Changed occurences of physiofit to physiofit4galaxy

MetaSys-LISBP · Aug 17, 2022 · 8f60da7 · 8f60da7
1 parent 84c3993
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Showing 12 changed files with 19 additions and 19 deletions.
diff --git 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
@@ -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 → physiofit4galaxy/__init__.py b/physiofit/__init__.py → physiofit4galaxy/__init__.py
diff --git a/physiofit/__main__.py → physiofit4galaxy/__main__.py b/physiofit/__main__.py → 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 → physiofit4galaxy/base/__init__.py b/physiofit/base/__init__.py → physiofit4galaxy/base/__init__.py
diff --git a/physiofit/base/fitter.py → physiofit4galaxy/base/fitter.py b/physiofit/base/fitter.py → 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 → physiofit4galaxy/base/io.py b/physiofit/base/io.py → 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 → physiofit4galaxy/logger.py b/physiofit/logger.py → physiofit4galaxy/logger.py
diff --git a/physiofit/tests/__init__.py → physiofit4galaxy/tests/__init__.py b/physiofit/tests/__init__.py → physiofit4galaxy/tests/__init__.py
diff --git a/physiofit/ui/__init__.py → physiofit4galaxy/ui/__init__.py b/physiofit/ui/__init__.py → physiofit4galaxy/ui/__init__.py
diff --git a/physiofit/ui/cli.py → physiofit4galaxy/ui/cli.py b/physiofit/ui/cli.py → physiofit4galaxy/ui/cli.py
diff --git 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 = [email protected]
 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