pyboolnet 3.0.16__tar.gz

pyboolnet-3.0.16/MANIFEST.in

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+global-exclude *~
+global-exclude *.pyc
+
+recursive-include pyboolnet/binaries *
+recursive-include pyboolnet/repository *

pyboolnet-3.0.16/PKG-INFO

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+Metadata-Version: 2.4
+Name: pyboolnet
+Version: 3.0.16
+Summary: Python toolbox for the generation, manipulation and analysis of Boolean networks.
+Home-page: https://github.com/hklarner/pyboolnet
+Author: Hannes Klarner
+Author-email: leevilux@yahoo.de
+Classifier: Programming Language :: Python
+Classifier: License :: OSI Approved :: GNU Library or Lesser General Public License (LGPL)
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Natural Language :: English
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Dist: networkx>=2.4
+Requires-Dist: pytest
+Requires-Dist: click>=8.0.1
+Requires-Dist: matplotlib>=3.3.3
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: home-page
+Dynamic: requires-dist
+Dynamic: summary

pyboolnet-3.0.16/README.md

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+
+
+## About pyboolnet
+pyboolnet is a Python package for the generation, modification and analysis of Boolean networks.
+The accompanying paper was published with [Bioinformatics](https://academic.oup.com/bioinformatics) and is available at
+
+ * https://doi.org/10.1093/bioinformatics/btw682
+
+For report bugs, request features and give feedback at [issues](http://github.com/hklarner/pyboolnet/issues) or contact
+
+ * hannes.klarner@fu-berlin.de (developer)
+ * heike.siebert@fu-berlin.de
+
+## Documentation
+The documentation and tutorials are hosted here:
+
+ * [https://pyboolnet.readthedocs.io/](https://pyboolnet.readthedocs.io/)
+
+## Model repository
+For examples of attractors, basins and phenotypes, browse the model repository here:
+
+ * [pyboolnet/repository](https://github.com/hklarner/pyboolnet/tree/master/pyboolnet/repository)
+
+## Installation
+To install the pyboolnet master branch use:
+
+``` 
+pip3 install pip --upgrade
+pip3 install --force-reinstall git+https://github.com/hklarner/pyboolnet
+```
+
+To install a tagged version use the `@`: 
+
+``` 
+pip3 install pip --upgrade
+pip3 install git+https://github.com/hklarner/pyboolnet@3.0.16
+```
+
+To list PyBoolNet as a dependency add the following line to your `requirements.txt`:
+
+```
+git+https://github.com/hklarner/pyboolnet@3.0.16
+```
+
+For release notes, see
+
+ * [pyboolnet/releasenotes.md](https://github.com/hklarner/pyboolnet/blob/master/RELEASENOTES.md)
+
+
+## Requirements
+clasp and gringo need to be on installed:
+```
+apt install clasp
+apt install gringo
+```
+ 
+## Command line tool
+```
+$ pyboolnet -h
+$ pyboolnet --trap-spaces --type min grieco_mapk.bnet
+```
+
+
+## Contributions
+- send pull requests to the `develop` branch
+- add tests to `pyboolnet/tests/`
+

pyboolnet-3.0.16/pyboolnet/__init__.py

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+
+
+import logging
+import os
+import sys
+
+from pyboolnet.helpers import read_executables
+from pyboolnet.version import read_version_txt
+
+VERSION = read_version_txt()
+NUSMV_KEYWORDS = ['MODULE', 'DEFINE', 'MDEFINE', 'CONSTANTS', 'VAR', 'IVAR', 'FROZENVAR', 'INIT', 'TRANS', 'INVAR', 'SPEC', 'CTLSPEC', 'LTLSPEC', 'PSLSPEC', 'COMPUTE', 'NAME', 'INVARSPEC', 'FAIRNESS', 'JUSTICE', 'COMPASSION', 'ISA', 'ASSIGN', 'CONSTRAINT', 'SIMPWFF', 'CTLWFF', 'LTLWFF', 'PSLWFF', 'COMPWFF', 'IN', 'MIN', 'MAX', 'MIRROR', 'PRED', 'PREDICATES', 'process', 'array', 'of', 'boolean', 'integer', 'real', 'word', 'word1', 'bool', 'signed', 'unsigned', 'extend', 'resize', 'sizeof', 'uwconst', 'swconst', 'EX', 'AX', 'EF', 'AF', 'EG', 'AG', 'E', 'F', 'O', 'G', 'H', 'X', 'Y', 'Z', 'A', 'U', 'S', 'V', 'T', 'BU', 'EBF', 'ABF', 'EBG', 'ABG', 'case', 'esac', 'mod', 'next', 'init', 'union', 'in', 'xor', 'xnor', 'self', 'TRUE', 'FALSE', 'count']
+COLOR_MAP = {"red1": "#df3e47", "green1": "#4bb93f", "blue1": "#7463b3", "yellow1": "#eecf1a", "pink1": "#db42a6", "green2": "#4cbd38", "red2": "#df3d47", "yellow2": "#efce1a"}
+COLORS = ["dodgerblue3", "firebrick2", "chartreuse3", "gold1", "aquamarine2", "darkorchid2"]
+UPDATES = ["synchronous", "asynchronous", "mixed"]
+GRAPHVIZ_LAYOUT_ENGINES = ["dot", "neato", "fdp", "sfdp", "circo", "twopi"]
+ROOT_DIR = os.path.join(os.path.dirname(__file__))
+EXECUTABLES = read_executables()
+
+logging.basicConfig(format="%(levelname)s %(message)s", stream=sys.stdout, level=logging.INFO)
+log = logging.getLogger(__name__)
+
+
+def find_command(name: str) -> str:
+    """
+    find the path to a command, in local binaries folder or in the shared execution PATH
+    """
+
+    if name in EXECUTABLES:
+        cmd = EXECUTABLES[name]
+        if cmd.startswith(":"):
+            cmd = cmd[1:]
+        else:
+            cmd = os.path.normpath(os.path.join(ROOT_DIR, "binaries", cmd))
+    else:
+        cmd = name
+
+    return cmd