From 6cedd0c0326125641fbe123e1e8332e7011d3c90 Mon Sep 17 00:00:00 2001
From: carsen <carsen.stringer@gmail.com>
Date: Thu, 16 Jan 2020 14:06:15 -0500
Subject: [PATCH] adding environment

---
 README.md       | 15 ++++++++++++++-
 environment.yml | 15 +++++++++++++++
 setup.py        |  4 ++--
 3 files changed, 31 insertions(+), 3 deletions(-)
 create mode 100644 environment.yml

diff --git a/README.md b/README.md
index 6f1becf..3e9b280 100644
--- a/README.md
+++ b/README.md
@@ -14,9 +14,22 @@ Here is what the output looks like for a recording of 64,000 neurons in a larval
 
 ## Installation
 
-You can pip install the package:
+Install an [Anaconda](https://www.anaconda.com/download/) distribution of Python -- Choose **Python 3.x** and your operating system. Note you might need to use an anaconda prompt if you did not add anaconda to the path.
+
+1. Download the [`environment.yml`](https://github.com/MouseLand/rastermap/blob/master/environment.yml) file from the repository. You can do this by cloning the repository, or copy-pasting the text from the file into a text document on your local computer.
+2. Open an anaconda prompt / command prompt with `conda` for **python 3** in the path
+3. Change directories to where the `environment.yml` is and run `conda env create -f environment.yml`
+4. To activate this new environment, run `conda activate rastermap`
+5. You should see `(rastermap)` on the left side of the terminal line. Now run `python -m rastermap` and you're all set.
+
+If you have an older `rastermap` environment you can remove it with `conda env remove -n rastermap` before creating a new one.
+
+Note you will always have to run **conda activate rastermap** before you run suite2p. Conda ensures pyqt and numba run correctly and quickly on your machine. If you want to run jupyter notebooks in this environment, then also `conda install jupyter`.
+
+... Or you can pip install the package and the pyqt5 requirements (not as recommended):
 
 ```
+pip install PyQt5 PyQt5.sip
 pip install rastermap
 ```
 
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..4e46c63
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,15 @@
+name: rastermap
+dependencies:
+  - python>=3.7
+  - pip
+  - numpy>=1.16
+  - numba>=0.43.1
+  - matplotlib
+  - scipy
+  - scikit-learn
+  - pyqt
+  - pip:
+    - pyqtgraph
+    - natsort
+    - scanimage-tiff-reader
+    - rastermap>0.1.0
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 6692011..2c0794e 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="rastermap",
-    version="0.1.1",
+    version="0.1.3",
     author="Marius Pachitariu and Carsen Stringer",
     author_email="carsen.stringer@gmail.com",
     description="Unsupervised clustering algorithm for 2D data",
@@ -13,7 +13,7 @@
     long_description_content_type="text/markdown",
     url="https://github.com/MouseLand/rastermap",
     packages=setuptools.find_packages(),
-	install_requires = ['numpy>=1.13.0', 'scipy', 'pyqtgraph', 'PyQt5', 'PyQt5.sip','matplotlib','numba','natsort'],
+	install_requires = ['numpy>=1.13.0', 'scipy','scikit-learn', 'pyqtgraph', 'matplotlib','numba','natsort'],
     include_package_data=True,
     classifiers=(
         "Programming Language :: Python :: 3",