Merge branch 'master' into check-links

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,6 +1,9 @@
 ---
 name: Bug report
 about: Report a problem/bug to help us improve
+title: ''
+labels: bug
+assignees: ''
 
 ---
 

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: true
+contact_links:
+  - name: GMT Community Forum
+    url: https://forum.generic-mapping-tools.org/c/questions/pygmt-q-a
+    about: Please ask questions here or find answers to common problems.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,6 +1,9 @@
 ---
 name: Feature request
 about: Request the addition of a new feature/functionality
+title: ''
+labels: feature request
+assignees: ''
 
 ---
 

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -1,8 +1,8 @@
 ---
 name: PyGMT release checklist
 about: Checklist for a new PyGMT release.
-title: 'Release PyGMT x.x.x'
-labels: 'maintenance'
+title: Release PyGMT x.x.x
+labels: maintenance
 assignees: ''
 
 ---

.github/PULL_REQUEST_TEMPLATE.md

@@ -16,6 +16,10 @@ Fixes #
 - [ ] Write detailed docstrings for all functions/methods.
 - [ ] If adding new functionality, add an example to docstrings or tutorials.
 
-**Notes**
+**Slash Commands**
 
-- You can write `/format` in the first line of a comment to lint the code automatically
+You can write slash commands (`/command`) in the first line of a comment to perform
+specific operations. Supported slash commands are:
+
+- `/format`: automatically format and lint the code
+- `/test-gmt-dev`: run full tests on the latest GMT development version

.github/workflows/cache_data.yaml

@@ -33,7 +33,7 @@ jobs:
           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_g
+                        @earth_relief_05m_p @earth_relief_05m_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

.github/workflows/ci_tests.yaml

@@ -7,6 +7,12 @@ on:
   push:
     branches: [ master ]
   pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - '*.md'
+      - '*.json'
+      - 'README.rst'
+      - 'LICENSE.txt'
   release:
     types:
       - published
@@ -15,38 +21,6 @@ on:
     - cron: '0 0 * * *'
 
 jobs:
-  style_check:
-    name: Style Checks
-    runs-on: ubuntu-latest
-
-    steps:
-      # Checkout current git repository
-      - name: Checkout
-        uses: actions/checkout@v2.3.1
-
-      # Setup Miniconda
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-
-      - name: Install packages
-        run: |
-          pip install black blackdoc flake8 pylint isort
-          sudo apt-get install dos2unix
-
-      - name: Formatting check (black and flake8)
-        run: make check
-
-      - name: Linting (pylint)
-        run: make lint
-
-      - name: Ensure files use UNIX line breaks and have 644 permission
-        run: |
-          find . -type f -not -path '*/\.git/*' -exec grep -Iq . {} \; -exec dos2unix --quiet {} \;
-          find . -type f -not -path '*/\.git/*' -exec grep -Iq . {} \; -exec chmod 644 {} \;
-          if [[ $(git ls-files -m) ]]; then git --no-pager diff HEAD; exit 1; fi
-
   test:
     name: ${{ matrix.os }} - Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}

.github/workflows/ci_tests_dev.yaml

@@ -1,13 +1,21 @@
-# This workflow installs PyGMT dependencies, builds documentation and runs tests on GMT latest
+# 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
 
-name: GMT Latest Tests
+name: GMT Dev Tests
 
 on:
   # push:
   #   branches: [ master ]
   pull_request:
-    types: [review_requested, ready_for_review]
+    types: [ready_for_review]
+    paths-ignore:
+      - 'doc/**'
+      - '*.md'
+      - '*.json'
+      - 'README.rst'
+      - 'LICENSE.txt'
+  repository_dispatch:
+    types: [test-gmt-dev-command]
   # Schedule daily tests
   schedule:
     - cron: '0 0 * * *'
@@ -36,10 +44,31 @@ jobs:
       # Checkout current git repository
       - name: Checkout
         uses: actions/checkout@v2.3.4
+        if: github.event_name != 'repository_dispatch'
         with:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
 
+      # Generate token from GenericMappingTools bot
+      - name: Generate token from GenericMappingTools bot
+        uses: tibdex/github-app-token@v1
+        if: github.event_name == 'repository_dispatch'
+        id: generate-token
+        with:
+          app_id: ${{ secrets.APP_ID }}
+          private_key: ${{ secrets.APP_PRIVATE_KEY }}
+
+      # Checkout the pull request branch
+      - name: Checkout
+        uses: actions/checkout@v2
+        if: github.event_name == 'repository_dispatch'
+        with:
+          token: ${{ steps.generate-token.outputs.token }}
+          repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
+          ref: ${{ github.event.client_payload.pull_request.head.ref }}
+          # fecth all history so that setuptools-scm works
+          fetch-depth: 0
+
       # Setup Miniconda
       - name: Setup Miniconda
         uses: conda-incubator/setup-miniconda@v2.0.0
@@ -106,3 +135,12 @@ jobs:
         with:
           name: artifact-GMT-${{ matrix.gmt_git_ref }}-${{ runner.os }}
           path: tmp-test-dir-with-unique-name
+
+      - name: Add reaction
+        uses: peter-evans/create-or-update-comment@v1
+        if: github.event_name == 'repository_dispatch'
+        with:
+          token: ${{ steps.generate-token.outputs.token }}
+          repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
+          comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
+          reaction-type: hooray

.github/workflows/format-command.yml

@@ -26,7 +26,7 @@ jobs:
       # Install formatting tools
       - name: Install formatting tools
         run: |
-          pip install black blackdoc flake8 isort
+          pip install black blackdoc docformatter flake8 isort
           sudo apt-get install dos2unix
 
       # Run "make format" and commit the change to the PR branch

.github/workflows/slash-command-dispatch.yml

@@ -21,5 +21,6 @@ jobs:
           token: ${{ steps.generate-token.outputs.token }}
           commands: |
             format
+            test-gmt-dev
           issue-type: pull-request
           permission: none

.github/workflows/style_checks.yaml

@@ -0,0 +1,42 @@
+name: Style Checks
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+  # Schedule daily tests
+  schedule:
+    - cron: '0 0 * * *'
+
+jobs:
+  style_check:
+    name: Style Checks
+    runs-on: ubuntu-latest
+
+    steps:
+      # Checkout current git repository
+      - name: Checkout
+        uses: actions/checkout@v2.3.4
+
+      # Setup Miniconda
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+
+      - name: Install packages
+        run: |
+          pip install black blackdoc docformatter flake8 pylint isort
+          sudo apt-get install dos2unix
+
+      - name: Formatting check (black, blackdoc, docformatter, flake8 and isort)
+        run: make check
+
+      - name: Linting (pylint)
+        run: make lint
+
+      - name: Ensure files use UNIX line breaks and have 644 permission
+        run: |
+          find . -type f -not -path '*/\.git/*' -exec grep -Iq . {} \; -exec dos2unix --quiet {} \;
+          find . -type f -not -path '*/\.git/*' -exec grep -Iq . {} \; -exec chmod 644 {} \;
+          if [[ $(git ls-files -m) ]]; then git --no-pager diff HEAD; exit 1; fi

.pylintrc

@@ -293,7 +293,7 @@ indent-string='    '
 max-line-length=100
 
 # Maximum number of lines in a module.
-max-module-lines=2000
+max-module-lines=3000
 
 # List of optional constructs for which whitespace checking is disabled. `dict-
 # separator` is used to allow tabulation in dicts, etc.: {1  : 1,\n222: 2}.

AUTHORS.md

@@ -8,6 +8,7 @@ Manoa.
 The following people have contributed code to the project (alphabetical by last name)
 and are considered the "PyGMT Developers":
 
+* [Michael Grund](https://github.com/michaelgrund)
 * [Wei Ji Leong](https://github.com/weiji14)
 * [Tyler Newton](http://www.tnewton.com/)
 * [William Schlitzer](https://github.com/willschlitzer)

AUTHORSHIP.md

@@ -0,0 +1,75 @@
+# Authorship guidelines for academic papers and software archives
+
+First of all, we are deeply thankful to everyone who has helped make PyGMT
+what it is today. Our goal for this document is to establish guidelines
+for giving credit to contributors for their work.
+To do so, we will attempt to define:
+
+- Fair and diverse ways of providing recognition for contributors' efforts.
+- Define _contributions_ in a broad way: writing code and/or documentation,
+  providing ideas, fostering the community, etc.
+
+The following are the ways in which individuals who have contributed will be
+recognized.
+
+> **Note**: These policies are not set in stone and may be changed to
+> accommodate the growth of the project or the preferences of the community.
+
+## The `AUTHORS.md` file
+
+Anyone who has contributed a pull request to the project is welcome to add
+themselves to the `AUTHORS.md` file. This file lives in the repository and is
+packaged with distributions. This is an optional process.
+
+## Changelog for each release
+
+Every time we make a release, everyone who has made a commit to the repository
+since the previous release will be mentioned in the changelog entry. If their
+full name is available on GitHub, we will use it. Otherwise, we will use the
+GitHub handle. This is a way of saying "Thank you".
+
+## Authorship on Zenodo archives of releases
+
+Anyone who has contributed to the repository (i.e., appears on `git log`) will
+be invited to be an author on the Zenodo archive of new releases.
+
+To be included as an author, you *must* add the following to the `AUTHORS.md`
+file of the repository:
+
+1. Full name
+2. Affiliation (if omitted, we will use "Unaffiliated")
+3. ORCID (optional)
+
+The order of authors will be defined by the number of commits to the repository
+(`git shortlog -sne`). The order can also be changed on a case-by-case basis.
+
+If you have contributed and do not wish to be included in Zenodo archives,
+there are a few options:
+
+1. Don't add yourself to `AUTHORS.md`
+2. Remove yourself from `AUTHORS.md`
+3. Indicate next to your name on `AUTHORS.md` that you do not wish to be
+   included with something like `(not included in Zenodo)`.
+
+## Scientific publications (papers)
+
+We aim to write academic papers for most of our software packages. Ideally, we
+will publish updated papers for major changes or significant new components of the
+package.
+
+To be included as an author on the paper, you *must* satisfy the following
+criteria:
+
+1. Have made multiple and regular contributions to the repository, or the GMT repository, in numerous facets, such as wrapping functions, testing, and/or writing documentation.
+2. Have made non-coding contributions, including project administration and decision making.
+3. Have participated in the writing and reviewing of the paper.
+2. Add your full name, affiliation, and (optionally) ORCID to the paper. These
+   can be submitted on pull requests to the corresponding paper repository.
+3. Write and/or read and review the manuscript in a timely manner and provide
+   comments on the paper (even if it's just an "OK", but preferably more).
+
+The order of authors will be defined by the number of commits made since the
+previous major release that has an associated paper (`git shortlog
+vX.0.0...HEAD -sne`). The order of any author who hasn't made any commits will
+be decided by all authors. The order can also be changed on a case-by-case
+basis.