Merge pull request #44 from MetaSys-LISBP/dev

Dev

physiofit/base/io.py

@@ -202,6 +202,19 @@ def get_models(self, data=None):
                 else:
                     self.models.append(model_class(self.data))
 
+    def get_local_model_folder(self) -> str:
+        """
+        Return the path towards the actual environment's used models folder
+        """
+
+        model_dir = Path(__file__).parent / "models"
+        return str(model_dir)
+
+    # TODO: Implement this function to add model to model folder and add button to GUI
+    @staticmethod
+    def add_model(model_file):
+        pass
+
     @staticmethod
     def read_yaml(yaml_file: str | bytes) -> ConfigParser:
 
@@ -227,7 +240,7 @@ def read_yaml(yaml_file: str | bytes) -> ConfigParser:
                 )
         return config_parser
 
-    def initialize_fitter(self, data, **kwargs):
+    def initialize_fitter(self, data: pd.DataFrame, **kwargs) -> PhysioFitter:
         """
         Initialize a PhysioFitter object
 
@@ -266,7 +279,7 @@ def initialize_fitter(self, data, **kwargs):
         return fitter
 
 
-    def output_pdf(self, fitter, export_path: str | Path = None):
+    def output_pdf(self, fitter: PhysioFitter, export_path: str | Path = None):
         """
         Handle the creation and output of a pdf file containing fit results as
         a plot

physiofit/ui/cli.py

@@ -1,5 +1,14 @@
 """
 Module containing the Command-Line Interface control logic.
+
+The Command-Line Interface has two goals:
+
+    i) Have a local CLI that can be used to launch jobs in a concise and quick manner, without use of the Graphical
+    User Interface. This can help when testing many different parameter sets, and also permits easy pipelining of the
+    tool, as described below.
+    ii) Have a version compatible with an integration onto the Galaxy W4M platform to be used in automated flux
+    calculation workflows
+
 """
 import argparse
 import logging

physiofit/ui/gui.py

@@ -163,7 +163,7 @@ def _initialize_opt_menu(self):
 
                     self.io.res_path = results_path / experiment
                     if not self.io.res_path.is_dir():
-                        self.io.res_path.mkdir()
+                        self.io.res_path.mkdir(parents=True)
                     # Initialize the fitter object
                     self.io.names = self.io.data.columns[1:].to_list()
                     kwargs = self._build_fitter_kwargs()
@@ -220,17 +220,21 @@ def _initialize_opt_menu_widgets(self, file_extension):
         model_options = [
             model.model_name for model in self.io.models
         ]
-        model_options.insert(0, "--")
+        if self.config_parser.model:
+            idx = model_options.index(self.config_parser.model["model_name"])
+        else:
+            idx = None
         model_name = st.selectbox(
             label="Model",
             options=model_options,
             key="model_selector",
-            help="Select the flux calculation model"
+            help="Select the flux calculation model",
+            index=idx
         )
 
         #if model_name == "Dynamic system (only substrates)":
         #    st.error("Not yet implemented...")
-        if model_name != "--":
+        if model_name:
             # Initialize selected model
             self.model = self.io.select_model(model_name)
             try:

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "physiofit"
-version = "3.1.1"
+version = "3.2.0"
 description = "Calculate extracellular fluxes from metabolite concentrations and biomass data"
 authors = ["llegregam <[email protected]>"]
 license = "GNU General Public License (GPL)"
@@ -16,7 +16,6 @@ numpy = "^1.24.2"
 scipy = "^1.10.1"
 streamlit = "^1.20.0"
 matplotlib = "^3.7.1"
-openpyxl = "^3.0.9"
 pyyaml = "^6.0"
 
 [tool.poetry.group.dev.dependencies]

validation/models/Monod_model/data.tsv

@@ -1,10 +1,10 @@
-time	X	S_GlcEq	P_ethanol
-0	1.1059872	75.04926	0
-2	1.1495275	73.038826	0.57032937
-4	1.9303926	70.92306	1.6142677
-6	2.7112577	68.06932	2.5530024
-10	5.3252807	58.518	6.1151433
-16	11.72252	33.73693	18.411366
-22	21.279594	1.3718239	31.23335
-34	21.328758	0	31.5461
-45	21.27246	0	31.384602
+experiments	time	X	S_GlcEq	P_ethanol
+A	0	1.1059872	75.04926	0
+A	2	1.1495275	73.038826	0.57032937
+A	4	1.9303926	70.92306	1.6142677
+A	6	2.7112577	68.06932	2.5530024
+A	10	5.3252807	58.518	6.1151433
+A	16	11.72252	33.73693	18.411366
+A	22	21.279594	1.3718239	31.23335
+A	34	21.328758	0	31.5461
+A	45	21.27246	0	31.384602

validation/models/Monod_model/physiofit_results/config_file.yml

@@ -18,7 +18,7 @@ model:
     S_GlcEq_s_0: 100
     X_0: 1
     y_BM: 1
-path_to_data: C:\Users\millard\Documents\GIT\PhysioFit\data_test\config_file.yml
+path_to_data: ..\data.tsv
 sds:
   P_ethanol: 3
   S_GlcEq: 7