From 34c295265845573ded0eb3d96d81d9a1adea1609 Mon Sep 17 00:00:00 2001
From: Armaan Bhojwani <me@armaanb.net>
Date: Fri, 6 Aug 2021 22:52:52 -0400
Subject: [PATCH] Restructure repository

---
 .gitignore                                |  4 +---
 README                                    | 25 ++++++++++++++++++++++-
 norepinephrine_wm/newmodel.py => model.py |  0
 old/.gitignore                            |  3 +++
 {norepinephrine_wm => old}/helper.py      |  0
 {norepinephrine_wm => old}/model.py       |  0
 {norepinephrine_wm => old}/parameters.txt |  0
 requirements.txt                          | 15 ++++++++++++++
 8 files changed, 43 insertions(+), 4 deletions(-)
 rename norepinephrine_wm/newmodel.py => model.py (100%)
 create mode 100644 old/.gitignore
 rename {norepinephrine_wm => old}/helper.py (100%)
 rename {norepinephrine_wm => old}/model.py (100%)
 rename {norepinephrine_wm => old}/parameters.txt (100%)
 create mode 100644 requirements.txt

diff --git a/.gitignore b/.gitignore
index 0ef23ea..8609bed 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,3 @@
-*.png
-*.pkl
 *.pyc
-params.json
 out/
+venv
diff --git a/README b/README
index 9b1367a..35378eb 100644
--- a/README
+++ b/README
@@ -8,5 +8,28 @@ Marianne Bezaire.
 
 The work in this repository was in-part derived from "Effects of Guanfacine and
 Phenylephrine on a Spiking Neuron Model of Working Memory" by Peter Duggins,
-Terry Stewart, Xuan Choo, Chris Eliasmith.
+Terry Stewart, Xuan Choo, Chris Eliasmith. Some of those original files are
+preserved in old/.
 <https://github.com/psipeter/drugs_and_working_memory>
+
+Usage
+=====
+
+Create and activate a new virtual environment:
+
+    python3 -m venv venv
+    . ./venv/bin/activate
+
+Install necesary dependencies:
+
+	pip install -r requirements.txt
+
+Modify conf.py as needed:
+
+	vi conf.py
+
+Run simulation (use the -h flag to see more options):
+
+	python3 model.py
+
+Results are stored in ./out/.
diff --git a/norepinephrine_wm/newmodel.py b/model.py
similarity index 100%
rename from norepinephrine_wm/newmodel.py
rename to model.py
diff --git a/old/.gitignore b/old/.gitignore
new file mode 100644
index 0000000..12579e0
--- /dev/null
+++ b/old/.gitignore
@@ -0,0 +1,3 @@
+*
+!.py
+!parameters.txt
diff --git a/norepinephrine_wm/helper.py b/old/helper.py
similarity index 100%
rename from norepinephrine_wm/helper.py
rename to old/helper.py
diff --git a/norepinephrine_wm/model.py b/old/model.py
similarity index 100%
rename from norepinephrine_wm/model.py
rename to old/model.py
diff --git a/norepinephrine_wm/parameters.txt b/old/parameters.txt
similarity index 100%
rename from norepinephrine_wm/parameters.txt
rename to old/parameters.txt
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..e2c606f
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,15 @@
+autopep8==1.5.7
+cycler==0.10.0
+kiwisolver==1.1.0
+matplotlib==3.4.2
+nengo==3.1.0
+numpy==1.21.1
+pandas==1.3.1
+Pillow==8.3.1
+pycodestyle==2.7.0
+pyparsing==2.4.7
+python-dateutil==2.8.2
+pytz==2021.1
+scipy==1.5.3
+six==1.16.0
+toml==0.10.2
-- 
2.39.2