updating setup

emissible · Mar 19, 2019 · 7b604c8 · 7b604c8
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diff --git a/README.md b/README.md
@@ -6,8 +6,6 @@
 
 Authors: **Joe Abbott**, **Ryan Beck**, **Hang Hu**, **Yang Liu**, **Lixin Lu**.
 
-<span style="color:red"> _**SPEEDCOM** is currently under development. We should be up and running soon._ </span>
-
 ## Overview
 
 _SPEEDCOM_ is an open source python package that aims to predict the fluorescence emission and absorption spectra of small conjugated organic molecules. These features are predicted using a convolutional neural network, implemented with [keras](https://github.com/keras-team/keras), and trained on data from the [PhotochemCAD database](http://www.photochemcad.com/PhotochemCAD.html). The software has a graphical-user-interface (GUI) where users can input the [SMILES](https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system) string for a given molecule and be returned its predicted spectra and associated characteristic quantities. For further details on the background science, and the operations of our program, please see our [use cases](https://github.com/emissible/SPEEDCOM/blob/master/use_cases.md).
@@ -27,11 +25,100 @@ Below shows the spectra and characteristics prediction of an example molecule, i
 
 * Python version 3.6.7 or later
 * conda version 4.6.8 or later
+* GitHub 
 
 ### Installation
-From your computer's terminal application, enter the following command:
 
-``conda install speedcom``
+You can execute the following ``commands`` from your computer's terminal application: 
+
+1. Either clone the _SPEEDCOM_ repository:
+
+	``git clone https://github.com/emissible/SPEEDCOM.git ``  
+
+	or download the zip file:  
+
+	`` curl -O https://github.com/emissible/SPEEDCOM/archive/master.zip ``
+
+2. `` cd SPEEDCOM ``
+
+2. ``conda env create -n speedcom_environment.yml``
+
+3. ``conda activate speedcom``
+
+4. ``cd speedcom && python runhtml.py``
+
+5. Find the isomeric SMILES string for the moelcule you want the spectra for and input it into the GUI!
+
+## Directory Structure
+
+	SPEEDCOM (master)  
+    |---data  
+        |--- 
+    |---doc  
+        |--- 
+    |---speedcom  
+        |---frontend
+            |---output
+            |--jquery.min.js
+            |--molecule_ex.png
+            |--spectra_ex.png
+            |--welcome.png
+        |---notebook_scripts
+            |--R2_plot.ipynb
+            |--encode_smiles.ipynb
+            |--rdkit_descriptor.ipynb
+            |--rdkit_exploration.ipynb
+            |--smiles_clean.ipynb
+            |--smiles_cnn.ipynb
+            |--to_help_write_tests.ipynb
+        |---saved_models
+            |--ems_dropna.best1.hdf5
+            |--epsilon.best_-1.hdf5
+            |--model_lstm_qy.json
+            |--model_smiles_cnn.json
+            |--model_smiles_ems_dropna.json
+            |--model_smiles_epsilon_lstm.json
+            |--smiles_wordmap.json
+            |--weights.best.hdf5
+            |--weight.qy_best.hdf5
+        |---tests
+            |---DATA_CLEAN_TEST_DIR
+            |--__init__.py
+            |--context,py
+            |--tests_NNModels.py
+            |--test_Prediction.py
+            |--test_dataUtils.py
+        	  |--test_data_extract.py
+         	  |--test_model_utils.py
+         	  |--test_readData_temp.tsv
+         	  |--test_speedcom.py
+         	  |--test_utilities.py
+        |--NNModels.py
+        |--Prediction.py
+        |--__init__.py
+        |--core.py
+        |--dataUtils.py
+        |--data_extract.py
+        |--matplotlibrc
+        |--model_utils.py
+        |--runhtml.py
+        |--speedcom.html
+        |--utilities.py
+        |--version.py  
+    |--.coveragerc
+    |--.gitignore  
+    |--.travis.yml
+    |--LICENSE  
+    |--README.md 
+    |--download.sh
+    |--numpyversion.py
+    |--requirements.txt
+    |--runtests.sh
+    |--setup.sh
+    |--speedcom_environment.yml 
+
+----
+
 
 ## Contributions
 

diff --git a/doc/source/_static/charac_screenshot.png b/doc/source/_static/charac_screenshot.png
diff --git a/setup.py b/setup.py
@@ -21,7 +21,7 @@
             platforms=PLATFORMS,
             version=VERSION,
             packages=PACKAGES,
-            # package_data=PACKAGE_DATA,
+            package_data=PACKAGE_DATA,
             install_requires=REQUIRES,
             include_package_data=True,
             requires=REQUIRES)

diff --git a/speedcom/version.py b/speedcom/version.py
@@ -67,5 +67,5 @@
 MICRO = _version_micro
 VERSION = __version__
 PACKAGES = ["speedcom"]
-# PACKAGE_DATA = {'nets': ['speedcom/nets/*.h5']}
+PACKAGE_DATA = {'nets': ['speedcom/saved_models/*']}
 REQUIRES = []