Merge pull request #117 from boschresearch/doctests

Use doctests
boschresearch · Oct 10, 2024 · c1acd0f · c1acd0f
2 parents 16324d4 + 0dad6d7
commit c1acd0f
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Showing 7 changed files with 101 additions and 79 deletions.
diff --git a/setup.cfg b/setup.cfg
@@ -115,15 +115,18 @@ extras =
 #          Comment those flags to avoid this py.test issue.
 addopts =
     --cov src/pylife --cov-append -m "not slow_acceptance and not demos"
+    --doctest-modules
+    --ignore=src/pylife/materialdata/woehler/bayesian.py
 
 norecursedirs =
     dist
     build
     .tox
-testpaths = tests
+testpaths = tests src/pylife
 markers =
 	slow_acceptance: long running acceptance test (not run by default)
 	demos: demo notebooks by testbook
+doctest_optionflags = NORMALIZE_WHITESPACE IGNORE_EXCEPTION_DETAIL
 
 [bdist_wheel]
 # Use this option if your package is pure-python

diff --git a/src/pylife/core/pylifesignal.py b/src/pylife/core/pylifesignal.py
@@ -273,10 +273,11 @@ def __init__(self, obj):
         def bar(df):
             return pd.DataFrame({'baz': df['foo'] + df['bar']})
 
-    >>> df = pd.DataFrame({'foo': [1.0, 2.0], 'bar': [-1.0, -2.0]})
-    >>> df.foo.bar()
-       baz
-    0  0.0
-    1  0.0
+        df = pd.DataFrame({'foo': [1.0, 2.0], 'bar': [-1.0, -2.0]})
+        df.foo.bar()
+
+           baz
+        0  0.0
+        1  0.0
     """
     return cls._register_method(method_name)
diff --git a/src/pylife/materialdata/woehler/bayesian.py b/src/pylife/materialdata/woehler/bayesian.py
@@ -34,6 +34,7 @@
 __author__ = "Mustapha Kassem"
 __maintainer__ = "Johannes Mueller"
 
+
 raise NotImplementedError(
     "pyLife's Bayesian Wöhler analyzer has been shutdown. "
     "See documentation for details."

diff --git a/src/pylife/mesh/meshsignal.py b/src/pylife/mesh/meshsignal.py
@@ -30,20 +30,25 @@
 --------
 Read in a mesh from a vmap file:
 
-
->>> df = (vm = pylife.vmap.VMAPImport('demos/plate_with_hole.vmap')
-             .make_mesh('1', 'STATE-2')
-             .join_variable('STRESS_CAUCHY')
-             .join_variable('DISPLACEMENT')
-             .to_frame())
+>>> from pylife.vmap import VMAPImport
+>>> df = (
+...     VMAPImport('demos/plate_with_hole.vmap')
+...     .make_mesh('1', 'STATE-2')
+...     .join_coordinates()
+...     .join_variable('STRESS_CAUCHY')
+...     .join_variable('DISPLACEMENT')
+...     .to_frame()
+... )
 >>> df.head()
-                            x         y    z        S11       S22  S33        S12  S13  S23        dx        dy   dz
-element_id node_id
-1          1734     14.897208  5.269875  0.0  27.080811  6.927080  0.0 -13.687358  0.0  0.0  0.005345  0.000015  0.0
-           1582     14.555333  5.355806  0.0  28.319006  1.178649  0.0 -10.732705  0.0  0.0  0.005285  0.000003  0.0
-           1596     14.630658  4.908741  0.0  47.701195  5.512213  0.0 -17.866833  0.0  0.0  0.005376  0.000019  0.0
-           4923     14.726271  5.312840  0.0  27.699907  4.052865  0.0 -12.210032  0.0  0.0  0.005315  0.000009  0.0
-           4924     14.592996  5.132274  0.0  38.010101  3.345431  0.0 -14.299768  0.0  0.0  0.005326  0.000013  0.0
+                            x         y    z  ...        dx        dy   dz
+element_id node_id                            ...
+1          1734     14.897208  5.269875  0.0  ...  0.005345  0.000015  0.0
+           1582     14.555333  5.355806  0.0  ...  0.005285  0.000003  0.0
+           1596     14.630658  4.908741  0.0  ...  0.005376  0.000019  0.0
+           4923     14.726271  5.312840  0.0  ...  0.005315  0.000009  0.0
+           4924     14.592996  5.132274  0.0  ...  0.005326  0.000013  0.0
+<BLANKLINE>
+[5 rows x 12 columns]
 
 Get the coordinates of the mesh.
 
@@ -210,10 +215,19 @@ def vtk_data(self):
         Example
         -------
         >>> import pyvista as pv
-        >>> grid = pv.UnstructuredGrid(*our_mesh.mesh.vtk_data())
+        >>> from pylife.vmap import VMAPImport
+        >>> df = (
+        ...     VMAPImport('demos/plate_with_hole.vmap')
+        ...     .make_mesh('1', 'STATE-2')
+        ...     .join_coordinates()
+        ...     .join_variable('STRESS_CAUCHY')
+        ...     .to_frame()
+        ... )
+
+        >>> grid = pv.UnstructuredGrid(*df.mesh.vtk_data())
         >>> plotter = pv.Plotter(window_size=[1920, 1080])
-        >>> plotter.add_mesh(grid, scalars=our_mesh.groupby('element_id')['val'].mean().to_numpy())
-        >>> plotter.show()
+        >>> plotter.add_mesh(grid, scalars=df.groupby('element_id')['S11'].mean().to_numpy())  # doctest: +SKIP
+        >>> plotter.show()  # doctest: +SKIP
 
         Note the `*` that needs to be added when calling ``pv.UnstructuredGrid()``.
         """

diff --git a/src/pylife/strength/meanstress.py b/src/pylife/strength/meanstress.py
@@ -59,11 +59,11 @@ def from_dict(cls, segments_dict):
 
         Example
         -------
-        >>> hd = MST.HaighDiagram.from_dict({
-        >>>    (1.0, np.inf): 0.0,
-        >>>    (-np.inf, 0.0): 0.5,
-        >>>    (0.0, 1.0): 0.167
-        >>> })
+        >>> hd = HaighDiagram.from_dict({
+        ...    (1.0, np.inf): 0.0,
+        ...    (-np.inf, 0.0): 0.5,
+        ...    (0.0, 1.0): 0.167
+        ... })
 
         sets up a FKM Goodman like Haigh diagram.
         """

diff --git a/src/pylife/utils/histogram.py b/src/pylife/utils/histogram.py
@@ -165,12 +165,6 @@ def rebin_histogram(histogram, binning, nan_default=False):
 
     Examples
     --------
-    >>> h
-    (0.0, 1.0]    1.0
-    (1.0, 2.0]    2.0
-    (2.0, 3.0]    3.0
-    (3.0, 4.0]    4.0
-    dtype: float64
     >>> h = pd.Series([10.0, 20.0, 30.0, 40.0], index=pd.interval_range(0.0, 4.0, 4))
     >>> h
     (0.0, 1.0]    10.0
@@ -203,12 +197,15 @@ def rebin_histogram(histogram, binning, nan_default=False):
 
     Define the target bin just by an int:
 
-    >>> rebin_histogram(h, 5)
-    (0.0, 0.8]     8.0
-    (0.8, 1.6]    14.0
-    (1.6, 2.4]    20.0
-    (2.4, 3.2]    26.0
-    (3.2, 4.0]    32.0
+    >>> rebin_histogram(h, 8)
+    (0.0, 0.5]     5.0
+    (0.5, 1.0]     5.0
+    (1.0, 1.5]    10.0
+    (1.5, 2.0]    10.0
+    (2.0, 2.5]    15.0
+    (2.5, 3.0]    15.0
+    (3.0, 3.5]    20.0
+    (3.5, 4.0]    20.0
     dtype: float64
 
     Limitations

diff --git a/src/pylife/vmap/vmap_import.py b/src/pylife/vmap/vmap_import.py
@@ -131,24 +131,29 @@ def make_mesh(self, geometry, state=None):
         --------
         Get the mesh data with the coordinates of geometry '1' and the stress tensor of 'STATE-2'
 
-        >>> (pylife.vmap.VMAPImport('demos/plate_with_hole.vmap')
-             .make_mesh('1', 'STATE-2')
-             .join_coordinates()
-             .join_variable('STRESS_CAUCHY')
-             .to_frame()
-                                    x         y    z        S11       S22  S33        S12  S13  S23
-        element_id node_id
-        1          1734     14.897208  5.269875  0.0  27.080811  6.927080  0.0 -13.687358  0.0  0.0
-                   1582     14.555333  5.355806  0.0  28.319006  1.178649  0.0 -10.732705  0.0  0.0
-                   1596     14.630658  4.908741  0.0  47.701195  5.512213  0.0 -17.866833  0.0  0.0
-                   4923     14.726271  5.312840  0.0  27.699907  4.052865  0.0 -12.210032  0.0  0.0
-                   4924     14.592996  5.132274  0.0  38.010101  3.345431  0.0 -14.299768  0.0  0.0
-        ...                       ...       ...  ...        ...       ...  ...        ...  ...  ...
-        4770       3812    -13.189782 -5.691876  0.0  36.527439  2.470588  0.0 -14.706686  0.0  0.0
-                   12418   -13.560289 -5.278386  0.0  32.868889  3.320898  0.0 -14.260107  0.0  0.0
-                   14446   -13.673285 -5.569107  0.0  34.291058  3.642457  0.0 -13.836027  0.0  0.0
-                   14614   -13.389065 -5.709927  0.0  36.063541  2.828889  0.0 -13.774759  0.0  0.0
-                   14534   -13.276068 -5.419206  0.0  33.804211  2.829817  0.0 -14.580153  0.0  0.0
+        >>> (
+        ...     VMAPImport('demos/plate_with_hole.vmap')
+        ...     .make_mesh('1', 'STATE-2')
+        ...     .join_coordinates()
+        ...     .join_variable('STRESS_CAUCHY')
+        ...     .to_frame()
+        ... )
+                                    x         y    z  ...        S12  S13  S23
+        element_id node_id                            ...
+        1          1734     14.897208  5.269875  0.0  ... -13.687358  0.0  0.0
+                   1582     14.555333  5.355806  0.0  ... -10.732705  0.0  0.0
+                   1596     14.630658  4.908741  0.0  ... -17.866833  0.0  0.0
+                   4923     14.726271  5.312840  0.0  ... -12.210032  0.0  0.0
+                   4924     14.592996  5.132274  0.0  ... -14.299768  0.0  0.0
+        ...                       ...       ...  ...  ...        ...  ...  ...
+        4770       3812    -13.189782 -5.691876  0.0  ... -14.706686  0.0  0.0
+                   12418   -13.560289 -5.278386  0.0  ... -14.260107  0.0  0.0
+                   14446   -13.673285 -5.569107  0.0  ... -13.836027  0.0  0.0
+                   14614   -13.389065 -5.709927  0.0  ... -13.774759  0.0  0.0
+                   14534   -13.276068 -5.419206  0.0  ... -14.580153  0.0  0.0
+        <BLANKLINE>
+        [37884 rows x 9 columns]
+
         """
         self._mesh = pd.DataFrame(index=self._mesh_index(geometry))
         self._geometry = geometry
@@ -219,7 +224,7 @@ def join_coordinates(self):
         --------
         Receive the mesh with the node coordinates
 
-        >>> pylife.vmap.VMAPImport('demos/plate_with_hole.vmap').make_mesh('1').join_coordinates().to_frame()
+        >>> VMAPImport('demos/plate_with_hole.vmap').make_mesh('1').join_coordinates().to_frame()
                                     x         y    z
         element_id node_id
         1          1734     14.897208  5.269875  0.0
@@ -233,9 +238,8 @@ def join_coordinates(self):
                    14446   -13.673285 -5.569107  0.0
                    14614   -13.389065 -5.709927  0.0
                    14534   -13.276068 -5.419206  0.0
-
+        <BLANKLINE>
         [37884 rows x 3 columns]
-
         """
         if self._mesh is None:
             raise APIUseError("Need to make_mesh() before joining the coordinates.")
@@ -340,25 +344,27 @@ def join_variable(self, var_name, state=None, column_names=None):
         --------
         Receiving the 'DISPLACEMENT' of 'STATE-1' , the stress and strain tensors of 'STATE-2'
 
-        >>> (pylife.vmap.VMAPImport('demos/plate_with_hole.vmap')
-             .make_mesh('1')
-             .join_variable('DISPLACEMENT', 'STATE-1')
-             .join_variable('STRESS_CAUCHY', 'STATE-2')
-             .join_variable('E').to_frame())
-                             dx   dy   dz        S11       S22  S33        S12  S13  S23       E11       E22  E33       E12  E13  E23
-        element_id node_id
-        1          1734     0.0  0.0  0.0  27.080811  6.927080  0.0 -13.687358  0.0  0.0  0.000119 -0.000006  0.0 -0.000169  0.0  0.0
-                   1582     0.0  0.0  0.0  28.319006  1.178649  0.0 -10.732705  0.0  0.0  0.000133 -0.000035  0.0 -0.000133  0.0  0.0
-                   1596     0.0  0.0  0.0  47.701195  5.512213  0.0 -17.866833  0.0  0.0  0.000219 -0.000042  0.0 -0.000221  0.0  0.0
-                   4923     0.0  0.0  0.0  27.699907  4.052865  0.0 -12.210032  0.0  0.0  0.000126 -0.000020  0.0 -0.000151  0.0  0.0
-                   4924     0.0  0.0  0.0  38.010101  3.345431  0.0 -14.299768  0.0  0.0  0.000176 -0.000038  0.0 -0.000177  0.0  0.0
-        ...                 ...  ...  ...        ...       ...  ...        ...  ...  ...       ...       ...  ...       ...  ...  ...
-        4770       3812     0.0  0.0  0.0  36.527439  2.470588  0.0 -14.706686  0.0  0.0  0.000170 -0.000040  0.0 -0.000182  0.0  0.0
-                   12418    0.0  0.0  0.0  32.868889  3.320898  0.0 -14.260107  0.0  0.0  0.000152 -0.000031  0.0 -0.000177  0.0  0.0
-                   14446    0.0  0.0  0.0  34.291058  3.642457  0.0 -13.836027  0.0  0.0  0.000158 -0.000032  0.0 -0.000171  0.0  0.0
-                   14614    0.0  0.0  0.0  36.063541  2.828889  0.0 -13.774759  0.0  0.0  0.000168 -0.000038  0.0 -0.000171  0.0  0.0
-                   14534    0.0  0.0  0.0  33.804211  2.829817  0.0 -14.580153  0.0  0.0  0.000157 -0.000035  0.0 -0.000181  0.0  0.0
-
+        >>> (
+        ...     VMAPImport('demos/plate_with_hole.vmap')
+        ...     .make_mesh('1')
+        ...     .join_variable('DISPLACEMENT', 'STATE-1')
+        ...     .join_variable('STRESS_CAUCHY', 'STATE-2')
+        ...     .join_variable('E').to_frame()
+        ... )
+                             dx   dy   dz        S11  ...  E33       E12  E13  E23
+        element_id node_id                            ...
+        1          1734     0.0  0.0  0.0  27.080811  ...  0.0 -0.000169  0.0  0.0
+                   1582     0.0  0.0  0.0  28.319006  ...  0.0 -0.000133  0.0  0.0
+                   1596     0.0  0.0  0.0  47.701195  ...  0.0 -0.000221  0.0  0.0
+                   4923     0.0  0.0  0.0  27.699907  ...  0.0 -0.000151  0.0  0.0
+                   4924     0.0  0.0  0.0  38.010101  ...  0.0 -0.000177  0.0  0.0
+        ...                 ...  ...  ...        ...  ...  ...       ...  ...  ...
+        4770       3812     0.0  0.0  0.0  36.527439  ...  0.0 -0.000182  0.0  0.0
+                   12418    0.0  0.0  0.0  32.868889  ...  0.0 -0.000177  0.0  0.0
+                   14446    0.0  0.0  0.0  34.291058  ...  0.0 -0.000171  0.0  0.0
+                   14614    0.0  0.0  0.0  36.063541  ...  0.0 -0.000171  0.0  0.0
+                   14534    0.0  0.0  0.0  33.804211  ...  0.0 -0.000181  0.0  0.0
+        <BLANKLINE>
         [37884 rows x 15 columns]
 
         TODO