Include error message and line numbers in GrainStats error reporting

.github/workflows/pypi.yaml

@@ -12,7 +12,7 @@ jobs:
     name: Build Package
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Setup Python
@@ -46,7 +46,7 @@ jobs:
       url: https://pypi.org/p/topostats
     steps:
       - name: Download all the dists
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           name: python-package-distributions
           path: dist/
@@ -72,7 +72,7 @@ jobs:
 
   #   steps:
   #     - name: Download all the dists
-  #       uses: actions/download-artifact@v4
+  #       uses: actions/download-artifact@v5
   #       with:
   #         name: python-package-distributions
   #         path: dist/

.github/workflows/sphinx_docs_to_gh_pages.yaml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     name: Sphinx docs to gh-pages
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Setup Python

.github/workflows/tests.yaml

@@ -30,7 +30,7 @@ jobs:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
         python-version: ["3.10", "3.11"]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Set up Python
         uses: actions/setup-python@v5
         with:

topostats/__init__.py

@@ -23,6 +23,10 @@
 __version__ = version("topostats")
 __release__ = ".".join(__version__.split(".")[:-2])
 
+TOPOSTATS_DETAILS = version("topostats").split("+g")
+TOPOSTATS_VERSION = TOPOSTATS_DETAILS[0]
+TOPOSTATS_COMMIT = TOPOSTATS_DETAILS[1].split(".d")[0]
+
 colormaps.register(cmap=Colormap("nanoscope").get_cmap())
 colormaps.register(cmap=Colormap("gwyddion").get_cmap())
 
@@ -269,3 +273,9 @@ def topostats_to_dict(self) -> dict[str, str | ImageGrainCrops | npt.NDArray]:
             Dictionary of ''TopoStats'' object.
         """
         return {re.sub(r"^_", "", key): value for key, value in self.__dict__.items()}
+
+
+def log_topostats_version() -> None:
+    """Log the TopoStats version, commit and date to system logger."""
+    LOGGER.info(f"TopoStats version : {TOPOSTATS_VERSION}")
+    LOGGER.info(f"Commit            : {TOPOSTATS_COMMIT}")

topostats/entry_point.py

@@ -8,7 +8,7 @@
 import sys
 from pathlib import Path
 
-from topostats import __version__, run_modules
+from topostats import __version__, log_topostats_version, run_modules
 from topostats.io import write_config_with_comments
 from topostats.plotting import run_toposum
 
@@ -1268,6 +1268,9 @@ def entry_point(manually_provided_args=None, testing=False) -> None:
     None
         Does not return anything.
     """
+    # Log topostats version and the commit id
+    log_topostats_version()
+
     # Parse command line options, load config (or default) and update with command line options
     parser = create_parser()
     args = parser.parse_args() if manually_provided_args is None else parser.parse_args(manually_provided_args)

topostats/grainstats.py

@@ -25,7 +25,7 @@
 # pylint: disable=line-too-long
 # pylint: disable=fixme
 # FIXME : The calculate_stats() and calculate_aspect_ratio() raise this error when linting, could consider putting
-#         variables into dictionar, see example of breaking code out to staticmethod extremes() and returning a
+#         variables into dictionary, see example of breaking code out to staticmethod extremes() and returning a
 #         dictionary of x_min/x_max/y_min/y_max
 # pylint: disable=too-many-locals
 # FIXME : calculate_aspect_ratio raises this error when linting it has 65 statements, recommended not to exceed 50.
@@ -238,6 +238,7 @@ def calculate_stats(self) -> tuple[pd.DataFrame, dict]:
                             f"[{self.image_name}] : Skipping subgrain due to being too small "
                             f"(size: {subgrain_tight_shape}) to calculate stats for."
                         )
+                        continue
 
                     # Calculate all the stats
                     points = self.calculate_points(subgrain_only_mask)

topostats/io.py

@@ -21,7 +21,7 @@
 from numpyencoder import NumpyEncoder
 from ruamel.yaml import YAML, YAMLError
 
-from topostats import __release__, grains
+from topostats import TOPOSTATS_COMMIT, TOPOSTATS_VERSION, __release__, grains
 from topostats.logs.logs import LOGGER_NAME
 
 LOGGER = logging.getLogger(LOGGER_NAME)
@@ -237,6 +237,11 @@ def write_yaml(
         header = f"# {header_message} : {get_date_time()}\n" + CONFIG_DOCUMENTATION_REFERENCE
     else:
         header = f"# Configuration from TopoStats run completed : {get_date_time()}\n" + CONFIG_DOCUMENTATION_REFERENCE
+
+    # Add comment to config with topostats version + commit
+    header += f"# TopoStats version: {TOPOSTATS_VERSION}\n"
+    header += f"# Commit: {TOPOSTATS_COMMIT}\n"
+
     output_config.write_text(header, encoding="utf-8")
 
     yaml = YAML(typ="safe")

topostats/processing.py

@@ -9,7 +9,7 @@
 import pandas as pd
 from art import tprint
 
-from topostats import __version__
+from topostats import TOPOSTATS_COMMIT, TOPOSTATS_VERSION
 from topostats.array_manipulation import re_crop_grain_image_and_mask_to_set_size_nm
 from topostats.filters import Filters
 from topostats.grains import GrainCrop, GrainCropsDirection, Grains, ImageGrainCrops
@@ -338,62 +338,73 @@ def run_grainstats(
         grainstats_config.pop("run")
         class_names = {index + 1: class_name for index, class_name in enumerate(grainstats_config.pop("class_names"))}
         # Grain Statistics :
+        LOGGER.info(f"[{filename}] : *** Grain Statistics ***")
+        grainstats_dict = {}
+        height_profiles_dict = {}
         try:
-            LOGGER.info(f"[{filename}] : *** Grain Statistics ***")
             grain_plot_dict = {
                 key: value
                 for key, value in plotting_config["plot_dict"].items()
                 if key in ["grain_image", "grain_mask", "grain_mask_image"]
             }
-            grainstats_dict = {}
-            height_profiles_dict = {}
+        except Exception as e:
+            LOGGER.error(
+                f"[{filename}] : An error occurred whilst creating a grain plots dictionary: {e}\nReturning empty dataframe."
+            )
+            return create_empty_dataframe(column_set="grainstats"), height_profiles_dict, {}
 
-            # There are two layers to process those above the given threshold and those below
-            grain_crops_direction: GrainCropsDirection
+        # There are two layers to process those above the given threshold and those below
+        grain_crops_direction: GrainCropsDirection
+        try:
             for direction, grain_crops_direction in image_grain_crops.__dict__.items():
                 if grain_crops_direction is None:
                     LOGGER.warning(
                         f"No grains exist for the {direction} direction. Skipping grainstats for {direction}."
                     )
                     continue
-                grainstats_calculator = GrainStats(
-                    grain_crops=grain_crops_direction.crops,
-                    direction=direction,
-                    base_output_dir=grain_out_path,
-                    image_name=filename,
-                    plot_opts=grain_plot_dict,
-                    **grainstats_config,
-                )
-                grainstats_dict[direction], height_profiles_dict[direction] = grainstats_calculator.calculate_stats()
-                grainstats_dict[direction]["threshold"] = direction
-            # Create results dataframe from above and below results
-            # Appease pylint and ensure that grainstats_df is always created
-            grainstats_df = create_empty_dataframe(column_set="grainstats")
-            if "above" in grainstats_dict and "below" in grainstats_dict:
-                grainstats_df = pd.concat([grainstats_dict["below"], grainstats_dict["above"]])
-            elif "above" in grainstats_dict:
-                grainstats_df = grainstats_dict["above"]
-            elif "below" in grainstats_dict:
-                grainstats_df = grainstats_dict["below"]
-            else:
-                raise ValueError(
-                    "grainstats dictionary has neither 'above' nor 'below' keys. This should be impossible."
-                )
-            grainstats_df["basename"] = basename.parent
-            grainstats_df["class_name"] = grainstats_df["class_number"].map(class_names)
-            LOGGER.info(f"[{filename}] : Calculated grainstats for {len(grainstats_df)} grains.")
-            LOGGER.info(f"[{filename}] : Grainstats stage completed successfully.")
-            return grainstats_df, height_profiles_dict, grainstats_calculator.grain_crops
-        except Exception:
-            LOGGER.info(
-                f"[{filename}] : Errors occurred whilst calculating grain statistics. Returning empty dataframe."
+                try:
+                    grainstats_calculator = GrainStats(
+                        grain_crops=grain_crops_direction.crops,
+                        direction=direction,
+                        base_output_dir=grain_out_path,
+                        image_name=filename,
+                        plot_opts=grain_plot_dict,
+                        **grainstats_config,
+                    )
+                    grainstats_dict[direction], height_profiles_dict[direction] = (
+                        grainstats_calculator.calculate_stats()
+                    )
+                    grainstats_dict[direction]["threshold"] = direction
+                except Exception as e:
+                    LOGGER.error(
+                        f"[{filename}] : An error occurred whilst calculating grain statistics: {e}\nReturning empty dataframe."
+                    )
+                    return create_empty_dataframe(column_set="grainstats"), height_profiles_dict, {}
+        except Exception as e:
+            LOGGER.error(
+                f"[{filename}] : An error occurred whilst trying to iterate over directions: {e}\nReturning empty dataframe."
             )
             return create_empty_dataframe(column_set="grainstats"), height_profiles_dict, {}
-    else:
-        LOGGER.info(
-            f"[{filename}] : Calculation of grainstats disabled, returning empty dataframe and empty height_profiles."
-        )
-        return create_empty_dataframe(column_set="grainstats"), {}, {}
+        # Create results dataframe from above and below results
+        # Appease pylint and ensure that grainstats_df is always created
+        grainstats_df = create_empty_dataframe(column_set="grainstats")
+        if "above" in grainstats_dict and "below" in grainstats_dict:
+            grainstats_df = pd.concat([grainstats_dict["below"], grainstats_dict["above"]])
+        elif "above" in grainstats_dict:
+            grainstats_df = grainstats_dict["above"]
+        elif "below" in grainstats_dict:
+            grainstats_df = grainstats_dict["below"]
+        else:
+            raise ValueError("grainstats dictionary has neither 'above' nor 'below' keys. This should be impossible.")
+        grainstats_df["basename"] = basename.parent
+        grainstats_df["class_name"] = grainstats_df["class_number"].map(class_names)
+        LOGGER.info(f"[{filename}] : Calculated grainstats for {len(grainstats_df)} grains.")
+        LOGGER.info(f"[{filename}] : Grainstats stage completed successfully.")
+        return grainstats_df, height_profiles_dict, grainstats_calculator.grain_crops
+    LOGGER.info(
+        f"[{filename}] : Calculation of grainstats disabled, returning empty dataframe and empty height_profiles."
+    )
+    return create_empty_dataframe(column_set="grainstats"), {}, {}
 
 
 def run_disordered_tracing(
@@ -1626,7 +1637,8 @@ def completion_message(config: dict, img_files: list, summary_config: dict, imag
     tprint("TopoStats", font="twisted")
     LOGGER.info(
         f"\n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ COMPLETE ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n"
-        f"  TopoStats Version           : {__version__}\n"
+        f"  TopoStats Version           : {TOPOSTATS_VERSION}\n"
+        f"  TopoStats Commit            : {TOPOSTATS_COMMIT}\n"
         f"  Base Directory              : {config['base_dir']}\n"
         f"  File Extension              : {config['file_ext']}\n"
         f"  Files Found                 : {len(img_files)}\n"