Merge pull request #83 from ABSESpy/dev

Version 0.6.5: Fixed two bugs.

CHANGELOG.md

@@ -1,4 +1,12 @@
 
+<a id='changelog-0.6.5'></a>
+# 0.6.5 — 2024-05-17
+
+## Fixed bugs
+
+- [x] #bug🐛 solving situation when entities with prob are not enough for expected size in random choose
+- [x] #bug🐛  Fixed shape `(1, x)` natural patch squeezed bug
+
 <a id='changelog-0.6.4'></a>
 # 0.6.4 — 2024-05-16
 

abses/__init__.py

@@ -31,7 +31,7 @@
     "load_data",
     "logger",
 ]
-__version__ = "v0.6.4"
+__version__ = "v0.6.5"
 
 from ._bases.logging import logger
 from .actor import Actor, alive_required, perception

abses/patch.py

@@ -614,12 +614,13 @@ def _add_attribute(
         flipud: bool = False,
         apply_mask: bool = False,
     ) -> None:
-        data = np.squeeze(data)
-        if data.shape != self.shape2d:
+        try:
+            data = data.reshape(self.shape2d)
+        except ValueError as e:
             raise ValueError(
                 f"Data shape does not match raster shape. "
                 f"Expected {self.shape2d}, received {data.shape}."
-            )
+            ) from e
         if apply_mask:
             set_null_values(data, ~self.mask)
         if attr_name is None:

abses/random.py

@@ -5,6 +5,9 @@
 # GitHub   : https://github.com/SongshGeo
 # Website: https://cv.songshgeo.com/
 
+"""在列表中随机操作主体
+"""
+
 from __future__ import annotations
 
 from itertools import combinations
@@ -89,7 +92,8 @@ def clean_p(self, prob: Union[np.ndarray, str]) -> np.ndarray:
         """
         if isinstance(prob, str):
             prob = self.actors.array(attr=prob)
-        prob = np.array(make_list(prob))
+        else:
+            prob = np.array(make_list(prob))
         length = len(prob)
         prob = np.nan_to_num(prob)
         prob[prob < 0] = 0.0
@@ -115,6 +119,7 @@ def choice(
         replace: bool = False,
         as_list: bool = False,
         when_empty: WHEN_EMPTY = "raise exception",
+        double_check: bool = False,
     ) -> Optional[Actor | ActorsList[Actor]]:
         """Randomly choose one or more actors from the current self object.
 
@@ -154,8 +159,14 @@ def choice(
             raise ABSESpyError(
                 f"Trying to choose {size} actors from {self.actors}."
             )
+        # 有概率的时候，先清理概率
         if prob is not None:
             prob = self.clean_p(prob=prob)
+            valid_prob = prob.astype(bool)
+            # 特别处理有概率的主体数量不足预期的情况
+            if valid_prob.sum() < size and not replace:
+                return self._when_p_not_enough(double_check, valid_prob, size)
+        # 其他情况就正常随机选择
         chosen = self.generator.choice(
             self.actors, size=size, replace=replace, p=prob
         )
@@ -165,6 +176,25 @@ def choice(
             else self._to_actors_list(chosen)
         )
 
+    def _when_p_not_enough(self, double_check, valid_prob, size):
+        if not double_check:
+            raise ABSESpyError(
+                f"Only {valid_prob.sum()} entities have possibility, "
+                f"but {size} entities are expected. "
+                "Please check the probability settings.\n"
+                "If you want to choose with replacement, set `replace=True`.\n"
+                "If you want to choose with equal probability, set `prob=None`.\n"
+                "If you want to choose the valid entities firstly, "
+                "and then choose others equally, set `double_check=True'`."
+            )
+        first_chosen = self.actors.select(valid_prob)
+        others = self.actors.select(~valid_prob)
+        remain_size = size - len(first_chosen)
+        second_chosen = self.generator.choice(
+            others, remain_size, replace=False
+        )
+        return self._to_actors_list([*first_chosen, *second_chosen])
+
     def new(
         self,
         actor_cls: Type[Actor],

docs/index.md

@@ -7,7 +7,7 @@ description: "Agent-Based Social-ecological systems Modelling Framework in Pytho
 
 <!-- Language: [English Readme](#) | [简体中文](README_ch) -->
 
-**Date**: January. 11, 2024, **Version**: 0.6.4
+**Date**: January. 11, 2024, **Version**: 0.6.5
 
 **Useful links**: [Install](home/Installation.md) | [Source Repository](https://github.com/ABSESpy/ABSESpy) | [Issues & Ideas](https://github.com/ABSESpy/ABSESpy/issues) | [Q&A Support](https://github.com/ABSESpy/ABSESpy/discussions)
 

pyproject.toml

@@ -31,7 +31,7 @@ line_length = 79
 
 [tool.poetry]
 name = "abses"
-version = "0.6.4"
+version = "0.6.5"
 description = "ABSESpy makes it easier to build artificial Social-ecological systems with real GeoSpatial datasets and fully incorporate human behaviour."
 authors = ["Shuang Song <[email protected]>"]
 license = "Apache 2.0 License"
@@ -51,15 +51,15 @@ abses = "hydra_plugins.abses_searchpath_plugin:ABSESpySearchPathPlugin"
 python = ">=3.9,<3.12"
 netcdf4 = ">=1.6"
 hydra-core = "~1.3"
-mesa-geo = "~0.7"
-xarray = "~2024"
+mesa-geo = ">=0.6"
+xarray = ">=2023"
 fiona = ">1.8"
-loguru = "~0.7"
+loguru = ">=0.7"
 rioxarray = ">=0.13"
 pendulum = "~2"
 geopandas = "~0"
 typing-extensions = "~4"
-fontawesome = "~5"
+fontawesome = ">=5"
 seaborn = ">=0.13"
 
 [tool.poetry.group.dev.dependencies]

requirements.txt

@@ -56,7 +56,7 @@ loguru==0.7.2 ; python_version >= "3.9" and python_version < "3.12"
 markdown-it-py==3.0.0 ; python_version >= "3.9" and python_version < "3.12"
 markupsafe==2.1.5 ; python_version >= "3.9" and python_version < "3.12"
 matplotlib-inline==0.1.7 ; python_version >= "3.9" and python_version < "3.12"
-matplotlib==3.8.4 ; python_version >= "3.9" and python_version < "3.12"
+matplotlib==3.9.0 ; python_version >= "3.9" and python_version < "3.12"
 mdurl==0.1.2 ; python_version >= "3.9" and python_version < "3.12"
 mesa-geo==0.7.1 ; python_version >= "3.9" and python_version < "3.12"
 mesa-viz-tornado==0.1.3 ; python_version >= "3.9" and python_version < "3.12"
@@ -73,7 +73,7 @@ parso==0.8.4 ; python_version >= "3.9" and python_version < "3.12"
 pendulum==2.1.2 ; python_version >= "3.9" and python_version < "3.12"
 pexpect==4.9.0 ; python_version >= "3.9" and python_version < "3.12" and sys_platform != "win32"
 pillow==10.3.0 ; python_version >= "3.9" and python_version < "3.12"
-platformdirs==4.2.1 ; python_version >= "3.9" and python_version < "3.12"
+platformdirs==4.2.2 ; python_version >= "3.9" and python_version < "3.12"
 prompt-toolkit==3.0.43 ; python_version >= "3.9" and python_version < "3.12"
 psutil==5.9.8 ; python_version >= "3.9" and python_version < "3.12"
 ptyprocess==0.7.0 ; python_version >= "3.9" and python_version < "3.12" and sys_platform != "win32"
@@ -93,7 +93,7 @@ rasterio==1.3.10 ; python_version >= "3.9" and python_version < "3.12"
 reacton==1.8.3 ; python_version >= "3.9" and python_version < "3.12"
 referencing==0.35.1 ; python_version >= "3.9" and python_version < "3.12"
 requests==2.31.0 ; python_version >= "3.9" and python_version < "3.12"
-rich-click==1.8.1 ; python_version >= "3.9" and python_version < "3.12"
+rich-click==1.8.2 ; python_version >= "3.9" and python_version < "3.12"
 rich==13.7.1 ; python_version >= "3.9" and python_version < "3.12"
 rioxarray==0.15.0 ; python_version >= "3.9" and python_version < "3.12"
 rpds-py==0.18.1 ; python_version >= "3.9" and python_version < "3.12"
@@ -105,10 +105,10 @@ shapely==2.0.4 ; python_version >= "3.9" and python_version < "3.12"
 six==1.16.0 ; python_version >= "3.9" and python_version < "3.12"
 sniffio==1.3.1 ; python_version >= "3.9" and python_version < "3.12"
 snuggs==1.4.7 ; python_version >= "3.9" and python_version < "3.12"
-solara-server[dev,starlette]==1.32.1 ; python_version >= "3.9" and python_version < "3.12"
-solara-ui==1.32.1 ; python_version >= "3.9" and python_version < "3.12"
-solara-ui[all]==1.32.1 ; python_version >= "3.9" and python_version < "3.12"
-solara==1.32.1 ; python_version >= "3.9" and python_version < "3.12"
+solara-server[dev,starlette]==1.32.2 ; python_version >= "3.9" and python_version < "3.12"
+solara-ui==1.32.2 ; python_version >= "3.9" and python_version < "3.12"
+solara-ui[all]==1.32.2 ; python_version >= "3.9" and python_version < "3.12"
+solara==1.32.2 ; python_version >= "3.9" and python_version < "3.12"
 soupsieve==2.5 ; python_version >= "3.9" and python_version < "3.12"
 stack-data==0.6.3 ; python_version >= "3.9" and python_version < "3.12"
 starlette==0.37.2 ; python_version >= "3.9" and python_version < "3.12"
@@ -127,6 +127,6 @@ wcwidth==0.2.13 ; python_version >= "3.9" and python_version < "3.12"
 websockets==12.0 ; python_version >= "3.9" and python_version < "3.12"
 widgetsnbextension==4.0.10 ; python_version >= "3.9" and python_version < "3.12"
 win32-setctime==1.1.0 ; python_version >= "3.9" and python_version < "3.12" and sys_platform == "win32"
-xarray==2024.3.0 ; python_version >= "3.9" and python_version < "3.12"
+xarray==2024.5.0 ; python_version >= "3.9" and python_version < "3.12"
 xyzservices==2024.4.0 ; python_version >= "3.9" and python_version < "3.12"
-zipp==3.18.1 ; python_version >= "3.9" and python_version < "3.10"
+zipp==3.18.2 ; python_version >= "3.9" and python_version < "3.10"

tests/api/test_random.py

@@ -10,6 +10,7 @@
 
 from abses import Actor, MainModel
 from abses._bases.errors import ABSESpyError
+from abses.sequences import ActorsList
 
 
 class TestRandomActorsList:
@@ -67,6 +68,7 @@ def test_clean_p(self, main: MainModel, actors_num, p, expected_p):
 
         # assert
         assert np.allclose(possibilities, expected_p)
+        assert np.sum(possibilities) == 1
 
     @pytest.mark.parametrize(
         "num, size, replace",
@@ -89,21 +91,27 @@ def test_bad_choose(self, main: MainModel, num, size, replace):
             (2, [0.1, 0.4], False, [0, 1]),
             (2, [np.nan, 1], True, [1, 1]),
             (1, [np.nan, 1], False, [1]),
+            (2, [0, 1], False, [0, 1]),
         ],
         ids=[
             "choose all two",
             "expected two, but only one to choose",
             "only one to choose",
+            "double_check choosing",
         ],
     )
     def test_random_choose(self, main: MainModel, size, p, replace, expected):
         """测试从列表中随机抽取"""
         # arrange
-        agents = main.agents.new(Actor, num=2)
+        agents: ActorsList = main.agents.new(Actor, num=2)
 
         # act
         chosen = agents.random.choice(
-            size=size, prob=p, as_list=True, replace=replace
+            size=size,
+            prob=p,
+            as_list=True,
+            replace=replace,
+            double_check=True,
         )
 
         # assert