Merge pull request #149 from pepkit/dev

Release 0.12.10

Author: khoroshevskyi

geofetch/_version.py

@@ -1 +1 @@
-__version__ = "0.12.9"
+__version__ = "0.12.10"

geofetch/cli.py

@@ -238,9 +238,7 @@ def _parse_cmdl(cmdl):
         default=_safe_echo("SRABAM"),
         help="""Optional: Specify folder of bam files. Geofetch will not
             download sra files when corresponding bam files already exist.
-            [Default: $SRABAM:"""
-        + _safe_echo("SRABAM")
-        + "]",
+            [Default: $SRABAM:""" + _safe_echo("SRABAM") + "]",
     )
 
     raw_group.add_argument(
@@ -250,9 +248,7 @@ def _parse_cmdl(cmdl):
         default=_safe_echo("SRAFQ"),
         help="""Optional: Specify folder of fastq files. Geofetch will not
             download sra files when corresponding fastq files already exist.
-            [Default: $SRAFQ:"""
-        + _safe_echo("SRAFQ")
-        + "]",
+            [Default: $SRAFQ:""" + _safe_echo("SRAFQ") + "]",
     )
 
     # Deprecated; these are for bam conversion which now happens in sra_convert

geofetch/geofetch.py

@@ -790,6 +790,7 @@ def _generate_processed_meta(
                 meta_processed_series,
                 pep_acc_path_exp,
                 just_object=self.just_object,
+                gse_meta_dict=gse_meta_dict,
             )
 
         elif self.supp_by == "samples":
@@ -814,6 +815,7 @@ def _generate_processed_meta(
                 meta_processed_series,
                 pep_acc_path_exp,
                 just_object=self.just_object,
+                gse_meta_dict=gse_meta_dict,
             )
 
         return return_objects