Merge pull request #243 from Loop3D/fix/qgis-plugin-fixes

Fix/qgis plugin fixes

Author: lachlangrose

.github/workflows/linting_and_testing.yml

@@ -46,9 +46,8 @@ jobs:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
         with:
+            auto-update-conda: true
             python-version: ${{ matrix.python-version }}
-            conda-remove-defaults: "true"
-      
       - name: Install dependencies for windows python 3.9 and 3.10
         if: ${{ matrix.os == 'windows-latest' && (matrix.python-version == '3.9' || matrix.python-version == '3.10') }}
         run: |
@@ -77,4 +76,4 @@ jobs:
 
       - name: Run tests
         run: |
-            conda run -n test  pytest -v
+            conda run -n test  pytest -v

map2loop/logging.py

@@ -66,3 +66,53 @@ def set_level(level: str):
         logger = logging.getLogger(name)
         logger.setLevel(level)
     logger.info(f"Logging level set to {level}")
+
+
+logger = getLogger(__name__)
+logger.info("Imported map2loop.logging module")
+
+
+def setLogging(level="info", handler=None):
+    """Set the logging parameters for log file or custom handler.
+
+    Parameters
+    ----------
+    level : str, optional
+        Logging level to set, by default "info"
+        Valid options: 'info', 'warning', 'error', 'debug'
+    handler : logging.Handler, optional
+        A logging handler to use instead of the default StreamHandler, by default None
+
+    Examples
+    --------
+    >>> from map2loop.logging import setLogging
+    >>> setLogging('debug')
+    >>> setLogging('info', logging.FileHandler('loop.log'))
+    """
+    levels = get_levels()
+    level_value = levels.get(level, logging.WARNING)
+
+    # Create default handler if none provided
+    if handler is None:
+        handler = logging.StreamHandler()
+
+    formatter = logging.Formatter(
+        "%(levelname)s: %(asctime)s: %(filename)s:%(lineno)d -- %(message)s"
+    )
+    handler.setFormatter(formatter)
+    handler.setLevel(level_value)
+
+    # Replace handlers in all known loggers
+    for name in loggers:
+        logger = logging.getLogger(name)
+        logger.handlers = []
+        logger.addHandler(handler)
+        logger.setLevel(level_value)
+
+    # Also apply to main module logger
+    main_logger = logging.getLogger(__name__)
+    main_logger.handlers = []
+    main_logger.addHandler(handler)
+    main_logger.setLevel(level_value)
+
+    main_logger.info(f"Set logging to {level}")

map2loop/project.py

@@ -614,6 +614,11 @@ def calculate_stratigraphic_order(self, take_best=False):
                 self.sorter.structure_data = self.map_data.get_map_data(Datatype.STRUCTURE)
             if hasattr(self.sorter, 'dtm_data') and self.sorter.dtm_data is None:
                 self.sorter.dtm_data = self.map_data.get_map_data(Datatype.DTM)
+            if hasattr(self.sorter, 'min_age_column') and self.sorter.min_age_column is None:
+                self.sorter.min_age_column = self.stratigraphic_column.get_min_age_column()
+            if hasattr(self.sorter, 'max_age_column') and self.sorter.max_age_column is None:
+                self.sorter.max_age_column = self.stratigraphic_column.get_max_age_column()
+            
             self.stratigraphic_column.column = self.sorter.sort(
                 self.stratigraphic_column.stratigraphicUnits,
             )

map2loop/sampler.py

@@ -52,7 +52,8 @@ def sample(
             pandas.DataFrame: data frame containing samples
         """
         pass
-
+    def __call__(self, **kwargs):
+        return self.sample(**kwargs)
 
 class SamplerDecimator(Sampler):
     """