docs corrections

docs/changelog.md

@@ -1,7 +1,7 @@
 # Changelog
 
-## [0.12.2] -- 2023-04-32
-- Added `max-prefetch-size` argument.
+## [0.12.2] -- 2023-04-25
+- Added `max-prefetch-size` argument. #113
 - Improved code and logger structure.
 
 ## [0.12.0] -- 2023-03-27

docs/usage.md

@@ -9,12 +9,10 @@
 usage: geofetch [<args>]
 
 The example how to use geofetch (to download GSE573030 just metadata):
-    geofetch -i GSE67303 -m `pwd` --just-metadata
+    geofetch -i GSE67303 -m <folder> --just-metadata
 
 To download all processed data of GSE57303:
-    geofetch -i GSE67303 --processed --geo-folder `pwd` -m `pwd`
-
-* where `pwd` is a current directory
+    geofetch -i GSE67303 --processed --geo-folder <folder> -m <folder>
 
 Automatic GEO and SRA data downloader
 
@@ -32,8 +30,7 @@ options:
   -u METADATA_FOLDER, --metadata-folder METADATA_FOLDER
                         Specify an absolute folder location to store metadata.
                         No subfolder will be added. Overrides value of
-                        --metadata-root [Default: Not used (--metadata-root is
-                        used by default)]
+                        --metadata-root.
   --just-metadata       If set, don't actually run downloads, just create
                         metadata
   -r, --refresh-metadata
@@ -56,8 +53,8 @@ options:
   --acc-anno            Optional: Produce annotation sheets for each
                         accession. Project combined PEP for the whole project
                         won't be produced.
-  --discard-soft        Optional: After creation of PEP files, all soft and
-                        additional files will be deleted
+  --discard-soft        Optional: After creation of PEP files, all .soft files
+                        will be deleted
   --const-limit-project CONST_LIMIT_PROJECT
                         Optional: Limit of the number of the constant sample
                         characters that should not be in project yaml.

geofetch/cli.py

@@ -18,12 +18,10 @@ def _parse_cmdl(cmdl):
         usage="""geofetch [<args>]
 
 The example how to use geofetch (to download GSE573030 just metadata):
-    geofetch -i GSE67303 -m `pwd` --just-metadata
+    geofetch -i GSE67303 -m <folder> --just-metadata
 
 To download all processed data of GSE57303:
-    geofetch -i GSE67303 --processed --geo-folder `pwd` -m `pwd`
-
-* where `pwd` is a current directory
+    geofetch -i GSE67303 --processed --geo-folder <folder> -m <folder>
 
 """,
     )
@@ -63,8 +61,7 @@ def _parse_cmdl(cmdl):
         "-u",
         "--metadata-folder",
         help="Specify an absolute folder location to store metadata. "
-        "No subfolder will be added. Overrides value of --metadata-root "
-        "[Default: Not used (--metadata-root is used by default)]",
+        "No subfolder will be added. Overrides value of --metadata-root.",
     )
 
     parser.add_argument(
@@ -127,7 +124,7 @@ def _parse_cmdl(cmdl):
     parser.add_argument(
         "--discard-soft",
         action="store_true",
-        help="Optional: After creation of PEP files, all soft and additional files will be deleted",
+        help="Optional: After creation of PEP files, all .soft files will be deleted",
     )
 
     parser.add_argument(
@@ -172,7 +169,8 @@ def _parse_cmdl(cmdl):
 
     parser.add_argument(
         "--max-prefetch-size",
-        help="Argument to pass to prefetch program's --max-size option, if prefetch will be used in this run of geofetch; for reference: https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump#check-the-maximum-size-limit-of-the-prefetch-tool",
+        help="Argument to pass to prefetch program's --max-size option, if prefetch will be used in this run of geofetch; "
+        "for reference: https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump#check-the-maximum-size-limit-of-the-prefetch-tool",
     )
 
     processed_group.add_argument(