diff --git a/.gitignore b/.gitignore index 68101ac..e708bd4 100644 --- a/.gitignore +++ b/.gitignore @@ -1,13 +1,13 @@ /venv/ -physiofit/__pycache__/__init__.cpython-310.pyc -physiofit/__pycache__/__main__.cpython-310.pyc -physiofit/__pycache__/logger.cpython-310.pyc -physiofit/base/__pycache__/__init__.cpython-310.pyc -physiofit/base/__pycache__/fitter.cpython-310.pyc -physiofit/base/__pycache__/io.cpython-310.pyc -physiofit/last_version.txt -physiofit/ui/__pycache__/__init__.cpython-310.pyc -physiofit/ui/__pycache__/cli.cpython-310.pyc +physiofit4galaxy/__pycache__/__init__.cpython-310.pyc +physiofit4galaxy/__pycache__/__main__.cpython-310.pyc +physiofit4galaxy/__pycache__/logger.cpython-310.pyc +physiofit4galaxy/base/__pycache__/__init__.cpython-310.pyc +physiofit4galaxy/base/__pycache__/fitter.cpython-310.pyc +physiofit4galaxy/base/__pycache__/io.cpython-310.pyc +physiofit4galaxy/last_version.txt +physiofit4galaxy/ui/__pycache__/__init__.cpython-310.pyc +physiofit4galaxy/ui/__pycache__/cli.cpython-310.pyc physiofit.egg-info/dependency_links.txt physiofit.egg-info/entry_points.txt physiofit.egg-info/PKG-INFO diff --git a/README.md b/README.md index c962e7d..ca8c773 100644 --- a/README.md +++ b/README.md @@ -12,8 +12,8 @@ PhysioFit4Galaxy is a fork of the original [PhysioFit package](https://github.co of the tool. ## Bug and feature requests -If you have an idea on how we could improve PhysioFit please submit a new *issue* -to [our GitHub issue tracker](https://github.com/MetaSys-LISBP/PhysioFit/issues). +If you have an idea on how we could improve PhysioFit on galaxy, please submit a new *issue* +to [our GitHub issue tracker](https://github.com/MetaSys-LISBP/PhysioFit4Galaxy/issues). ## How to cite Peiro C., Millard P., de Simone A., Cahoreau E., Peyriga L., Enjalbert B., and Heux S. Chemical and metabolic controls on dihydroxyacetone metabolism lead to suboptimal growth of *Escherichia coli*. Appl Environ Microbiol, 2019, [doi: 10.1128/AEM.00768-19](https://doi.org/10.1128/AEM.00768-19) diff --git a/physiofit/__init__.py b/physiofit4galaxy/__init__.py similarity index 100% rename from physiofit/__init__.py rename to physiofit4galaxy/__init__.py diff --git a/physiofit/__main__.py b/physiofit4galaxy/__main__.py similarity index 90% rename from physiofit/__main__.py rename to physiofit4galaxy/__main__.py index fbcebe3..5b8761b 100644 --- a/physiofit/__main__.py +++ b/physiofit4galaxy/__main__.py @@ -1,6 +1,6 @@ import sys -import physiofit.ui.cli +import physiofit4galaxy.ui.cli def main(): """The main routine""" diff --git a/physiofit/base/__init__.py b/physiofit4galaxy/base/__init__.py similarity index 100% rename from physiofit/base/__init__.py rename to physiofit4galaxy/base/__init__.py diff --git a/physiofit/base/fitter.py b/physiofit4galaxy/base/fitter.py similarity index 99% rename from physiofit/base/fitter.py rename to physiofit4galaxy/base/fitter.py index a6b3328..6a5267d 100644 --- a/physiofit/base/fitter.py +++ b/physiofit4galaxy/base/fitter.py @@ -9,7 +9,7 @@ from scipy.optimize import minimize, differential_evolution from scipy.stats import chi2 -from physiofit.logger import initialize_fitter_logger +from physiofit4galaxy.logger import initialize_fitter_logger mod_logger = logging.getLogger("PhysioFit.base.fitter") diff --git a/physiofit/base/io.py b/physiofit4galaxy/base/io.py similarity index 99% rename from physiofit/base/io.py rename to physiofit4galaxy/base/io.py index 1cc3ee0..fcda28f 100644 --- a/physiofit/base/io.py +++ b/physiofit4galaxy/base/io.py @@ -8,7 +8,7 @@ from matplotlib.backends.backend_pdf import PdfPages from pandas import DataFrame, read_csv -from physiofit.base.fitter import PhysioFitter +from physiofit4galaxy.base.fitter import PhysioFitter mod_logger = logging.getLogger("PhysioFit.base.io") diff --git a/physiofit/logger.py b/physiofit4galaxy/logger.py similarity index 100% rename from physiofit/logger.py rename to physiofit4galaxy/logger.py diff --git a/physiofit/tests/__init__.py b/physiofit4galaxy/tests/__init__.py similarity index 100% rename from physiofit/tests/__init__.py rename to physiofit4galaxy/tests/__init__.py diff --git a/physiofit/ui/__init__.py b/physiofit4galaxy/ui/__init__.py similarity index 100% rename from physiofit/ui/__init__.py rename to physiofit4galaxy/ui/__init__.py diff --git a/physiofit/ui/cli.py b/physiofit4galaxy/ui/cli.py similarity index 100% rename from physiofit/ui/cli.py rename to physiofit4galaxy/ui/cli.py diff --git a/setup.cfg b/setup.cfg index 0fc5b47..58f27ac 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,14 +1,14 @@ [metadata] -name = physiofit -version = attr: physiofit.__version__ +name = physiofit4galaxy +version = attr: physiofit4galaxy.__version__ author = Loïc Le Grégam author_email = legregam@insa-toulouse.fr description = Calculate extracellular fluxes from metabolite concentrations and biomass data long_description = file: README.md long_description_content_type = text/markdown -url = https://github.com/MetaSys-LISBP/PhysioFit +url = https://github.com/MetaSys-LISBP/PhysioFit4Galaxy project_urls = - Bug Tracker = https://github.com/MetaSys-LISBP/PhysioFit/issues + Bug Tracker = https://github.com/MetaSys-LISBP/PhysioFit4Galaxy/issues classifiers = Programming Language :: Python :: 3 License :: OSI Approved :: GNU General Public License (GPL) @@ -26,4 +26,4 @@ install_requires = [options.entry_points] console_scripts = - physiofit = physiofit.__main__:main + physiofit4galaxy = physiofit4galaxy.__main__:main