fix: add logger lines, wrongly skipped during merge + fix MPI workflow action

Author: elenafuengar

.github/workflows/pull_request_MPI.yml

@@ -24,6 +24,10 @@ jobs:
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        path: wakis
     - name: Setup Miniforge
       uses: conda-incubator/setup-miniconda@v2
       with:
@@ -37,13 +41,8 @@ jobs:
       run:  |
         cd wakis
         pip install .['notebook']
-
     - name: Print versions
       run: conda list
-    - name: Checkout wakis
-      uses: actions/checkout@v4
-      with:
-        path: wakis
     - name: Run pytest
       run:  |
         cd wakis

wakis/gridFIT3D.py

@@ -83,27 +83,11 @@ def __init__(self, xmin=None, xmax=None,
                 stl_colors=None, stl_tol=1e-3,
                 load_from_h5=None, verbose=1,):
 
+        t0 = time.time()
+        self.logger = Logger()
         self.verbose = verbose
         self.use_mpi = use_mpi
 
-        # stl info
-        self.stl_solids = stl_solids
-        self.stl_materials = stl_materials
-        self.stl_rotate = stl_rotate
-        self.stl_translate = stl_translate
-        self.stl_scale = stl_scale
-        self.stl_colors = stl_colors
-        self.update_logger(['stl_solids', 'stl_materials'])
-        if stl_rotate != [0., 0., 0.]:
-            self.update_logger(['stl_rotate'])
-        if stl_translate != [0., 0., 0.]:
-            self.update_logger(['stl_translate'])
-        if stl_scale != 1.0:
-            self.update_logger(['stl_scale'])
-
-        if stl_solids is not None:
-            self._prepare_stl_dicts()
-
         # Grid data
         # generate from file
         if load_from_h5 is not None:
@@ -149,13 +133,33 @@ def __init__(self, xmin=None, xmax=None,
         self.dy = np.min(np.diff(self.y))
         #self.dz = np.min(np.diff(self.z))
         self.dz = (self.zmax - self.zmin)/self.Nz
+        self.update_logger(['Nx', 'Ny', 'Nz', 'dx', 'dy', 'dz'])
+
+        # stl info
+        self.stl_solids = stl_solids
+        self.stl_materials = stl_materials
+        self.stl_rotate = stl_rotate
+        self.stl_translate = stl_translate
+        self.stl_scale = stl_scale
+        self.stl_colors = stl_colors
+        self.update_logger(['stl_solids', 'stl_materials'])
+        if stl_rotate != [0., 0., 0.]:
+            self.update_logger(['stl_rotate'])
+        if stl_translate != [0., 0., 0.]:
+            self.update_logger(['stl_translate'])
+        if stl_scale != 1.0:
+            self.update_logger(['stl_scale'])
+
+        if stl_solids is not None:
+            self._prepare_stl_dicts()
 
         # refine self.x, self.y, self.z using snap points
         self.use_mesh_refinement = use_mesh_refinement
         self.refinement_method = refinement_method
         self.snap_points = snap_points
         self.snap_tol = snap_tol
         self.snap_solids = snap_solids # if None, use all stl_solids
+        self.update_logger(['use_mesh_refinement'])
 
         if self.use_mesh_refinement:
             if verbose:
@@ -171,7 +175,6 @@ def __init__(self, xmin=None, xmax=None,
                     x:[{xmin:.3f}, {xmax:.3f}],\n\
                     y:[{ymin:.3f}, {ymax:.3f}],\n\
                     z:[{zmin:.3f}, {zmax:.3f}]')
-            t0 = time.time()
 
         # MPI subdivide domain
         if self.use_mpi:
@@ -1039,6 +1042,17 @@ def load_from_h5(self, filename):
                 {list(self.stl_solids.keys())}')
             print(f' * STL solids assigned materials [eps_r, mu_r, sigma]:\n\
                 {list(self.stl_materials.values())}')
+
+        # update logger [TODO: add domain bounds info]
+        self.update_logger(['Nx', 'Ny', 'Nz', 'dx', 'dy', 'dz'])
+        self.update_logger(['stl_solids', 'stl_materials'])
+        if self.stl_rotate != [0., 0., 0.]:
+            self.update_logger(['stl_rotate'])
+        if self.stl_translate != [0., 0., 0.]:
+            self.update_logger(['stl_translate'])
+        if self.stl_scale != 1.0:
+            self.update_logger(['stl_scale'])
+
     def update_logger(self, attrs):
         """
         Assigns the parameters handed via attrs to the logger