Merge branch 'master' into gmt-master-gh-actions

Author: weiji14

.azure-pipelines.yml

@@ -63,194 +63,3 @@ jobs:
       make lint
     displayName: Linting (pylint)
     condition: succeededOrFailed()
-
-
-# Mac
-########################################################################################
-- job:
-  displayName: 'Mac'
-
-  pool:
-    vmImage: 'macOS-10.14'
-
-  variables:
-    CONDA_REQUIREMENTS: requirements.txt
-    CONDA_REQUIREMENTS_DEV: requirements-dev.txt
-    CONDA_INSTALL_EXTRA: "codecov gmt=6.0.0"
-
-  strategy:
-    matrix:
-      Python38:
-        python.version: '3.8'
-        PYTHON: '3.8'
-      Python37:
-        python.version: '3.7'
-        PYTHON: '3.7'
-      Python36:
-        python.version: '3.6'
-        PYTHON: '3.6'
-
-  steps:
-
-  - bash: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
-
-  # Get the Fatiando CI scripts
-  - bash: git clone --branch=1.2.0 --depth=1 https://github.com/fatiando/continuous-integration.git
-    displayName: Fetch the Fatiando CI scripts
-
-  # On Hosted macOS, the agent user doesn't have ownership of Miniconda's installation
-  # directory. We need to take ownership if we want to update conda or install packages
-  # globally.
-  - bash: sudo chown -R $USER $CONDA
-    displayName: Take ownership of conda installation
-
-  # Setup dependencies and build a conda environment
-  - bash: source continuous-integration/azure/setup-miniconda.sh
-    displayName: Setup Miniconda
-
-  # Show installed pkg information for postmortem diagnostic
-  - bash: |
-      set -x -e
-      source activate testing
-      conda list
-    displayName: List installed packages
-
-  # Cache the ${HOME}/.gmt directory, for docs and testing
-  - task: Cache@2
-    inputs:
-      key: cachedata | 20200524
-      path: $(HOME)/.gmt
-      cacheHitVar: CACHE_CACHEDATA_RESTORED
-    displayName: Cache GMT remote data for testing
-
-  # Download remote files, if not already cached
-  - bash: |
-      set -x -e
-      source activate testing
-      gmt which -Gu @earth_relief_10m @earth_relief_01d @ridge.txt @Table_5_11.txt @tut_bathy.nc @tut_quakes.ngdc @tut_ship.xyz
-    displayName: Download remote data
-    condition: ne(variables['CACHE_CACHEDATA_RESTORED'], true)
-
-  # Install the package
-  - bash: |
-      set -x -e
-      source activate testing
-      python setup.py bdist_wheel
-      pip install dist/*
-    displayName: Install the package
-
-  # Run the tests
-  - bash: |
-      set -x -e
-      source activate testing
-      make test PYTEST_EXTRA="-r P"
-    displayName: Test
-
-  # Build the documentation
-  - bash: |
-      set -x -e
-      source activate testing
-      make -C doc clean all
-    displayName: Build the documentation
-
-  # Upload test coverage if there were no failures
-  - bash: |
-      set -x -e
-      source activate testing
-      coverage xml
-      echo "Uploading coverage to Codecov"
-      codecov -e PYTHON AGENT_OS
-    env:
-      CODECOV_TOKEN: $(codecov.token)
-    condition: succeeded()
-    displayName: Upload coverage
-
-
-# Windows
-########################################################################################
-- job:
-  displayName: 'Windows'
-
-  pool:
-    vmImage: 'vs2017-win2016'
-
-  variables:
-    CONDA_REQUIREMENTS: requirements.txt
-    CONDA_REQUIREMENTS_DEV: requirements-dev.txt
-    CONDA_INSTALL_EXTRA: "codecov gmt=6.0.0"
-
-  strategy:
-    matrix:
-      Python38:
-        python.version: '3.8'
-        PYTHON: '3.8'
-      Python37:
-        python.version: '3.7'
-        PYTHON: '3.7'
-      Python36:
-        python.version: '3.6'
-        PYTHON: '3.6'
-
-  steps:
-
-  - powershell: Write-Host "##vso[task.prependpath]$env:CONDA\Scripts"
-    displayName: Add conda to PATH
-
-  # Get the Fatiando CI scripts
-  - script: git clone --branch=1.2.0 --depth=1 https://github.com/fatiando/continuous-integration.git
-    displayName: Fetch the Fatiando CI scripts
-
-  # Setup dependencies and build a conda environment
-  - script: continuous-integration/azure/setup-miniconda.bat
-    displayName: Setup Miniconda
-
-  # Show installed pkg information for postmortem diagnostic
-  - bash: |
-      set -x -e
-      source activate testing
-      conda list
-    displayName: List installed packages
-
-  # Cache the ${HOME}/.gmt directory, for docs and testing
-  - task: Cache@2
-    inputs:
-      key: cachedata | 20200524
-      path: $(HOMEPATH)/.gmt
-      cacheHitVar: CACHE_CACHEDATA_RESTORED
-    displayName: Cache GMT remote data for testing
-
-  # Download remote files, if not already cached
-  - bash: |
-      set -x -e
-      source activate testing
-      gmt which -Gu @earth_relief_10m @earth_relief_01d @ridge.txt @Table_5_11.txt @tut_bathy.nc @tut_quakes.ngdc @tut_ship.xyz
-    displayName: Download remote data
-    condition: ne(variables['CACHE_CACHEDATA_RESTORED'], true)
-
-  # Install the package that we want to test
-  - bash: |
-      set -x -e
-      source activate testing
-      python setup.py sdist --formats=zip
-      pip install dist/*
-    displayName: Install the package
-
-  # Run the tests
-  - bash: |
-      set -x -e
-      source activate testing
-      make test PYTEST_EXTRA="-r P"
-    displayName: Test
-
-  # Upload test coverage if there were no failures
-  - bash: |
-      set -x -e
-      source activate testing
-      coverage report -m
-      coverage xml
-      codecov -e PYTHON AGENT_OS
-    env:
-      CODECOV_TOKEN: $(codecov.token)
-    condition: succeeded()
-    displayName: Upload coverage

.github/release-drafter.yml

@@ -15,7 +15,7 @@ categories:
     label: 'deprecation'
 exclude-labels:
   - 'skip-changelog'
-change-template: '* $TITLE (#$NUMBER) @$AUTHOR'
+change-template: '* $TITLE (#$NUMBER)'
 template: |
   [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3781524.svg)](https://doi.org/10.5281/zenodo.3781524)
 
@@ -24,3 +24,7 @@ template: |
   *
 
   $CHANGES
+
+  ## Contributors
+
+  $CONTRIBUTORS

.github/workflows/ci_tests.yaml

@@ -1,4 +1,4 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# This workflow installs PyGMT dependencies, build documentation and run tests
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
 name: Tests
@@ -7,7 +7,6 @@ on:
   push:
     branches: [ master ]
   pull_request:
-    branches: [ master ]
   # Schedule daily tests
   schedule:
     - cron: '0 0 * * *'
@@ -19,21 +18,25 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7]
-        os: [ubuntu-latest, macOS-latest, windows-latest]
+        python-version: [3.6, 3.7, 3.8]
+        #os: [ubuntu-latest, macOS-latest, windows-latest]
+        os: [ubuntu-latest, macOS-latest]
+    # environmental variables used in coverage
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python-version }}
 
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected]
-
-      # Workaround for versioneer, see https://github.com/warner/python-versioneer/issues/206
-      - name: Fetch all history for all tags and branches
-        run: git fetch --prune --unshallow
+        uses: actions/[email protected]
+        with:
+          # fecth all history so that versioneer works
+          fetch-depth: 0
 
       # Setup Miniconda
       - name: Setup Miniconda
-        uses: goanpeca/setup-miniconda@v1.3.1
+        uses: goanpeca/setup-miniconda@v1.6.0
         with:
           python-version: ${{ matrix.python-version }}
           channels: conda-forge
@@ -45,8 +48,9 @@ jobs:
           requirements_file=full-conda-requirements.txt
           cat requirements.txt requirements-dev.txt > $requirements_file
           cat << EOF >> $requirements_file
-          gmt=6.0.0
+          gmt=6.1.0
           make
+          codecov
           EOF
           conda install --yes --file $requirements_file
 
@@ -63,28 +67,30 @@ jobs:
           path: |
             ~/.gmt/cache
             ~/.gmt/server
-          key: cache-gmt-${{ runner.os }}-20200609
-          restore-keys: cache-gmt-refs/heads/master-
+          key: cache-gmt-${{ runner.os }}-${{ github.ref }}-20200711
+          restore-keys: cache-gmt-${{ runner.os }}-refs/heads/master-
 
       # Workaround for the timeouts of 'gmt which' on Linux and Windows
       - name: Download remote data using wget (Linux & Windows)
         shell: bash -l {0}
         run: |
           if [ "$RUNNER_OS" == "Windows" ]; then choco install wget; fi  # install wget on Windows
-          mkdir ~/.gmt ~/.gmt/cache ~/.gmt/server
+          mkdir -p ~/.gmt ~/.gmt/cache ~/.gmt/server/earth/earth_relief/
           wget --no-check-certificate https://oceania.generic-mapping-tools.org/gmt_hash_server.txt -P ~/.gmt/server/
-          for data in earth_relief_01d.grd earth_relief_30m.grd earth_relief_10m.grd; do
-            wget --no-check-certificate https://oceania.generic-mapping-tools.org/${data} -P ~/.gmt/server/
+          for data in earth_relief_01d_p.grd earth_relief_01d_g.grd earth_relief_30m_p.grd earth_relief_30m_g.grd earth_relief_10m_p.grd earth_relief_10m_g.grd; do
+            wget --no-check-certificate https://oceania.generic-mapping-tools.org/server/earth/earth_relief/${data} -P ~/.gmt/server/earth/earth_relief/
           done
-          for data in ridge.txt Table_5_11.txt tut_bathy.nc tut_quakes.ngdc tut_ship.xyz usgs_quakes_22.txt; do
+          for data in ridge.txt Table_5_11.txt test.dat.nc tut_bathy.nc tut_quakes.ngdc tut_ship.xyz usgs_quakes_22.txt; do
             wget --no-check-certificate https://oceania.generic-mapping-tools.org/cache/${data} -P ~/.gmt/cache/
           done
         if: steps.cache.outputs.cache-hit != 'true' && runner.os != 'macOS'
 
       # Download remote files, if not already cached
       - name: Download remote data (macOS)
         shell: bash -l {0}
-        run: gmt which -Gu @earth_relief_01d @earth_relief_30m @earth_relief_10m @ridge.txt @Table_5_11.txt @tut_bathy.nc @tut_quakes.ngdc @tut_ship.xyz @usgs_quakes_22.txt
+        run: |
+          gmt which -Ga @earth_relief_10m_p @earth_relief_10m_g @earth_relief_30m_p @earth_relief_30m_g @earth_relief_01d_p @earth_relief_01d_g
+          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
         if: steps.cache.outputs.cache-hit != 'true' && runner.os == 'macOS'
 
       # Install the package that we want to test
@@ -99,6 +105,19 @@ jobs:
         shell: bash -l {0}
         run: make test PYTEST_EXTRA="-r P"
 
+      # Build the documentation
+      #- name: Build the documentation
+      #  shell: bash -l {0}
+      #  run: make -C doc clean all
+
+      # Upload coverage to Codecov
+      - name: Upload coverage to Codecov
+        uses: codecov/[email protected]
+        with:
+          file: ./coverage.xml # optional
+          env_vars: OS,PYTHON
+          fail_ci_if_error: true
+
   test_gmt_master:
     name: GMT master - ${{ matrix.os }} - Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}

.gitignore

@@ -12,6 +12,7 @@ MANIFEST
 .ipynb_checkpoints/
 .vscode/
 tmp-test-dir-with-unique-name/
+coverage.xml
 htmlcov
 build/
 dist/

.travis.yml

@@ -26,7 +26,7 @@ env:
         # The file with the listed requirements to be installed by conda
         - CONDA_REQUIREMENTS=requirements.txt
         - CONDA_REQUIREMENTS_DEV=requirements-dev.txt
-        - CONDA_INSTALL_EXTRA="codecov twine gmt=6.0.0"
+        - CONDA_INSTALL_EXTRA="codecov twine gmt=6.1.0"
         # These variables control which actions are performed in a build
         - DEPLOY=false
 
@@ -70,7 +70,6 @@ script:
 # Things to do if the build is successful
 after_success:
     # Upload coverage information
-    - coverage xml
     - codecov -e PYTHON
 
 deploy:

MAINTENANCE.md

@@ -100,8 +100,8 @@ publishing the actual release notes at https://www.pygmt.org/latest/changes.html
 
 2. Edit the changes list to remove any trivial changes (updates to the README, typo
    fixes, CI configuration, etc).
-3. Replace the PR number in the commit titles with a link to the Github PR page. In Vim,
-   use `` %s$#\([0-9]\+\)$`#\1 <https://github.com/GenericMappingTools/pygmt/pull/\1>`__$g ``
+3. Replace the PR number in the commit titles with a link to the Github PR page.
+   Use ``sed -i.bak -E 's$\(#([0-9]*)\)$(`#\1 <https://github.com/GenericMappingTools/pygmt/pull/\1>`__)$g' changes.rst``
    to make the change automatically.
 4. Copy the remaining changes to `doc/changes.rst` under a new section for the
    intended release.

Makefile

@@ -1,7 +1,10 @@
 # Build, package, test, and clean
 PROJECT=pygmt
 TESTDIR=tmp-test-dir-with-unique-name
-PYTEST_ARGS=--cov-config=../.coveragerc --cov-report=term-missing --cov=$(PROJECT) --doctest-modules -v --mpl --mpl-results-path=results --pyargs
+PYTEST_ARGS=--cov=$(PROJECT) --cov-config=../.coveragerc \
+			--cov-report=term-missing --cov-report=xml --cov-report=html \
+			--doctest-modules -v --mpl --mpl-results-path=results \
+			--pyargs ${PYTEST_EXTRA}
 BLACK_FILES=$(PROJECT) setup.py doc/conf.py examples
 FLAKE8_FILES=$(PROJECT) setup.py
 LINT_FILES=$(PROJECT) setup.py
@@ -27,7 +30,8 @@ test:
 	@cd $(TESTDIR); python -c "import $(PROJECT); $(PROJECT).show_versions()"
 	@echo ""
 	cd $(TESTDIR); pytest $(PYTEST_ARGS) $(PROJECT)
-	cp $(TESTDIR)/.coverage* . && coverage html
+	cp $(TESTDIR)/coverage.xml .
+	cp -r $(TESTDIR)/htmlcov .
 	rm -r $(TESTDIR)
 
 format:
@@ -43,6 +47,6 @@ lint:
 clean:
 	find . -name "*.pyc" -exec rm -v {} \;
 	find . -name "*~" -exec rm -v {} \;
-	rm -rvf build dist MANIFEST *.egg-info __pycache__ .coverage .cache htmlcov
+	rm -rvf build dist MANIFEST *.egg-info __pycache__ .coverage .cache htmlcov coverage.xml
 	rm -rvf $(TESTDIR)
 	rm -rvf baseline