Merge branch 'i63-fix-linting-nexus' into '63-clean-nexus-s-codebase'

fix linting nexus module

See merge request !43

conda-recipe/meta.yaml

 package:
   name: nexus-passoft
-  version: "2023.4.6.2"
+  version: "2023.4.6.3"
 
 source:
   path: ../
@@ -17,6 +17,7 @@ requirements:
   build:
     - python >=3.9
     - pip
+    - setuptools
 
   run:
     - python >=3.9

nexus/__init__.py

@@ -4,4 +4,4 @@
 
 __author__ = """IRIS PASSCAL"""
 __email__ = 'software-support@passcal.nmt.edu'
-__version__ = '2023.4.6.2'
+__version__ = '2023.4.6.3'

nexus/obspy_improved.py

@@ -15,6 +15,7 @@ from obspy import Inventory
 from obspy import UTCDateTime
 from obspy.core.inventory import (Network, Station, Channel,
                                   Site, Equipment)
+from obspy.core.inventory.util import Comment
 from obspy.io.mseed.core import _is_mseed
 from obspy.io.mseed import util
 
@@ -298,6 +299,9 @@ class InventoryIm(Inventory):
             inv_cha = inv_sta.channels[inv_sta.channels.index(inv_cha)]
             if self.extend_epoch(inv_cha, start, end):
                 inv_cha._new = new
+        # add Comment object to Channel
+        comment = Comment('')
+        inv_cha.comments.append(comment)
 
     def extend_epoch(self, inv, start: UTCDateTime, end: UTCDateTime) -> bool:
         """
@@ -386,6 +390,7 @@ class InventoryIm(Inventory):
             return True
         return False
 
+
     def populate_from_streams_old(self, streams, new=False):
         """
         Deprecated.
@@ -847,3 +852,31 @@ def utc_from_str(value: str) -> UTCDateTime:
         hour=hour, minute=minute,
         second=second, microsecond=microsecond
     )
+
+def scan_ms(dir_name, status_message=print):
+    # Remove timing test
+    import time
+    start = time.time()
+
+    mseed_files = []
+    streams = []
+    for root, dirs, files in os.walk(dir_name):
+        for name in files:
+            abs_path = os.path.join(root, name)
+            status_message('Scanning {}...'.format(abs_path))
+            if ( os.path.isfile(abs_path) and
+                 _is_mseed(abs_path) ):
+                mseed_files.append(abs_path)
+                try:
+                    st = obspy_read(abs_path, headonly=True)
+                except:
+                    print('Failed to read file {}'.format(abs_path))
+                streams.append(st)
+    print(f'Scan took: {time.time() - start}')
+    return streams, mseed_files
+
+def quick_scan_ms(dir_name, status_message=print):
+    import time
+    start = time.time()
+
+    print(f'Scan took: {time.time() - start}')
\ No newline at end of file

setup.cfg

 [bumpversion]
-current_version = 2023.4.0.0
+current_version = 2023.4.6.3
 commit = True
 tag = True
 

setup.py

@@ -52,6 +52,6 @@ setup(
     packages=find_packages(include=['nexus']),
     test_suite='tests',
     url='https://git.passcal.nmt.edu/software_public/passoft/nexus',
-    version='2023.4.6.2',
+    version='2023.4.6.3',
     zip_safe=False,
 )