Merge branch 'master' into hlines-module

Author: michaelgrund

.codecov.yml

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

.dvc/.gitignore

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

.dvc/config

@@ -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

.dvcignore

@@ -1,24 +1,35 @@
 ---
 name: PyGMT release checklist
 about: Checklist for a new PyGMT release.
-title: Release PyGMT x.x.x
+title: Release PyGMT vX.Y.Z
 labels: maintenance
 assignees: ''
 
 ---
 
-**Release**: [v0.x.x](https://github.com/GenericMappingTools/pygmt/milestones/0.x.x)
+**Release**: [v0.x.x](https://github.com/GenericMappingTools/pygmt/milestones/?)
 **Scheduled Date**: YYYY/MM/DD
+**Pull request due date**: YYYY/MM/DD
+
+**Priority PRs/issues to complete prior to release**
+- [ ] Wrap X ()
+- [ ] Wrap Y ()
 
 **Before release**:
 - [ ] Reserve a DOI on [Zenodo](https://zenodo.org) by clicking on "New Version"
-- [ ] Update Changelog
-- [ ] Add a new entry in `doc/_static/version_switch.js` for documentation switcher
-- [ ] Update citation information https://github.com/GenericMappingTools/pygmt#citing-pygmt
+- [ ] Finish up 'Changelog entry for v0.x.x' Pull Request:
+  - [ ] Add a new entry in `doc/_static/version_switch.js` for documentation switcher
+  - [ ] Update citation information https://github.com/GenericMappingTools/pygmt#citing-pygmt
+  - [ ] Add the documentation link https://github.com/GenericMappingTools/pygmt#documentation-for-other-versions
+  - [ ] Add compatibility information https://github.com/GenericMappingTools/pygmt#compatibility-with-python-and-gmt-versions
+  - [ ] Copy draft changelog from Release Drafter and edit it to look nice
 
 **Release**:
-- [ ] Go to [GitHub Release](https://github.com/GenericMappingTools/pygmt/releases) and make a release, this will automatically create a tag too
-- [ ] Manually upload the pygmt-vX.Y.Z.zip file to https://zenodo.org/deposit, make sure you file it under the correct reserved DOI
+- [ ] At the [PyGMT release page on GitHub](https://github.com/GenericMappingTools/pygmt/releases):
+  - [ ] Edit the draft release notes with the finalized changelog
+  - [ ] Set the tag version and release title to vX.Y.Z
+  - [ ] Make a release by clicking the 'Publish Release' button, this will automatically create a tag too
+- [ ] Manually upload the pygmt-vX.Y.Z.zip file to https://zenodo.org/deposit, ensure that it is filed under the correct reserved DOI
 
 **After release**:
 - [ ] Update conda-forge [pygmt-feedstock](https://github.com/conda-forge/pygmt-feedstock) [Usually done automatically by conda-forge's bot]
@@ -27,7 +38,7 @@ assignees: ''
   - [ ] GMT [forum](https://forum.generic-mapping-tools.org/c/news/)
   - [ ] [Major/Minor releases only] GMT [website](https://github.com/GenericMappingTools/website) (News)
   - [ ] [ResearchGate](https://www.researchgate.net/project/PyGMT-A-Python-interface-for-the-Generic-Mapping-Tools)
-
+  - [ ] [Twitter](https://twitter.com/gmt_dev)
 ---
 
 - [ ] Party :tada: (don't tick before all other checkboxes are ticked!)

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -0,0 +1,19 @@
+codecov:
+  notify:
+    require_ci_to_pass: no
+
+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%  # >=90% of new changes should be tested
+        if_not_found: success
+        if_ci_failed: failure
+
+comment: off

.github/codecov.yml

@@ -1,5 +1,10 @@
-name-template: 'v$NEXT_PATCH_VERSION'
-tag-template: 'v$NEXT_PATCH_VERSION'
+name-template: 'v$RESOLVED_VERSION'
+tag-template: 'v$RESOLVED_VERSION'
+version-resolver:
+  minor:
+    labels:
+      - 'feature'
+  default: patch
 categories:
   - title: 'New Features'
     label: 'feature'
@@ -18,9 +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/release-drafter.yml

@@ -12,31 +12,39 @@ jobs:
   gmt_cache:
     name: Cache GMT artifacts
     runs-on: macOS-latest
+    defaults:
+      run:
+        shell: bash -l {0}
 
     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"
 
       # Install GMT
       - name: Install GMT
-        shell: bash -l {0}
         run: conda install -c conda-forge gmt=6.1.1
 
       # Download remote files
       - name: Download remote data
-        shell: bash -l {0}
         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 \
                         @earth_relief_05m_p @earth_relief_05m_g
+          # Download one tile of the 03s srtm data.
+          # @N35E135.earth_relief_03s_g.nc is for internal use only.
+          # 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/cache_data.yaml

@@ -26,12 +26,14 @@ 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: >
           --accept 429
+          --exclude "^https://doi.org/10.5281/zenodo$"
           --exclude "^https://zenodo.org/badge/DOI/$"
+          --exclude "^https://zenodo.org/badge/DOI/10.5281/zenodo$"
           --exclude "^https://github.com/GenericMappingTools/pygmt/pull/[0-9]*$"
           --exclude "^https://github.com/GenericMappingTools/pygmt/issues/[0-9]*$"
           --exclude "^https://www.generic-mapping-tools.org/_static/gmt-logo.png/$"
@@ -40,6 +42,7 @@ jobs:
           --exclude "^git"
           --exclude "^file://"
           --exclude "^https://docs.generic-mapping-tools.org/latest/%s$"
+          --exclude "https://hackmd.io/@pygmt"
           --verbose
           "repository/**/*.rst"
           "repository/**/*.md"

.github/workflows/check-links.yml

@@ -0,0 +1,164 @@
+# This workflow installs PyGMT, builds and deploys documentation
+
+name: Docs
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    types: [opened, reopened, synchronize, ready_for_review]
+    paths-ignore:
+      - 'pygmt/tests/**'
+      - '*.md'
+      - '*.json'
+      - 'LICENSE.txt'
+      - '.gitignore'
+      - '.pylintrc'
+  release:
+    types:
+      - published
+
+jobs:
+  docs:
+    name: ${{ matrix.os }} - Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.9]
+        os: [ubuntu-latest, macOS-latest, windows-latest]
+        # Is it a draft Pull Request (true or false)?
+        isDraft:
+          - ${{ github.event.pull_request.draft }}
+        # Only run one job (Ubuntu + Python 3.9) for draft PRs
+        exclude:
+          - os: macOS-latest
+            isDraft: true
+          - os: windows-latest
+            isDraft: true
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      # Cancel previous runs that are not completed
+      - name: Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.8.0
+        with:
+          access_token: ${{ github.token }}
+
+      # Checkout current git repository
+      - name: Checkout
+        uses: actions/checkout@v2.3.4
+        with:
+          # fecth all history so that setuptools-scm works
+          fetch-depth: 0
+
+      # Setup Miniconda
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v2.1.0
+        with:
+          activate-environment: pygmt
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge
+          miniconda-version: "latest"
+
+      # Install GMT and other required dependencies from conda-forge
+      - name: Install dependencies
+        run: |
+          conda install gmt=6.1.1 numpy pandas xarray netCDF4 packaging \
+                        ipython make myst-parser \
+                        sphinx sphinx-copybutton sphinx-gallery sphinx_rtd_theme=0.5.1
+
+      # Show installed pkg information for postmortem diagnostic
+      - name: List installed packages
+        run: conda list
+
+      # Download cached remote files (artifacts) from GitHub
+      - name: Download remote data from GitHub
+        uses: dawidd6/action-download-artifact@v2.13.0
+        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: |
+          python setup.py sdist --formats=zip
+          pip install dist/*
+
+      # Build the documentation
+      - name: Build the documentation
+        run: make -C doc clean all
+
+      - name: Checkout the gh-pages branch
+        uses: actions/checkout@28c7f3d2b5162b5ddd3dfd9a45aa55eaf396478b
+        with:
+          ref: gh-pages
+          # Checkout to this folder instead of the current one
+          path: deploy
+          # Download the entire history
+          fetch-depth: 0
+        if: (github.event_name == 'release' || github.event_name == 'push') && (matrix.os == 'ubuntu-latest')
+
+      - name: Push the built HTML to gh-pages
+        run: |
+          # Detect if this is a release or from the master branch
+          if [[ "${GITHUB_EVENT_NAME}" == "release" ]]; then
+              # Get the tag name without the "refs/tags/" part
+              version="${GITHUB_REF#refs/*/}"
+          else
+              version=dev
+          fi
+          echo "Deploying version: $version"
+          # Make the new commit message. Needs to happen before cd into deploy
+          # to get the right commit hash.
+          message="Deploy $version from $(git rev-parse --short HEAD)"
+          cd deploy
+          # Need to have this file so that Github doesn't try to run Jekyll
+          touch .nojekyll
+          # Delete all the files and replace with our new  set
+          echo -e "\nRemoving old files from previous builds of ${version}:"
+          rm -rvf ${version}
+          echo -e "\nCopying HTML files to ${version}:"
+          cp -Rvf ../doc/_build/html/ ${version}/
+          # If this is a new release, update the link from /latest to it
+          if [[ "${version}" != "dev" ]]; then
+              echo -e "\nSetup link from ${version} to 'latest'."
+              rm -f latest
+              ln -sf ${version} latest
+          fi
+          # Stage the commit
+          git add -A .
+          echo -e "\nChanges to be applied:"
+          git status
+          # Configure git to be the GitHub Actions account
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git config user.name "github-actions[bot]"
+          # If this is a dev build and the last commit was from a dev build
+          # (detect if "dev" was in the previous commit message), reuse the
+          # same commit
+          if [[ "${version}" == "dev" && `git log -1 --format='%s'` == *"dev"* ]]; then
+              echo -e "\nAmending last commit:"
+              git commit --amend --reset-author -m "$message"
+          else
+              echo -e "\nMaking a new commit:"
+              git commit -m "$message"
+          fi
+          # Make the push quiet just in case there is anything that could leak
+          # sensitive information.
+          echo -e "\nPushing changes to gh-pages."
+          git push -fq origin gh-pages 2>&1 >/dev/null
+          echo -e "\nFinished uploading generated files."
+        if: (github.event_name == 'release' || github.event_name == 'push') && (matrix.os == 'ubuntu-latest')