fixed all tests

festim-dev · Dec 20, 2024 · f5ae452 · f5ae452
1 parent 8c72a2f
commit f5ae452
Show file tree

Hide file tree

Showing 4 changed files with 21 additions and 13 deletions.
diff --git a/docs/environment.yml b/docs/environment.yml
@@ -9,6 +9,8 @@ dependencies:
   - sphinx==7
   - folium
   - numpy==1.24
+  - tqdm
+  - scifem>=0.2.8
   - pip:
       - sympy
       - sphinx_book_theme==1.1.2

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -86,7 +86,7 @@ Create a conda environment with ``dolfinx``::
 
     conda create -n festim-env
     conda activate festim-env       
-    conda install -c conda-forge fenics-dolfinx
+    conda install -c conda-forge fenics-dolfinx tqdm
 
 Install the correct FESTIM version with::
 

diff --git a/docs/source/userguide/troubleshooting.rst b/docs/source/userguide/troubleshooting.rst
@@ -56,6 +56,7 @@ Then increase the absolute tolerance of the solver:
 
     import festim as F
 
+    my_model = F.HydrogenTransportProblem()
     my_model.settings = F.Settings(
         atol=1e10,
         rtol=1e-10,

diff --git a/src/festim/boundary_conditions/flux_bc.py b/src/festim/boundary_conditions/flux_bc.py
@@ -159,13 +159,16 @@ class ParticleFluxBC(FluxBCBase):
 
 
     Usage:
-        >>> from festim import ParticleFluxBC
-        >>> ParticleFluxBC(subdomain=my_subdomain, value=1, species="H")
-        >>> ParticleFluxBC(subdomain=my_subdomain, value=lambda x: 1 + x[0], species="H")
-        >>> ParticleFluxBC(subdomain=my_subdomain, value=lambda t: 1 + t, species="H")
-        >>> ParticleFluxBC(subdomain=my_subdomain, value=lambda T: 1 + T, species="H")
-        >>> ParticleFluxBC(subdomain=my_subdomain, value=lambda x, t: 1 + x[0] + t, species="H")
-        >>> ParticleFluxBC(subdomain=my_subdomain, value=lambda c1: 2 * c1**2, species="H", species_dependent_value={"c1": species1})
+    .. testcode::
+
+        from festim import ParticleFluxBC
+
+        ParticleFluxBC(subdomain=my_subdomain, value=1, species="H")
+        ParticleFluxBC(subdomain=my_subdomain, value=lambda x: 1 + x[0], species="H")
+        ParticleFluxBC(subdomain=my_subdomain, value=lambda t: 1 + t, species="H")
+        ParticleFluxBC(subdomain=my_subdomain, value=lambda T: 1 + T, species="H")
+        ParticleFluxBC(subdomain=my_subdomain, value=lambda x, t: 1 + x[0] + t, species="H")
+        ParticleFluxBC(subdomain=my_subdomain, value=lambda c1: 2 * c1**2, species="H", species_dependent_value={"c1": species1})
     """
 
     def __init__(self, subdomain, value, species, species_dependent_value={}):
@@ -240,11 +243,13 @@ class HeatFluxBC(FluxBCBase):
 
 
     Usage:
-        >>> from festim import HeatFluxBC
-        >>> HeatFluxBC(subdomain=my_subdomain, value=1)
-        >>> HeatFluxBC(subdomain=my_subdomain, value=lambda x: 1 + x[0])
-        >>> HeatFluxBC(subdomain=my_subdomain, value=lambda t: 1 + t)
-        >>> HeatFluxBC(subdomain=my_subdomain, value=lambda x, t: 1 + x[0] + t)
+    .. testcode::
+
+        from festim import HeatFluxBC
+        HeatFluxBC(subdomain=my_subdomain, value=1)
+        HeatFluxBC(subdomain=my_subdomain, value=lambda x: 1 + x[0])
+        HeatFluxBC(subdomain=my_subdomain, value=lambda t: 1 + t)
+        HeatFluxBC(subdomain=my_subdomain, value=lambda x, t: 1 + x[0] + t)
     """
 
     def __init__(self, subdomain, value):