Release 0.12.13

geofetch/__init__.py

@@ -1,18 +1,8 @@
 """Package-level data"""
 
-import coloredlogs
-import logmuse
-
 from geofetch._version import __version__
 from geofetch.finder import Finder
 from geofetch.geofetch import Geofetcher
 
 __author__ = ["Oleksandr Khoroshevskyi", "Vince Reuter", "Nathan Sheffield"]
 __all__ = ["Finder", "Geofetcher", "__version__"]
-
-_LOGGER = logmuse.init_logger("geofetch")
-coloredlogs.install(
-    logger=_LOGGER,
-    datefmt="%H:%M:%S",
-    fmt="[%(levelname)s] [%(asctime)s] %(message)s",
-)

geofetch/finder.py

@@ -3,7 +3,6 @@
 import re
 from datetime import datetime, timedelta
 
-import coloredlogs
 import requests
 import xmltodict
 
@@ -19,11 +18,6 @@
 __author__ = "Oleksandr Khoroshevskyi"
 
 _LOGGER = logging.getLogger("__name__")
-coloredlogs.install(
-    logger=_LOGGER,
-    datefmt="%H:%M:%S",
-    fmt="[%(levelname)s] [%(asctime)s] %(message)s",
-)
 
 
 class Finder:

geofetch/geofetch.py

@@ -117,63 +117,63 @@ def __init__(
         :param input: GSEnumber or path to the input file
         :param name: Specify a project name. Defaults to GSE number or name of accessions file name
         :param metadata_root:  Specify a parent folder location to store metadata.
-                The project name will be added as a subfolder [Default: $SRAMETA:]
+                The project name will be added as a subfolder (Default: $SRAMETA:)
         :param 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)]
+                Overrides value of --metadata-root (Default: Not used, --metadata-root is used by default)
         :param just_metadata: If set, don't actually run downloads, just create metadata
         :param refresh_metadata: If set, re-download metadata even if it exists.
         :param config_template: Project config yaml file template.
         :param pipeline_samples: Specify one or more filepaths to SAMPLES pipeline interface yaml files.
                 These will be added to the project config file to make it immediately compatible with looper.
-                [Default: null]
+                (Default: null)
         :param pipeline_project: Specify one or more filepaths to PROJECT pipeline interface yaml files.
                 These will be added to the project config file to make it immediately compatible with looper.
-                [Default: null]
+                (Default: null)
         :param acc_anno:  Produce annotation sheets for each accession.
                 Project combined PEP for the whole project won't be produced.
         :param discard_soft: Create project without downloading soft files on the disc
         :param add_dotfile: Add .pep.yaml file that points .yaml PEP file
         :param disable_progressbar: Set true to disable progressbar
 
         :param const_limit_project: Optional: Limit of the number of the constant sample characters
-                that should not be in project yaml. [Default: 50]
+                that should not be in project yaml. (Default: 50)
         :param const_limit_discard: Optional: Limit of the number of the constant sample characters
-                that should not be discarded [Default: 250]
+                that should not be discarded (Default: 250)
         :param attr_limit_truncate: Optional: Limit of the number of sample characters.
                 Any attribute with more than X characters will truncate to the first X, where X is a number of characters
-                [Default: 500]
+                (Default: 500)
 
         :param max_soft_size: Optional: Max size of soft file.
-                Supported input formats : 12B, 12KB, 12MB, 12GB. [Default value: 1GB]
+                Supported input formats : 12B, 12KB, 12MB, 12GB. (Default: 1GB)
 
-        :param processed: Download processed da_soft_sizeta [Default: download raw data].
+        :param processed: Download processed data (Default: download raw data).
         :param data_source: Specifies the source of data on the GEO record to retrieve processed data,
                 which may be attached to the collective series entity, or to individual samples. Allowable values are:
-                samples, series or both (all). Ignored unless 'processed' flag is set. [Default: samples]
-        :param filter: Filter regex for processed filenames [Default: None].Ignored unless 'processed' flag is set.
-        :param filter_size: Filter size for processed files that are stored as sample repository [Default: None].
+                samples, series or both (all). Ignored unless 'processed' flag is set. (Default: samples)
+        :param filter: Filter regex for processed filenames (Default: None). Ignored unless 'processed' flag is set.
+        :param filter_size: Filter size for processed files that are stored as sample repository (Default: None).
                 Works only for sample data. Supported input formats : 12B, 12KB, 12MB, 12GB.
                 Ignored unless 'processed' flag is set.
         :param geo_folder: Specify a location to store processed GEO files.
-                Ignored unless 'processed' flag is set.[Default: $GEODATA:]
+                Ignored unless 'processed' flag is set. (Default: $GEODATA:)
 
         :param split_experiments: Split SRR runs into individual samples. By default, SRX experiments with multiple SRR
                 Runs will have a single entry in the annotation table, with each run as a separate row in the
-                subannotation table. This setting instead treats each run as a separate sample [Works with raw data]
+                subannotation table. This setting instead treats each run as a separate sample (Works with raw data)
         :param bam_folder: Optional: Specify folder of bam files. Geofetch will not download sra files when
-                corresponding bam files already exist. [Default: $SRABAM:] [Works with raw data]
+                corresponding bam files already exist. (Default: $SRABAM:) (Works with raw data)
         :param fq_folder: Optional: Specify folder of fastq files. Geofetch will not download sra files when corresponding
-                fastq files already exist. [Default: $SRAFQ:] [Works with raw data]
-        :param use_key_subset: Use just the keys defined in this module when writing out metadata. [Works with raw data]
+                fastq files already exist. (Default: $SRAFQ:) (Works with raw data)
+        :param use_key_subset: Use just the keys defined in this module when writing out metadata. (Works with raw data)
         :param sra_folder: Optional: Specify a location to store sra files
-                [Default: $SRARAW:" + safe_echo("SRARAW") + ]
-        :param bam_conversion: Optional: set True to convert bam files  [Works with raw data]
+                (Default: $SRARAW:" + safe_echo("SRARAW") + )
+        :param bam_conversion: Optional: set True to convert bam files  (Works with raw data)
         :param picard_path:  Specify a path to the picard jar, if you want to convert fastq to bam
-                [Default: $PICARD:" + safe_echo("PICARD") + "]  [Works with raw data]
+                (Default: $PICARD:" + safe_echo("PICARD") + ")  (Works with raw data)
         :param add_convert_modifier: Add looper SRA convert modifier to config file.
 
-        :param skip: Skip some accessions. [Default: no skip].
-        :param opts: opts object [Optional]
+        :param skip: Skip some accessions. (Default: no skip).
+        :param opts: opts object (Optional)
         :param str | int max_prefetch_size: argmuent to prefetch command's --max-size option;
             for reference: https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump#check-the-maximum-size-limit-of-the-prefetch-tool
         :param kwargs: other values

requirements/requirements-all.txt

@@ -1,10 +1,9 @@
 colorama>=0.3.9
-logmuse>=0.2.6
+logmuse>=0.3.0
 ubiquerg>=0.6.2
 requests>=2.28.1
 xmltodict>=0.13.0
 pandas>=1.5.3
 peppy>=0.40.6
 rich>=12.5.1
-coloredlogs>=15.0.1
 piper>=0.14.4