Revert 158 commits

Author: seisman

.dvcignore

@@ -1,2 +1,3 @@
-# Add patterns of files dvc should ignore, which could improve the performance.
-# Learn more at https://dvc.org/doc/user-guide/project-structure/dvcignore-files
+# 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/1-bug_report.yaml

@@ -23,7 +23,7 @@ body:
         For more details, check out:
 
         - [Minimal Complete Verifiable Examples](https://stackoverflow.com/help/mcve)
-        - [Craft Minimal Bug Reports](https://matthewrocklin.com/minimal-bug-reports)
+        - [Craft Minimal Bug Reports](http://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
 
       placeholder: "PASTE CODE HERE"
       render: python

.github/ISSUE_TEMPLATE/4-release_checklist.md

@@ -8,52 +8,49 @@ assignees: ''
 ---
 
 **Release**: [v0.x.x](https://github.com/GenericMappingTools/pygmt/milestones/?)
-**Scheduled Date**: 20YY/MM/DD
-**Pull request due date**: 20YY/MM/DD
-**DOI**: `10.5281/zenodo.XXXXXXX`
+**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**:
-
-- [ ] Check [SPEC 0](https://scientific-python.org/specs/spec-0000/) to see if we need to bump the minimum supported versions of GMT, Python and
-      core package dependencies (NumPy, pandas, Xarray)
-- [ ] Review the ["PyGMT Team" page](https://www.pygmt.org/dev/team.html)
+- [ ] Check [SPEC 0](https://scientific-python.org/specs/spec-0000/) to see if we need to bump the minimum supported versions of GMT, Python and core package dependencies (NumPy/Pandas/Xarray)
+- [ ] Run `make codespell` to check common misspellings. If there are any, either fix them or add them to `ignore-words-list` in `pyproject.toml`
 - [ ] Check to ensure that:
-  - [ ] Deprecations and related tests are removed for this version by running `grep --include="*.py" -r vX.Y.Z` from the base of the repository
   - [ ] All tests pass in the ["GMT Legacy Tests" workflow](https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_tests_legacy.yaml)
   - [ ] All tests pass in the ["GMT Dev Tests" workflow](https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_tests_dev.yaml)
   - [ ] All tests pass in the ["Doctests" workflow](https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_doctests.yaml)
-- [ ] Update warnings in `pygmt/_show_versions.py` as well as notes in
-      [Not working transparency](https://www.pygmt.org/dev/install.html#not-working-transparency)
-      regarding GMT-Ghostscript incompatibility
+  - [ ] Deprecations and related tests are removed for this version by running `grep --include="*.py" -r 'remove_version="vX.Y.Z"' pygmt` from the base of the repository
+- [ ] Update warnings in `pygmt.show_versions()` as well as notes in [Common installation issues](https://www.pygmt.org/dev/install.html#not-working-transparency)
+      and [Testing your install]((https://www.pygmt.org/dev/install.html#testing-your-install) regarding GMT-Ghostscript incompatibility
 - [ ] Reserve a DOI on [Zenodo](https://zenodo.org) by clicking on "New Version"
-- [ ] Finish up the "Changelog entry for v0.x.x" Pull Request (Use the previous changelog PR as a reference)
-- [ ] Run `make codespell` to check common misspellings. If there are any, either fix them or add them to `ignore-words-list` in `pyproject.toml`
-- [ ] Draft the announcement on https://hackmd.io/@pygmt
+- [ ] Review the ["PyGMT Team" page](https://www.pygmt.org/dev/team.html)
+- [ ] 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.cff` and BibTeX at https://github.com/GenericMappingTools/pygmt#citing-pygmt
+    - [ ] Update authorship list
+    - [ ] Update DOI (and url for BibTeX)
+    - [ ] Update version
+    - [ ] Update date released
+  - [ ] Add the documentation link `doc/minversions.md`
+  - [ ] Add minimum required version information `doc/minversions.md`
+  - [ ] Copy draft changelog from Release Drafter and edit it to look nice ([see maintainers guide for details](https://www.pygmt.org/dev/maintenance.html#updating-the-changelog))
 
 **Release**:
-
 - [ ] 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
-- [ ] Download pygmt-X.Y.Z.zip (rename to pygmt-vX.Y.Z.zip) and baseline-images.zip from
-      the release page, and upload the two zip files to https://zenodo.org/deposit,
-      ensure that they are filed under the correct reserved DOI
+- [ ] Manually upload the pygmt-vX.Y.Z.zip and baseline-images.zip files 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)
-      [Done automatically by conda-forge's bot. Remember to pin Python and SPEC0 versions]
+- [ ] Update conda-forge [pygmt-feedstock](https://github.com/conda-forge/pygmt-feedstock) [Done automatically by conda-forge's bot, but remember to pin SPEC0 versions]
 - [ ] Bump PyGMT version on https://github.com/GenericMappingTools/try-gmt (after conda-forge update)
 - [ ] Announce the release on:
-  - [ ] GMT [forum](https://forum.generic-mapping-tools.org/c/news/) (do this announcement first! Requires moderator status)
+  - [ ] GMT [forum](https://forum.generic-mapping-tools.org/c/news/) (do this announcement first! draft on https://hackmd.io/@pygmt. requires moderator status)
   - [ ] [ResearchGate](https://www.researchgate.net) (after forum announcement, add new version as research item via the **code** category, be sure to include the corresponding new Zenodo DOI)
-
 ---
 
 - [ ] Party :tada: (don't tick before all other checkboxes are ticked!)

.github/PULL_REQUEST_TEMPLATE.md

@@ -8,10 +8,6 @@
 Fixes #
 
 
-<!-- If significant changes to the documentation are made, please insert the link to the documentation page after it has been built. -->
-**Preview**:
-
-
 **Reminders**
 
 - [ ] Run `make format` and `make check` to make sure the code follows the style guide.

.github/release-drafter.yml

@@ -24,8 +24,6 @@ exclude-contributors:
   - 'actions-bot'
   - 'dependabot'
   - 'dependabot[bot]'
-  - 'pre-commit-ci'
-  - 'pre-commit-ci[bot]'
 category-template: '### $TITLE'
 change-template: '* $TITLE ([#$NUMBER]($URL))'
 sort-by: 'title'

.github/workflows/benchmarks.yml

@@ -25,7 +25,7 @@ concurrency:
 
 jobs:
   benchmarks:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     if: github.repository == 'GenericMappingTools/pygmt' && (github.event_name != 'pull_request' || contains(github.event.pull_request.labels.*.name, 'run/benchmark'))
     defaults:
       run:
@@ -34,7 +34,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v4.2.2
+        uses: actions/checkout@v4.1.7
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -45,7 +45,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.1
+        uses: mamba-org/setup-micromamba@v1.9.0
         with:
           environment-name: pygmt
           condarc: |
@@ -87,8 +87,8 @@ jobs:
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@v3.1.0
+        uses: CodSpeedHQ/action@v3.0.0
         with:
           # 'bash -el -c' is needed to use the custom shell.
           # See https://github.com/CodSpeedHQ/action/issues/65.
-          run: bash -el -c "python -c \"import pygmt; pygmt.show_versions()\"; PYGMT_USE_EXTERNAL_DISPLAY=false python -m pytest -r P --pyargs pygmt --codspeed --override-ini addopts='--verbose'"
+          run: bash -el -c "python -c \"import pygmt; pygmt.show_versions()\"; PYGMT_USE_EXTERNAL_DISPLAY=false python -m pytest -r P --pyargs pygmt --codspeed"

.github/workflows/cache_data.yaml

@@ -36,14 +36,14 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v4.2.2
+        uses: actions/checkout@v4.1.7
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.1
+        uses: mamba-org/setup-micromamba@v1.9.0
         with:
           environment-name: pygmt
           condarc: |
@@ -76,10 +76,9 @@ jobs:
 
       # Upload the downloaded files as artifacts to GitHub
       - name: Upload artifacts to GitHub
-        uses: actions/upload-artifact@v4.4.3
+        uses: actions/upload-artifact@v4
         with:
           name: gmt-cache
-          include-hidden-files: true
           path: |
             ~/.gmt/cache
             ~/.gmt/server

.github/workflows/check-links.yml

@@ -23,41 +23,44 @@ jobs:
 
     steps:
     - name: Checkout the repository
-      uses: actions/checkout@v4.2.2
+      uses: actions/checkout@v4.1.7
       with:
         path: repository
 
     - name: Checkout the documentation
-      uses: actions/checkout@v4.2.2
+      uses: actions/checkout@v4.1.7
       with:
         ref: gh-pages
         path: documentation
 
     - name: Link Checker
       id: lychee
-      uses: lycheeverse/lychee-action@v2.0.2
+      uses: lycheeverse/lychee-action@v1.10.0
       with:
-        fail: false  # Don't fail action on broken links
         output: /tmp/lychee-out.md
         # 429: Too many requests
         args: >
           --accept 429
-          --exclude "^https://docs.generic-mapping-tools.org/6.[0-9]?/%s$"
-          --exclude "^https://docs.generic-mapping-tools.org/6.[0-9]?/%3Cmodule-name%3E.html$"
-          --exclude "^https://doi.org"
+          --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]*$"
           --exclude "^https://github.com/GenericMappingTools/gmt/releases/tag/X.Y.Z$"
           --exclude "^https://github.com/GenericMappingTools/pygmt/edit"
           --exclude "^https://github.com/GenericMappingTools/pygmt/issues/new"
-          --exclude "^https://github.com/GenericMappingTools/pygmt/pull/[0-9]*$"
-          --exclude "^https://github.com/GenericMappingTools/pygmt/issues/[0-9]*$"
           --exclude "^https://github.com/GenericMappingTools/pygmt/releases/tag/%7B%7Bpath%7D%7D"
-          --exclude "^https://hackmd.io/@pygmt"
-          --exclude "^https://test.pypi.org/simple/"
-          --exclude "^https://www.adobe.com/jp/print/postscript/pdfs/PLRM.pdf"
-          --exclude "^https://www.generic-mapping-tools.org/remote-datasets/%s$"
           --exclude "^https://www.pygmt.org/%7B%7Bpath%7D%7D"
+          --exclude "^git"
+          --exclude "^file://"
+          --exclude "https://www.adobe.com/jp/print/postscript/pdfs/PLRM.pdf"
+          --exclude "^https://docs.generic-mapping-tools.org/6.5/%s$"
+          --exclude "^https://docs.generic-mapping-tools.org/6.5/%3Cmodule-name%3E.html$"
+          --exclude "^https://www.generic-mapping-tools.org/remote-datasets/%s$"
+          --exclude "^https://hackmd.io/@pygmt"
+          --exclude "^https://doi.org"
           --exclude "^https://www.researchgate.net/"
-          --exclude "^https://zenodo.org/badge/DOI/"
+          --exclude "^https://test.pypi.org/simple/"
           --verbose
           "repository/**/*.rst"
           "repository/**/*.md"

.github/workflows/ci_docs.yml

@@ -69,7 +69,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v4.2.2
+        uses: actions/checkout@v4.1.7
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -80,7 +80,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.1
+        uses: mamba-org/setup-micromamba@v1.9.0
         with:
           environment-name: pygmt
           condarc: |
@@ -94,7 +94,7 @@ jobs:
           create-args: >-
             python=3.12
             gmt=6.5.0
-            ghostscript=10.04.0
+            ghostscript=10.03.1
             numpy
             pandas
             xarray
@@ -103,7 +103,6 @@ jobs:
             contextily
             geopandas<1.0
             ipython
-            pyarrow
             rioxarray
             make
             pip
@@ -115,7 +114,7 @@ jobs:
             sphinx-copybutton
             sphinx-design
             sphinx-gallery
-            sphinx_rtd_theme<3.0
+            sphinx_rtd_theme
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
@@ -139,7 +138,7 @@ jobs:
         run: make -C doc clean all
 
       - name: Checkout the gh-pages branch
-        uses: actions/checkout@v4.2.2
+        uses: actions/checkout@v4.1.7
         with:
           ref: gh-pages
           # Checkout to this folder instead of the current one

.github/workflows/ci_doctests.yaml

@@ -35,14 +35,14 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v4.2.2
+        uses: actions/checkout@v4.1.7
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.1
+        uses: mamba-org/setup-micromamba@v1.9.0
         with:
           environment-name: pygmt
           condarc: |