Merge pull request #1 from DNA-and-Natural-Algorithms-Group/development

Development

.travis.yml

@@ -0,0 +1,18 @@
+language: python
+python:
+  - "3.8"
+  - "3.9"
+
+# command to install dependencies
+install:
+  - pip install -r requirements.txt
+  - pip install pytest-cov pytest
+  - pip install codecov
+  - pip install .
+
+# command to run tests
+script:
+  - pytest --cov-report term --cov=nuskell/
+
+after_success:
+  - codecov

LICENSE

@@ -1,7 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2010-2017 Seung Woo Shin, Qing Dong, Robert Johnson, 
-  Stefan Badelt, Erik Winfree <[email protected]>
+Copyright (c) 2010-2020 Stefan Badelt, Seung Woo Shin, Robert Johnson, Qing Dong, Erik Winfree <[email protected]>
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in

README.md

@@ -1,53 +1,62 @@
-# Nuskell: Nucleic acid strand displacement compiler
+# Nuskell: nucleic acid strand displacement compiler
 
-``Nuskell`` compiles formal chemical reaction networks (CRNs) into domain-level
-strand displacement (DSD) systems. It provides a library of ``translation
-schemes`` (i.e. variations of CRN-to-DSD translations) to exploit the diversity
-of DSD circuits implementing the same CRN.
+[![GitHub tag (latest by date)](https://img.shields.io/github/v/tag/DNA-and-Natural-Algorithms-Group/nuskell)](https://github.com/DNA-and-Natural-Algorithms-Group/nuskell/tags)
+[![GitHub release (latest by date)](https://img.shields.io/github/v/release/DNA-and-Natural-Algorithms-Group/nuskell?include_prereleases)](https://github.com/DNA-and-Natural-Algorithms-Group/nuskell/releases)
+[![PyPI version](https://badge.fury.io/py/nuskell.svg)](https://badge.fury.io/py/nuskell)
+[![PyPI - License](https://img.shields.io/pypi/l/nuskell)](https://opensource.org/licenses/MIT)
+[![Build Status](https://travis-ci.com/DNA-and-Natural-Algorithms-Group/nuskell.svg?branch=master)](https://travis-ci.com/github/DNA-and-Natural-Algorithms-Group/nuskell)
+[![Codecov branch](https://img.shields.io/codecov/c/github/DNA-and-Natural-Algorithms-Group/nuskell/master)](https://codecov.io/gh/DNA-and-Natural-Algorithms-Group/nuskell)
 
-In order to proof/disproof the correctness of a particular translation,
-``Nuskell`` includes the domain-level reaction enumerator ``Peppercorn`` [Grun
-et al. (2014)] to find intended and unintended reaction pathways and then
-provides two notions of stochastic trajectory-type CRN equivalence:
-bisimulation [Johnson et al. (2016)] and pathway decomposition [Shin et al. (2014)].
+``Nuskell`` is software framework to compile formal chemical reaction networks
+(CRNs) into domain-level strand displacement (DSD) systems.  As there are many
+ways to do such a translation, we provide a library of [translation schemes]
+(i.e. variations of CRN-to-DSD translations) that the user can select from. 
 
-The domain-level reactions and their approximate rates can be exported in form
-of an ODE system to simulate the dynamics of the compiled DSD network.
+In order to proof/disproof the correctness of a particular translation,
+``Nuskell`` includes the domain-level reaction enumeration package
+[Peppercorn][] [[Badelt et al. (2020)]] and the CRN verification package
+[crnverifier][].  
+Peppercorn finds intended and potentially unintended reaction pathways, the
+crnverifier then checks if the implementation CRN is a correct implementation
+of the formal CRN using the stochastic trajectory-type CRN correctness notions
+of bisimulation [[Johnson et al. (2019)]] and pathway decomposition 
+[[Shin et al.  (2019)]].
 
 ### Examples
 
 Implement a formal CRN using a particular translation-scheme:
 
 ```
-  $ echo "A + B <=> X + Y; X -> A" | nuskell --ts scheme.ts --verify modular-bisimulation
+  $ echo "A + B <=> X + Y; X -> A" | nuskell --ts srinivas2017.ts --verify crn-bisimulation
 ```
 for options see:
 ```
   $ nuskell --help
 ```
 ## Translation Schemes
-Detailed information about translation schemes can be found in the ``/schemes`` directory.
+Detailed information about translation schemes can be found in the [translation
+schemes] directory.
 
 ## Installation
 ```
   $ python setup.py install
 ```
-or
-```
-  $ python setup.py install --user
-```
 
 ## Documentation
 A preview of the documentation for release v1.0 can be found at: [documentation].
 
 ## Version
-0.5.1
+0.8 -- basically a complete rewrite, python>=3.8 only.
+  * nuskell.dsdcompiler is now a subpackage to compile from CRN to DSD.
+  * crnverifier is now an independent package and therefore a dependency.
+  * enumeration interface updated to peppercornenumerator-v1.1.
+  * nuskell now uses the prototype objects provided by the dsdobjects library.
 
 ### Authors
+  - Stefan Badelt
   - Seung Woo Shin
-  - Qing Dong
   - Robert Johnson
-  - Stefan Badelt
+  - Qing Dong
   - Erik Winfree
 
 ### License
@@ -60,9 +69,12 @@ Stefan Badelt, Seung Woo Shin, Robert F. Johnson, Qing Dong, Chris Thachuk, and
 
 
 [//]: References
+[Peppercorn]: <https://github.com/DNA-and-Natural-Algorithms-Group/peppercornenumerator>
+[crnverifier]: <https://github.com/DNA-and-Natural-Algorithms-Group/crnverifier>
+[translation schemes]: <https://github.com/DNA-and-Natural-Algorithms-Group/nuskell/tree/master/nuskell/dsdcompiler/schemes>
 [Badelt et al. (2017)]: <https://doi.org/10.1007/978-3-319-66799-7_15>
-[Grun et al. (2014)]: <https://arxiv.org/abs/1505.03738>
-[Shin et al. (2014)]: <http://dna.caltech.edu/DNAresearch_publications.html#PathwayDecomposition>
-[Johnson et al. (2016)]: <http://dna.caltech.edu/DNAresearch_publications.html#CRN-Bisimulation>
+[Badelt et al. (2020)]: <https://doi.org/10.1098/rsif.2019.0866>
+[Shin et al. (2019)]: <https://doi.org/10.1016/j.tcs.2017.10.011> 
+[Johnson et al. (2019)]: <https://doi.org/10.1016/j.tcs.2018.01.002>
 [documentation]: <http://dna.caltech.edu/~badelt/nuskell/index.html>
 

nuskell/__init__.py

@@ -1,11 +1,9 @@
-##############################################
-# Initiation of the nuskell compiler package #
-##############################################
+#
+#  nuskell/__init__.py
+#  NuskellCompilerProject
+#
+__version__ = "0.8"
 
-__version__ = "0.5.1"
-
-# Import the main interface to the compiler #
-from nuskell.compiler import translate, genCRN
-from nuskell.verifier import verify
-from nuskell.interpreter.environment import NuskellExit
+import logging
+logging.getLogger(__name__).addHandler(logging.NullHandler())