Merge pull request #51 from MetaSys-LISBP/dev

Dev

.gitignore

@@ -15,3 +15,4 @@ physiofit.egg-info/requires.txt
 physiofit.egg-info/SOURCES.txt
 physiofit.egg-info/top_level.txt
 /versions publi/
+/physiofit/data/

physiofit/base/io.py

@@ -49,7 +49,7 @@ def __init__(self):
         self.simulated_data_sds = None
         self.simulated_data = None
         self.experimental_data = None
-        self.home_path = None
+        self.wkdir = None
         self.data_path = None
         self.res_path = None
         self.has_config_been_read = False
@@ -145,16 +145,16 @@ def _verify_data(data: DataFrame):
                 "DataFrame has not been generated"
             )
 
-        for x in ["time", "X"]:
+        for x in ["time", "X", "experiments"]:
             if x not in data.columns:
                 raise ValueError(f"Column {x} is missing from the dataset")
+        if data.columns[0] != "experiments":
+            raise ValueError("First column should be 'experiments'")
+        if data.columns[1] != "time":
+            raise ValueError("Second column should be 'time'")
 
-        if "experiment" in data.columns:
-            if len(data.columns) <= 3:
-                raise ValueError(f"Data does not contain any metabolite columns")
-        else:
-            if len(data.columns) <= 2:
-                raise ValueError(f"Data does not contain any metabolite columns")
+        if len(data.columns) <= 3:
+            raise ValueError(f"Data does not contain any metabolite columns")
 
         for x in data.columns:
             if x != "experiments" and data[x].dtypes != np.int64 and data[x].dtypes != np.float64:
@@ -219,7 +219,7 @@ def add_model(model_file):
     def read_yaml(yaml_file: str | bytes) -> ConfigParser:
 
         """
-        Import raml configuration file and parse keyword arguments
+        Import yaml configuration file and parse keyword arguments
 
         :param yaml_file: path to the yaml file or json file
         :return config_parser: Dictionary containing arguments parsed from yaml file

physiofit/ui/cli.py

@@ -14,7 +14,6 @@
 import logging
 from pathlib import Path
 import sys
-# import shutil
 
 import pandas as pd
 
@@ -93,8 +92,11 @@ def run(data, args, logger, experiments):
         io = IoHandler()
         exp_data = data.loc[exp, :].sort_values("time").copy()
         logger.info(f"Input Data: \n{exp_data}")
-        io.home_path = Path(args.data).parent
-        logger.info(f"Home path: {io.home_path}")
+        if hasattr(args, 'galaxy'):
+            io.wkdir = Path('.')
+        else:
+            io.wkdir = Path(args.data).parent
+        logger.info(f"Home path: {io.wkdir}")
         logger.info(f"Reading configuration file at {args.config}")
         io.configparser = io.read_yaml(args.config)
         logger.info(f"Config File:\n{io.configparser}")
@@ -128,9 +130,9 @@ def run(data, args, logger, experiments):
             io.multiple_experiments = []
         io.multiple_experiments.append(df)
         if exp is not None:
-            res_path = io.home_path / (io.home_path.name + "_res") / exp
+            res_path = io.wkdir / (io.wkdir.name + "_res") / exp
         else:
-            res_path = io.home_path / (io.home_path.name + "_res")
+            res_path = io.wkdir / (io.wkdir.name + "_res")
         logger.info(res_path)
         if not res_path.is_dir():
             res_path.mkdir(parents=True)

physiofit/ui/gui.py

@@ -94,7 +94,7 @@ def _initialize_opt_menu(self):
             except Exception:
                 st.error("An error has occurred when reading the yaml configuration file.")
                 raise
-        elif file_extension  in ["tsv", "txt"]:
+        elif file_extension in ["tsv", "txt"]:
             try:
                 self.io.data = self.io.read_data(self.data_file)
                 # Initialize default SDs
@@ -141,10 +141,10 @@ def _initialize_opt_menu(self):
             except Exception:
                 st.error("An error has occurred when initializing the model")
                 raise
-            if not self.io.home_path:
+            if not self.io.wkdir:
                 raise ValueError("No output directory selected")
             self.config_parser = ConfigParser(
-                path_to_data = self.io.home_path / self.data_file.name,
+                path_to_data =self.io.wkdir / self.data_file.name,
                 selected_model= self.model,
                 sds = self.sd,
                 mc = self.mc,
@@ -284,8 +284,8 @@ def _initialize_opt_menu_widgets(self, file_extension):
                     self._output_directory_selector()
 
                 else:
-                    self.io.home_path = Path(self.config_parser.path_to_data).resolve().parent
-                    self.io.res_path = self.io.home_path / (self.io.home_path.name + "_res")
+                    self.io.wkdir = Path(self.config_parser.path_to_data).resolve().parent
+                    self.io.res_path = self.io.wkdir / (self.io.wkdir.name + "_res")
 
             # Build the form for advanced parameters
             form = st.form("Parameter_form")
@@ -500,28 +500,28 @@ def _output_directory_selector(self):
 
             # Initialize home path from directory selector and add
             # to session state
-            st.session_state.home_path = Path(st.text_input(
+            st.session_state.wkdir = Path(st.text_input(
                 "Selected output data directory:",
                 filedialog.askdirectory(master=root)
             ))
-            if st.session_state.home_path == Path(".") \
-                    or not st.session_state.home_path.exists():
+            if st.session_state.wkdir == Path(".") \
+                    or not st.session_state.wkdir.exists():
                 raise RuntimeError("Please provide a valid output directory")
-            self.io.home_path = copy(
-                st.session_state.home_path)
+            self.io.wkdir = copy(
+                st.session_state.wkdir)
 
-        elif hasattr(st.session_state, "home_path"):
+        elif hasattr(st.session_state, "wkdir"):
 
-            self.io.home_path = Path(st.text_input(
+            self.io.wkdir = Path(st.text_input(
                 "Selected output data directory:",
-                st.session_state.home_path
+                st.session_state.wkdir
             ))
-            if self.io.home_path == Path(".") \
-                    or not self.io.home_path.exists():
+            if self.io.wkdir == Path(".") \
+                    or not self.io.wkdir.exists():
                 raise RuntimeError("Please provide a valid output directory")
 
             # Initialize the result export directory
-            self.io.res_path = self.io.home_path / (self.io.home_path.name + "_res")
+            self.io.res_path = self.io.wkdir / (self.io.wkdir.name + "_res")
             if not clicked:
                 if not self.io.res_path.is_dir():
                     self.io.res_path.mkdir()

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "physiofit"
-version = "3.3.1"
+version = "3.3.2"
 description = "Calculate extracellular fluxes from metabolite concentrations and biomass data"
 authors = ["llegregam <[email protected]>"]
 license = "GNU General Public License (GPL)"

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: ..\data.tsv
+path_to_data: ".\\validation\\models\\Monod_model\\physiofit_results\\data.tsv"
 sds:
   P_ethanol: 3
   S_GlcEq: 7

validation/models/Steady-state_model/physiofit_results/results/config_file.yml

@@ -16,7 +16,7 @@ model:
     Glc_q: 1
     X_0: 1
     growth_rate: 1
-path_to_data: C:\Users\millard\Documents\GIT\PhysioFit\data_test\Steady-state_model\data.txt
+path_to_data: ".\\validation\\models\\Steady-state_model\\physiofit_results\\results\\config_file.yml"
 sds:
   Ace: 0.2
   Glc: 0.46