Fix for Issue #2, SIGALRM error

.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

README.md

@@ -1,77 +1,49 @@
-# Nuskell: a nucleic acid strand displacement compiler
+# Nuskell: nucleic acid strand displacement compiler
 
 [![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)
-![build](https://github.com/DNA-and-Natural-Algorithms-Group/nuskell/actions/workflows/python-package.yml/badge.svg)
-[![Codecov](https://img.shields.io/codecov/c/github/dna-and-natural-algorithms-group/nuskell)](https://codecov.io/gh/dna-and-natural-algorithms-group/nuskell)
+[![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)
 
-**Nuskell** is a compiler framework to translate formal chemical reaction
-networks (CRNs) into domain-level strand displacement (DSD) systems. 
-To support the diversity of proposed CRN-to-DSD translation methods 
-from literature, as well as potential new CRN-to-DSD translation
-methods that are yet to be developed, Nuskell provides a *domain-specific
-programming language*. In this language, CRN-to-DSD translations can be 
-formulated as algorithms: so-called *translation schemes*.  We provide a
-library of selected existing [translation schemes] that users can use 
-without understanding the details of the Nuskell programming language. 
+``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. 
 
-A notion of correctness for a particular translation is established on a
-case-by-case basis using the domain-level reaction enumeration package
+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][], which implements the rate-independent, stochastic-level
-theories of pathway decomposition equivalence [[Shin et al.  (2019)]] and/or
-CRN bisimulation [[Johnson et al. (2019)]].
+[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)]].
 
-Peppercorn first finds intended and potentially unintended reaction pathways,
-then the crnverifier checks if the implementation CRN is a correct
-implementation of the formal CRN.  Nuskell is a first step to integrate
-biophysical modeling of nucleic acids with rigorous abstraction hierarchies of
-modern compilers to design and characterize DSD systems. For more details, see
-[[Badelt et al. (2017)]].
+### Examples
 
-## Installation
-Nuskell must be installed directly from this repository, we recommend clining
-the repository and then using:
-```bash
-pip install .
-```
+Implement a formal CRN using a particular translation-scheme:
 
-For debugging, or if you are planning a contribution to the repository, please
-install the development version and make sure all tests pass:
-```bash
-pip install .[dev]
-pytest 
 ```
-
-## Quickstart: the nuskell executable 
-Upon installation, the package provides an executable `nuskell`, which is the
-main interface combining CRN-to-DSD translation, DSD enumeration and CRN
-verification.  For example, to implement the formal CRN
+  $ echo "A + B <=> X + Y; X -> A" | nuskell --ts srinivas2017.ts --verify crn-bisimulation
 ```
-A + B <=> X + Y
-X -> A
+for options see:
 ```
-using the translation-scheme from [Srinivas (2015)], and to verify that
-the translation is correct with CRN bisimulation, use the command line call:
-```bash
-echo "A + B <=> X + Y; X -> A" | nuskell --ts srinivas2015.ts --verify crn-bisimulation
+  $ nuskell --help
 ```
-New users may also appreciate the `-v` flag to get more detailed information on
-the individual compilation steps, as well as the option `--pilfile` to print the 
-DNA complexes generated in different stages of the compilation. 
-Detailed information about existing translation schemes can be found in the
-[translation schemes] directory.
-
-For more options see:
-```bash
-nuskell --help
+## Translation Schemes
+Detailed information about translation schemes can be found in the [translation
+schemes] directory.
+
+## Installation
+```
+  $ python setup.py install
 ```
 
-## Nuskell documentation
-A (preliminary) documentation can be found online: [documentation].  Most
-importantly, the documentation provides more details on what kind of
-translation schemes are supported and how to write them.  Suggestions and
-contributions that improve the documentation are very welcome.
+## Documentation
+A preview of the documentation for release v1.0 can be found at: [documentation].
 
 ## Version
 0.8 -- basically a complete rewrite, python>=3.8 only.
@@ -80,23 +52,26 @@ contributions that improve the documentation are very welcome.
   * enumeration interface updated to peppercornenumerator-v1.1.
   * nuskell now uses the prototype objects provided by the dsdobjects library.
 
-## Authors
+### Authors
   - Stefan Badelt
   - Seung Woo Shin
-  - Hope Amber Johnson
+  - Robert Johnson
   - Qing Dong
   - Erik Winfree
 
+### License
+MIT
+
 ## Cite
 Stefan Badelt, Seung Woo Shin, Robert F. Johnson, Qing Dong, Chris Thachuk, and Erik Winfree (2017)
 "A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities"
 [[Badelt et al. (2017)]].
 
+
 [//]: 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>
-[Srinivas (2015)]: <https://github.com/DNA-and-Natural-Algorithms-Group/nuskell/tree/master/nuskell/dsdcompiler/schemes/literature/srinivas2015.ts>
 [Badelt et al. (2017)]: <https://doi.org/10.1007/978-3-319-66799-7_15>
 [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> 

docs/Makefile

@@ -1,20 +1,177 @@
-# Minimal makefile for Sphinx documentation
+# Makefile for Sphinx documentation
 #
 
-# You can set these variables from the command line, and also
-# from the environment for the first two.
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = .
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
 BUILDDIR      = _build
 
-# Put it first so that "make" without argument is like "make help".
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
 help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/nuskell.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/nuskell.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/nuskell"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/nuskell"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
 
-.PHONY: help Makefile
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
 
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

docs/compiler.rst

@@ -0,0 +1,6 @@
+nuskell.compiler
+==========================
+
+.. automodule:: nuskell.compiler
+  :members: translate, genCRN, InvalidSchemeError
+