Merge pull request #676 from KulaginVladimir/main

festim/exports/txt_export.py

@@ -9,30 +9,39 @@
 
 class TXTExport(festim.Export):
     """
-
     Args:
         field (str): the exported field ("solute", "1", "retention",
             "T"...)
-        label (str): label of the field. Will also be the filename.
-        folder (str): the export folder
+        filename (str): the filename (must end with .txt).
         times (list, optional): if provided, the field will be
             exported at these timesteps. Otherwise exports at all
             timesteps. Defaults to None.
+        header_format (str, optional): the format of column headers.
+            Defautls to ".2e".
     """
 
-    def __init__(self, field, label, folder, times=None) -> None:
+    def __init__(self, field, filename, times=None, header_format=".2e") -> None:
         super().__init__(field=field)
         if times:
             self.times = sorted(times)
         else:
             self.times = times
-        self.label = label
-        self.folder = folder
+        self.filename = filename
+        self.header_format = header_format
         self._first_time = True
 
     @property
     def filename(self):
-        return f"{self.folder}/{self.label}.txt"
+        return self._filename
+
+    @filename.setter
+    def filename(self, value):
+        if value is not None:
+            if not isinstance(value, str):
+                raise TypeError("filename must be a string")
+            if not value.endswith(".txt"):
+                raise ValueError("filename must end with .txt")
+        self._filename = value
 
     def is_it_time_to_export(self, current_time):
         if self.times is None:
@@ -57,11 +66,6 @@ def write(self, current_time, steady):
         solution = f.project(self.function, V_DG1)
         solution_column = np.transpose(solution.vector()[:])
         if self.is_it_time_to_export(current_time):
-            if steady:
-                header = "x,t=steady"
-            else:
-                header = "x,t={}s".format(current_time)
-
             # if the directory doesn't exist
             # create it
             dirname = os.path.dirname(self.filename)
@@ -72,6 +76,10 @@ def write(self, current_time, steady):
             # write data
             # else append new column to the existing file
             if steady or self._first_time:
+                if steady:
+                    header = "x,t=steady"
+                else:
+                    header = f"x,t={format(current_time, self.header_format)}s"
                 x = f.interpolate(f.Expression("x[0]", degree=1), V_DG1)
                 x_column = np.transpose([x.vector()[:]])
                 data = np.column_stack([x_column, solution_column])
@@ -81,7 +89,7 @@ def write(self, current_time, steady):
                 old_file = open(self.filename)
                 old_header = old_file.readline().split("\n")[0]
                 old_file.close()
-                header = old_header + ",t={}s".format(current_time)
+                header = old_header + f",t={format(current_time, self.header_format)}s"
                 # Append new column
                 old_columns = np.loadtxt(self.filename, delimiter=",", skiprows=1)
                 data = np.column_stack([old_columns, solution_column])
@@ -90,16 +98,36 @@ def write(self, current_time, steady):
 
 
 class TXTExports:
-    def __init__(self, fields=[], times=[], labels=[], folder=None) -> None:
+    """
+    Args:
+        fields (list): list of exported fields ("solute", "1", "retention",
+            "T"...)
+        filenames (list): list of the filenames for each field (must end with .txt).
+        times (list, optional): if provided, fields will be
+            exported at these timesteps. Otherwise exports at all
+            timesteps. Defaults to None.
+        header_format (str, optional): the format of column headers.
+            Defautls to ".2e".
+    """
+
+    def __init__(
+        self, fields=[], filenames=[], times=None, header_format=".2e"
+    ) -> None:
+        msg = "TXTExports class will be depricated in future versions of FESTIM"
+        warnings.warn(msg, DeprecationWarning)
+
         self.fields = fields
-        if len(self.fields) != len(labels):
+        if len(self.fields) != len(filenames):
             raise ValueError(
                 "Number of fields to be exported "
-                "doesn't match number of labels in txt exports"
+                "doesn't match number of filenames in txt exports"
             )
-        self.times = sorted(times)
-        self.labels = labels
-        self.folder = folder
+        if times:
+            self.times = sorted(times)
+        else:
+            self.times = times
+        self.filenames = filenames
+        self.header_format = header_format
         self.exports = []
-        for function, label in zip(self.fields, self.labels):
-            self.exports.append(TXTExport(function, label, folder, times))
+        for function, filename in zip(self.fields, self.filenames):
+            self.exports.append(TXTExport(function, filename, times, header_format))

festim/generic_simulation.py

@@ -2,6 +2,7 @@
 from festim.h_transport_problem import HTransportProblem
 from fenics import *
 import numpy as np
+import warnings
 
 
 class Simulation:
@@ -273,6 +274,20 @@ def initialise(self):
             self.mesh.dx, self.mesh.ds, self.materials
         )
 
+        # needed to ensure that data is actually exported at TXTExport.times
+        # see issue 675
+        for export in self.exports.exports:
+            if isinstance(export, festim.TXTExport) and export.times:
+                if not self.dt.milestones:
+                    self.dt.milestones = []
+                for time in export.times:
+                    if time not in self.dt.milestones:
+                        msg = "To ensure that TXTExport exports data at the desired times "
+                        msg += "TXTExport.times are added to milestones"
+                        warnings.warn(msg)
+                        self.dt.milestones.append(time)
+                self.dt.milestones.sort()
+
     def run(self, completion_tone=False):
         """Runs the model.
 

test/simulation/test_initialise.py

@@ -1,4 +1,5 @@
 import festim as F
+from pathlib import Path
 
 
 def test_initialise_changes_nb_of_sources():
@@ -71,3 +72,34 @@ def test_initialise_initialise_dt():
 
     # test
     assert my_model.dt.value(2) == 3
+
+
+def test_TXTExport_times_added_to_milestones(tmpdir):
+    """Creates a Simulation object and checks that, if no dt.milestones
+     are given and TXTExport.times are given, TXTExport.times are
+    are added to dt.milestones by .initialise()
+    """
+    # tmpdir
+    d = tmpdir.mkdir("test_folder")
+
+    # build
+    my_model = F.Simulation()
+    my_model.mesh = F.MeshFromVertices([1, 2, 3])
+    my_model.materials = F.Material(id=1, D_0=1, E_D=0, thermal_cond=1)
+    my_model.T = F.Temperature(100)
+    my_model.dt = F.Stepsize(initial_value=3)
+    my_model.settings = F.Settings(
+        absolute_tolerance=1e-10, relative_tolerance=1e-10, final_time=4
+    )
+    txt_export = F.TXTExport(
+        field="solute",
+        filename="{}/solute_label.txt".format(str(Path(d))),
+        times=[1, 2, 3],
+    )
+    my_model.exports = [txt_export]
+
+    # run
+    my_model.initialise()
+
+    # test
+    assert my_model.dt.milestones == txt_export.times

test/system/test_chemical_potential.py

@@ -83,7 +83,7 @@ def run(h):
         my_exports = festim.Exports(
             [
                 festim.TXTExport(
-                    "solute", times=[100], label="solute", folder=str(Path(d))
+                    "solute", times=[100], filename="{}/solute.txt".format(str(Path(d)))
                 ),
             ]
         )

test/system/test_misc.py

@@ -134,17 +134,17 @@ def test_txt_export_desired_times(tmp_path):
     my_model.dt = F.Stepsize(0.1)
 
     my_export = F.TXTExport(
-        "solute", label="mobile_conc", times=[0.2, 0.5], folder=tmp_path
+        "solute", times=[0.2, 0.5], filename="{}/mobile_conc.txt".format(tmp_path)
     )
     my_model.exports = [my_export]
 
     my_model.initialise()
     my_model.run()
 
-    assert os.path.exists("{}/{}.txt".format(my_export.folder, my_export.label))
+    assert os.path.exists(my_export.filename)
 
     data = np.genfromtxt(
-        "{}/{}.txt".format(my_export.folder, my_export.label),
+        my_export.filename,
         skip_header=1,
         delimiter=",",
     )
@@ -163,16 +163,16 @@ def test_txt_export_all_times(tmp_path):
     my_model.T = F.Temperature(500)
     my_model.dt = F.Stepsize(0.1)
 
-    my_export = F.TXTExport("solute", label="mobile_conc", folder=tmp_path)
+    my_export = F.TXTExport("solute", filename="{}/mobile_conc.txt".format(tmp_path))
     my_model.exports = [my_export]
 
     my_model.initialise()
     my_model.run()
 
-    assert os.path.exists("{}/{}.txt".format(my_export.folder, my_export.label))
+    assert os.path.exists(my_export.filename)
 
     data = np.genfromtxt(
-        "{}/{}.txt".format(my_export.folder, my_export.label),
+        my_export.filename,
         skip_header=1,
         delimiter=",",
     )
@@ -190,15 +190,15 @@ def test_txt_export_steady_state(tmp_path):
     my_model.settings = F.Settings(1e-10, 1e-10, transient=False)
     my_model.T = F.Temperature(500)
 
-    my_export = F.TXTExport("solute", label="mobile_conc", folder=tmp_path)
+    my_export = F.TXTExport("solute", filename="{}/mobile_conc.txt".format(tmp_path))
     my_model.exports = [my_export]
 
     my_model.initialise()
     my_model.run()
 
-    assert os.path.exists("{}/{}.txt".format(my_export.folder, my_export.label))
+    assert os.path.exists(my_export.filename)
 
-    txt = open("{}/{}.txt".format(my_export.folder, my_export.label))
+    txt = open(my_export.filename)
     header = txt.readline().rstrip()
     txt.close()
 

test/system/test_system.py

@@ -344,7 +344,7 @@ def run(h):
         my_exports = festim.Exports(
             [
                 festim.TXTExport(
-                    "solute", times=[100], label="solute", folder=str(Path(d))
+                    "solute", times=[100], filename="{}/solute.txt".format(str(Path(d)))
                 ),
             ]
         )

test/unit/test_exports/test_txt_export.py

@@ -25,7 +25,11 @@ def function_subspace(self):
     @pytest.fixture
     def my_export(self, tmpdir):
         d = tmpdir.mkdir("test_folder")
-        my_export = TXTExport("solute", "solute_label", str(Path(d)), times=[1, 2, 3])
+        my_export = TXTExport(
+            "solute",
+            times=[1, 2, 3],
+            filename="{}/solute_label.txt".format(str(Path(d))),
+        )
 
         return my_export
 
@@ -34,37 +38,54 @@ def test_file_exists(self, my_export, function):
         my_export.function = function
         my_export.write(current_time=current_time, steady=False)
 
-        assert os.path.exists("{}/{}.txt".format(my_export.folder, my_export.label))
+        assert os.path.exists(my_export.filename)
 
     def test_file_doesnt_exist(self, my_export, function):
         current_time = 10
         my_export.function = function
         my_export.write(current_time=current_time, steady=False)
 
-        assert not os.path.exists("{}/{}.txt".format(my_export.folder, my_export.label))
+        assert not os.path.exists(my_export.filename)
 
     def test_create_folder(self, my_export, function):
         """Checks that write() creates the folder if it doesn't exist"""
         current_time = 1
         my_export.function = function
-        my_export.folder += "/folder2"
+        slash_indx = my_export.filename.rfind("/")
+        my_export.filename = (
+            my_export.filename[:slash_indx]
+            + "/folder2"
+            + my_export.filename[slash_indx:]
+        )
         my_export.write(current_time=current_time, steady=False)
 
-        assert os.path.exists("{}/{}.txt".format(my_export.folder, my_export.label))
+        assert os.path.exists(my_export.filename)
 
     def test_subspace(self, my_export, function_subspace):
         current_time = 1
         my_export.function = function_subspace
         my_export.write(current_time=current_time, steady=False)
 
-        assert os.path.exists("{}/{}.txt".format(my_export.folder, my_export.label))
+        assert os.path.exists(my_export.filename)
+
+    def test_error_filename_endswith_txt(self, my_export):
+        with pytest.raises(ValueError, match="filename must end with .txt"):
+            my_export.filename = "coucou"
+
+    def test_error_filename_not_a_str(self, my_export):
+        with pytest.raises(TypeError, match="filename must be a string"):
+            my_export.filename = 2
 
 
 class TestIsItTimeToExport:
     @pytest.fixture
     def my_export(self, tmpdir):
         d = tmpdir.mkdir("test_folder")
-        my_export = TXTExport("solute", "solute_label", str(Path(d)), times=[1, 2, 3])
+        my_export = TXTExport(
+            "solute",
+            times=[1, 2, 3],
+            filename="{}/solute_label.txt".format(str(Path(d))),
+        )
 
         return my_export
 
@@ -84,7 +105,11 @@ class TestWhenIsNextTime:
     @pytest.fixture
     def my_export(self, tmpdir):
         d = tmpdir.mkdir("test_folder")
-        my_export = TXTExport("solute", "solute_label", str(Path(d)), times=[1, 2, 3])
+        my_export = TXTExport(
+            "solute",
+            times=[1, 2, 3],
+            filename="{}/solute_label.txt".format(str(Path(d))),
+        )
 
         return my_export
 

test/unit/test_exports/test_txt_exports.py

@@ -6,11 +6,16 @@
 
 
 class TestWrite:
-    @pytest.fixture
-    def my_export(self, tmpdir):
+    @pytest.fixture(params=[[1, 2, 3], None])
+    def my_export(self, tmpdir, request):
         d = tmpdir.mkdir("test_folder")
         my_export = TXTExports(
-            ["solute", "T"], [1, 2, 3], ["solute_label", "T_label"], str(Path(d))
+            fields=["solute", "T"],
+            filenames=[
+                "{}/solute_label.txt".format(str(Path(d))),
+                "{}/T_label.txt".format(str(Path(d))),
+            ],
+            times=request.param,
         )
 
         return my_export
@@ -22,4 +27,4 @@ def test_txt_exports_times(self, my_export):
 
 def test_error_when_fields_and_labels_have_different_lengths():
     with pytest.raises(ValueError, match="Number of fields to be exported"):
-        TXTExports(["solute", "T"], [1], ["solute_label"])
+        TXTExports(["solute", "T"], ["solute_label.txt"], [1])