From 786db811e5b19ff6707610912e4db7e02a92b012 Mon Sep 17 00:00:00 2001 From: llegregam Date: Tue, 17 Oct 2023 15:03:00 +0200 Subject: [PATCH 1/7] Made it so that model is initialized when configuration file is given --- physiofit/ui/gui.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/physiofit/ui/gui.py b/physiofit/ui/gui.py index 3036b94..a0c3a20 100644 --- a/physiofit/ui/gui.py +++ b/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: From 76e38c777ff573149a1d1a8bded7697720c71d79 Mon Sep 17 00:00:00 2001 From: llegregam Date: Tue, 17 Oct 2023 15:03:36 +0200 Subject: [PATCH 2/7] Added a way to get models folder path --- physiofit/base/io.py | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/physiofit/base/io.py b/physiofit/base/io.py index dec385c..562d6bd 100644 --- a/physiofit/base/io.py +++ b/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 From 73230522e21dcb4d2b0a796fb3ba1b7ca083224f Mon Sep 17 00:00:00 2001 From: llegregam Date: Tue, 17 Oct 2023 15:04:48 +0200 Subject: [PATCH 3/7] Removed unused openpyxl dependency bump to 3.2.0 --- pyproject.toml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index dc27d8c..d38e508 100644 --- a/pyproject.toml +++ b/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 "] 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] From b3001a6814636aa056af398ad8f2995ac1f2b85c Mon Sep 17 00:00:00 2001 From: llegregam Date: Tue, 17 Oct 2023 15:06:17 +0200 Subject: [PATCH 4/7] Fixed path in config_file.yml --- validation/models/Monod_model/physiofit_results/config_file.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/validation/models/Monod_model/physiofit_results/config_file.yml b/validation/models/Monod_model/physiofit_results/config_file.yml index ada66fa..8769f50 100644 --- a/validation/models/Monod_model/physiofit_results/config_file.yml +++ b/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 From ac284be8ab56df3406837d4e6f4eeafbd51fda7f Mon Sep 17 00:00:00 2001 From: llegregam Date: Tue, 17 Oct 2023 15:06:30 +0200 Subject: [PATCH 5/7] Fixed data by adding experiments column --- validation/models/Monod_model/data.tsv | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/validation/models/Monod_model/data.tsv b/validation/models/Monod_model/data.tsv index 867e816..abfe37c 100644 --- a/validation/models/Monod_model/data.tsv +++ b/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 From c742c14877d57a2ea472e49dc6c11e895431a11e Mon Sep 17 00:00:00 2001 From: llegregam Date: Tue, 17 Oct 2023 15:06:44 +0200 Subject: [PATCH 6/7] New lockfile 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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