improved Mac install permissions

Mac/README.txt

@@ -1,8 +1,8 @@
 This README file is for the Smoldyn distribution for Mac OS X.
 
-This distribution contains pre-compiled Smoldyn software for running on standard Macs.  It assumes that you have an Intel Mac running OS 10.6 or higher, that your system is configured in a typical way, and that you want the default Smoldyn installation.
+This distribution contains pre-compiled Smoldyn software for running on standard Macs.  It assumes that you have an M1 or Intel Mac running OS 10.9 or higher, that your system is configured in a typical way, and that you want the default Smoldyn installation.
 
-To install Smoldyn, open your "Terminal" application, which is in your Applications/Utilities directory.  Change directories to this download directory (probably type "cd Desktop/smoldyn-2.xx-mac", or something similar).  Then type "sudo ./install.sh", and enter your computer password when prompted.  If you get a warning about Python bindings not being installed, that's okay; just install pip at some point and re-run the install script.  If you are asked whether you want the installer to update your environment PATH variable, you should generally say yes (enter 'y').  This will add the directory /usr/local/bin to the list of places where your computer will look for executable files, which means that it will find Smoldyn correctly.  Next, test Smoldyn by typing "smoldyn examples/S1_intro/bounce3.txt".  If it runs, congratulations, you have a successful Smoldyn installation!  If not, see below.
+To install Smoldyn, open your "Terminal" application, which is in your Applications/Utilities directory.  Change directories to this download directory (probably type "cd Desktop/smoldyn-2.xx-mac", or something similar).  Then type "./install.sh" and enter your computer password when prompted.  If you get a warning about Python bindings not being installed, that's okay; just install pip at some point and re-run the install script.  If you are asked whether you want the installer to update your environment PATH variable, you should generally say yes (enter 'y').  This will add the directory /usr/local/bin to the list of places where your computer will look for executable files, which means that it will find Smoldyn correctly.  Next, test Smoldyn by typing "smoldyn examples/S1_intro/bounce3.txt".  If it runs, congratulations, you have a successful Smoldyn installation!  If not, see below.
 
 Particularly useful files in the download directory:
 SmoldynQuickGuide.pdf - a 2 page Smoldyn quick reference guide, in documentation directory

Mac/install.sh

@@ -1,29 +1,29 @@
 #!/bin/bash
 
 echo "Installing Smoldyn"
-mkdir -p /usr/local/bin
-cp bin/smoldyn /usr/local/bin
-chmod +x /usr/local/bin/smoldyn
-cp -r bin/BioNetGen /usr/local/bin
-chmod +x /usr/local/bin/BioNetGen/BNG2.pl
-chmod +x /usr/local/bin/BioNetGen/Perl2
+sudo mkdir -p /usr/local/bin
+sudo cp bin/smoldyn /usr/local/bin
+sudo chmod +x /usr/local/bin/smoldyn
+sudo cp -r bin/BioNetGen /usr/local/bin
+sudo chmod +x /usr/local/bin/BioNetGen/BNG2.pl
+sudo chmod +x /usr/local/bin/BioNetGen/Perl2
 
 echo "Installing SmolCrowd"
-cp bin/SmolCrowd /usr/local/bin
-chmod +x /usr/local/bin/SmolCrowd
+sudo cp bin/SmolCrowd /usr/local/bin
+sudo chmod +x /usr/local/bin/SmolCrowd
 
 echo "Installing wrl2smol"
-cp bin/wrl2smol /usr/local/bin
-chmod +x /usr/local/bin/wrl2smol
+sudo cp bin/wrl2smol /usr/local/bin
+sudo chmod +x /usr/local/bin/wrl2smol
 
 echo "Installing Libsmoldyn"
-mkdir -p /usr/local/include
-mkdir -p /usr/local/lib
-cp include/libsmoldyn.h /usr/local/include
-cp include/smoldyn.h /usr/local/include
-cp include/smoldynconfigure.h /usr/local/include
-cp lib/libsmoldyn_static.a /usr/local/lib
-cp lib/libsmoldyn_shared.dylib /usr/local/lib
+sudo mkdir -p /usr/local/include
+sudo mkdir -p /usr/local/lib
+sudo cp include/libsmoldyn.h /usr/local/include
+sudo cp include/smoldyn.h /usr/local/include
+sudo cp include/smoldynconfigure.h /usr/local/include
+sudo cp lib/libsmoldyn_static.a /usr/local/lib
+sudo cp lib/libsmoldyn_shared.dylib /usr/local/lib
 
 echo "Installing Python bindings"
 if command -v pip &> /dev/null; then

Mac/uninstall.sh

@@ -1,21 +1,21 @@
 #!/bin/bash
 
 echo "Uninstalling Smoldyn"
-rm /usr/local/bin/smoldyn
-rm -r /usr/local/bin/BioNetGen
+sudo rm /usr/local/bin/smoldyn
+sudo rm -r /usr/local/bin/BioNetGen
 
 echo "Uninstalling SmolCrowd"
-rm /usr/local/bin/SmolCrowd
+sudo rm /usr/local/bin/SmolCrowd
 
 echo "Uninstalling wrl2smol"
-rm /usr/local/bin/wrl2smol
+sudo rm /usr/local/bin/wrl2smol
 
 echo "Uninstalling Libsmoldyn"
-rm /usr/local/include/libsmoldyn.h
-rm /usr/local/include/smoldyn.h
-rm /usr/local/include/smoldynconfigure.h
-rm /usr/local/lib/libsmoldyn_static.a
-rm /usr/local/lib/libsmoldyn_shared.dylib
+sudo rm /usr/local/include/libsmoldyn.h
+sudo rm /usr/local/include/smoldyn.h
+sudo rm /usr/local/include/smoldynconfigure.h
+sudo rm /usr/local/lib/libsmoldyn_static.a
+sudo rm /usr/local/lib/libsmoldyn_shared.dylib
 
 echo "Uninstalling Python bindings"
 if command -v pip &> /dev/null; then

docs/Smoldyn/SmoldynCodeDoc.tex

@@ -7067,6 +7067,8 @@ \subsection*{Modifications for version 2.73 (released 2/27/24)}
 \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.
 
+\subsection*{Modifications for version 2.74 (not released yet)}
+\item Changed Mac install and uninstall scripts so that individual commands use sudo, but the whole script does not. This is important because sudo should not be used with pip.
 
 \end{itemize}