minor bug fixes

docs/release-history.md

@@ -1,12 +1,14 @@
 # Release History
 
+## v1.6.2
+- Minor bug fixes 
+
 ## v1.6.1
 - samplesheet: ensures csv and meta_data pickle match
 - better error message when multiple samplesheet csvs are detected, and more stringent detection parameters
 - updated CI/CD with github actions, faster testing, dropped flaky unit tests
 - updated documentation
 
-
 ## v1.6.0
 - qualityMask: All versions of 1.5.x used a different convention for probes to drop or keep. In version 1.6.0 and above,
 methylprep reverts to the previous convention used in v1.4.6 and below: For the `quality_mask` column in the processed output

methylprep/cli.py

@@ -636,8 +636,16 @@ def cli_sample_sheet(cmd_args):
 def cli_alert(cmd_args):
     parser = DefaultParser(
         prog='methylprep alert',
-        description="Regularly search GEO for new data, filtered by keyword, and updating only if new data found."
-        )
+        description="""Searches GEO for datasets, filtered by keyword, and saves results to <keyword-pattern>_meta.csv.""",
+    )
+    parser.add_argument(
+        '-v', '--verbose',
+        required=False,
+        help="""Verbose reports to page and saves csv.""",
+        type=str,
+        default=''
+    )
+
     parser.add_argument(
         '-k', '--keyword',
         required=False,

methylprep/models/raw_dataset.py

@@ -10,7 +10,7 @@
 from ..models.probes import FG_PROBE_SUBSETS
 from ..files import IdatDataset
 from ..utils import inner_join_data
-from ..utils.progress_bar import * # checks environment and imports tqdm appropriately.
+# from ..utils.progress_bar import * # checks environment and imports tqdm appropriately.
 from collections import Counter
 
 __all__ = ['RawDataset', 'MethylationDataset', 'get_raw_datasets', 'get_array_type']
@@ -82,10 +82,10 @@ def get_raw_datasets(sample_sheet, sample_name=None, from_s3=None, meta_only=Fal
     elif from_s3 and not meta_only:
         parser = RawDataset.from_sample_s3
         zip_reader = from_s3
-        raw_datasets = tqdm([parser(zip_reader, sample) for sample in samples], total=len(samples), desc='Getting raw datasets')
+        raw_datasets = [parser(zip_reader, sample) for sample in samples]
     elif not from_s3 and not meta_only:
         parser = RawDataset.from_sample
-        raw_datasets = tqdm([parser(sample) for sample in samples], total=len(samples), desc='Getting raw datasets')
+        raw_datasets = [parser(sample) for sample in samples]
 
     if not meta_only:
         # ensure all idat files have same number of probes

methylprep/version.py

@@ -2,4 +2,4 @@
 # 1) we don't load dependencies by storing it in __init__.py
 # 2) we can import it in setup.py for the same reason
 # 3) we can import it into your module module
-__version__ = '1.6.1'
+__version__ = '1.6.2'