Merge branch 'main' into refactor/virtualfile_in

GenericMappingTools · Oct 3, 2024 · b051239 · b051239
2 parents 8e80bb5 + 68a17a0
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diff --git a/.github/ISSUE_TEMPLATE/1-bug_report.yaml b/.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](http://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+        - [Craft Minimal Bug Reports](https://matthewrocklin.com/minimal-bug-reports)
 
       placeholder: "PASTE CODE HERE"
       render: python

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -34,7 +34,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v4.1.7
+        uses: actions/checkout@v4.2.0
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0

diff --git a/.github/workflows/cache_data.yaml b/.github/workflows/cache_data.yaml
@@ -36,7 +36,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v4.1.7
+        uses: actions/checkout@v4.2.0
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0

diff --git a/.github/workflows/check-links.yml b/.github/workflows/check-links.yml
@@ -23,12 +23,12 @@ jobs:
 
     steps:
     - name: Checkout the repository
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.0
       with:
         path: repository
 
     - name: Checkout the documentation
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.0
       with:
         ref: gh-pages
         path: documentation

diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml
@@ -69,7 +69,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v4.1.7
+        uses: actions/checkout@v4.2.0
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -138,7 +138,7 @@ jobs:
         run: make -C doc clean all
 
       - name: Checkout the gh-pages branch
-        uses: actions/checkout@v4.1.7
+        uses: actions/checkout@v4.2.0
         with:
           ref: gh-pages
           # Checkout to this folder instead of the current one

diff --git a/.github/workflows/ci_doctests.yaml b/.github/workflows/ci_doctests.yaml
@@ -35,7 +35,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v4.1.7
+        uses: actions/checkout@v4.2.0
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0

diff --git a/.github/workflows/ci_tests.yaml b/.github/workflows/ci_tests.yaml
@@ -71,8 +71,8 @@ jobs:
         include:
           - python-version: '3.10'
             numpy-version: '1.24'
-            pandas-version: '=1.5'
-            xarray-version: '=2022.09'
+            pandas-version: '=2.0'
+            xarray-version: '=2023.04'
             optional-packages: ''
           - python-version: '3.12'
             numpy-version: '2.1'
@@ -103,7 +103,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v4.1.7
+        uses: actions/checkout@v4.2.0
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -178,7 +178,7 @@ jobs:
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4.5.0
+        uses: codecov/codecov-action@v4.6.0
         if: success() || failure()
         with:
           use_oidc: true

diff --git a/.github/workflows/ci_tests_dev.yaml b/.github/workflows/ci_tests_dev.yaml
@@ -46,7 +46,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v4.1.7
+        uses: actions/checkout@v4.2.0
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -88,7 +88,7 @@ jobs:
 
       # Checkout current GMT repository
       - name: Checkout the GMT source from ${{ matrix.gmt_git_ref }} branch
-        uses: actions/checkout@v4.1.7
+        uses: actions/checkout@v4.2.0
         with:
           repository: 'GenericMappingTools/gmt'
           ref: ${{ matrix.gmt_git_ref }}

diff --git a/.github/workflows/ci_tests_legacy.yaml b/.github/workflows/ci_tests_legacy.yaml
@@ -35,7 +35,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-20.04, macos-12, windows-2019]
-        gmt_version: ['6.3', '6.4']
+        gmt_version: ['6.4']
     timeout-minutes: 30
     defaults:
       run:
@@ -44,7 +44,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v4.1.7
+        uses: actions/checkout@v4.2.0
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0

diff --git a/.github/workflows/dvc-diff.yml b/.github/workflows/dvc-diff.yml
@@ -21,7 +21,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.0
       with:
         # fetch all history so that dvc diff works
         fetch-depth: 0

diff --git a/.github/workflows/format-command.yml b/.github/workflows/format-command.yml
@@ -18,7 +18,7 @@ jobs:
           private-key: ${{ secrets.APP_PRIVATE_KEY }}
 
       # Checkout the pull request branch
-      - uses: actions/checkout@v4.1.7
+      - uses: actions/checkout@v4.2.0
         with:
           token: ${{ steps.generate-token.outputs.token }}
           repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}

diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -45,7 +45,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.0
       with:
         # fetch all history so that setuptools-scm works
         fetch-depth: 0

diff --git a/.github/workflows/release-baseline-images.yml b/.github/workflows/release-baseline-images.yml
@@ -23,7 +23,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.0
 
     - name: Setup data version control (DVC)
       uses: iterative/[email protected]

diff --git a/.github/workflows/style_checks.yaml b/.github/workflows/style_checks.yaml
@@ -24,7 +24,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v4.1.7
+        uses: actions/checkout@v4.2.0
 
       # Setup Python
       - name: Set up Python

diff --git a/.github/workflows/type_checks.yml b/.github/workflows/type_checks.yml
@@ -33,7 +33,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v4.1.7
+        uses: actions/checkout@v4.2.0
 
       # Setup Python
       - name: Set up Python

diff --git a/AUTHORS.md b/AUTHORS.md
@@ -13,16 +13,16 @@ The following people have contributed code and/or documentation to the project
 | [Abhishek Anant](https://twitter.com/itsabhianant) | [0000-0002-5751-2010](https://orcid.org/0000-0002-5751-2010) | Unaffiliated |
 | [Andre L. Belem](https://github.com/andrebelem) | [0000-0002-8865-6180](https://orcid.org/0000-0002-8865-6180) | Fluminense Federal University, Brazil |
 | [Dongdong Tian](https://seisman.info/) | [0000-0001-7967-1197](https://orcid.org/0000-0001-7967-1197) | China University of Geosciences, China |
-| [Jamie Quinn](http://jamiejquinn.com) | [0000-0002-0268-7032](https://orcid.org/0000-0002-0268-7032) | University College London, United Kingdom |
+| [Jamie Quinn](https://jamiejquinn.com) | [0000-0002-0268-7032](https://orcid.org/0000-0002-0268-7032) | University College London, United Kingdom |
 | [Jiayuan Yao](https://github.com/core-man) | [0000-0001-7036-4238](https://orcid.org/0000-0001-7036-4238) | Nanyang Technological University, Singapore |
 | [Jing-Hui Tong](https://github.com/jhtong33) | [0009-0002-7195-3071](https://orcid.org/0009-0002-7195-3071) | National Taiwan Normal University, Taiwan |
 | [Kathryn Materna](https://github.com/kmaterna) | [0000-0002-6687-980X](https://orcid.org/0000-0002-6687-980X) | US Geological Survey, USA |
-| [Leonardo Uieda](http://www.leouieda.com/) | [0000-0001-6123-9515](https://orcid.org/0000-0001-6123-9515) | University of Liverpool, United Kingdom |
+| [Leonardo Uieda](https://www.leouieda.com/) | [0000-0001-6123-9515](https://orcid.org/0000-0001-6123-9515) | University of Liverpool, United Kingdom |
 | [Liam Toney](https://liam.earth/) | [0000-0003-0167-9433](https://orcid.org/0000-0003-0167-9433) | University of Alaska Fairbanks, USA |
 | [Malte Ziebarth](https://github.com/mjziebarth) | [0000-0002-5190-4478](https://orcid.org/0000-0002-5190-4478) | GFZ German Research Centre for Geosciences, Germany |
 | [Max Jones](https://github.com/maxrjones) | [0000-0003-0180-8928](https://orcid.org/0000-0003-0180-8928) | University of Hawaiʻi at Mānoa, USA |
 | [Michael Grund](https://github.com/michaelgrund) | [0000-0001-8759-2018](https://orcid.org/0000-0001-8759-2018) | SNP Innovation Lab GmbH, Germany |
-| [Tyler Newton](http://www.tnewton.com/) | [0000-0002-1560-6553](https://orcid.org/0000-0002-1560-6553) | University of Oregon, USA |
+| [Tyler Newton](https://www.tnewton.com/) | [0000-0002-1560-6553](https://orcid.org/0000-0002-1560-6553) | University of Oregon, USA |
 | [Wei Ji Leong](https://github.com/weiji14) | [0000-0003-2354-1988](https://orcid.org/0000-0003-2354-1988) | Development Seed, USA |
 | [William Schlitzer](https://github.com/willschlitzer) | [0000-0002-5843-2282](https://orcid.org/0000-0002-5843-2282) | Unaffiliated |
 | [Yohai Magen](https://github.com/yohaimagen) | [0000-0002-4892-4013](https://orcid.org/0000-0002-4892-4013) | Tel Aviv University, Israel |

diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@
 
 [Documentation (development version)](https://www.pygmt.org/dev) | [Contact](https://forum.generic-mapping-tools.org) | [TryOnline](https://github.com/GenericMappingTools/try-gmt)
 
-[![Latest version on PyPI](http://img.shields.io/pypi/v/pygmt.svg?style=flat-square)](https://pypi.python.org/pypi/pygmt)
+[![Latest version on PyPI](https://img.shields.io/pypi/v/pygmt.svg?style=flat-square)](https://pypi.python.org/pypi/pygmt)
 [![Latest version on conda-forge](https://img.shields.io/conda/v/conda-forge/pygmt?style=flat-square)](https://anaconda.org/conda-forge/pygmt)
 [![GitHub Actions Tests status](https://github.com/GenericMappingTools/pygmt/workflows/Tests/badge.svg)](https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_tests.yaml)
 [![GitHub Actions GMT Dev Tests status](https://github.com/GenericMappingTools/pygmt/workflows/GMT%20Dev%20Tests/badge.svg)](https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_tests_dev.yaml)

diff --git a/doc/_static/style.css b/doc/_static/style.css
@@ -48,38 +48,6 @@ p {
     font-size: 4em;
 }
 
-.api-module {
-	margin-bottom: 80px;
-}
-
-.youtube-embed {
-    max-width: 600px;
-    margin-bottom: 24px;
-}
-
-.video-container {
-    position:relative;
-    padding-bottom:56.25%;
-    padding-top:30px;
-    height:0;
-    overflow:hidden;
-}
-
-.video-container iframe, .video-container object, .video-container embed {
-    position:absolute;
-    top:0;
-    left:0;
-    width:100%;
-    height:100%;
-}
-
-/*.wy-menu-vertical header, .wy-menu-vertical p.caption {*/
-    /*font-size: 90%;*/
-    /*font-weight: bold;*/
-    /*color: #eeeeee;*/
-    /*letter-spacing: 0.12em;*/
-/*}*/
-
 .wy-nav-content {
     max-width: 1000px;
 }
@@ -137,22 +105,6 @@ html.writer-html5 .rst-content dl.field-list {
     }
 }
 
-/* Style for the copy button */
-/* Safe to remove for sphinx-copybutton>0.3.1
- * https://github.com/executablebooks/sphinx-copybutton/pull/107
- */
-a.copybtn {
-    position: absolute;
-    top: .2em;
-    right: .2em;
-    width: 1.3em;
-    height: 1.3em;
-    opacity: .3;
-    transition: opacity 0.5s;
-    border: none;
-    user-select: none;
-}
-
 /* Atkinson Hyperlegible regular */
 @font-face {
     font-family: "Atkinson Hyperlegible";
@@ -189,9 +141,6 @@ a.copybtn {
 .sphx-glr-thumbcontainer {
     border: solid #d6d6d6 1px!important;
     text-align: center!important;
-}
-
-.sphx-glr-thumbcontainer {
     min-height: 240px!important;
     min-width: 180px!important;
 }

diff --git a/doc/_static/version_switch.js b/doc/_static/version_switch.js
@@ -74,7 +74,7 @@
            window.location.href = new_url;
         },
         error: function() {
-            window.location.href = 'http://' + doc_url + '/' + selected;
+            window.location.href = 'https://' + doc_url + '/' + selected;
         }
       });
     }

diff --git a/doc/_templates/footer.html b/doc/_templates/footer.html
@@ -3,7 +3,7 @@
 
 {%- block extrafooter %}
 <p>
-Built with <a href="http://sphinx-doc.org/">Sphinx</a>
+Built with <a href="https://sphinx-doc.org/">Sphinx</a>
 using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
 provided by <a href="https://readthedocs.org">Read the Docs</a>
 </p>

diff --git a/doc/api/index.rst b/doc/api/index.rst
@@ -218,6 +218,8 @@ and store them in GMT's user data directory.
     :toctree: generated
 
     datasets.list_sample_data
+    datasets.load_black_marble
+    datasets.load_blue_marble
     datasets.load_earth_age
     datasets.load_earth_free_air_anomaly
     datasets.load_earth_geoid

diff --git a/doc/changes.md b/doc/changes.md
@@ -101,6 +101,7 @@
 
 ### Enhancements
 
+* **Breaking**: (Unneeded) extra double quotes around text strings (containing whitespaces) are now considered as part of the text string ([#3132](https://github.com/GenericMappingTools/pygmt/pull/3132), [#3457](https://github.com/GenericMappingTools/pygmt/issues/3457))
 * pygmt.project: Add 'output_type' parameter for output in pandas/numpy/file formats ([#3110](https://github.com/GenericMappingTools/pygmt/pull/3110))
 * pygmt.grdtrack: Add 'output_type' parameter for output in pandas/numpy/file formats ([#3106](https://github.com/GenericMappingTools/pygmt/pull/3106))
 * pygmt.blockm*: Add 'output_type' parameter for output in pandas/numpy/file formats ([#3103](https://github.com/GenericMappingTools/pygmt/pull/3103))
@@ -241,7 +242,7 @@
 * Switch away from Stamen basemaps ([#2717](https://github.com/GenericMappingTools/pygmt/pull/2717))
 * Add the "validate_output_table_type" function to check the "output_type" parameter ([#2772](https://github.com/GenericMappingTools/pygmt/pull/2772))
 * Create "skip_if_no" helper function to skip tests when missing a package ([#2883](https://github.com/GenericMappingTools/pygmt/pull/2883))
-* Fix "fixture_xr_image" to open "earth_day_01d_p" directly with rioxarray ([#2963](https://github.com/GenericMappingTools/pygmt/pull/2963))
+* Fix "fixture_xr_image" to open "earth_day_01d" directly with rioxarray ([#2963](https://github.com/GenericMappingTools/pygmt/pull/2963))
 * Improve the way to import optional modules ([#2809](https://github.com/GenericMappingTools/pygmt/pull/2809))
 * Move variable `__gmt_version__` to pygmt.clib to avoid cyclic-import errors ([#2713](https://github.com/GenericMappingTools/pygmt/pull/2713))
 * Refactor the internal "_load_remote_dataset function" to simplify datasets' definitions ([#2917](https://github.com/GenericMappingTools/pygmt/pull/2917))

diff --git a/doc/contributing.md b/doc/contributing.md
@@ -64,7 +64,7 @@ the problem:
 
       python <test>.py 2>&1 | awk -F': ' '$2=="GMT_Call_Command string" {print $3}'
 
-  where `<test>` is the name of your test script. Note that this script works only with GMT>=6.4
+  where `<test>` is the name of your test script.
 * If the bug is produced when passing an in-memory data object (e.g., a
   pandas.DataFrame or xarray.DataArray) to a PyGMT function, try writing the
   data to a file (e.g., a netCDF or ASCII txt file) and passing the data file
@@ -100,7 +100,7 @@ Please take a look at these resources to learn about Git and pull requests (don'
 hesitate to [ask questions](contributing.md#getting-help)):
 
 * [How to Contribute to Open Source](https://opensource.guide/how-to-contribute/).
-* [Git Workflow Tutorial](http://www.asmeurer.com/git-workflow/) by Aaron Meurer.
+* [Git Workflow Tutorial](https://www.asmeurer.com/git-workflow/) by Aaron Meurer.
 * [How to Contribute to an Open Source Project on GitHub](https://egghead.io/courses/how-to-contribute-to-an-open-source-project-on-github).
 
 ### Getting Help
@@ -111,7 +111,7 @@ the project where you can ask questions.
 
 ### Pull Request Workflow
 
-We follow the [git pull request workflow](http://www.asmeurer.com/git-workflow)
+We follow the [git pull request workflow](https://www.asmeurer.com/git-workflow)
 to make changes to our codebase. Every change made goes through a pull request, even
 our own, so that our
 [continuous integration](https://en.wikipedia.org/wiki/Continuous_integration)
@@ -168,7 +168,7 @@ To increase the chances of getting your pull request accepted quickly, try to:
     or [Tutorials](contributing.md#contributing-tutorials).
 * Have a good coding style
   - Use readable code, as it is better than clever code (even with comments).
-  - Follow the [PEP8](http://pep8.org) style guide for code and the
+  - Follow the [PEP8](https://pep8.org) style guide for code and the
     [NumPy style guide](https://numpydoc.readthedocs.io/en/latest/format.html)
     for docstrings. Please refer to [Code style](contributing.md#code-style).
 
@@ -251,7 +251,7 @@ There are four main components to PyGMT's documentation:
 
 The documentation is written primarily in
 [reStructuredText](https://docutils.sourceforge.io/rst.html) and built by
-[Sphinx](http://www.sphinx-doc.org/). Please refer to
+[Sphinx](https://www.sphinx-doc.org/). Please refer to
 {gmt-docs}`reStructuredText Cheatsheet <devdocs/rst-cheatsheet.html>`
 if you are new to reStructuredText. When contributing documentation, be sure to
 follow the general guidelines in the [pull request workflow](contributing.md#pull-request-workflow)
@@ -473,7 +473,7 @@ code, be sure to follow the general guidelines in the
 ### Code Style
 
 We use the [ruff](https://docs.astral.sh/ruff) tool to format the code, so we
-don't have to think about it. It loosely follow the [PEP8](http://pep8.org) guide
+don't have to think about it. It loosely follow the [PEP8](https://pep8.org) guide
 but with a few differences. Regardless, you won't have to worry about formatting
 the code yourself. Before committing, run it to automatically format your code:
 

diff --git a/doc/install.md b/doc/install.md
@@ -308,5 +308,5 @@ especially regarding transparency. If the transparency doesn't work in your figu
 please check your GMT and Ghostscript versions (you can run `pygmt.show_versions()`).
 We recommend:
 
-- Ghostscript 9.53-9.56 for GMT 6.3.0/6.4.0
+- Ghostscript 9.53-9.56 for GMT 6.4.0 (or below)
 - Ghostscript 10.03 or later for GMT 6.5.0