BUGFIX: Typos in GH workflow #54
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Changes in the behavior of flake8 caused the test to fail. Adding W503 to the ignored errors fixes this. W503 is currently the recommended way according to PEP8.
removal of mypy pre-commit hook UPDATE: Project updated to use pyproject.toml. Setup.py and mypy.ini removed. NEW: Installation dependency of escher is now optional. Users can install dependency to use Escher. This chance is can be seen in module pathway from subpackage pathway.
UPDATE: subpackate parsing imports are not specific anymore. UPDATE: module kegg.py, bigg.py and biocyc.py include new functions parse_reaction_attributes and parse_metabolites_attributes. These function extract the main information for the data. Biocyc includes new function such reaction_str_from_xml, get_direction_from_xml. Kegg includes data_from_string. NEW: New module retrieval.py. This module is in charge of downloading data from the multiple databases and writing them into disk. Additionally, the parsing of the data to reactions and metabolites is also done by this module. UDPATE: cobramod.utils include new functions such convert_to_transport and is_compound
UPDATE: removal of shebang for multiple modules that are not supposed to be run as scripts UPDATE: In bigg.py and kegg.py, few functions renamed (retrieve_kegg_genes, parse_genes) UPDATE: in core.creation.py, some functions renamed (metabolite_from_string, metabolite_from_data, convert_string_metabolite, string_to_reaction). Old functions commented. Main function from the module refactor to use new data type. Argumnets for multiple function updated to be optional. Only main function use kwargs. Main function refactor to be more concise and use new functions. FIX: in crossreferences.py, issue were the path that is a string, was not absolute. UPDATE: in genes.py, rename of function genes_to_reaction UPDATE: test_creation.py updated to use new functions. Some blocks were commented until new function in other modules are updated
UPDATED: in extension.py, multiple reactions renamed e.g yield_reaction_from_list, find_problem, recursive_flux_test, non_zero_core, add_reactions_to_Pathway, remove_avoid_reactions, add_pathway_from_file, add_pathway_from_data, add_pathway_from_strings. Main core function add_function internally modified to use refactored reactions. add_pathway_from_data uses new data structure in retrieval.py. For multiple functions, arguments were updated to include optional arguments. UPDATED: in graph.py, function renamed to get_graph_dict, build_lineal_graph. Removal of old deprecated code REMOVED: module retrieval.py UPDATED: in parsing, kegg.py, bigg.py and biocyc.py have deprecated code removed. NEW: in retrieval.py, data can parse pathway information. Additionally, subdatabase from Biocyc can be used FIX: in utils.py, arrows for equations had the wrong bounds. New functions inform_new_sinks, reaction_is_minimize, confirm_sink FIX: in mapping.py, function uses correct name
UPDATED: in retrieval.py. Requesting files from biocyc needs credentials. Credentials come from function in utils.py. Additionally, Data needs new argument "model_id" UPDATED: in crossreferences.py deprecated pandas function replaced UPDATED: in extension.py, function add_pathway_from_data now uses tuples instead of list. Tuples are used for the visualization of pathways UPDATED: in graph.py, function find_cycle refactor to make it simpler. Additionally, multiple funcitions had their types added. UPDATED: in pathway.py, reaction_strings does not need a cobra.Model UPDATED: in summary.py, function summmary uses filename as Optional argument BUGFIX: in bigg.py, when retrieving files, metabolites will come from "universal". UPDATED: multiple test updated to use new refactored functions
UPDATED: in creation.py, parsing of genes modified to be taken care of by parsing subpackage. This change applies to bigg, biocyc, kegg. For plantcyc and solcyc, this is also true and old code was either commented or removed UPDATED: data directory structure for solcyc modified
NEW: in utils, new function kegg_info_to_version moved from kegg.py NEW: in retrieval.py, Data class now expects a version. This is needed to comply with the previous data versioning. Additionally, when querying, a encoded identifier is needed to avoid problems with servers. All databases directory are uppercase. UPDATE: for plantcyc and solcyc, enconding also happens for gene information. Additionally, removing deprecated code. Problem with gene directory fixed. UPDATE: in kegg.py, old code removed. Function renamed to ko_generator. When querying genes, cobramod will try to obtain genes for reactions. Sometimes the query can be stopped server-side. To avoid this, we make sequentially requests instead of a large one FIXED: in biocyc.py, problem with nameless reactions fixed. UPDATE: in bigg.py, HTTPError raised from find_url now shows the model_id from the query. NEW: new module db_version.py. This module is in charge to track and compare the data versions for cobramod. It uses a Singleton as configurator. Methods come from original module base.py REMOVED: methods moved to db_version.py or removed
FIXED: Missing RNA parsing for Biocyc family databases
SuperpathwayWarning is now an Exception UPDATE:Enviroment updated to be OS-independent NEW: Test for PMN:ARA in test_creation.py
UPDATED: class Database in retrieval UPDATED: Refactor of plantcyc, solcyc modules to only gene parsing. Modules in parsing got their docstrings updated REMOVED: deprecated code in creation.py UPDATED: the module test.py, uses pkg_resouces to retrieve models from cobra
ADDED: Memote-example files added UPDATED: jupyter files for all example updated to reflect new changes
UPDATED: Test data 15.01.24 UPDATED: Test files use new changes. Deprecated code removed. Superpatwathway Warning changed to exception. Usage of pkgresources for textbook models
REMOVED: old test. ADDED: missing figure
UPDATED: in extension.py, fn yield_reaction_from list will only create an object if the object is not already in the model.
UPDATE: pre commit with ruff fmt and linting
UPDATE: .yml for test and publish updated with more recents actions NEW: changelog UPDATE: environment.yml includes all deps for developement UPDATE: in pyproject.toml, updating dependencies NEW: logging information is more human-friendly and includes colors
UPDATED: Test data updated to 19.02.2024 REMOVED: Test with Solcyc data FIXED: some test for pathways used deprecated statements NEW: Alternative optional dependency 'dev' UPDATE: in Readme, badge with python versions
UPDATE: debug_log has a new format. This applies to the visualization sub-package. REMOVE: long text in README.md for the abstract UPDATE: dev dependencies in pyproject.py includes docs build NEW: fun change_to_debug takes care of changing format for the tests UPDATE: all tests included this new function
UPDATED: Most modules uses rather the logging module than the warning module to print warnings REMOVED: AbbreviationWarning UPDATED: readthedocs.yml uses py310 UPDATED: typo in README UPDATED: Test instances modified to show changes
for converter.py
UPDATED: docs sources REMOVED: make.bat UPDATED: sphinx-autoapi reverted in environment.yml and pyproject UPDATED: changing log lvevel for non-zero flux test and genes_to_reaction. Fixing typos in kegg.py and utils.py
FIXED: missing warning for wrong chemical formula
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