Merge branch 'wrap-histogram' of github.com:GenericMappingTools/pygmt into wrap-histogram

Author: willschlitzer

.dvc/.gitignore

@@ -0,0 +1,3 @@
+/config.local
+/tmp
+/cache

.dvc/config

@@ -0,0 +1,4 @@
+[core]
+    remote = upstream
+['remote "upstream"']
+    url = https://dagshub.com/GenericMappingTools/pygmt.dvc

.dvcignore

@@ -0,0 +1,3 @@
+# Add patterns of files dvc should ignore, which could improve
+# the performance. Learn more at
+# https://dvc.org/doc/user-guide/dvcignore

.github/codecov.yml

@@ -4,10 +4,15 @@ codecov:
 
 coverage:
   status:
+    project:
+      default:
+        target: auto  # increase overall coverage on each pull request
+        threshold: 0.25%  # Allow the coverage to drop by X%
+        if_not_found: success
+        if_ci_failed: failure
     patch:
       default:
-        target: '90'
-        if_no_uploads: error
+        target: 90%  # >=90% of new changes should be tested
         if_not_found: success
         if_ci_failed: failure
 

.github/release-drafter.yml

@@ -23,9 +23,9 @@ exclude-labels:
 category-template: '### $TITLE'
 change-template: '* $TITLE ([#$NUMBER]($URL))'
 template: |
-  ## Release v$NEXT_PATCH_VERSION (20YY/MM/DD)
+  ## Release v$RESOLVED_VERSION (20YY/MM/DD)
 
-  [![Digital Object Identifier for PyGMT v$NEXT_PATCH_VERSION](https://zenodo.org/badge/DOI/10.5281/zenodo.3781524.svg)](https://doi.org/10.5281/zenodo.3781524)
+  [![Digital Object Identifier for PyGMT v$RESOLVED_VERSION](https://zenodo.org/badge/DOI/10.5281/zenodo.3781524.svg)](https://doi.org/10.5281/zenodo.3781524)
 
   ### Highlights
 

.github/workflows/cache_data.yaml

@@ -19,7 +19,7 @@ jobs:
     steps:
       # Setup Miniconda
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2.0.1
+        uses: conda-incubator/setup-miniconda@v2.1.0
         with:
           channels: conda-forge
           miniconda-version: "latest"
@@ -40,9 +40,11 @@ jobs:
           # The naming scheme may change.
           # DO NOT USE IT IN SCRIPTS.
           gmt which -Ga @N35E135.earth_relief_03s_g.nc
+          # @srtm_tiles.nc is needed for 03s and 01s relief data
+          gmt which -Ga @srtm_tiles.nc
           gmt which -Ga @ridge.txt @Table_5_11.txt @test.dat.nc \
                         @tut_bathy.nc @tut_quakes.ngdc @tut_ship.xyz \
-                        @usgs_quakes_22.txt
+                        @usgs_quakes_22.txt @fractures_06.txt
 
       # Upload the downloaded files as artifacts to GitHub
       - name: Upload artifacts to GitHub

.github/workflows/check-links.yml

@@ -26,7 +26,7 @@ jobs:
         path: documentation
 
     - name: Link Checker
-      uses: lycheeverse/lychee-action@v1.0.4
+      uses: lycheeverse/lychee-action@v1.0.6
       with:
         # 429: Too many requests
         args: >

.github/workflows/ci_docs.yml

@@ -56,7 +56,7 @@ jobs:
 
       # Setup Miniconda
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2.0.1
+        uses: conda-incubator/setup-miniconda@v2.1.0
         with:
           activate-environment: pygmt
           python-version: ${{ matrix.python-version }}
@@ -68,7 +68,7 @@ jobs:
         run: |
           conda install gmt=6.1.1 numpy pandas xarray netCDF4 packaging \
                         ipython make myst-parser \
-                        sphinx sphinx-copybutton sphinx-gallery sphinx_rtd_theme=0.4.3
+                        sphinx sphinx-copybutton sphinx-gallery sphinx_rtd_theme=0.5.1
 
       # Show installed pkg information for postmortem diagnostic
       - name: List installed packages

.github/workflows/ci_tests.yaml

@@ -25,12 +25,12 @@ on:
 
 jobs:
   test:
-    name: ${{ matrix.os }} - Python ${{ matrix.python-version }}
+    name: ${{ matrix.os }} - Python ${{ matrix.python-version }} / NumPy ${{ matrix.numpy-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.7, 3.9]
         os: [ubuntu-latest, macOS-latest, windows-latest]
         # Is it a draft Pull Request (true or false)?
         isDraft:
@@ -41,20 +41,24 @@ jobs:
             isDraft: true
           - os: windows-latest
             isDraft: true
-          - os: ubuntu-latest
-            python-version: 3.7
-            isDraft: true
-          - os: ubuntu-latest
-            python-version: 3.8
-            isDraft: true
+          # - os: ubuntu-latest
+          #   python-version: 3.7
+          #   isDraft: true
+        # Pair Python 3.7 with NumPy 1.17 and Python 3.9 with NumPy 1.20
+        include:
+          - python-version: 3.7
+            numpy-version: '1.17'
+          - python-version: 3.9
+            numpy-version: '1.20'
     defaults:
       run:
         shell: bash -l {0}
 
-    # environmental variables used in coverage
+    # Environment variables used by codecov
     env:
       OS: ${{ matrix.os }}
       PYTHON: ${{ matrix.python-version }}
+      NUMPY: ${{ matrix.numpy-version }}
 
     steps:
       # Cancel previous runs that are not completed
@@ -72,7 +76,7 @@ jobs:
 
       # Setup Miniconda
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2.0.1
+        uses: conda-incubator/setup-miniconda@v2.1.0
         with:
           activate-environment: pygmt
           python-version: ${{ matrix.python-version }}
@@ -82,8 +86,9 @@ jobs:
       # Install GMT and other required dependencies from conda-forge
       - name: Install dependencies
         run: |
-          conda install gmt=6.1.1 numpy pandas xarray netCDF4 packaging \
-                        codecov coverage[toml] ipython make \
+          conda install gmt=6.1.1 numpy=${{ matrix.numpy-version }} \
+                        pandas xarray netCDF4 packaging \
+                        codecov coverage[toml] dvc ipython make \
                         pytest-cov pytest-mpl pytest>=6.0 \
                         sphinx-gallery
 
@@ -109,6 +114,12 @@ jobs:
           touch ~/.gmt/server/gmt_data_server.txt ~/.gmt/server/gmt_hash_server.txt
           ls -lhR ~/.gmt
 
+      # Pull baseline image data from dvc remote (DAGsHub)
+      - name: Pull baseline image data from dvc remote
+        run: |
+          dvc pull
+          ls -lhR pygmt/tests/baseline/
+
       # Install the package that we want to test
       - name: Install the package
         run: |
@@ -129,8 +140,8 @@ jobs:
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1.2.2
+        uses: codecov/codecov-action@v1.3.1
         with:
           file: ./coverage.xml # optional
-          env_vars: OS,PYTHON
+          env_vars: OS,PYTHON,NUMPY
           fail_ci_if_error: false

.github/workflows/ci_tests_dev.yaml

@@ -1,5 +1,4 @@
-# This workflow installs PyGMT dependencies, builds documentation and runs tests on GMT dev version
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+# This workflow installs PyGMT and runs tests on GMT dev version
 
 name: GMT Dev Tests
 
@@ -10,10 +9,13 @@ on:
     types: [ready_for_review]
     paths-ignore:
       - 'doc/**'
+      - 'examples/**'
       - '*.md'
       - '*.json'
       - 'README.rst'
       - 'LICENSE.txt'
+      - '.gitignore'
+      - '.pylintrc'
   repository_dispatch:
     types: [test-gmt-dev-command]
   # Schedule daily tests
@@ -28,7 +30,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: [3.9]
-        os: [ubuntu-20.04, macOS-10.15, windows-latest]
+        os: [ubuntu-latest, macOS-11.0, windows-latest]
         gmt_git_ref: [master]
     defaults:
       run:
@@ -71,17 +73,20 @@ jobs:
 
       # Setup Miniconda
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2.0.1
+        uses: conda-incubator/setup-miniconda@v2.1.0
         with:
+          activate-environment: pygmt
           python-version: ${{ matrix.python-version }}
           channels: conda-forge
           miniconda-version: "latest"
 
-      # Install build dependencies from conda-forge
-      - name: Install build dependencies
+      # Install dependencies from conda-forge
+      - name: Install dependencies
         run: |
-          conda install ninja cmake libblas libcblas liblapack fftw gdal ghostscript \
-                        libnetcdf hdf5 zlib curl pcre ipython pytest pytest-cov pytest-mpl
+          conda install ninja cmake libblas libcblas liblapack fftw gdal \
+                        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
 
       # Build and install latest GMT from GitHub
       - name: Install GMT ${{ matrix.gmt_git_ref }} branch (Linux/macOS)
@@ -113,6 +118,12 @@ jobs:
           touch ~/.gmt/server/gmt_data_server.txt ~/.gmt/server/gmt_hash_server.txt
           ls -lhR ~/.gmt
 
+      # Pull baseline image data from dvc remote (DAGsHub)
+      - name: Pull baseline image data from dvc remote
+        run: |
+          dvc pull
+          ls -lhR pygmt/tests/baseline/
+
       # Install the package that we want to test
       - name: Install the package
         run: |