Merge pull request #30 from MetaSys-LISBP/dev

bump to 3.0.4

.gitignore

@@ -14,4 +14,4 @@ physiofit.egg-info/PKG-INFO
 physiofit.egg-info/requires.txt
 physiofit.egg-info/SOURCES.txt
 physiofit.egg-info/top_level.txt
-/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/
+/versions publi/

physiofit/base/fitter.py

@@ -468,11 +468,12 @@ def khi2_test(self):
         )
 
         logger.info(f"khi2 test results:\n"
-                         f"khi2 value: {cost}\n"
-                         f"Number of measurements: {number_measurements}\n"
-                         f"Number of parameters to fit: {number_params}\n"
-                         f"Degrees of freedom: {dof}\n"
-                         f"p-value = {p_val}\n")
+                     f"khi2 value: {cost}\n"
+                     f"Number of measurements: {number_measurements}\n"
+                     f"Number of parameters to fit: {number_params}\n"
+                     f"Degrees of freedom: {dof}\n"
+                     f"p-value = {p_val}\n"
+                    )
 
         if p_val < 0.95:
             logger.info(

physiofit/data/data_example.tsv

@@ -0,0 +1,17 @@
+time	X	Glc	Ace
+1.7	6.2E-2	NA	NA
+2.3	8.6E-2	NA	NA
+2.7	0.11	NA	NA
+3.4	0.17	NA	NA
+3.8	0.21	NA	NA
+4.2	0.3	NA	NA
+4.6	0.38	NA	NA
+5	0.55	NA	NA
+5.4	0.61	NA	NA
+1.4	NA	13.63	0.22
+1.9	NA	13.58	0.37
+2.9	NA	12.62	0.71
+4	NA	11.25	1.46
+4.8	NA	9.37	2.14
+5.2	NA	8.20	2.55
+5.6	NA	6.55	2.89

physiofit/tests/conftest.py

@@ -0,0 +1,30 @@
+
+"""
+Configuration variables for the tests
+
+Shared pre-defined parameters
+The return value of fixture function will be available as a predefined
+parameter for all test functions. The test's parameter name must be the same as
+the fixture function's name.
+"""
+
+import pytest
+from physiofit.base.io import IoHandler
+from physiofit.models.base_model import StandardDevs
+
+@pytest.fixture
+def data():
+    """Test data to use in tests"""
+
+    return IoHandler.read_data(
+        r"C:\Users\legregam\PycharmProjects\PhysioFit\physiofit\data\data_example.tsv"
+    )
+
+@pytest.fixture
+def sds():
+    return StandardDevs(
+        X = 0.2,
+        Glc = 0.5,
+        Ace = 0.5
+    )
+

physiofit/tests/test_fitter.py

@@ -0,0 +1,28 @@
+"""
+Test the creation and use of the PhysioFitter
+"""
+
+import pytest
+import physiofit as phyfit
+from pandas import read_csv
+
+
+def test_physiofitter(data, sds):
+    """
+    Test that the model and PhysioFitter can be safely instanciated from IoHandler
+    """
+
+    io = phyfit.base.io.IoHandler()
+    model = io.select_model("Steady-state batch model", data)
+    assert isinstance(model, phyfit.models.base_model.Model)
+    model.get_params()
+    fitter = io.initialize_fitter(
+        model.data,
+        model=model,
+        sd=sds,
+        debug_mode=True
+    )
+    assert isinstance(fitter, phyfit.base.fitter.PhysioFitter)
+
+def test_simulation(data, sds):
+    pass

physiofit/ui/gui.py

@@ -143,7 +143,7 @@ def _initialize_opt_menu(self):
             if not self.io.home_path:
                 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.home_path / self.data_file.name,
                 selected_model= self.model,
                 sds = self.sd,
                 mc = self.mc,

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "physiofit"
-version = "3.0.2"
+version = "3.0.4"
 description = "Calculate extracellular fluxes from metabolite concentrations and biomass data"
 authors = ["llegregam <[email protected]>"]
 license = "GNU General Public License (GPL)"
@@ -27,6 +27,10 @@ Sphinx = "^6.1.3"
 sphinx-argparse = "^0.4.0"
 sphinx-rtd-theme = "^1.2.0"
 
+
+[tool.poetry.group.test.dependencies]
+pytest = "^7.3.1"
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"