Merge pull request #9 from MetaSys-LISBP/dev

v2.0.3

docs/faq.rst

@@ -24,14 +24,11 @@ What units should be used for input data?
 ------------------------------
 
 Input data (biomass concentration, metabolites concentrations, and time) can be provided to PhysioFit using any unit. Still, we recommand to use units for which values are as close to unity as
-possible to ensure numerical stability (e.g. 3 mM instead of 3e3 µM). Importantly, units of the estimated fluxes depend on units of time and metabolites and biomass concentrations.
+possible to ensure numerical stability (e.g. 3 mM instead of 3e3 µM). Importantly, units of the estimated fluxes depend on units of time and metabolites and biomass concentrations. The concentration of different metabolites can 
+be provided using different units, but a single unit must be used for all measurements of a given metabolite.
 
 .. seealso:: :ref:`flux units` 
 
-To avoid any numerical instabilities, provide values in a range not too far from unity (e.g. if a metabolite 
-concentration is 2 mM, provide the value directly in mM and not as 2e-3 M). The concentration of different metabolites can 
-be provided using different units, but a single unit must be used for all measurements of a given metabolite.
-
 ..  _`flux units`:
 
 What are the flux units?

physiofit/__init__.py

@@ -1 +1 @@
-__version__ = "2.0.2"
+__version__ = "2.0.3"

physiofit/base/io.py

@@ -67,15 +67,15 @@ def _read_data(path_to_data: str) -> DataFrame:
 
         data_path = Path(path_to_data).resolve()
 
-        if data_path.suffix == ".tsv":
+        if data_path.suffix in [".txt", ".tsv"]:
             data = read_csv(str(data_path), sep="\t")
         elif data_path.suffix == ".csv":
             data = read_csv(str(data_path), sep=";")
         else:
             if not data_path.exists():
                 raise ValueError(f"{data_path} is not a valid file")
             else:
-                raise TypeError(f"{data_path} is not a valid format. Accepted formats are .csv or .tsv")
+                raise TypeError(f"{data_path} is not a valid format. Accepted formats are .csv, .txt or .tsv")
 
         IoHandler._verify_data(data)
         return data

physiofit/ui/cli.py

@@ -82,7 +82,7 @@ def parse_args():
     parser = argparse.ArgumentParser("Physiofit: Extracellular flux estimation software")
 
     # Parse data arguments (tsv + json)
-    parser.add_argument("-t", "--data", type=str, help="Path to data file in tsv format")
+    parser.add_argument("-t", "--data", type=str, help="Path to data file in tabulated format (txt or tsv)")
     parser.add_argument("-c", "--config", type=str, help="Path to config file in json format")
 
     # Parse basic parameters

physiofit/ui/gui.py

@@ -78,7 +78,7 @@ def _initialize_opt_menu(self):
         if file_extension == "json":
             config = IoHandler.read_json_config(self.data_file)
             input_values.update(config)
-        elif file_extension != "tsv":
+        elif file_extension not in ["tsv", "txt"]:
             raise KeyError(
                 f"Wrong input file format. Accepted formats are tsv for data files or json for configuration "
                 f"files. Detected file: {self.data_file.name}")
@@ -94,7 +94,7 @@ def _initialize_opt_menu(self):
         submitted = self._initialize_opt_menu_widgets(input_values, file_extension)
 
         if submitted:
-            if file_extension == "tsv":
+            if file_extension in ["tsv", "txt"]:
                 self.io_handler.data = data
                 self.io_handler.data = self.io_handler.data.sort_values("time", ignore_index=True)
                 self.io_handler.names = self.io_handler.data.columns[1:].to_list()
@@ -145,7 +145,7 @@ def _initialize_opt_menu_widgets(self, input_values, file_extension):
                 disabled=enable_mc
             )
 
-            if file_extension == "tsv":
+            if file_extension in ["tsv", "txt"]:
 
                 # Set up tkinter for directory chooser
                 root = tk.Tk()

requirements.txt

@@ -1,4 +1,6 @@
-pandas
-matplotlib
-numpy
-scipy
+pandas >= 1.1.5
+numpy >= 1.21.6
+scipy >= 1.5.2
+streamlit>=1.8.0
+matplotlib >= 3.5.1
+openpyxl >= 3.0.9

setup.cfg

@@ -16,14 +16,14 @@ classifiers =
 
 [options]
 packages = find:
-python_requires = >=3.6
+python_requires = >=3.7
 install_requires =
-    pandas
-    numpy
-    scipy
-    streamlit>=1.5.0
-    matplotlib
-    openpyxl
+    pandas >= 1.1.5
+    numpy >= 1.21.6
+    scipy >= 1.5.2
+    streamlit>=1.8.0
+    matplotlib >= 3.5.1
+    openpyxl >= 3.0.9
 
 [options.entry_points]
 console_scripts =