fixed error in GitHub action for Linux

.github/workflows/bag_on_linux.yml

@@ -23,6 +23,7 @@ jobs:
       run: |
         conda config --add channels conda-forge
         conda install appdirs cartopy gdal matplotlib-base numpy psutil pyproj qt-material
+        conda install h5py dateutil lxml
         pip install PySide6
         sudo apt-get install -y libegl1
         pip install hyo2.abc2

hyo2/bag/__init__.py

@@ -4,7 +4,7 @@
 """
 
 name = 'BAG'
-__version__ = '1.2.3'
+__version__ = '1.2.4'
 __author__ = 'gmasetti@ccom.unh.edu'
 __license__ = 'LGPLv3 license'
 __copyright__ = 'Copyright (c) 2024, University of New Hampshire, Center for Coastal and Ocean Mapping'

hyo2/bag/bag.py

@@ -3,7 +3,7 @@
 from typing import Tuple
 
 import numpy as np
-from lxml import etree
+from lxml import etree, isoschematron
 
 from hyo2.bag.base import is_bag, File
 from hyo2.bag.helper import BAGError, Helper
@@ -353,8 +353,8 @@ def tracking_list_types(self):
         return self[BAGFile._bag_tracking_list].dtype
 
     def has_valid_row_in_tracking_list(self):
-        rows, cols = self.elevation_shape()
-        # logger.info('rows: %s, cols: %s' % (rows, cols))
+        rows, _ = self.elevation_shape()
+        # logger.info('rows: %s, cols: %s' % (rows, _))
 
         tl = self.tracking_list()
         for idx, row in enumerate(tl['row']):
@@ -363,7 +363,7 @@ def has_valid_row_in_tracking_list(self):
                 return False
 
         return True
-    
+
     def has_valid_col_in_tracking_list(self):
         rows, cols = self.elevation_shape()
         # logger.info('rows: %s, cols: %s' % (rows, cols))
@@ -432,7 +432,7 @@ def substitute_metadata(self, path):
 
         is_valid = self.validate_metadata(xml_string)
         if not is_valid:
-            logger.info("the passed medatadata file is not valid")
+            logger.info("the passed metadata file is not valid")
             return
 
         del self[BAGFile._bag_metadata]
@@ -441,7 +441,7 @@ def substitute_metadata(self, path):
         for i, bt in enumerate(xml_string):
             ds[i] = bytes([bt])
 
-    def validate_metadata(self, xml_string=None):
+    def validate_metadata(self, xml_string: None | bytes = None) -> bool:
         """ Validate metadata based on XML Schemas and schematron. """
         # clean metadata error list
         self.meta_errors = list()
@@ -454,7 +454,7 @@ def validate_metadata(self, xml_string=None):
         try:
             xml_tree = etree.fromstring(xml_string)
         except etree.Error as e:
-            logger.warning("unabled to parse XML metadata: %s" % e)
+            logger.warning("unable to parse XML metadata: %s" % e)
             self.meta_errors.append(e)
             return False
 
@@ -463,7 +463,7 @@ def validate_metadata(self, xml_string=None):
             schema_doc = etree.parse(schema_path)
             schema = etree.XMLSchema(schema_doc)
         except etree.Error as e:
-            logger.warning("unabled to parse XML schema: %s" % e)
+            logger.warning("unable to parse XML schema: %s" % e)
             self.meta_errors.append(e)
             return False
 
@@ -483,22 +483,14 @@ def validate_metadata(self, xml_string=None):
             schematron_path = os.path.join(Helper.iso19757_3_folder(), 'bag_metadata_profile.sch')
             schematron_doc = etree.parse(schematron_path)
         except etree.DocumentInvalid as e:
-            logger.warning("unabled to parse BAG schematron: %s" % e)
-            self.meta_errors.append(e)
-            return False
-
-        try:
-            from lxml import isoschematron
-        except IOError as e:
-            msg = "Unable to load lxml isoschematron files"
-            logger.warning("%s: %s" % (msg, e))
+            logger.warning("unable to parse BAG schematron: %s" % e)
             self.meta_errors.append(e)
             return False
 
         try:
             schematron = isoschematron.Schematron(schematron_doc, store_report=True)
         except etree.DocumentInvalid as e:
-            logger.warning("unabled to load BAG schematron: %s" % e)
+            logger.warning("unable to load BAG schematron: %s" % e)
             self.meta_errors.append(e)
             return False
 

hyo2/bag/tracklist.py

@@ -29,7 +29,7 @@ def __init__(self, track_list: np.ndarray, csv_file=None, header=None, comment=N
         self.header = header
         if self.header is None:
             self.header = str()
-        if type(self.header) is tuple:
+        if isinstance(self.header, tuple):
             self.header = ",".join(fld for fld in self.header)
             self.header += "\n"
         logger.debug("header: %s" % self.header)