0.4.0 Documentation <https://www.pygmt.org/v0.4.0>`_
       - >=6.2.0
       - >=3.7
-      - >=1.17.0
+      - >=1.17
     * - `v0.3.1 <https://github.com/GenericMappingTools/pygmt/releases/tag/v0.3.1>`_
       - `v0.3.1 Documentation <https://www.pygmt.org/v0.3.1>`_
       - >=6.1.1
@@ -273,6 +278,3 @@ Compatibility with GMT/Python/NumPy versions
       - >=6.0.0
       - 3.6 - 3.8
       -
-
-The unstable development documentation, which reflects the `main branch <https://github.com/GenericMappingTools/pygmt>`_
-on GitHub, can be found at https://www.pygmt.org/dev/.

doc/api/index.rst

@@ -81,6 +81,7 @@ Operations on tabular data:
 
     blockmean
     blockmedian
+    blockmode
     surface
 
 Operations on grids:
@@ -92,11 +93,13 @@ Operations on grids:
     grdcut
     grdfill
     grdfilter
+    grdgradient
     grdhisteq
     grdlandmask
-    grdgradient
+    grdproject
     grdsample
     grdtrack
+    sphdistance
     xyz2grd
 
 Crossover analysis with x2sys:
@@ -107,6 +110,14 @@ Crossover analysis with x2sys:
     x2sys_init
     x2sys_cross
 
+Input/output
+------------
+
+.. autosummary::
+    :toctree: generated
+
+    load_dataarray
+
 GMT Defaults
 ------------
 
@@ -162,6 +173,7 @@ and store them in the GMT cache folder.
     datasets.load_sample_bathymetry
     datasets.load_usgs_quakes
     datasets.load_fractures_compilation
+    datasets.load_hotspots
 
 .. automodule:: pygmt.exceptions
 

doc/conf.py

@@ -127,11 +127,9 @@
 release = __version__
 
 # These enable substitutions using |variable| in the rst files
-rst_epilog = """
+rst_epilog = f"""
 .. |year| replace:: {year}
-""".format(
-    year=year
-)
+"""
 
 html_last_updated_fmt = "%b %d, %Y"
 html_title = "PyGMT"

doc/install.rst

@@ -80,7 +80,7 @@ Dependencies
 
 PyGMT requires the following libraries to be installed:
 
-* `numpy <https://numpy.org>`__ (>= 1.17)
+* `numpy <https://numpy.org>`__ (>= 1.18)
 * `pandas <https://pandas.pydata.org>`__
 * `xarray <https://xarray.pydata.org>`__
 * `netCDF4 <https://unidata.github.io/netcdf4-python>`__