From d6a50e5e68d94e07e998e00d9aac2feb09367860 Mon Sep 17 00:00:00 2001
From: alexPatrie <alexanderpatrie@gmail.com>
Date: Mon, 8 Jan 2024 14:49:53 -0500
Subject: [PATCH] updated readme for smoldyn mac instructions and added intel
 smoldyn installer

---
 README.md                                     | 28 ++++++++++------
 scripts/install-with-smoldyn-for-mac-intel.sh | 32 +++++++++++++++++++
 2 files changed, 51 insertions(+), 9 deletions(-)
 create mode 100755 scripts/install-with-smoldyn-for-mac-intel.sh

diff --git a/README.md b/README.md
index 93a3047a7..2c475fb85 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@ Core implementations of `process-bigraph.composite.Process()` aligning with BioS
 tools.
 
 
-## Getting Started (PyPI)
+## Installation
 
 The easiest way to download this tool is via the Python Package Index. You may download
 core-processes with: 
@@ -19,23 +19,33 @@ install the dependencies required for your use.
 
 ### Using `biosimulator_processes.smoldyn_process.SmoldynProcess()`: 
 
-#### PLEASE NOTE: 
+#### Mac Users PLEASE NOTE: 
 Due to the multi-lingual nature of Smoldyn, which is primarily 
 developed in C++, the installation process for utilizing 
 the `SmoldynProcess` process implementation requires separate handling. This is particularly 
 relevant for macOS and Windows users, where setting up the Python bindings can be more complex.
 
-Please follow the detailed installation instructions provided below to ensure proper setup 
-of Smoldyn for your system.
+For your convienience, we have created an installation shell script that will install the correct distribution of 
+Smoldyn based on your Mac processor along with the codebase of this repo. To install Smoldyn and this repo on your 
+Mac, please adhere to the following instructions:
 
-To download Smoldyn, please follow these steps:
+1. Clone this repo from Github:
 
-1. Visit the [Smoldyn Download Page](https://www.smoldyn.org/download.html).
-2. Choose the version appropriate for your operating system.
-3. Follow the instructions or links provided on the page to complete the download.
+        git clone https://github.com/vivarium-collective/biosimulator-processes.git
 
-For more detailed instructions and information, refer to the official Smoldyn documentation.
+2. Provide adminstrative access to the `scripts` directory within the cloned repo:
 
+        cd biosimulator-processes 
+        chmod +x scripts 
+
+3. Look for the install-with-smoldyn-for-mac-<YOUR MAC PROCESSOR> shell script where <YOUR MAC PROCESSOR> corresponds 
+    to your machine's processor:
+
+        ls scripts 
+
+4. Run the appropriate shell script (for example, using mac silicon):
+
+        scripts/install-with-smoldyn-for-mac-silicon.sh 
 
 ### Quick Start Example:
 #### TODO: Add quickstart example of instance declarations.
diff --git a/scripts/install-with-smoldyn-for-mac-intel.sh b/scripts/install-with-smoldyn-for-mac-intel.sh
new file mode 100755
index 000000000..80d25a859
--- /dev/null
+++ b/scripts/install-with-smoldyn-for-mac-intel.sh
@@ -0,0 +1,32 @@
+#!/bin/bash
+
+# The following script serves as a utility for installing this repository with the Smoldyn requirement on a Intel Mac
+
+set -e
+
+# set installation parameters
+dist_url=https://www.smoldyn.org/smoldyn-2.72-mac-Intel.tgz
+tarball_name=smoldyn-2.72-mac.tgz
+dist_dir=${tarball_name%.tgz}
+
+# uninstall existing version
+pip uninstall smoldyn || return
+
+# download the appropriate distribution from smoldyn
+wget $dist_url
+
+# extract the source from the tarball
+tar -xzvf $tarball_name
+
+# delete the tarball
+rm $tarball_name
+
+# install smoldyn from the source
+cd $dist_dir
+sudo -H ./install.sh
+
+# install the repo
+cd ..
+pip install -e .
+
+