0.2.5

See readme

.gitignore

@@ -50,6 +50,8 @@ coverage.xml
 .hypothesis/
 .pytest_cache/
 cover/
+tests/biomodels/*
+tests/test_biomodels.py
 
 # Translations
 *.mo
@@ -67,6 +69,7 @@ instance/
 
 # Scrapy stuff:
 .scrapy
+.DS_Store
 
 # Sphinx documentation
 docs/_build/

MANIFEST.in

@@ -0,0 +1,30 @@
+# Include the README, LICENSE, and CHANGELOG files
+include README.md
+include LICENSE
+include CHANGELOG.md
+
+# Include JSON data files in the specified package directory
+recursive-include ratesb_python/common *.json
+
+# Exclude all bytecode
+global-exclude *.pyc
+global-exclude __pycache__
+global-exclude *.pyo
+
+# Exclude files and directories related to development, version control, or builds
+exclude .gitignore
+exclude .gitattributes
+exclude .devcontainer
+exclude .coverage
+exclude dist
+exclude tests
+exclude venv
+exclude paper
+exclude *.egg-info
+recursive-exclude *.egg-info *
+recursive-exclude build *
+recursive-exclude .devcontainer *
+recursive-exclude dist *
+recursive-exclude tests *
+recursive-exclude venv *
+recursive-exclude paper *

README.md

@@ -29,6 +29,12 @@ results = analyzer.results
 # Display all errors and warnings
 print(results)
 
+# Check selected errors and warnings
+analyzer.checks([1, 2, 1001, 1002])
+
+# No need to set results = analyzer.results again as results updates automatically
+print(results)
+
 # Display only warnings
 warnings = results.get_warnings()
 for reaction, messages in warnings.items():
@@ -183,6 +189,11 @@ python -m unittest
 ### 0.2.4
 * updated instructions in readme
 
+### 0.2.5
+* Separated model reading from analysis
+* Tested on 1054 biomodels and fixed bugs
+* Added check_model method to allow user to use the package with one line
+
 ## Contributing
 
 Contributions to `ratesb_python` are welcomed! Whether it's bug reports, feature requests, or new code contributions, we value your feedback and contributions. Please submit a pull request or open an issue on our [GitHub repo](https://github.com/sys-bio/ratesb_python).
@@ -199,6 +210,7 @@ Contributions to `ratesb_python` are welcomed! Whether it's bug reports, feature
 
 * Implement stoichiometry checks for mass actions.
 * Perform checks after default classification to optimize performance.
+* Give user option to not use the default rate law classification to improve performance
 
 ## Known Issues
 

ratesb_python/__init__.py

@@ -1 +1,2 @@
-from ratesb_python.common.analyzer import Analyzer
+from ratesb_python.common.analyzer import Analyzer
+from ratesb_python.common.analyzer import check_model