Merge pull request #7 from GazzolaLab/wip/geometry

Complete `geometry.py` module: handling sphere and cylinder
GazzolaLab · Jun 18, 2024 · d4f1f48 · d4f1f48
2 parents e497c68 + 6fb6ba6
commit d4f1f48
Show file tree

Hide file tree

Showing 25 changed files with 1,492 additions and 272 deletions.
diff --git a/docs/api/collective.rst b/docs/api/collective.rst
@@ -0,0 +1,14 @@
+Collective Geometry
+===================
+
+Rod-like geometry
+-----------------
+
+.. automodule:: bsr.rod
+   :members:
+
+Stacked geometry
+----------------
+
+.. automodule:: bsr.stack
+   :members:
diff --git a/docs/conf.py b/docs/conf.py
@@ -25,6 +25,7 @@
     "sphinx.ext.viewcode",
     "sphinx.ext.mathjax",
     "sphinx.ext.autosectionlabel",
+    "sphinx.ext.viewcode",
     "sphinx_autodoc_typehints",
     "sphinx_click",
     "numpydoc",
@@ -38,6 +39,7 @@
     "undoc-members",
     "private-members",
     "special-members",
+    "inherited-members",
 ]
 source_suffix = [".rst", ".md"]
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -22,6 +22,7 @@ TODO: Description of the project.
 
    api/file
    api/geometry
+   api/collective
 
 .. toctree::
    :maxdepth: 2

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -173,4 +173,6 @@ branch = true
 omit = [
     "*/.local/*",
 	"setup.py",
+    "*/protocol.py",
+    "macros.py",
 ]
diff --git a/src/bsr/__init__.py b/src/bsr/__init__.py
@@ -1,10 +1,10 @@
 import sys
 from importlib import metadata as importlib_metadata
 
-from .collections import *
 from .file import *
 from .macros import *
 from .rod import *
+from .stack import *
 
 
 def get_version() -> str:

diff --git a/src/bsr/collections.py b/src/bsr/collections.py