Uh oh!
There was an error while loading. Please reload this page.
Fixes to several github issues - #64
Closed
akutuva21 wants to merge 3 commits into
Closed
Conversation
Fixes#55 — get_rule_mod() had three bugs in xmlparsers.py: - TotalRate never detected: string "1" compared to int 1 (always False) - DeleteMolecules: KeyError if @DeleteMolecules attribute absent on any op - MoveConnected list branch: appended from move_op[...] instead of mo[...] Fixes#57 — NFsim version now detected and reported in --version/info commands via PATH lookup with fallback to BNG2.pl-adjacent bin/. Fixes#58, #61 — Remove distutils usage throughout: - distutils.spawn → shutil.which in utils.py - distutils.ccompiler → setuptools._distutils with distutils fallback - setup.py: add python_requires>=3.8, promote missing deps to install_requires - ci.yml: replace deprecated setup.py install/sdist/bdist_wheel with pip Fixes#60 — Add release-test.yml workflow that installs from PyPI and runs smoke tests + pytest on every published release across all platforms. Fixes#21 — Add test_action_parsing.py covering pyparsing rejection of malformed actions (unclosed braces). Also adds bionetgen/__main__.py to support python -m bionetgen invocation, and tests/test_rule_modifiers.py with full coverage of the three get_rule_mod bug fixes.
wshlavacek added a commit
to wshlavacek/PyBioNetGen
that referenced
this pull request
May 24, 2026
SYMBOL_RENAMES registry + rename_symbols() (whole-word, both stacks), mirroring TOL_OVERRIDES. Rescues the 3 V19xx endemic models whose parameter 'frac' collides with ExprTk's reserved 'frac' in bngsim NFsim (RuleWorld#63/RuleWorld#64) — rename frac->fracsym is semantically null (scalar coefficient, never a .gdat column). All 3 now run on both stacks and PASS. TIMEOUT_OVERRIDES['mlnr.bngl']=300: the slow-tier sweep timed it out at 180s under 2-worker contention, but it runs in ~82s idle; 300s covers it and it PASSES. 6 rename_symbols unit tests added.
jrfaeder pushed a commit
that referenced
this pull request
Jul 20, 2026
* Refactor gather_terms array sums Replaced manual explicit summation loops with pythonic sum() operations in gather_terms. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #64 remove forbidden artifacts and run black --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
This PR addresses a cluster of bugs and long-standing CI/packaging issues, primarily around Python 3.12 compatibility, broken rule modifier parsing, and the lack of automated release testing.
Changes
Bug fixes
bionetgen/modelapi/xmlparsers.py— closes#55Three bugs in
get_rule_mod():TotalRatenever appliedratelaw["@totalrate"] == 1compared string to int, alwaysFalsestr(ratelaw.get("@totalrate")) == "1"DeleteMoleculesKeyErrorop.get("@DeleteMolecules")+ stricterall()checkMoveConnectedwrong idsmonever used — all appends read from the outer listmove_opmo["@id"],mo["@source"], etc. across all 4 linesPython 3.12 compatibility — closes#58, #61
distutils.spawn.find_executable→shutil.whichinutils.pydistutils.ccompiler→setuptools._distutils.ccompiler(withdistutilsfallback) incsimulator.pyci.yml: replacedpython setup.py install && python setup.py sdist bdist_wheelwithpython -m pip install .(eliminates double BNG binary download and deprecation warnings)setup.py: addedpython_requires=">=3.8"and promotedpyyed,matplotlib,pandasintoinstall_requiresNFsim version reporting — closes#57
BNGInfo.gatherInfo()now detects the NFsim binary and reports its version underNFsim version. Lookup order: PATH first, thenbin/adjacent to BNG2.pl. Gracefully falls back to"not found"if unavailable.Automated PyPI release testing — closes#60
Adds
.github/workflows/release-test.yml, triggered on every published release. Installsbionetgenfrom PyPI, runs a smoke test (bionetgen -h,import bionetgen), then the full pytest suite across Ubuntu / Windows / macOS × Python 3.9–3.12.Action exception tests — closes#21
Adds
tests/test_action_parsing.pywith a test confirming pyparsing raises on malformed actions (e.g. missing closing braces).Other
bionetgen/__main__.pysopython -m bionetgenworks as an invocation pathtests/test_rule_modifiers.pywith full unit test coverage of all threeget_rule_mod()bug fixesIssues closed
Closes#21
Closes#55
Closes#57
Closes#58
Closes#60
Closes#61
Testing
test_rule_modifiers.pydirectly exercises each of the three fixed code paths with targeted fixturestest_action_parsing.pyconfirms the pyparsing grammar rejects malformed input