Merge branch 'main' into geographic2cell_ids

xarray-contrib · Nov 22, 2024 · 2877a77 · 2877a77
2 parents 743d2d7 + ce81a17
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -45,7 +45,7 @@ jobs:
       fail-fast: false
 
       matrix:
-        os: ["ubuntu-latest", "macos-latest"]
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
         python-version: ["3.10", "3.11", "3.12"]
 
     steps:
@@ -61,13 +61,13 @@ jobs:
       - name: Setup micromamba
         uses: mamba-org/setup-micromamba@v2
         with:
+          micromamba-version: "1.5.10-0"
           environment-file: ${{ env.CONDA_ENV_FILE }}
           environment-name: xdggs-tests
           cache-environment: true
           cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{matrix.python-version}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
           create-args: >-
             python=${{matrix.python-version}}
-            conda
 
       - name: Install xdggs
         run: |

diff --git a/.gitignore b/.gitignore
@@ -70,7 +70,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
-docs/generated/
+docs/**/generated/
 
 # PyBuilder
 .pybuilder/
@@ -163,3 +163,7 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+# bibtex
+.auctex-auto
+*.bib.untidy
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -5,13 +5,22 @@ repos:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-docstring-first
-      - id: check-yaml
-      - id: check-toml
   - repo: https://github.com/rbubley/mirrors-prettier
     rev: v3.3.3
     hooks:
       - id: prettier
         args: [--cache-location=.prettier_cache/cache]
+  - repo: https://github.com/ComPWA/taplo-pre-commit
+    rev: v0.9.3
+    hooks:
+      - id: taplo-format
+        args: [--option, array_auto_collapse=false]
+      - id: taplo-lint
+        args: [--no-schema]
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.23
+    hooks:
+      - id: validate-pyproject
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.7.2
     hooks:
@@ -27,11 +36,27 @@ repos:
       - id: blackdoc
         additional_dependencies: ["black==24.10.0"]
       - id: blackdoc-autoupdate-black
+  - repo: https://github.com/citation-file-format/cffconvert
+    rev: b6045d78aac9e02b039703b030588d54d53262ac
+    hooks:
+      - id: validate-cff
   - repo: https://github.com/kynan/nbstripout
     rev: 0.8.0
     hooks:
       - id: nbstripout
         args: [--extra-keys=metadata.kernelspec metadata.langauge_info.version]
+  - repo: https://github.com/FlamingTempura/bibtex-tidy
+    rev: v1.14.0
+    hooks:
+      - id: bibtex-tidy
+        stages: [manual]
+        args:
+          - "--modify"
+          - "--blank-lines"
+          - "--sort=-year,name"
+          - "--duplicates"
+          - "--escape"
+          - "--trailing-commas"
 
 ci:
   autofix_prs: true

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,45 @@
+cff-version: 1.2.0
+title: xdggs
+message: "If you use this software, please cite it as below."
+type: software
+authors:
+  - family-names: "Magin"
+    given-names: "Justus"
+    orcid: "https://orcid.org/0000-0002-4254-8002"
+  - family-names: "Bovy"
+    given-names: "Benoît"
+    orcid: "https://orcid.org/0009-0001-4011-3574"
+  - family-names: "Kmoch"
+    given-names: "Alexander"
+    orcid: "https://orcid.org/0000-0003-4386-4450"
+  - family-names: "Abernathey"
+    given-names: "Ryan"
+    orcid: "https://orcid.org/0000-0001-5999-4917"
+  - family-names: "Coca-Castro"
+    given-names: "Alejandro"
+    orcid: "https://orcid.org/0000-0002-9264-1539"
+  - family-names: "Strobl"
+    given-names: "Peter"
+    orcid: "https://orcid.org/0000-0003-2733-1822"
+  - family-names: "Fouilloux"
+    given-names: "Anne"
+    orcid: "https://orcid.org/0000-0002-1784-2920"
+  - family-names: "Loos"
+    given-names: "Daniel"
+    orcid: "https://orcid.org/0000-0002-4024-4443"
+  - family-names: "Chan"
+    given-names: "Wai Tik"
+    orcid: "https://orcid.org/0009-0005-3779-139X"
+  - family-names: "Delouis"
+    given-names: "Jean-Marc"
+    orcid: "https://orcid.org/0000-0002-0713-1658"
+  - family-names: "Odaka"
+    given-names: "Tina"
+    orcid: "https://orcid.org/0000-0002-1500-0156"
+repository-code: "https://github.com/xarray-contrib/xdggs"
+url: "https://xdggs.readthedocs.io"
+keywords:
+  - xarray
+  - discrete global grid systems
+  - dggs
+license: Apache-2.0
diff --git a/README.md b/README.md
@@ -83,4 +83,4 @@ We welcome contributions to `xdggs`! Please follow these steps to get involved:
 
 ## Acknowledgments
 
-This project was inspired by the increasing need for scalable geospatial data analysis using DGGS and is built upon the robust ecosystem of Xarray.
+This project was initiated using funding from CNES (PANGEO IAOCEA, contract R&T R-S23/DU-0002-025-01) and the European Union (ERC, WaterSmartLand, 101125476, Interreg-BSR, HyTruck, #C031).
diff --git a/ci/docs.yml b/ci/docs.yml
@@ -10,8 +10,8 @@ dependencies:
   - sphinx-copybutton
   - sphinx-design
   - sphinx-inline-tabs
+  - sphinxcontrib-bibtex
   - xarray
-  - healpy
   - h5netcdf
   - netcdf4
   - pooch
@@ -27,4 +27,5 @@ dependencies:
   - pip
   - pip:
       - h3ronpy
+      - cdshealpix
       - -e ..
diff --git a/ci/environment.yml b/ci/environment.yml
@@ -2,7 +2,6 @@ channels:
   - conda-forge
 dependencies:
   - xarray
-  - healpy
   - h5netcdf
   - netcdf4
   - pooch
@@ -18,3 +17,4 @@ dependencies:
   - pip
   - pip:
       - h3ronpy
+      - cdshealpix
diff --git a/ci/install-upstream-wheels.sh b/ci/install-upstream-wheels.sh
@@ -10,7 +10,7 @@ fi
 $conda remove -y --force \
     xarray \
     pandas \
-    healpy
+    cdshealpix
 python -m pip uninstall -y h3ronpy
 
 # install from scientific-python wheels
@@ -36,23 +36,5 @@ python -m pip install \
 python -m pip install --no-deps --upgrade \
     git+https://github.com/Unidata/cftime \
     git+https://github.com/astropy/astropy \
-    "git+https://github.com/nmandery/h3ronpy#subdirectory=h3ronpy"
-
-# install healpy from github
-# need to run `auditwheel` to include the shared libs
-python -m pip install auditwheel
-
-# build and repair the wheel
-# - manual clone
-mkdir deps
-git clone --filter=blob:none --quiet https://github.com/healpy/healpy deps/healpy
-pushd deps/healpy
-git submodule update --init --recursive -q
-# - build and repair the wheel
-mkdir -p built_wheel repaired_wheel
-python -m pip wheel --no-deps . --wheel-dir built_wheel
-auditwheel repair --plat linux_x86_64 -w repaired_wheel built_wheel/healpy-*.whl
-# - install the repaired wheel
-python -m pip install --upgrade --no-deps repaired_wheel/healpy-*.whl
-# - clean up
-popd; rm -rf deps
+    "git+https://github.com/nmandery/h3ronpy#subdirectory=h3ronpy" \
+    git+https://github.com/cds-astro/cds-healpix-python
diff --git a/docs/conf.py b/docs/conf.py
@@ -29,6 +29,7 @@
     "IPython.sphinxext.ipython_console_highlighting",
     "sphinx_autosummary_accessors",
     "myst_nb",
+    "sphinxcontrib.bibtex",
 ]
 
 extlinks = {
@@ -96,10 +97,15 @@
     "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
     "lonboard": ("https://developmentseed.org/lonboard/latest", None),
     "healpy": ("https://healpy.readthedocs.io/en/latest", None),
+    "cdshealpix-python": ("https://cds-astro.github.io/cds-healpix-python", None),
     "shapely": ("https://shapely.readthedocs.io/en/stable", None),
 }
 
 # -- myst-nb options ---------------------------------------------------------
 
 nb_execution_timeout = -1
 nb_execution_cache_path = "_build/myst-nb"
+
+# -- sphinxcontrib-bibtex ----------------------------------------------------
+
+bibtex_bibfiles = ["reference_guide/publications.bib"]
diff --git a/docs/index.md b/docs/index.md
@@ -14,28 +14,28 @@ maxdepth: 3
 caption: Tutorials
 hidden: true
 ---
-
-Tutorials <tutorials/index>
+tutorials/h3
+tutorials/healpix
 ```
 
-```{toctree}
----
-maxdepth: 3
-caption: User guide
-hidden: true
----
-Publications <user_guide/publications>
-```
+<!-- ```{toctree} -->
+<!-- --- -->
+<!-- maxdepth: 3 -->
+<!-- caption: User guide -->
+<!-- hidden: true -->
+<!-- --- -->
+<!-- ``` -->
 
 ```{toctree}
 ---
 maxdepth: 3
-caption: Technical information
+caption: Reference guide
 hidden: true
 ---
 
 Changelog <changelog>
 API Reference <api>
+Publications <reference_guide/publications>
 ```
 
 # Welcome to `xdggs`

diff --git a/docs/reference_guide/publications.bib b/docs/reference_guide/publications.bib
@@ -0,0 +1,33 @@
+@misc{magin_2024_13934967,
+  author        = {Magin, Justus and Bovy, Benoit and Delouis, Jean-Marc and Fouilloux, Anne and Coca-Castro, Alejandro and Abernathey, Ryan and Strobl, Peter and Kmoch, Alexander and Odaka, Tina Erica},
+  title         = "{Advancing Geospatial Data Analysis with XDGGS}",
+  year          = 2024,
+  month         = oct,
+  doi           = {10.5281/zenodo.13934967},
+  publisher     = {Zenodo},
+  url           = {https://doi.org/10.5281/zenodo.13934967},
+  version       = {1.0},
+}
+
+@article{isprs-archives-XLVIII-4-W12-2024-75-2024,
+  author        = {Kmoch, A. and Bovy, B. and Magin, J. and Abernathey, R. and Coca-Castro, A. and Strobl, P. and Fouilloux, A. and Loos, D. and Uuemaa, E. and Chan, W. T. and Delouis, J.-M. and Odaka, T.},
+  title         = "{XDGGS: A community-developed Xarray package to support planetary DGGS data cube computations}",
+  journal       = {The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences},
+  year          = 2024,
+  volume        = {XLVIII-4/W12-2024},
+  pages         = {75--80},
+  doi           = {10.5194/isprs-archives-XLVIII-4-W12-2024-75-2024},
+  url           = {https://isprs-archives.copernicus.org/articles/XLVIII-4-W12-2024/75/2024/},
+}
+
+@inproceedings{kmoch2024,
+  title         = {{{XDGGS}}: {{Xarray Extension}} for {{Discrete Global Grid Systems}} ({{DGGS}})},
+  shorttitle    = {{XDGGS}},
+  author        = {Kmoch, Alexander and Bovy, Beno{\^i}t and Magin, Justus and Abernathey, Ryan and Strobl, Peter and {Coca-Castro}, Alejandro and Fouilloux, Anne and Loos, Daniel and Odaka, Tina},
+  year          = {2024},
+  month         = Apr,
+  booktitle     = {{{EGU General Assembly}} 2024},
+  address       = {Vienna, Austria, 14-19 Apr 2024},
+  doi           = {10.5194/egusphere-egu24-15416},
+  urldate       = {2024-11-18},
+}
diff --git a/docs/reference_guide/publications.md b/docs/reference_guide/publications.md
@@ -0,0 +1,9 @@
+# Publications mentioning `xdggs`
+
+```{bibliography} publications.bib
+---
+all: true
+list: bullet
+style: alpha
+---
+```
diff --git a/docs/tutorials/healpix.ipynb b/docs/tutorials/healpix.ipynb
@@ -152,19 +152,29 @@
     "derived_ds"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "11",
+   "metadata": {},
+   "source": [
+    "```{note}\n",
+    "We need to use {py:func}`xarray.testing.assert_allclose` to compare cell centers because the cell center coordinates were computed using a [different library](https://github.com/healpy/healpy) with a slightly different implementation, resulting in small floating point differences.\n",
+    "```"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
-    "xr.testing.assert_equal(derived_ds, original_ds)"
+    "xr.testing.assert_allclose(derived_ds, original_ds)"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "12",
+   "id": "13",
    "metadata": {},
    "source": [
     "### Cell boundary polygons\n",
@@ -175,7 +185,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -185,7 +195,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "14",
+   "id": "15",
    "metadata": {},
    "source": [
     "## Plotting\n",
@@ -200,7 +210,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -219,7 +229,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.7"
+   "version": "3.11.6"
   }
  },
  "nbformat": 4,
Original file line number	Diff line number	Diff line change
Expand Up		@@ -83,4 +83,4 @@ We welcome contributions to `xdggs`! Please follow these steps to get involved:

		## Acknowledgments

		This project was inspired by the increasing need for scalable geospatial data analysis using DGGS and is built upon the robust ecosystem of Xarray.
		This project was initiated using funding from CNES (PANGEO IAOCEA, contract R&T R-S23/DU-0002-025-01) and the European Union (ERC, WaterSmartLand, 101125476, Interreg-BSR, HyTruck, #C031).