Implement logging

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name="cifkit",
-    version="0.20",
+    version="0.21",
     package_dir={"": "src"},
     packages=find_packages(where="src"),
     install_requires=[],  # List your dependencies here

src/cifkit/figures/polyhedron.py

@@ -34,7 +34,15 @@ def generate_color_mapping(labels):
     return color_map
 
 
-def plot(points, vertex_labels, file_path, formula, is_displayed, output_dir=None):
+def plot(
+    points,
+    vertex_labels,
+    file_path,
+    formula,
+    show_labels,
+    is_displayed,
+    output_dir=None,
+):
     """
     Generate and save a 3D plot of a molecular structure.
     """
@@ -46,7 +54,7 @@ def plot(points, vertex_labels, file_path, formula, is_displayed, output_dir=Non
     central_atom_coord = points[-1]
     central_atom_label = vertex_labels[-1]
     # Coordination numbers
-    coordination_number = len(points) - 1    
+    coordination_number = len(points) - 1
 
     # Title
     title = f"Formula: {formula}, Central atom: {central_atom_label}, CN: {coordination_number},\n{file_path}"
@@ -60,26 +68,26 @@ def plot(points, vertex_labels, file_path, formula, is_displayed, output_dir=Non
         sphere = pv.Sphere(radius=radius, center=point)
         plotter.add_mesh(sphere, color=label_colors[label])
 
-        # Add labels with index
-        indexed_label = (
-            f"{idx + 1}. {label}"  # Creating a label with numbering
-        )
+        # Creating a label with numbering
+        indexed_label = f"{idx + 1}. {label}"
         adjusted_point = point + [
             0.3,
             0.3,
             0.3,
         ]  # Offset to avoid overlapping with the sphere
-        if idx != len(points) - 1:
-            plotter.add_point_labels(
-                adjusted_point,
-                [indexed_label],  # Use the indexed label
-                font_size=50,
-                text_color=label_colors[label],
-                always_visible=True,
-                shape=None,
-                margin=0,
-                reset_camera=False,
-            )
+
+        if show_labels:
+            if idx != len(points) - 1:
+                plotter.add_point_labels(
+                    adjusted_point,
+                    [indexed_label],  # Use the indexed label
+                    font_size=50,
+                    text_color=label_colors[label],
+                    always_visible=True,
+                    shape=None,
+                    margin=0,
+                    reset_camera=False,
+                )
 
     delaunay = Delaunay(points)
     hull = ConvexHull(points)
@@ -144,5 +152,3 @@ def plot(points, vertex_labels, file_path, formula, is_displayed, output_dir=Non
     """
     # Save the screenshot
     plotter.screenshot(save_path)
-
-

src/cifkit/models/cif.py

@@ -4,8 +4,10 @@
 
 # Polyhedron
 import os
+import logging
 from cifkit.figures import polyhedron
 from cifkit.utils.unit import round_dict_values
+from cifkit.utils.log_messages import CifLog
 
 # Parser .cif file
 from cifkit.utils.cif_parser import (
@@ -96,12 +98,18 @@ def wrapper(self, *args, **kwargs):
     return wrapper
 
 
-class Cif:
-    def __init__(self, file_path: str, display=True) -> None:
+# Global logging
+logging.basicConfig(
+    level=logging.INFO,
+    format="%(asctime)s - %(levelname)s - %(message)s",
+)
 
+
+class Cif:
+    def __init__(self, file_path: str, logging_enabled=False) -> None:
         self.file_path = file_path
-        if display:
-            print(f"Processing {self.file_path}")
+        self.logging_enabled = logging_enabled
+
         """Initialize the Cif object with the file path."""
         self.file_name = os.path.basename(file_path)
         self.file_name_without_ext = os.path.splitext(self.file_name)[0]
@@ -110,15 +118,22 @@ def __init__(self, file_path: str, display=True) -> None:
         self._preprocess()
         self._load_data()
 
+    def _log_info(self, message):
+        """Log a formatted message if logging is enabled."""
+        if self.logging_enabled:
+            formatted_message = message.format(file_path=self.file_path)
+            logging.info(formatted_message)
+
     def _preprocess(self):
         """Preprocess each .cif file and check any error."""
+        self._log_info(CifLog.PREPROCESSING.value)
         check_unique_atom_site_labels(self.file_path)
         remove_author_loop(self.file_path)
         preprocess_label_element_loop_values(self.file_path)
 
     def _load_data(self):
         """Load data from the .cif file and process it."""
-
+        self._log_info(CifLog.LOADING_DATA.value)
         self._block = get_cif_block(self.file_path)
         self._parse_cif_data()
         self._generate_supercell()
@@ -162,6 +177,7 @@ def _generate_supercell(self):
     """
 
     def compute_connections(self, cutoff_radius=10.0):
+        self._log_info(CifLog.COMPUTE_CONNECTIONS.value)
         """Compute nearest neighbor connections per site label."""
         self.connections = get_site_connections(
             [
@@ -403,7 +419,9 @@ def get_polyhedron_labels_by_CN_best_methods(
         )
 
     @ensure_connections
-    def plot_polyhedron(self, site_label, is_displayed=False, output_dir=None):
+    def plot_polyhedron(
+        self, site_label, show_labels=True, is_displayed=False, output_dir=None
+    ):
         coords, vertex_labels = get_polyhedron_coordinates_labels(
             self.CN_connections_by_best_methods, site_label
         )
@@ -412,6 +430,7 @@ def plot_polyhedron(self, site_label, is_displayed=False, output_dir=None):
             vertex_labels,
             self.file_path,
             self.formula,
+            show_labels,
             is_displayed,
             output_dir,
         )

src/cifkit/utils/log_messages.py

@@ -0,0 +1,7 @@
+from enum import Enum
+
+
+class CifLog(Enum):
+    PREPROCESSING = "Preprocessing {file_path}"
+    LOADING_DATA = "Parsing .cif file and generating a supercell"
+    COMPUTE_CONNECTIONS = "Computing pair distances and coordination numbers"

tests/conftest.py

@@ -7,9 +7,8 @@
 from cifkit.utils import cif_parser, folder
 from cifkit import Cif
 from cifkit import CifEnsemble
-from cifkit.preprocessors import environment
 from cifkit.coordination import composition
-from cifkit.coordination import method, filter
+from cifkit.coordination import filter
 
 """
 CifEnsemble - histogram test

tests/core/models/test_cif.py

@@ -1,8 +1,10 @@
 import os
 import shutil
 import pytest
+import logging
 from cifkit import Cif
 from cifkit.utils.error_messages import CifParserError
+from cifkit.utils.log_messages import CifLog
 from cifkit.utils import folder
 
 
@@ -90,6 +92,38 @@ def test_lazy_loading(cif_URhIn):
     assert cif_URhIn.connections is not None
 
 
+"""
+Test log
+"""
+
+
+@pytest.mark.fast
+def test_init_log(caplog):
+    file_path = "tests/data/cif/URhIn.cif"
+    cif = Cif(file_path, logging_enabled=True)
+
+    with caplog.at_level(logging.INFO):
+        assert (
+            CifLog.PREPROCESSING.value.format(file_path=file_path)
+            in caplog.text
+        )
+
+        assert CifLog.LOADING_DATA.value in caplog.text
+
+    cif.compute_connections()
+    with caplog.at_level(logging.INFO):
+        assert CifLog.COMPUTE_CONNECTIONS.value in caplog.text
+
+
+@pytest.mark.fast
+def test_init_no_log(caplog):
+    file_path = "tests/data/cif/URhIn.cif"
+    Cif(file_path)
+
+    with caplog.at_level(logging.INFO):
+        assert caplog.text == ""
+
+
 @pytest.mark.fast
 def test_shortest_distance(cif_URhIn):
     assert cif_URhIn.shortest_distance == 2.697
@@ -342,10 +376,6 @@ def test_plot_polyhedron_default_output_folder(cif_URhIn):
     expected_output_dir = "tests/data/cif/polyhedrons"
     output_file_path = os.path.join(expected_output_dir, "URhIn_In1.png")
 
-    # Ensure the directory exists
-    if not os.path.exists(expected_output_dir):
-        os.makedirs(expected_output_dir)
-
     # Define the output file path
     cif_URhIn.plot_polyhedron("In1")
 
@@ -359,13 +389,9 @@ def test_plot_polyhedron_with_output_folder_given(cif_URhIn):
     expected_output_dir = "tests/data/cif/polyhedrons_user"
     output_file_path = os.path.join(expected_output_dir, "URhIn_In1.png")
 
-    # Ensure the directory exists
-    if not os.path.exists(expected_output_dir):
-        os.makedirs(expected_output_dir)
-
     # Define the output file path
     cif_URhIn.plot_polyhedron(
-        "In1", is_displayed=True, output_dir="tests/data/cif/polyhedrons_user"
+        "In1", is_displayed=False, output_dir="tests/data/cif/polyhedrons_user"
     )
 
     assert os.path.exists(output_file_path)
@@ -378,16 +404,12 @@ def test_plot_polyhedrons(cif_ensemble_test):
     # Define the directory to store the output
     expected_output_dir = "tests/data/cif/ensemble_test/polyhedrons"
     # Ensure the directory exists
-    if not os.path.exists(expected_output_dir):
-        os.makedirs(expected_output_dir)
 
     cifs = cif_ensemble_test.cifs
     for cif in cifs:
         labels = cif.site_labels
-        print("Label from the cif object")
-        print(labels)
         for label in labels:
-            cif.plot_polyhedron(label)
+            cif.plot_polyhedron(label, show_labels=True)
 
     # Check the number of files
     image_file_count = folder.get_file_count(expected_output_dir, ".png")