all open statements and file paths use os.path.join

updated post

pyelmer/elmer.py

@@ -121,7 +121,7 @@ def write_boundary_ids(self, simulation_dir):
             simulation_dir (str): Path of simulation directory
         """
         data = {boundary.id: name for name, boundary in self.boundaries.items()}
-        with open(simulation_dir + "/boundaries.yml", "w") as f:
+        with open(os.path.join(simulation_dir + "/boundaries.yml"), "w") as f:
             yaml.dump(data, f, sort_keys=False)
 
     def _dict_to_str(self, dictionary, *, key_value_separator=" = "):
@@ -425,7 +425,7 @@ def load_simulation(name, setup_file=""):
         Simulation object.
     """
     if setup_file == "":
-        setup_file = f"{data_dir}/simulations.yml"
+        setup_file = os.path.join(data_dir, "simulations.yml")
     with open(setup_file) as f:
         settings = yaml.safe_load(f)[name]
     sim = Simulation()
@@ -445,7 +445,7 @@ def load_material(name, simulation, setup_file=""):
         Material object.
     """
     if setup_file == "":
-        setup_file = f"{data_dir}/materials.yml"
+        setup_file = os.path.join(data_dir, "materials.yml")
     with open(setup_file) as f:
         data = yaml.safe_load(f)[name]
     return Material(simulation, name, data)
@@ -463,7 +463,7 @@ def load_solver(name, simulation, setup_file=""):
         Solver object.
     """
     if setup_file == "":
-        setup_file = f"{data_dir}/solvers.yml"
+        setup_file = os.path.join(data_dir, "solvers.yml")
     with open(setup_file) as f:
         data = yaml.safe_load(f)[name]
     return Solver(simulation, name, data)
@@ -481,7 +481,7 @@ def load_boundary(name, simulation, setup_file=""):
         Boundary object.
     """
     if setup_file == "":
-        setup_file = f"{data_dir}/boundaries.yml"
+        setup_file = os.path.join(data_dir, "boundaries.yml")
     with open(setup_file) as f:
         data = yaml.safe_load(f)[name]
     return Boundary(simulation, name, data=data)
@@ -499,7 +499,7 @@ def load_initial_condition(name, simulation, setup_file=""):
         InitialCondition object.
     """
     if setup_file == "":
-        setup_file = f"{data_dir}/initial_conditions.yml"
+        setup_file = os.path.join(data_dir, "initial_conditions.yml")
     with open(setup_file) as f:
         data = yaml.safe_load(f)[name]
     return InitialCondition(simulation, name, data)

pyelmer/execute.py

@@ -24,7 +24,7 @@ def run_elmer_grid(sim_dir, meshfile, elmergrid=None):
             elmergrid = "ElmerGrid"
 
     args = [elmergrid, "14", "2", meshfile]
-    with open(sim_dir + "/elmergrid.log", "w") as f:
+    with open(os.path.join(sim_dir, "elmergrid.log"), "w") as f:
         subprocess.run(args, cwd=sim_dir, stdout=f, stderr=f)
 
     mesh_dir = sim_dir + "/" + ".".join(meshfile.split(".")[:-1])
@@ -72,7 +72,7 @@ def run_elmer_solver(sim_dir, elmersolver=None):
             elmersolver = "ElmerSolver"
 
     args = [elmersolver, "case.sif"]
-    with open(sim_dir + "/elmersolver.log", "w") as f:
+    with open(os.path.join(sim_dir, "elmersolver.log"), "w") as f:
         subprocess.run(args, cwd=sim_dir, stdout=f, stderr=f)
 
 

pyelmer/post.py

@@ -64,7 +64,7 @@ def scan_logfile(sim_dir):
     Returns:
         list[str], list[str], dict: error messages, warnings, statistics
     """
-    with open(sim_dir + "/elmersolver.log", "r") as f:
+    with open(os.path.join(sim_dir, "elmersolver.log"), "r") as f:
         log = f.readlines()
     for i in range(len(log)):
         log[i] = log[i][:-1]
@@ -92,7 +92,7 @@ def plot_residuals(sim_dir, solvers, save=False):
         solvers (list): solvers to analyze - currently works only for
         'heat equation' and 'statmagsolver'
     """
-    with open(sim_dir + "/elmersolver.log", "r") as f:
+    with open(os.path.join(sim_dir, "elmersolver.log"), "r") as f:
         log = f.readlines()
     for i in range(len(log)):
         log[i] = log[i][:-1]

pyelmer/test/test_elmer.py

@@ -159,7 +159,7 @@ def test_equation():
 
 
 def test_load_simulation():
-    with open(file_dir + "/test_data/simulations.yml") as f:
+    with open(os.path.join(file_dir, "test_data", "simulations.yml") as f:
         settings = yaml.safe_load(f)["test_simulation"]
     assert (
         elmer.load_simulation(
@@ -170,7 +170,7 @@ def test_load_simulation():
 
 
 def test_load_material():
-    with open(file_dir + "/test_data/materials.yml") as f:
+    with open(os.path.join(file_dir, "test_data", "materials.yml") as f:
         data = yaml.safe_load(f)["test_material"]
     sim = elmer.Simulation()
     assert (
@@ -182,7 +182,7 @@ def test_load_material():
 
 
 def test_load_solver():
-    with open(file_dir + "/test_data/solvers.yml") as f:
+    with open(os.path.join(file_dir, "test_data", "solvers.yml") as f:
         data = yaml.safe_load(f)["test_solver"]
     sim = elmer.Simulation()
     assert (
@@ -194,7 +194,7 @@ def test_load_solver():
 
 
 def test_load_body_force():
-    with open(file_dir + "/test_data/body_forces.yml") as f:
+    with open(os.path.join(file_dir, "test_data", "body_forces.yml") as f:
         data = yaml.safe_load(f)["test_body_force"]
     sim = elmer.Simulation()
     assert (
@@ -206,7 +206,7 @@ def test_load_body_force():
 
 
 def test_load_boundary():
-    with open(file_dir + "/test_data/boundaries.yml") as f:
+    with open(os.path.join(file_dir, "test_data", "boundaries.yml") as f:
         data = yaml.safe_load(f)["test_boundary"]
     sim = elmer.Simulation()
     assert elmer.load_boundary(
@@ -218,7 +218,7 @@ def test_load_boundary():
 
 
 def test_load_initial_condition():
-    with open(file_dir + "/test_data/initial_conditions.yml") as f:
+    with open(os.path.join(file_dir, "test_data", "initial_conditions.yml") as f:
         data = yaml.safe_load(f)["test_initial_condition"]
     sim = elmer.Simulation()
     assert (