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

KEGG entries

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