RuleWorld/PyBioNetGen issues and pull requests

#59 - pkg_resources update breaks bngl

Issue - State: open - Opened by luciansmith 4 months ago

#58 - distutils was deprecated in Python 3.12

Issue - State: open - Opened by aadibiasi 6 months ago

#57 - NFsim version in bionetgen --version and info commands

Issue - State: open - Opened by jrfaeder 9 months ago
Labels: enhancement

#56 - Strings generated from Parameter objects do not print the correct value

Issue - State: closed - Opened by aadibiasi 9 months ago - 1 comment
Labels: bug

#55 - Model writing omits keywords in reaction rules

Issue - State: open - Opened by jrfaeder 10 months ago - 3 comments
Labels: bug

#54 - Adding molecule types

Issue - State: closed - Opened by Hamzaahmed0 about 1 year ago - 2 comments

#53 - Installing PyBioNetFit on Intel Macs

Issue - State: closed - Opened by ColinGros about 1 year ago - 1 comment

#52 - Fixed argument name in example

Pull Request - State: closed - Opened by ChocolateCharlie over 1 year ago - 1 comment

#51 - Is it possible to import the model as python string ?

Issue - State: closed - Opened by LifeWorks about 2 years ago - 2 comments
Labels: enhancement

#50 - Test Suite Reorganization

Pull Request - State: closed - Opened by cjarmstrong97 over 2 years ago

#49 - Network parsing

Pull Request - State: closed - Opened by ASinanSaglam over 2 years ago

#48 - Typo fix

Pull Request - State: closed - Opened by cjarmstrong97 over 2 years ago

#47 - restructuring where utilities are placed

Pull Request - State: closed - Opened by ASinanSaglam over 2 years ago

#46 - Removing `pexpect` dependency

Pull Request - State: closed - Opened by ASinanSaglam over 2 years ago

#45 - `pexpect` is unnecessary and `winpexpect` causes dependency issues

Issue - State: closed - Opened by ASinanSaglam over 2 years ago
Labels: enhancement

#44 - Loading a model from a .net file

Issue - State: closed - Opened by TorkelE over 2 years ago - 2 comments

#43 - Fixed docstring for bngmodel.add_action()

Pull Request - State: closed - Opened by cjarmstrong97 over 2 years ago

#42 - How to change initial conditions of loaded BioNetGen model?

Issue - State: closed - Opened by TorkelE over 2 years ago - 11 comments

#41 - Provide more informative error message for when Perl is not available

Issue - State: closed - Opened by jonrkarr over 2 years ago - 1 comment

#40 - Added Arrhenius rate law option for reaction rules

Pull Request - State: closed - Opened by cjarmstrong97 almost 3 years ago

#39 - Population map parsing support; minor formatting changes

Pull Request - State: closed - Opened by cjarmstrong97 almost 3 years ago

#38 - Action parsing with Pyparsing

Pull Request - State: closed - Opened by ASinanSaglam almost 3 years ago

#37 - Mostly functional energy pattern parsing & printing

Pull Request - State: closed - Opened by cjarmstrong97 almost 3 years ago - 2 comments

#36 - Graphdiff Updates & Fixes

Pull Request - State: closed - Opened by cjarmstrong97 almost 3 years ago

#35 - Parsing - RuleModifier

Pull Request - State: closed - Opened by cjarmstrong97 about 3 years ago

#34 - Model Format Checking

Pull Request - State: closed - Opened by cjarmstrong97 about 3 years ago

#33 - Add links in documentation to online validation, introspection, and execution of BNGL models through runBioSimulations

Issue - State: open - Opened by jonrkarr about 3 years ago

#32 - Model parser incorrectly succeeds on completely different formats (e.g., CellML) where it should fail

Issue - State: closed - Opened by jonrkarr about 3 years ago

#31 - Provide more information errors for alternative model formats

Issue - State: closed - Opened by jonrkarr about 3 years ago - 1 comment

#30 - fixing a minor import issue

Pull Request - State: closed - Opened by ASinanSaglam about 3 years ago

#29 - Parsing - PatternMods

Pull Request - State: closed - Opened by cjarmstrong97 about 3 years ago - 1 comment

#28 - Parsing - RateLaw & PatternMod

Pull Request - State: closed - Opened by cjarmstrong97 about 3 years ago

#27 - Provide more informative error for empty `sample_times` argument

Issue - State: closed - Opened by jonrkarr about 3 years ago - 1 comment

#26 - BUG: `sample_times` is not parsed correctly

Issue - State: closed - Opened by jonrkarr about 3 years ago - 2 comments

#25 - Parsing - PatternQuantifier

Pull Request - State: closed - Opened by cjarmstrong97 about 3 years ago

#24 - Package fails to parse several models in RuleHub

Issue - State: closed - Opened by jonrkarr about 3 years ago - 3 comments
Labels: bug

#23 - Some issue fixing

Pull Request - State: closed - Opened by cjarmstrong97 about 3 years ago

#22 - Suggestion: use py-perl5 for more seamless bridge to `BNGL2.pl`

Issue - State: open - Opened by jonrkarr about 3 years ago - 2 comments
Labels: enhancement

#21 - Raise exceptions on ill-formatted actions

Issue - State: open - Opened by jonrkarr about 3 years ago - 3 comments
Labels: bug

#20 - PyTest testing suite revamp

Pull Request - State: closed - Opened by cjarmstrong97 about 3 years ago

#19 - Info Subcommand Beginning

Pull Request - State: closed - Opened by cjarmstrong97 over 3 years ago

#18 - Parse all actions (e.g., including `setModelName`)

Issue - State: closed - Opened by jonrkarr over 3 years ago - 4 comments
Labels: bug

#17 - BUG: `bionetgen.bngmodel` fails when action block is empty or undefined

Issue - State: closed - Opened by jonrkarr over 3 years ago - 3 comments

#16 - BUG: `sample_times` action argument is not parsed correctly

Issue - State: closed - Opened by jonrkarr over 3 years ago - 2 comments
Labels: bug

#15 - Make `bionetgen.modelapi.structs.Action.args` a dictionary

Issue - State: closed - Opened by jonrkarr over 3 years ago - 5 comments
Labels: bug

#14 - BUG: Only one action of each type can be parsed

Issue - State: closed - Opened by jonrkarr over 3 years ago - 1 comment

#13 - Documentation Updates

Pull Request - State: closed - Opened by cjarmstrong97 over 3 years ago

#12 - visualize command gives error

Issue - State: closed - Opened by jrfaeder over 3 years ago - 1 comment
Labels: bug

#11 - Installation requires numpy

Issue - State: closed - Opened by jonrkarr over 3 years ago - 4 comments
Labels: enhancement

#10 - Parse actions from BNGL files

Issue - State: closed - Opened by jonrkarr over 3 years ago - 4 comments
Labels: enhancement

#9 - Current directory restoration is missing from one of the cases of `bionetgen.modelapi.bngfile.write_xml`

Issue - State: closed - Opened by jonrkarr over 3 years ago
Labels: bug

#8 - Reading invalid BNGL files should fail with a more informative error message

Issue - State: closed - Opened by jonrkarr over 3 years ago - 2 comments
Labels: enhancement

#7 - Messages from BNG2.pl should display immediately when running from terminal

Issue - State: closed - Opened by jrfaeder over 3 years ago - 3 comments

#6 - Suggestion: remove requirement for specific file extensions

Issue - State: open - Opened by jonrkarr over 3 years ago
Labels: enhancement

#5 - Suggestion: different PyPI name or equate version number to the version of BNG2

Issue - State: open - Opened by jonrkarr over 3 years ago
Labels: enhancement

#4 - `bionetgen.xmlapi.structs.Species.pattern` and `bionetgen.xmlapi.structs.Species.gen_string` include compartments twice

Issue - State: closed - Opened by jonrkarr over 3 years ago - 3 comments
Labels: bug

#3 - Provide option to read the raw model definition rather than the resolved description

Issue - State: closed - Opened by jonrkarr over 3 years ago - 3 comments
Labels: enhancement

#2 - In some cases it would be helpful to parse comments from BNGL files

Issue - State: open - Opened by jonrkarr over 3 years ago - 1 comment
Labels: enhancement

#1 - `bionetgen.xmlapi.model.bngmodel.compartments` attribute is absent for non-compartmentalized models rather than an empty dict

Issue - State: closed - Opened by jonrkarr over 3 years ago - 5 comments

GitHub / RuleWorld/PyBioNetGen issues and pull requests