Merge pull request #50 from MetaSys-LISBP/dev

Dev

docs/cite.rst

@@ -3,8 +3,8 @@ How to cite
 
 Thank you for using PhysioFit and citing us in your work! It means a lot to us and encourage us to continue its development.
 
-  PhysioFit: quantifying cell growth parameters and uptake and production fluxes.
+  PhysioFit: a software to quantify cell growth parameters and extracellular fluxes.
 
   Le Grégam L., Guitton Y., Bellvert F., Jourdan F., Portais J.C., Millard P.
 
-  **doi**: https://doi.org/10.1101/2023.10.12.561695
+  bioRxiv preprint, doi: https://doi.org/10.1101/2023.10.12.561695

docs/faq.rst

@@ -76,7 +76,7 @@ The quality of the fit can be evaluated based on:
 What is a χ² test?
 ------------------------------------------------------------------
 
-A χ² test describes how well a model fits a set of observations. Measures of goodness of fit typically summarize the discrepancy between observed values and the values expected under the model used in PhysioFit (see the :doc:`models` section). It is calculated as the sum of differences between measured and simulated values, each squared and divided by the simulated value.
+A χ² test describes how well a model fits a set of observations. Measures of goodness of fit typically summarize the discrepancy between observed values and the values expected under the model used in PhysioFit (see the :doc:`method` section). It is calculated as the sum of differences between measured and simulated values, each squared and divided by the simulated value.
 A good fit corresponds to small differences between measured and simulated values, thereby the χ² value is low. In contrast, a bad fit corresponds to large differences between simulations and measurements, and the χ² value is high. 
 
 The resulting χ² value can then be compared with a χ² distribution to determine the goodness of fit. The p-value of one-tail χ² test is calculated by PhysioFit from the best fit and is given in the log file (have a look to the :doc:`usage` section). A p-value close to 0 means poor fitting, and a p-value close to 1 means good fitting (keeping in mind that a p-value very close to 1 can be an evidence that standard deviations might be overestimated). A 

docs/method.rst

@@ -52,8 +52,8 @@ more details on the interpretation of the khi2 test results.
 Sensitivity analysis
 *********************
 
-To determine the precision on the fit and on the estimated parameters (including fluxes), PhysioFit performs a Monte Carlo analysis. Briefly, several 
-noisy datasets are generated from the simulated dynamics of the best fit (i.e defined in parameter :samp:`number of iterations` of the GUI) and calculate fluxes and other growth 
+To determine the precision on the fit and on the estimated parameters (including fluxes), PhysioFit performs a Monte Carlo analysis. Briefly, PhysioFit generates several 
+datasets by adding noise to the dynamics simulated from the best fit, and calculated fluxes and other growth 
 parameters for each of these synthetic datasets. This enables PhysioFit to compute statistics (mean, median, standard deviation and 95% confidence interval) for 
-each parameter. We recommend always running a sensitivity analysis when using PhysioFit.
+each parameter (including fluxes). We recommend always running a sensitivity analysis when using PhysioFit.
 

docs/models.rst

@@ -1,6 +1,12 @@
 Models
 =========
 
+Some common flux calculation models are provided with PhysioFit, and users can also build their own models.
+
+.. note:: We would be happy to broaden the types of models shipped with PhysioFit. If you have developed a new model, it might be 
+          usefull and valuable to the fluxomics community! Please, keep in touch with us to discuss and see if we can include your 
+          model in the built-in models shipped with PhysioFit! :)
+
 
 Models shipped with PhysioFit
 ******************************

physiofit/ui/gui.py

@@ -34,6 +34,7 @@ def start_app(self):
 
         st.set_page_config(page_title=f"PhysioFit (v{physiofit.__version__})")
         st.title(f"Welcome to PhysioFit (v{physiofit.__version__})")
+        st.write("Documentation available at [https://physiofit.readthedocs.io](https://physiofit.readthedocs.io).")
         self.update_info = st.empty()
         self.check_uptodate()
         self.select_menu = st.selectbox(
@@ -220,8 +221,13 @@ def _initialize_opt_menu_widgets(self, file_extension):
         model_options = [
             model.model_name for model in self.io.models
         ]
-        if self.config_parser.model:
-            idx = model_options.index(self.config_parser.model["model_name"])
+        if self.config_parser:
+            if self.config_parser.model:
+                try:
+                    idx = model_options.index(self.config_parser.model["model_name"])
+                except Exception:
+                    st.error("Error while reading model name from configuration file")
+                    raise
         else:
             idx = None
         model_name = st.selectbox(

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "physiofit"
-version = "3.3.0"
+version = "3.3.1"
 description = "Calculate extracellular fluxes from metabolite concentrations and biomass data"
 authors = ["llegregam <[email protected]>"]
 license = "GNU General Public License (GPL)"