Merge pull request #32 from knubez/pygeos

Remove PyGEOS
knubez · Aug 8, 2024 · 0096017 · 0096017
2 parents 29c2edf + 48def48
commit 0096017
Show file tree

Hide file tree

Showing 4 changed files with 19 additions and 4 deletions.
diff --git a/docs/examples/sample-mpas-ug-data.ipynb b/docs/examples/sample-mpas-ug-data.ipynb
@@ -342,7 +342,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%watermark -v -w -p cartopy,dask,gdown,geopandas,joblib,matplotlib,netCDF4,numpy,pandas,pygeos,regionmask,scipy,seaborn,shapely,skimage,xarray"
+    "%watermark -v -w -p cartopy,dask,gdown,geopandas,joblib,matplotlib,netCDF4,numpy,pandas,regionmask,scipy,seaborn,shapely,skimage,xarray"
    ]
   }
  ],

diff --git a/docs/index.md b/docs/index.md
@@ -62,6 +62,21 @@ with `matplotlib` 3.8.0 (mid Sep 2023), but 3.8.1 (end of Oct 2023)
 restored the previous behavior.
 ```
 
+```{note}
+In the past (before TAMS v0.1.5, mid Aug 2024),
+the TAMS conda-forge recipe included PyGEOS,
+in order to make certain GeoPandas and regionmask operations faster.
+[In Shapely v2](https://shapely.readthedocs.io/en/stable/release/2.x.html)
+(mid Dec 2022, but not relevant to TAMS
+[until mid 2023](https://geopandas.org/en/stable/docs/user_guide/pygeos_to_shapely.html)),
+[PyGEOS is part of Shapely](https://shapely.readthedocs.io/en/stable/migration_pygeos.html)
+and doesn't need to be installed separately.
+GeoPandas dropped support for Shapely v1 and PyGEOS in
+[their v1 release](https://github.com/geopandas/geopandas/releases/tag/v1.0.0) (late Jun 2024).
+[PyGEOS on conda-forge](https://github.com/conda-forge/pygeos-feedstock) has been retired,
+so you likely won't be able to install it in new Conda environments in any case.
+```
+
 ### Development install
 
 If you want to modify the code, you can first clone the repo

diff --git a/environment-dev.yml b/environment-dev.yml
@@ -20,7 +20,6 @@ dependencies:
   - gdown
   - joblib
   - netcdf4
-  - pygeos
   - regionmask >=0.9
   - scipy
   - seaborn >=0.13.2

diff --git a/tams/core.py b/tams/core.py
@@ -380,7 +380,8 @@ def _data_in_contours_regionmask(
     # Form regionmask(s)
     shapes = contours[["geometry"]]
     regions = regionmask.from_geopandas(shapes)
-    mask = regions.mask(data)  # works but takes long (though shorter with pygeos)!
+    mask = regions.mask(data)
+    # Note: before Shapely v2, having `pygeos` installed made this faster
 
     # Aggregate points inside contour
     new_data_ = {
@@ -1126,7 +1127,7 @@ def f(g):
     # Trying regionmask
     shapes = cs235[["geometry"]]
     regions = regionmask.from_geopandas(shapes)
-    mask = regions.mask(tb)  # works but takes long (though shorter with pygeos)!
+    mask = regions.mask(tb)
 
     regions.plot(ax=ax)