Merge remote-tracking branch 'origin/wrap/fitcircle' into wrap/fitcircle

GenericMappingTools · Nov 6, 2021 · 3e57da6 · 3e57da6
2 parents d131d2f + 899a93f
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diff --git a/.github/ISSUE_TEMPLATE/release_checklist.md b/.github/ISSUE_TEMPLATE/release_checklist.md
@@ -16,10 +16,11 @@ assignees: ''
 - [ ] Wrap Y ()
 
 **Before release**:
+- [ ] Run `grep --include="*.py" -r 'remove_version="vX.Y.Z"' pygmt` from the base of the repository to check if any deprecations and related tests should be removed in this version
 - [ ] Reserve a DOI on [Zenodo](https://zenodo.org) by clicking on "New Version"
 - [ ] 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
+  - [ ] Update `CITATION.cff` and BibTeX at 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-gmt-and-pythonnumpy-versions
   - [ ] 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))

diff --git a/.github/workflows/cache_data.yaml b/.github/workflows/cache_data.yaml
@@ -19,7 +19,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v2.3.4
+        uses: actions/checkout@v2.4.0
         with:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
@@ -51,6 +51,8 @@ jobs:
       - name: Download remote data
         run: |
           python -c "from pygmt.helpers.testing import download_test_data; download_test_data()"
+        env:
+          GMT_DATA_SERVER: https://oceania.generic-mapping-tools.org/
 
       # Upload the downloaded files as artifacts to GitHub
       - name: Upload artifacts to GitHub

diff --git a/.github/workflows/check-links.yml b/.github/workflows/check-links.yml
@@ -15,18 +15,18 @@ jobs:
 
     steps:
     - name: Checkout the repository
-      uses: actions/checkout@v2.3.4
+      uses: actions/checkout@v2.4.0
       with:
         path: repository
 
     - name: Checkout the documentation
-      uses: actions/checkout@v2.3.4
+      uses: actions/checkout@v2.4.0
       with:
         ref: gh-pages
         path: documentation
 
     - name: Link Checker
-      uses: lycheeverse/lychee-action@v1.0.8
+      uses: lycheeverse/lychee-action@v1.0.9
       with:
         # 429: Too many requests
         args: >

diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml
@@ -49,7 +49,7 @@ jobs:
 
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v2.3.4
+        uses: actions/checkout@v2.4.0
         with:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
@@ -80,7 +80,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.14.1
+        uses: dawidd6/action-download-artifact@v2.15.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success
@@ -107,7 +107,7 @@ jobs:
         run: make -C doc clean all
 
       - name: Checkout the gh-pages branch
-        uses: actions/checkout@28c7f3d2b5162b5ddd3dfd9a45aa55eaf396478b
+        uses: actions/checkout@v2.4.0
         with:
           ref: gh-pages
           # Checkout to this folder instead of the current one

diff --git a/.github/workflows/ci_tests.yaml b/.github/workflows/ci_tests.yaml
@@ -72,7 +72,7 @@ jobs:
 
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v2.3.4
+        uses: actions/checkout@v2.4.0
         with:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
@@ -96,16 +96,16 @@ jobs:
           mamba install gmt=6.2.0 numpy=${{ matrix.numpy-version }} \
                         pandas xarray netCDF4 packaging \
                         ${{ matrix.optional-packages }} \
-                        coverage[toml] dvc=2.3.0 make pytest>=6.0 \
-                        pytest-cov pytest-mpl sphinx-gallery
+                        dvc make pytest>=6.0 \
+                        pytest-cov pytest-mpl sphinx-gallery tomli
 
       # Show installed pkg information for postmortem diagnostic
       - name: List installed packages
         run: mamba list
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.14.1
+        uses: dawidd6/action-download-artifact@v2.15.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success

diff --git a/.github/workflows/ci_tests_dev.yaml b/.github/workflows/ci_tests_dev.yaml
@@ -45,7 +45,7 @@ jobs:
 
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v2.3.4
+        uses: actions/checkout@v2.4.0
         if: github.event_name != 'repository_dispatch'
         with:
           # fecth all history so that setuptools-scm works
@@ -62,12 +62,12 @@ jobs:
 
       # Checkout the pull request branch
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v2.4.0
         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 }}
+          ref: ${{ github.event.pull_request.head.sha }}
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
 
@@ -88,7 +88,7 @@ jobs:
       - name: Install dependencies
         run: |
           mamba install ninja cmake libblas libcblas liblapack fftw gdal geopandas \
-                        ghostscript libnetcdf hdf5 zlib curl pcre make dvc=2.3.0
+                        ghostscript libnetcdf hdf5 zlib curl pcre make dvc
           pip install --pre numpy pandas xarray netCDF4 packaging \
                             ipython pytest-cov pytest-mpl pytest>=6.0 sphinx-gallery \
                             tomli
@@ -107,7 +107,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.14.1
+        uses: dawidd6/action-download-artifact@v2.15.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success

diff --git a/.github/workflows/dvc-diff.yml b/.github/workflows/dvc-diff.yml
@@ -13,7 +13,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v2.3.4
+      uses: actions/checkout@v2.4.0
       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
@@ -14,11 +14,11 @@ jobs:
           private_key: ${{ secrets.APP_PRIVATE_KEY }}
 
       # Checkout the pull request branch
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v2.4.0
         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 }}
+          ref: ${{ github.event.pull_request.head.sha }}
 
       # Setup Python environment
       - uses: actions/setup-python@v2.2.2

diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -23,15 +23,15 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v2.3.4
+      uses: actions/checkout@v2.4.0
       with:
         # fetch all history so that setuptools-scm works
         fetch-depth: 0
 
     - name: Set up Python
       uses: actions/setup-python@v2.2.2
       with:
-        python-version: 3.9
+        python-version: '3.10'
 
     - name: Install dependencies
       run: python -m pip install setuptools wheel

diff --git a/.github/workflows/release-baseline-images.yml b/.github/workflows/release-baseline-images.yml
@@ -16,7 +16,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v2.3.4
+      uses: actions/checkout@v2.4.0
 
     - name: Setup data version control (DVC)
       uses: iterative/setup-dvc@v1.0.3

diff --git a/.github/workflows/style_checks.yaml b/.github/workflows/style_checks.yaml
@@ -16,13 +16,13 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v2.3.4
+        uses: actions/checkout@v2.4.0
 
       # Setup Miniconda
       - name: Set up Python
         uses: actions/setup-python@v2.2.2
         with:
-          python-version: 3.9
+          python-version: '3.10'
 
       - name: Install packages
         run: |

diff --git a/AUTHORS.md b/AUTHORS.md
@@ -10,6 +10,7 @@ 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
 * [Dongdong Tian](https://seisman.info/) | [0000-0001-7967-1197](https://orcid.org/0000-0001-7967-1197) | Michigan State University
+* [Jamie Quinn](http://jamiejquinn.com) | [0000-0002-0268-7032](https://orcid.org/0000-0002-0268-7032) | University College London
 * [Jiayuan Yao](https://github.com/core-man) | [0000-0001-7036-4238](https://orcid.org/0000-0001-7036-4238) | Nanyang Technological University
 * [Kathryn Materna](https://github.com/kmaterna) | [0000-0002-6687-980X](https://orcid.org/0000-0002-6687-980X) | US Geological Survey
 * [Leonardo Uieda](http://www.leouieda.com/) | [0000-0001-6123-9515](https://orcid.org/0000-0001-6123-9515) | University of Liverpool

diff --git a/AUTHORSHIP.md b/AUTHORSHIP.md
@@ -58,6 +58,11 @@ there are a few options:
 3. Indicate next to your name on `AUTHORS.md` that you do not wish to be
    included with something like `(not included in Zenodo)`.
 
+Note that authors included in the Zenodo archive will also have their name
+listed in the `CITATION.cff` file. This is a machine (and human) readable file
+that enables people to cite the PyGMT software easily, and the file will be
+updated by the PyGMT maintainers each time a new release is made.
+
 ## Scientific publications (papers)
 
 We aim to write academic papers for most of our software packages. Ideally, we

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,72 @@
+# YAML 1.2
+# Metadata for citation of this software according to the CFF format (https://citation-file-format.github.io/)
+cff-version: 1.2.0
+message: If you use this software, please cite it as follows.
+title: 'PyGMT: A Python interface for the Generic Mapping Tools'
+authors:
+- given-names: Leonardo
+  family-names: Uieda
+  affiliation: University of Liverpool, United Kingdom
+  orcid: https://orcid.org/0000-0001-6123-9515
+- given-names: Dongdong
+  family-names: Tian
+  affiliation: Michigan State University, USA
+  orcid: https://orcid.org/0000-0001-7967-1197
+- given-names: Wei Ji
+  family-names: Leong
+  affiliation: Victoria University of Wellington, New Zealand
+  orcid: https://orcid.org/0000-0003-2354-1988
+- given-names: Meghan
+  family-names: Jones
+  affiliation: University of Hawai'i at Mānoa, USA
+  orcid: https://orcid.org/0000-0003-0180-8928
+- given-names: William
+  family-names: Schlitzer
+  affiliation: Unaffiliated
+  orcid: https://orcid.org/0000-0002-5843-2282
+- given-names: Liam
+  family-names: Toney
+  affiliation: University of Alaska Fairbanks, USA
+  orcid: https://orcid.org/0000-0003-0167-9433
+- given-names: Michael
+  family-names: Grund
+  affiliation: Innoplexia GmbH, Germany
+  orcid: https://orcid.org/0000-0001-8759-2018
+- given-names: Jiayuan
+  family-names: Yao
+  affiliation: Nanyang Technological University, Singapore
+  orcid: https://orcid.org/0000-0001-7036-4238
+- given-names: Yohai
+  family-names: Magen
+  affiliation: Tel Aviv University
+  orcid: https://orcid.org/0000-0002-4892-4013
+- given-names: Kathryn
+  family-names: Materna
+  affiliation: US Geological Survey, USA
+  orcid: https://orcid.org/0000-0002-6687-980X
+- given-names: Tyler
+  family-names: Newton
+  affiliation: University of Oregon, USA
+  orcid: https://orcid.org/0000-0002-1560-6553
+- given-names: Abhishek
+  family-names: Anant
+  affiliation: Unaffiliated
+  orcid: https://orcid.org/0000-0002-5751-2010
+- given-names: Malte
+  family-names: Ziebarth
+  affiliation: GFZ German Research Centre for Geosciences, Germany
+  orcid: https://orcid.org/0000-0002-5190-4478
+- given-names: Jamie
+  family-names: Quinn
+  affiliation: University College London
+  orcid: https://orcid.org/0000-0002-0268-7032
+- given-names: Paul
+  family-names: Wessel
+  affiliation: University of Hawai'i at Mānoa, USA
+  orcid: https://orcid.org/0000-0001-5708-7336
+date-released: 2021-10-29
+doi: 10.5281/zenodo.5607255
+license: BSD-3-Clause
+repository-code: https://github.com/GenericMappingTools/pygmt
+type: software
+version: 0.5.0
diff --git a/README.rst b/README.rst
@@ -50,22 +50,6 @@ or visit the `PyGMT Gallery <https://www.pygmt.org/latest/gallery>`__.
     :align: center
     :target: https://www.youtube.com/watch?v=SSIGJEe0BIk
 
-
-Disclaimer
-----------
-
-🚨 **This package is still undergoing rapid development.** 🚨
-
-All of the API (functions/classes/interfaces) is subject to change until we reach v1.0.0
-as per the `semantic versioning specification <https://semver.org/spec/v2.0.0.html>`__.
-There may be non-backward compatible changes as we experiment with new design ideas and
-implement new features. **This is not a finished product, use with caution.**
-
-We welcome any feedback and ideas!
-Let us know by submitting
-`issues on GitHub <https://github.com/GenericMappingTools/pygmt/issues>`__
-or by posting on our `Discourse forum <https://forum.generic-mapping-tools.org>`__.
-
 About
 -----
 
@@ -78,7 +62,6 @@ We rely heavily on new features that have been implemented in GMT 6.0. In partic
 a new *modern execution mode* that greatly simplifies figure creation. **These features
 are not available in the 5.4 version of GMT**.
 
-
 Project goals
 -------------
 
@@ -154,28 +137,29 @@ Developers". Feel free to cite our work in your research using the following Bib
 
 .. code-block::
 
-    @software{pygmt_2021_5162003,
+    @software{pygmt_2021_5607255,
       author       = {Uieda, Leonardo and
                       Tian, Dongdong and
                       Leong, Wei Ji and
+                      Jones, Meghan and
                       Schlitzer, William and
                       Toney, Liam and
                       Grund, Michael and
-                      Jones, Meghan and
                       Yao, Jiayuan and
+                      Magen, Yohai and
                       Materna, Kathryn and
                       Newton, Tyler and
                       Anant, Abhishek and
                       Ziebarth, Malte and
-                      Magen, Yohai and
+                      Quinn, Jamie and
                       Wessel, Paul},
       title        = {{PyGMT: A Python interface for the Generic Mapping Tools}},
-      month        = aug,
+      month        = oct,
       year         = 2021,
       publisher    = {Zenodo},
-      version      = {v0.4.1},
-      doi          = {10.5281/zenodo.5162003},
-      url          = {https://doi.org/10.5281/zenodo.5162003}
+      version      = {v0.5.0},
+      doi          = {10.5281/zenodo.5607255},
+      url          = {https://doi.org/10.5281/zenodo.5607255}
     }
 
 To cite a specific version of PyGMT, go to our Zenodo page at
@@ -228,12 +212,17 @@ Compatibility with GMT/Python/NumPy versions
       - GMT
       - Python
       - Numpy
-    * - `v0.5.0 <https://github.com/GenericMappingTools/pygmt/milestone/8>`_ (upcoming release)
+    * - `Dev <https://github.com/GenericMappingTools/pygmt/milestone/9>`_ (upcoming release)
       - `Dev Documentation <https://www.pygmt.org/dev>`_ (reflects `main branch <https://github.com/GenericMappingTools/pygmt>`_)
       - >=6.2.0
       - >=3.7
       - >=1.18
-    * - `v0.4.1 <https://github.com/GenericMappingTools/pygmt/releases/tag/v0.4.1>`_ (latest release)
+    * - `v0.5.0 <https://github.com/GenericMappingTools/pygmt/releases/tag/v0.5.0>`_ (latest release)
+      - `v0.5.0 Documentation <https://www.pygmt.org/v0.5.0>`_
+      - >=6.2.0
+      - >=3.7
+      - >=1.18
+    * - `v0.4.1 <https://github.com/GenericMappingTools/pygmt/releases/tag/v0.4.1>`_
       - `v0.4.1 Documentation <https://www.pygmt.org/v0.4.1>`_
       - >=6.2.0
       - >=3.7