version 2.71

ssandrews · Feb 5, 2023 · b117127 · b117127
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,12 @@
 ## Changelog
 
+### 2.71 (2/5/23)
+
+- Fixed bug in which graphics were called by Python API even when turned off.
+- Made it an error for command timing to have non-integer values for integer commands.
+- Improved command timing so that command execution order is consistent.
+- Added translatemol command and improved longrangeforce command.
+
 ### 2.70.1 (12/28/22)
 
 - Added wheels for Python 3.11 (Windows, OSX).

diff --git a/CMakeLists.txt b/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 "2.71.dev${STAMP}")
+            set(SMOLDYN_VERSION "2.72.dev${STAMP}")
         endif()
     endif()
 endif()

diff --git a/docs/Smoldyn/SmoldynCodeDoc.pdf b/docs/Smoldyn/SmoldynCodeDoc.pdf
diff --git a/docs/Smoldyn/SmoldynCodeDoc.tex b/docs/Smoldyn/SmoldynCodeDoc.tex
@@ -5,6 +5,7 @@
 \usepackage{longtable}
 \usepackage{listings}
 \usepackage{url}
+\usepackage{hyperref}
 
 % settings for listings package
 \lstset{
@@ -42,8 +43,8 @@
 \pretolerance=10000
 
 \title{Smoldyn Code Documentation} 
-\subtitle{Version 2.70}
-\date{\copyright October, 2022}
+\subtitle{Version 2.71}
+\date{\copyright February, 2023}
 \author{Steve Andrews}
 \maketitle
 
@@ -6914,7 +6915,7 @@ \subsection*{Modifications for version 2.69 (released 10/17/22)}
 \subsection*{Modifications for version 2.70 (released 10/24/22)}
 \item Fixed bug, or maybe just a lack of feature availablility, in libsmoldyn and Python interface in which reaction probabilities could not be set for bimolecular reactions.
 
-\subsection*{Modifications for version 2.71 (not released yet)}
+\subsection*{Modifications for version 2.71 (released 2/5/23)}
 \item Fixed bug in which graphics were being called from Python API even when they were turned off. This arose from \ttt{gl2glutInit} being called in Simulation.cpp \ttt{Simulation::runSim} for all cases; it's now called in smolgraphics.c \ttt{smolsimulategl} instead.
 \item Made it an error to enter command timing with either non-integer values for integer type commands, or to enter timing steps that are less than or equal to zero.
 \item Improved command timing so that all commands that execute at a particular time are performed with integer commands first, then float commands (unchanged from before) and also, within these lists, in the order that they are listed in the configuration file (new functionality).

diff --git a/docs/Smoldyn/SmoldynManual.pdf b/docs/Smoldyn/SmoldynManual.pdf
diff --git a/docs/Smoldyn/SmoldynManual.tex b/docs/Smoldyn/SmoldynManual.tex
@@ -92,8 +92,8 @@
 
 
 \title{Smoldyn User's Manual}
-\subtitle{Version 2.70}
-\date{\copyright October, 2022}
+\subtitle{Version 2.71}
+\date{\copyright February, 2023}
 \author{Steve Andrews}
 \maketitle
 

diff --git a/examples/S95_regression/output_271/translatemol2_271_out.txt b/examples/S95_regression/output_271/translatemol2_271_out.txt
@@ -0,0 +1,150 @@
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+blue(up) 5.88991 -1.79111 150
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diff --git a/examples/S95_regression/regression.py b/examples/S95_regression/regression.py
@@ -10,7 +10,7 @@
 					'polymer_end','polymer_mid','rafts','rafts3D','ReflectToNewSpecies',
 					'structexpansion','surf1','surf2','surf3','surfaceboundjump','surfacedrift2',
 					'surfacedrift3','surfacereact','stick',
-					'surfacediffuse','tracking','tracking2','trisphere']
+					'surfacediffuse','tracking','tracking2','translatemol2','trisphere']
 
 suffix=input('Enter suffix for new simulations: ')
 reference=input('Enter suffix for reference simulations or "none": ')

diff --git a/windows/install.bat b/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-2.70-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-2.71-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"