From 1f5621383b8eed9bec77ff8a9509014faf9d64f5 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 29 Oct 2025 09:22:33 +0000 Subject: [PATCH 1/4] chore(master): release 0.9.0 --- CHANGELOG.md | 24 ++++++++++++++++++++++++ pyproject.toml | 2 +- 2 files changed, 25 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 73bc9791..bf812d59 100644 --- a/CHANGELOG.md +++ b/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+* **examples:** :sparkles: Remove outdated agent and analysis files, add configuration and quick start notebook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) diff --git a/pyproject.toml b/pyproject.toml index 737c7d6e..062b52d5 100644 --- a/pyproject.toml +++ b/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"} From 6e1dd9e813e40700ce7a823bd0f8d08276eb1630 Mon Sep 17 00:00:00 2001 From: SongshGeo Date: Wed, 29 Oct 2025 10:33:57 +0100 Subject: [PATCH 2/4] fix(dependencies): :bug: reorganize documentation dependencies in pyproject.toml so that mkdocs-jupyter is not required anymore This commit refactors the `pyproject.toml` file to separate documentation-related dependencies into an optional group. The previous direct dependencies for documentation tools have been moved under `[project.optional-dependencies]` to enhance clarity and organization. Additionally, the version constraints for `mkdocs` and related plugins have been updated to ensure compatibility and improve the documentation build process. --- pyproject.toml | 45 ++++++++++++++++++++++++++++++++------------- 1 file changed, 32 insertions(+), 13 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 062b52d5..3c2f7b82 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -41,16 +41,6 @@ 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] @@ -58,6 +48,31 @@ 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", From c9b99fe96effdfc373d9c7a960ee32f47915b62e Mon Sep 17 00:00:00 2001 From: SongshGeo Date: Wed, 29 Oct 2025 10:39:16 +0100 Subject: [PATCH 3/4] fix(ci): :wrench: update GitHub Actions workflows to install documentation dependencies This commit modifies the GitHub Actions workflows for both documentation deployment and notebook testing. The installation commands for dependencies are updated to use `uv sync --group docs --dev`, ensuring that the necessary documentation tools, including mkdocs and related plugins, are installed correctly. This change enhances the clarity and efficiency of the CI/CD process for documentation management. --- .github/workflows/gh-page.yml | 3 ++- .github/workflows/test-notebooks.yml | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/gh-page.yml b/.github/workflows/gh-page.yml index 1ab1e53a..fb3e1070 100644 --- a/.github/workflows/gh-page.yml +++ b/.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 diff --git a/.github/workflows/test-notebooks.yml b/.github/workflows/test-notebooks.yml index 8dd7360e..c52e7734 100644 --- a/.github/workflows/test-notebooks.yml +++ b/.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: From 7b7ed83fb3de131a4fd2dfa2eb56dcd2b486c4cf Mon Sep 17 00:00:00 2001 From: SongshGeo Date: Wed, 29 Oct 2025 10:57:15 +0100 Subject: [PATCH 4/4] chore(dependencies): :arrow_up: update package versions and reorganize optional dependencies in uv.lock This commit updates the version of the "abses" package to 0.9.0 and reorganizes the optional dependencies in the `uv.lock` file. Documentation-related dependencies have been grouped under `[package.optional-dependencies]`, enhancing clarity and organization. Additionally, several development dependencies have been added or updated to ensure compatibility and improve the development workflow. --- abses/space/patch.py | 19 +++++-- uv.lock | 121 ++++++++++++++++++++++++++++--------------- 2 files changed, 94 insertions(+), 46 deletions(-) diff --git a/abses/space/patch.py b/abses/space/patch.py index 4e037866..4c1086b3 100644 --- a/abses/space/patch.py +++ b/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 diff --git a/uv.lock b/uv.lock index 2cd60b1c..5500e679 100644 --- a/uv.lock +++ b/uv.lock @@ -8,7 +8,7 @@ resolution-markers = [ [[package]] name = "abses" -version = "0.7.5" +version = "0.9.0" source = { editable = "." } dependencies = [ { name = "fiona" }, @@ -20,21 +20,39 @@ dependencies = [ { name = "loguru" }, { name = "mesa" }, { name = "mesa-geo" }, - { name = "mkdocs" }, - { name = "mkdocs-jupyter" }, - { name = "mkdocs-static-i18n" }, - { name = "mkdocstrings" }, { name = "netcdf4" }, { name = "numpy" }, { name = "pendulum" }, { name = "rioxarray" }, { name = "seaborn" }, - { name = "solara" }, { name = "typing-extensions" }, { name = "urllib3" }, { name = "xarray" }, ] +[package.optional-dependencies] +docs = [ + { name = "mike" }, + { name = "mkdocs" }, + { name = "mkdocs-awesome-pages-plugin" }, + { name = "mkdocs-bibtex" }, + { name = "mkdocs-callouts" }, + { name = "mkdocs-exclude" }, + { name = "mkdocs-git-authors-plugin" }, + { name = "mkdocs-git-revision-date-localized-plugin" }, + { name = "mkdocs-glightbox" }, + { name = "mkdocs-jupyter" }, + { name = "mkdocs-macros-plugin" }, + { name = "mkdocs-minify-plugin" }, + { name = "mkdocs-redirects" }, + { name = "mkdocs-simple-hooks" }, + { name = "mkdocs-static-i18n" }, + { name = "mkdocstrings", extra = ["python"] }, + { name = "nbconvert" }, + { name = "nbmake" }, + { name = "pymdown-extensions" }, +] + [package.dev-dependencies] dev = [ { name = "allure-pytest" }, @@ -49,6 +67,22 @@ dev = [ { name = "jupyterlab-execute-time" }, { name = "lxml" }, { name = "matplotlib" }, + { name = "mypy" }, + { name = "nbstripout" }, + { name = "pre-commit" }, + { name = "pre-commit-hooks" }, + { name = "pydocstyle" }, + { name = "pylint" }, + { name = "pytest" }, + { name = "pytest-clarity" }, + { name = "pytest-cov" }, + { name = "pytest-sugar" }, + { name = "ruff" }, + { name = "scriv" }, + { name = "sourcery" }, + { name = "tox" }, +] +docs = [ { name = "mike" }, { name = "mkdocs" }, { name = "mkdocs-awesome-pages-plugin" }, @@ -65,23 +99,9 @@ dev = [ { name = "mkdocs-simple-hooks" }, { name = "mkdocs-static-i18n" }, { name = "mkdocstrings", extra = ["python"] }, - { name = "mypy" }, { name = "nbconvert" }, { name = "nbmake" }, - { name = "nbstripout" }, - { name = "pre-commit" }, - { name = "pre-commit-hooks" }, - { name = "pydocstyle" }, - { name = "pylint" }, { name = "pymdown-extensions" }, - { name = "pytest" }, - { name = "pytest-clarity" }, - { name = "pytest-cov" }, - { name = "pytest-sugar" }, - { name = "ruff" }, - { name = "scriv" }, - { name = "sourcery" }, - { name = "tox" }, ] [package.metadata] @@ -95,20 +115,36 @@ requires-dist = [ { name = "loguru", specifier = ">=0.7" }, { name = "mesa", specifier = ">=3.1.0" }, { name = "mesa-geo", specifier = ">=0.9.1" }, - { name = "mkdocs", specifier = ">=1.6.1" }, - { name = "mkdocs-jupyter", specifier = ">=0.25.1" }, - { name = "mkdocs-static-i18n", specifier = ">=1.3.0" }, - { name = "mkdocstrings", specifier = ">=0.30.1" }, + { name = "mike", marker = "extra == 'docs'", specifier = ">=2.0.0" }, + { name = "mkdocs", marker = "extra == 'docs'", specifier = ">=1.6.1" }, + { name = "mkdocs-awesome-pages-plugin", marker = "extra == 'docs'", specifier = ">=2.9.2" }, + { name = "mkdocs-bibtex", marker = "extra == 'docs'", specifier = ">=2.11.0" }, + { name = "mkdocs-callouts", marker = "extra == 'docs'", specifier = ">=1.9.1" }, + { name = "mkdocs-exclude", marker = "extra == 'docs'", specifier = ">=1.0.2" }, + { name = "mkdocs-git-authors-plugin", marker = "extra == 'docs'", specifier = ">=0.7.2" }, + { name = "mkdocs-git-revision-date-localized-plugin", marker = "extra == 'docs'", specifier = ">=1.2.0" }, + { name = "mkdocs-glightbox", marker = "extra == 'docs'", specifier = ">=0.3.4" }, + { name = "mkdocs-jupyter", marker = "extra == 'docs'", specifier = ">=0.25.1" }, + { name = "mkdocs-macros-plugin", marker = "extra == 'docs'", specifier = ">=1.0.4" }, + { name = "mkdocs-minify-plugin", marker = "extra == 'docs'", specifier = ">=0.7.1" }, + { name = "mkdocs-redirects", marker = "extra == 'docs'", specifier = ">=1.2.1" }, + { name = "mkdocs-simple-hooks", marker = "extra == 'docs'", specifier = ">=0.1.5" }, + { name = "mkdocs-static-i18n", marker = "extra == 'docs'", specifier = ">=1.3.0" }, + { name = "mkdocstrings", marker = "extra == 'docs'", specifier = ">=0.30.1" }, + { name = "mkdocstrings", extras = ["python"], marker = "extra == 'docs'", specifier = ">=0.24.0" }, + { name = "nbconvert", marker = "extra == 'docs'", specifier = ">=7.16.6" }, + { name = "nbmake", marker = "extra == 'docs'", specifier = ">=1.5.5" }, { name = "netcdf4", specifier = ">=1.6" }, { name = "numpy", specifier = "<2" }, { name = "pendulum", specifier = ">=3.0.0" }, + { name = "pymdown-extensions", marker = "extra == 'docs'", specifier = ">=10.7" }, { name = "rioxarray", specifier = ">=0.13" }, { name = "seaborn", specifier = ">=0.13" }, - { name = "solara" }, { name = "typing-extensions", specifier = ">=4,<5" }, { name = "urllib3" }, { name = "xarray", specifier = ">=2023" }, ] +provides-extras = ["docs"] [package.metadata.requires-dev] dev = [ @@ -124,8 +160,24 @@ dev = [ { name = "jupyterlab-execute-time", specifier = ">=3.0.1" }, { name = "lxml", specifier = ">=5.2.1" }, { name = "matplotlib", specifier = ">=3.7.2" }, + { name = "mypy", specifier = ">=1.6.1" }, + { name = "nbstripout", specifier = ">=0.6.2" }, + { name = "pre-commit", specifier = ">=3.0.1" }, + { name = "pre-commit-hooks", specifier = ">=4.4.0" }, + { name = "pydocstyle", specifier = ">=6.3.0" }, + { name = "pylint", specifier = ">=3.0.1" }, + { name = "pytest", specifier = ">=7.2.1" }, + { name = "pytest-clarity" }, + { name = "pytest-cov", specifier = ">=4.1.0" }, + { name = "pytest-sugar", specifier = ">=0.9.7" }, + { name = "ruff", specifier = ">=0.1.0" }, + { name = "scriv", specifier = ">=1.2.0" }, + { name = "sourcery", specifier = ">=1.0.6" }, + { name = "tox", specifier = ">=4.11.3" }, +] +docs = [ { name = "mike", specifier = ">=2.0.0" }, - { name = "mkdocs", specifier = ">=1.5.3" }, + { name = "mkdocs", specifier = ">=1.6.1" }, { name = "mkdocs-awesome-pages-plugin", specifier = ">=2.9.2" }, { name = "mkdocs-bibtex", specifier = ">=2.11.0" }, { name = "mkdocs-callouts", specifier = ">=1.9.1" }, @@ -133,30 +185,17 @@ dev = [ { name = "mkdocs-git-authors-plugin", specifier = ">=0.7.2" }, { name = "mkdocs-git-revision-date-localized-plugin", specifier = ">=1.2.0" }, { name = "mkdocs-glightbox", specifier = ">=0.3.4" }, - { name = "mkdocs-jupyter", specifier = ">=0.24.5" }, + { name = "mkdocs-jupyter", specifier = ">=0.25.1" }, { name = "mkdocs-macros-plugin", specifier = ">=1.0.4" }, { name = "mkdocs-minify-plugin", specifier = ">=0.7.1" }, { name = "mkdocs-redirects", specifier = ">=1.2.1" }, { name = "mkdocs-simple-hooks", specifier = ">=0.1.5" }, { name = "mkdocs-static-i18n", specifier = ">=1.3.0" }, + { name = "mkdocstrings", specifier = ">=0.30.1" }, { name = "mkdocstrings", extras = ["python"], specifier = ">=0.24.0" }, - { name = "mypy", specifier = ">=1.6.1" }, { name = "nbconvert", specifier = ">=7.16.6" }, { name = "nbmake", specifier = ">=1.5.5" }, - { name = "nbstripout", specifier = ">=0.6.2" }, - { name = "pre-commit", specifier = ">=3.0.1" }, - { name = "pre-commit-hooks", specifier = ">=4.4.0" }, - { name = "pydocstyle", specifier = ">=6.3.0" }, - { name = "pylint", specifier = ">=3.0.1" }, { name = "pymdown-extensions", specifier = ">=10.7" }, - { name = "pytest", specifier = ">=7.2.1" }, - { name = "pytest-clarity" }, - { name = "pytest-cov", specifier = ">=4.1.0" }, - { name = "pytest-sugar", specifier = ">=0.9.7" }, - { name = "ruff", specifier = ">=0.1.0" }, - { name = "scriv", specifier = ">=1.2.0" }, - { name = "sourcery", specifier = ">=1.0.6" }, - { name = "tox", specifier = ">=4.11.3" }, ] [[package]]