Packaged

.gitignore

@@ -128,5 +128,12 @@ trna_ssa/
 # Pylint
 .pylint.d/
 
+# packaged stuff
+build/
+dist/
+obsolete/
+*.egg-info/
+
+.vscode*
 
 

MANIFEST.in

@@ -1,4 +1,19 @@
-recursive-include include *.pxd
-recursive-include include *.pyx
-recursive-include include *.cpp
-recursive-include include *.h
+recursive-exclude rsnapsim/ssa_cpp/*
+recursive-exclude rsnapsim/ssa_cpp
+recursive-exclude trna_ssa *
+recursive-exclude models *
+recursive-exclude test *
+recursive-exclude test_files *
+recursive-exclude paper_figures *
+
+recursive-include blank_model.pyx
+recursive-include blank_model.cpp
+recursive-include blank_model.h
+
+recursive-include rsnapsim/blank_model.pyx
+recursive-include rsnapsim/blank_model.cpp
+recursive-include rsnapsim/blank_model.h
+
+
+
+prune ssa_cpp/

README.md

@@ -7,6 +7,15 @@ Translated by Will Raymond - 2018/2019
 ------------------------------
 ### **rSNAPsim** - **R**NA **S**equence to **NA**scent **P**rotein **Sim**ulation
 -------------------------------
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![PyPI version](https://badge.fury.io/py/rsnapsim.svg)](https://badge.fury.io/py/rsnapsim)
+
+ssa c++ library [![PyPI version](https://badge.fury.io/py/rsnapsim-ssa-cpp.svg)](https://badge.fury.io/py/rsnapsim-ssa-cpp)
+
+
+![alt text](https://github.com/MunskyGroup/rSNAPsim/blob/packaged/rsnapsim/docs/images/rsnapsim_figure1_tmp.png?raw=true)
+
+
 ### Project Goal
 
 Provide a Python module that takes nucleotide sequence as an input and does the following: 
@@ -31,17 +40,29 @@ Dependencies:
  * [matplotlib](https://matplotlib.org/)
  * [pandas](https://pandas.pydata.org/)
  * [SnapGene Reader](https://github.com/IsaacLuo/SnapGeneFileReader)
-
+ * [DnaFeaturesViewer](https://edinburgh-genome-foundry.github.io/DnaFeaturesViewer/index.html)
 -----------------------------------
 ### Instillation 
 
 #### Within a conda enviroment:
 
-```conda install eigen ```
+```
+conda install eigen 
+pip install rsnapsim-ssa-cpp 
+pip install rsnapsim
+```
+
 
-```pip install -i https://test.pypi.org/simple/ rsnapsim-ssa-cpp ```
+#### Within a Google Colab:
+
+```
+!apt install libeigen3-dev
+!ln -sf /usr/include/eigen3/Eigen /usr/include/Eigen
+!pip install rsnapsim-ssa-cpp
+!pip install rsnapsim
+!pip install --upgrade rsnapsim 
+```
 
-```pip install -i https://test.pypi.org/simple/ rsnapsim```
 
 ##### Compilation of the C++ 
 
@@ -54,6 +75,19 @@ The c++ model should attempt to compile when you pip install the ssa-cpp module,
 
 -------------------------------------
 
+--------------------
+### Example Colab Notebooks
+
+* Simulating Translation [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1yT0bt39GEB3fS9iO73_a-Bad9uorl_I5?usp=sharing)
+* Simulating Constructs with Different codon usages  [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1Amy9Mvf0IZDJsy9ZQ3sxAENSFOmiNJMQ?usp=sharing) 
+* Intensity Analyses  [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1G0sWY4ul-mAb51JT9F7GfyK49Dkxui9V?usp=sharing) 
+* Harringtonine / FRAP simulations  [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1_Y9l_EYIRIUwg7FYgVxoTfb6fYNo5NrJ?usp=sharing) 
+* Model Maker/ Designer [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1l3KXD0MWeH6crGLp2EbmOzNrvJphFyf_?usp=sharing)
+* MW/Diffusion Calculations [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/17l7oMcNTaoiR0FSVbc46DEv8DCBG6IFO?usp=sharing)
+
+
+
+
 #### Future work
 
 - Example notebooks of all functions