Preparing for version 2.73

CHANGELOG.md

@@ -1,5 +1,23 @@
 ## Changelog
 
+### 2.73 (2/27/24)
+
+- Changed default bounce interactions from the reflection method to the overlap method.
+- Added PYTHON_VERSION as a compile option.
+- Trying to reduce warnings from gitHub dependabot.
+- Fixed bug in cmdsetreactionratemolcount command.
+
+### 2.72 (8/17/23)
+
+- Minor improvements to Tiff saving.
+- Support for diffusion coefficient changes at surfaces.
+- Improved error handling, command line input, and logging functionality.
+- Added command line options with double hyphens.
+- Fixed some issues that caused compiler warnings.
+- Fixed a bug in the rate_rule statement.
+- Increased standard string lengths from 256 to 512 characters, and long strings to 4096 characters.
+- Fixed sphere reflection algorithm for the "bounce -2" setting.
+
 ### 2.71 (2/5/23)
 
 - Fixed bug in which graphics were called by Python API even when turned off.

CMakeLists.txt

@@ -30,7 +30,7 @@ if(NOT SMOLDYN_VERSION)
         else()
             # minute-ly release.
             string(TIMESTAMP STAMP "%Y%m%d%H%M")
-            set(SMOLDYN_VERSION "2.72.dev${STAMP}")
+            set(SMOLDYN_VERSION "2.73.dev${STAMP}")
         endif()
     endif()
 endif()

docs/Smoldyn/SmoldynCodeDoc.tex

@@ -43,8 +43,8 @@
 \pretolerance=10000
 
 \title{Smoldyn Code Documentation} 
-\subtitle{Version 2.72}
-\date{\copyright August, 2023}
+\subtitle{Version 2.73}
+\date{\copyright February, 2024}
 \author{Steve Andrews}
 \maketitle
 
@@ -7060,9 +7060,9 @@ \subsection*{Modifications for version 2.72 (released 8/17/23)}
 \item Merged an automated pull request that might fix dependabot alerts about out of date scipy.
 \item Removed \ttt{public std::unary\_function<type, type>} instances from tree\_iterator.hpp (part of NSV code) because this is deprecated.
 
-\subsection*{Modifications for version 2.73 (not released yet)}
+\subsection*{Modifications for version 2.73 (released 2/27/24)}
 \item Investigated diffusion coefficients in crowded systems. I now believe that the overlap method is better than the reflection method. This is discussed in the reactions chapter of the Smoldyn manual. I changed the default behavior to overlap method.
-\item Added a line to the CMake file. In the Python module section, edited a line to read \ttt{find\_package(Python3 3.10 EXACT COMPONENTS Interpreter Development REQUIRED)}, where the new portion is the Python 3.10 requirement. This prevents an error of \ttt{invalid command 'bdist\_wheel'} because it now uses the same Python version for everything. ... This was reverted by someone. The below \ttt{PYTHON\_VERSION} update fixes this problem.
+\item Added a line to the CMake file. In the Python module section, edited a line to read \ttt{find\_package(Python3 3.10 EXACT COMPONENTS Interpreter Development REQUIRED)}, where the new portion is the Python 3.10 requirement. This prevents an error of \ttt{invalid command 'bdist\_wheel'} because it now uses the same Python version for everything. This was reverted afterward. The below \ttt{PYTHON\_VERSION} update fixes this problem.
 \item Edited Smoldyn/source/pybind11/tests/requirements.txt to simplify the file and hopefully stop warnings from the gitHub dependabot.
 \item Added \ttt{PYTHON\_VERSION} as an option to the build, with new code in the master CMakeLists.txt file. Using this fixes the problem of building for one Python version and running a different one.
 \item Fixed bug in cmdsetreactionratemolcount. It wasn't loading the species name correctly, leading to a non-functional command. I'm not sure why it wasn't caught earlier, but it wasn't.

docs/Smoldyn/SmoldynManual.tex

@@ -92,8 +92,8 @@
 
 
 \title{Smoldyn User's Manual}
-\subtitle{Version 2.72}
-\date{\copyright August, 2023}
+\subtitle{Version 2.73}
+\date{\copyright February, 2024}
 \author{Steve Andrews}
 \maketitle
 

windows/install.bat

@@ -28,7 +28,7 @@ copy "%FROMDIR%lib\libsmoldyn_shared.dll" "%DESTDIR%lib"
 
 echo Installing Python bindings
 where pip /q
-if %ERRORLEVEL% == 0 (pip install "%FROMDIR%bin\smoldyn-2.72-cp39-cp39-win_amd64.whl") else (echo WARNING: Not installing Python bindings because pip cannot be found)
+if %ERRORLEVEL% == 0 (pip install "%FROMDIR%bin\smoldyn-2.73-cp39-cp39-win_amd64.whl") else (echo WARNING: Not installing Python bindings because pip cannot be found)
 
 echo Adding Smoldyn directory to local and system path
 echo.%PATH% > "%DESTDIR%PATH_old.txt"