Merge branch 'master' into hlines-module

.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/ISSUE_TEMPLATE/release_checklist.md

@@ -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/codecov.yml

@@ -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/release-drafter.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/workflows/cache_data.yaml

@@ -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/check-links.yml

@@ -26,12 +26,14 @@ jobs:
  path: documentation
 
  - name: Link Checker
- uses: lycheeverse/[email protected].4
+ uses: lycheeverse/[email protected].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:https://"
  --exclude "^https://docs.generic-mapping-tools.org/latest/%s$"
+ --exclude "https://hackmd.io/@pygmt"
  --verbose
  "repository/**/*.rst"
  "repository/**/*.md"

.github/workflows/ci_docs.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/[email protected]
+ with:
+ access_token: ${{ github.token }}
+
+ # Checkout current git repository
+ - name: Checkout
+ uses: actions/[email protected]
+ with:
+ # fecth all history so that setuptools-scm works
+ fetch-depth: 0
+
+ # Setup Miniconda
+ - name: Setup Miniconda
+ uses: conda-incubator/[email protected]
+ with:
+ activate-environment: pygmt
+ python-version: ${{ matrix.python-version }}
+ channels: conda-forge
+ miniconda-version: "latest"
+
+ # Install GMT and other required dependencies from conda-forge
+ - name: Install dependencies
+ run: |
+ conda install gmt=6.1.1 numpy pandas xarray netCDF4 packaging \
+ ipython make myst-parser \
+ sphinx sphinx-copybutton sphinx-gallery sphinx_rtd_theme=0.5.1
+
+ # Show installed pkg information for postmortem diagnostic
+ - name: List installed packages
+ run: conda list
+
+ # Download cached remote files (artifacts) from GitHub
+ - name: Download remote data from GitHub
+ uses: dawidd6/[email protected]
+ with:
+ workflow: cache_data.yaml
+ workflow_conclusion: success
+ name: gmt-cache
+ path: .gmt
+
+ # Move downloaded files to ~/.gmt directory and list them
+ - name: Move and list downloaded remote files
+ run: |
+ mkdir -p ~/.gmt
+ mv .gmt/* ~/.gmt
+ # Change modification times of the two files, so GMT won't refresh it
+ touch ~/.gmt/server/gmt_data_server.txt ~/.gmt/server/gmt_hash_server.txt
+ ls -lhR ~/.gmt
+
+ # Install the package that we want to test
+ - name: Install the package
+ run: |
+ python setup.py sdist --formats=zip
+ pip install dist/*
+
+ # Build the documentation
+ - name: Build the documentation
+ run: make -C doc clean all
+
+ - name: Checkout the gh-pages branch
+ uses: actions/checkout@28c7f3d2b5162b5ddd3dfd9a45aa55eaf396478b
+ with:
+ ref: gh-pages
+ # Checkout to this folder instead of the current one
+ path: deploy
+ # Download the entire history
+ fetch-depth: 0
+ if: (github.event_name == 'release' || github.event_name == 'push') && (matrix.os == 'ubuntu-latest')
+
+ - name: Push the built HTML to gh-pages
+ run: |
+ # Detect if this is a release or from the master branch
+ if [[ "${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')