fix(dependencies): 🐛 reorganize dependencies

.github/workflows/gh-page.yml

@@ -41,7 +41,8 @@ jobs:
       - name: Install dependencies (uv)
         run: |
           set -e
-          uv sync
+          # Install runtime + docs group (mkdocs, plugins, nb toolchain)
+          uv sync --group docs --dev
           if [ -n "${{ secrets.GH_TOKEN }}" ]; then
             uv pip install git+https://${{ secrets.GH_TOKEN }}@github.com/squidfunk/mkdocs-material-insiders.git
           else

.github/workflows/test-notebooks.yml

@@ -22,7 +22,8 @@ jobs:
 
       - name: Install deps
         run: |
-          uv sync --dev
+          # Need docs stack to execute notebooks via mkdocs-jupyter/nbmake
+          uv sync --group docs --dev
 
       - name: Run nbmake
         env:

CHANGELOG.md

@@ -1,5 +1,29 @@
 # Changelog
 
+## [0.9.0](https://github.com/SongshGeoLab/ABSESpy/compare/v0.8.5...v0.9.0) (2025-10-29)
+
+
+### Features
+
+* **actor, patch:** :sparkles: Add move_to method in Actor and count_agents method in PatchModule ([11e63b2](https://github.com/SongshGeoLab/ABSESpy/commit/11e63b2a95fc72232a5ab96d840bf9ad66743b30))
+* **actor:** :sparkles: Add evaluate method to Actor for scoring candidates with rollback functionality ([bad83ac](https://github.com/SongshGeoLab/ABSESpy/commit/bad83ac22e769cafa092584414a83a603dda3c9b))
+* **agents, space:** :sparkles: Enhance agent and cell functionality with new properties and methods ([cacf3d0](https://github.com/SongshGeoLab/ABSESpy/commit/cacf3d04957ddf54d949277c86e3bc80af415dad))
+* **core:** Protocol-based architecture refactoring ([12534d8](https://github.com/SongshGeoLab/ABSESpy/commit/12534d8c93517336c57f0d86a57aaab366fb6af7))
+* **examples:** :sparkles: Remove outdated agent and analysis files, add configuration and quick start notebook ([d1fed62](https://github.com/SongshGeoLab/ABSESpy/commit/d1fed623172cdeb8cddcfe3a560f0be94c340c68))
+* **examples:** :white_check_mark: Introduce configuration file and enhance model dynamics ([1fa3e0c](https://github.com/SongshGeoLab/ABSESpy/commit/1fa3e0cc879c4c7e01f19b4040160e410006105e))
+* **patch:** :sparkles: Implement __getitem__ method for PatchModule with numpy-style indexing ([1c66edb](https://github.com/SongshGeoLab/ABSESpy/commit/1c66edb3e833d145295e0ae139e54d89340e2c18))
+
+
+### Bug Fixes
+
+* **sequences:** Fix attribute access in better() method ([2f1089f](https://github.com/SongshGeoLab/ABSESpy/commit/2f1089f40267cb2b7b5967f2d7519fec6fff3a15))
+
+
+### Documentation
+
+* **docs:** :memo: Enhance UML documentation and integrate Mermaid diagrams ([62a9cdd](https://github.com/SongshGeoLab/ABSESpy/commit/62a9cdd62715c6c72439def968a1a8a896b16aae))
+* **tutorials, docs:** :memo: Expand tutorial content and enhance documentation structure ([316c972](https://github.com/SongshGeoLab/ABSESpy/commit/316c97203b21c94c0a797bb9199d2a8ca4818c60))
+
 ## [0.7.5](https://github.com/SongshGeoLab/ABSESpy/compare/v0.7.4...v0.7.5) (2025-02-16)
 
 

abses/space/patch.py

@@ -573,12 +573,20 @@ def _select_by_geometry(
                 Args pass to the function `rasterasterio.mask.mask`.
 
         Returns:
-            A numpy array of clipped cells.
+            A boolean numpy 2D array mask where True indicates selected cells.
         """
-        # TODO 研究一下为什么需要转换为整数，转换bool结果不一样了
-        return self.xda.astype(np.int32, casting="safe").rio.clip(
+        # Use float dtype so rioxarray can represent out-of-geometry as NaN.
+        # Boolean selection must be based on NaN mask, not on underlying cell values
+        # (otherwise cells with value 0 would be incorrectly excluded).
+        clipped = self.xda.astype(np.float32).rio.clip(
             [geometry], all_touched=False, drop=False, **kwargs
         )
+        # Convert to boolean mask: True where data is finite (inside geometry)
+        mask_da = np.isfinite(clipped.to_numpy())
+        # Ensure 2D mask (squeeze potential band dimension)
+        if mask_da.ndim == 3:
+            mask_da = np.squeeze(mask_da, axis=0)
+        return mask_da
 
     def select(
         self,
@@ -620,8 +628,9 @@ def select(
             mask_ = self._attr_or_array(where).reshape(self.shape2d)
         else:
             raise TypeError(f"{type(where)} is not supported for selecting cells.")
-        mask_ = np.nan_to_num(mask_, nan=0.0).astype(bool)
-        return ActorsList(self.model, self.array_cells[mask_])
+        # mask_ is expected to be boolean here
+        mask_bool = mask_.astype(bool)
+        return ActorsList(self.model, self.array_cells[mask_bool])
 
     sel = select
 

pyproject.toml

@@ -9,7 +9,7 @@ line_length = 79
 
 [project]
 name = "abses"
-version = "0.7.5"
+version = "0.9.0"
 description = "ABSESpy makes it easier to build artificial Social-ecological systems with real GeoSpatial datasets and fully incorporate human behaviour."
 authors = [{name = "Shuang Song", email = "songshgeo@gmail.com"}]
 license = {text = "Apache 2.0 License"}
@@ -41,23 +41,38 @@ dependencies = [
     "numpy<2",
     "urllib3",
     "icons",
-    "solara",
-    "mkdocs>=1.6.1",
-    # Note: mkdocs-material-insiders requires authentication and MUST NOT be declared here
-    # to avoid build backend variable expansion errors (e.g. Unknown context field).
-    # Install locally via environment variable before building docs, e.g.:
-    #   export MKDOCS_INSIDER=your_token
-    #   uv pip install "git+https://${MKDOCS_INSIDER}@github.com/squidfunk/mkdocs-material-insiders.git"
-    "mkdocs-jupyter>=0.25.1",
-    "mkdocstrings>=0.30.1",
-    "mkdocs-static-i18n>=1.3.0",
 ]
 
 [project.urls]
 Homepage = "https://github.com/SongshGeoLab/ABSESpy"
 Documentation = "https://absespy.github.io/ABSESpy/"
 Repository = "https://github.com/SongshGeoLab/ABSESpy"
 
+[project.optional-dependencies]
+# Optional docs-related dependencies. Not required at runtime.
+docs = [
+    "mkdocs>=1.6.1",
+    "mkdocs-git-revision-date-localized-plugin>=1.2.0",
+    "mkdocs-minify-plugin>=0.7.1",
+    "mkdocs-redirects>=1.2.1",
+    "mkdocs-awesome-pages-plugin>=2.9.2",
+    "mkdocs-git-authors-plugin>=0.7.2",
+    "mkdocstrings>=0.30.1",
+    "mkdocstrings[python]>=0.24.0",
+    "mkdocs-bibtex>=2.11.0",
+    "mkdocs-macros-plugin>=1.0.4",
+    "mkdocs-jupyter>=0.25.1",
+    "mkdocs-callouts>=1.9.1",
+    "mkdocs-glightbox>=0.3.4",
+    "mkdocs-exclude>=1.0.2",
+    "mkdocs-simple-hooks>=0.1.5",
+    "mkdocs-static-i18n>=1.3.0",
+    "pymdown-extensions>=10.7",
+    "mike>=2.0.0",
+    "nbmake>=1.5.5",
+    "nbconvert>=7.16.6",
+]
+
 [project.entry-points."hydra.searchpath"]
 abses = "hydra_plugins.abses_searchpath_plugin:ABSESpySearchPathPlugin"
 
@@ -89,17 +104,21 @@ dev = [
     "tox>=4.11.3",
     "lxml>=5.2.1",
     "griffe>=1.14.0",
-    # Docs dependencies
-    "mkdocs>=1.5.3",
+]
+
+# Dedicated group for docs build. Install with: uv sync --group docs
+docs = [
+    "mkdocs>=1.6.1",
     "mkdocs-git-revision-date-localized-plugin>=1.2.0",
     "mkdocs-minify-plugin>=0.7.1",
     "mkdocs-redirects>=1.2.1",
     "mkdocs-awesome-pages-plugin>=2.9.2",
     "mkdocs-git-authors-plugin>=0.7.2",
+    "mkdocstrings>=0.30.1",
     "mkdocstrings[python]>=0.24.0",
     "mkdocs-bibtex>=2.11.0",
     "mkdocs-macros-plugin>=1.0.4",
-    "mkdocs-jupyter>=0.24.5",
+    "mkdocs-jupyter>=0.25.1",
     "mkdocs-callouts>=1.9.1",
     "mkdocs-glightbox>=0.3.4",
     "mike>=2.0.0",