feat(fixes): shebangs and cmd-line standards

aodntools/timeseries_products/aggregated_timeseries.py

@@ -414,29 +414,28 @@ def main_aggregator(files_to_agg, var_to_agg, site_code, input_dir='', output_di
                             (var_to_agg + "-" + product_type),
                             ('END-'+ time_end_filename), 'C-' + datetime.utcnow().strftime(file_timeformat)]) + '.nc'
     ncout_path = os.path.join(output_dir, output_name)
-    shutil.move(temp_outfile, os.path.join(output_dir, ncout_path))
+    shutil.move(temp_outfile, ncout_path)
 
     return ncout_path, bad_files
 
 
 if __name__ == "__main__":
 
-    parser = argparse.ArgumentParser(description="Aggregate ONE variable from ALL instruments from ALL deployments from ONE site")
-    parser.add_argument('-site', dest='site_code', help='site code, like NRMMAI',  required=True)
-    parser.add_argument('-var', dest='varname', help='variable to aggregate, like TEMP', required=True)
-    parser.add_argument('-files', dest='filenames',
-                        help='name of the file that contains the source URLs (relative to inpath, if given)',
-                        required=True)
-    parser.add_argument('-indir', dest='input_dir', help='base path of input files', default='', required=False)
-    parser.add_argument('-outdir', dest='output_dir', help='path where the result file will be written. Default ./',
-                        default='./', required=False)
-    parser.add_argument('-download_url', dest='download_url', help='path to the download_url_prefix',
-                        default='', required=False)
-    parser.add_argument('-opendap_url', dest='opendap_url', help='path to the opendap_url_prefix',
-                        default='', required=False)
+    parser = argparse.ArgumentParser(
+        description="Aggregate ONE variable from ALL instruments from ALL deployments from ONE site"
+    )
+    parser.add_argument('site_code', help='site code, like NRSMAI')
+    parser.add_argument('varname', help='variable to aggregate, like TEMP')
+    parser.add_argument('filenames',
+                        help='path of file listing the source URLs (relative to input_dir, if given)')
+    parser.add_argument('-i', '--input_dir', help='base path of input files', default='')
+    parser.add_argument('-o', '--output_dir', help='path where the result file will be written. Default ./',
+                        default='./')
+    parser.add_argument('--download_url', help='path to the download_url_prefix', default='')
+    parser.add_argument('--opendap_url', help='path to the opendap_url_prefix', default='')
     args = parser.parse_args()
 
-    with open(os.path.join(args.input_dir,args.filenames)) as ff:
+    with open(args.filenames) as ff:
         files_to_agg = [line.rstrip() for line in ff]
 
     print(main_aggregator(files_to_agg=files_to_agg, var_to_agg=args.varname, site_code=args.site_code,

aodntools/timeseries_products/gridded_timeseries.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import numpy as np
 import bisect
 import argparse
@@ -318,17 +320,24 @@ def grid_variable(input_file, VoI, depth_bins=None, max_separation=50, depth_bin
 
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description="Gridded time series: interpolate ONE variable from ALL instruments from ALL deployments from ONE site into 1hr timestamps and fixed depth bins")
-    parser.add_argument('-var', dest='var', help='name of the variable to concatenate. Like TEMP, PSAL', default='TEMP', required=False)
-    parser.add_argument('-file', dest='filename', help='name of the Hourly Time Series Product file that contains the data', default=None, required=False)
-    parser.add_argument('-depth_bins', dest='depth_bins', help='list of depth where the VoI will be interpolated', default=None, nargs='+', required=False)
-    parser.add_argument('-max_separation', dest='max_separation', help='maximum difference between instruments to allow interpolation', default=50, required=False)
-    parser.add_argument('-depth_bins_increment', dest='depth_bins_increment', help='increment in meters for the automatic generated depth bins', default=10, required=False)
-    parser.add_argument('-indir', dest='input_dir', help='base path of input file. Default .', default='.',
-                        required=False)
-    parser.add_argument('-outdir', dest='output_dir', help='path where the result file will be written. Default .',
-                        default='.', required=False)
-    parser.add_argument('-config', dest='config_file', help='JSON configuration file', default=None, required=False)
+    parser = argparse.ArgumentParser(
+        description="Gridded time series: interpolate ONE variable from ALL instruments from ALL deployments"
+                    " from ONE site into 1hr timestamps and fixed depth bins"
+    )
+    parser.add_argument('input_file',
+                        help='name of the Hourly Time Series Product file that contains the data')
+    parser.add_argument('-v', '--var', default='TEMP',
+                        help='name of the variable to grid (default TEMP)')
+    parser.add_argument('--depth_bins', help='list of depth where the variable will be interpolated',
+                        nargs='+', type=float)
+    parser.add_argument('--max_separation',  default=50,
+                        help='maximum difference between instruments to allow interpolation (default 50m)')
+    parser.add_argument('--depth_bins_increment', default=10,
+                        help='increment in meters for the automatic generated depth bins (default 10)')
+    parser.add_argument('-i', '--input_dir', help='base path of input files', default='')
+    parser.add_argument('-o', '--output_dir', help='path where the result file will be written. Default ./',
+                        default='./')
+    parser.add_argument('--config_file', help='JSON configuration file', default=None)
     args = parser.parse_args()
 
     if args.config_file:
@@ -348,8 +357,6 @@ def grid_variable(input_file, VoI, depth_bins=None, max_separation=50, depth_bin
         input_dir = args.input_dir
         output_dir = args.output_dir
 
-    file_name = args.filename
-
-    print(grid_variable(input_file=file_name, VoI=VoI, depth_bins=depth_bins,
+    print(grid_variable(input_file=args.input_file, VoI=VoI, depth_bins=depth_bins,
                         max_separation=int(max_separation), depth_bins_increment=int(depth_bins_increment),
                         input_dir=input_dir, output_dir=output_dir))

aodntools/timeseries_products/hourly_timeseries.py

@@ -641,18 +641,25 @@ def hourly_aggregator(files_to_aggregate, site_code, qcflags, input_dir='', outp
 
 if __name__ == "__main__":
 
-    parser = argparse.ArgumentParser(description="Concatenate ALL variables from ALL instruments from ALL deployments from ONE site at 1hr time bin")
-    parser.add_argument('-site', dest='site_code', help='site code, like NRMMAI',  required=True)
-    parser.add_argument('-files', dest='filenames', help='name of the file that contains the source URLs', required=True)
-    parser.add_argument('-qc', dest='qcflags', help='list of QC flags to select variable values to keep', nargs='+', required=True)
-    parser.add_argument('-indir', dest='input_dir', help='base path of input files', default='', required=False)
-    parser.add_argument('-outdir', dest='output_dir', help='path where the result file will be written. Default ./',
-                        default='./', required=False)
+    parser = argparse.ArgumentParser(
+        description="Concatenate ALL variables from ALL instruments from ALL deployments from ONE site at 1hr time bin"
+    )
+    parser.add_argument('site_code', help='site code, like NRSMAI')
+    parser.add_argument('filenames',
+                        help='path of file listing the source URLs (relative to input_dir, if given)')
+    parser.add_argument('--qcflags', default='1,2',
+                        help='QC flags to select variable values to keep (comma-separated, no spaces; default=1,2)')
+    parser.add_argument('-i', '--input_dir', help='base path of input files', default='')
+    parser.add_argument('-o', '--output_dir', help='path where the result file will be written. Default ./',
+                        default='./')
+    parser.add_argument('--download_url', help='path to the download_url_prefix', default='')
+    parser.add_argument('--opendap_url', help='path to the opendap_url_prefix', default='')
     args = parser.parse_args()
 
     with open(args.filenames, 'r') as file:
         files_to_aggregate = [i.strip() for i in file.readlines()]
-    qcflags = [int(i) for i in args.qcflags]
+    qcflags = [int(i) for i in args.qcflags.split(',')]
 
     hourly_aggregator(files_to_aggregate=files_to_aggregate, site_code=args.site_code, qcflags=qcflags,
-                      input_dir=args.input_dir, output_dir=args.output_path)
+                      input_dir=args.input_dir, output_dir=args.output_dir,
+                      download_url_prefix=args.download_url, opendap_url_prefix=args.opendap_url)

aodntools/timeseries_products/velocity_aggregated_timeseries.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import os
 import sys
 import tempfile
@@ -306,15 +308,14 @@ def velocity_aggregated(files_to_agg, site_code, input_dir='', output_dir='./',
 if __name__ == "__main__":
 
     parser = argparse.ArgumentParser(description="Concatenate X,Y,Z velocity variables from ALL instruments from ALL deployments from ONE site")
-    parser.add_argument('-site', dest='site_code', help='site code, like NRMMAI',  required=True)
-    parser.add_argument('-files', dest='filenames', help='name of the file that contains the source URLs', required=True)
-    parser.add_argument('-indir', dest='input_dir', help='base path of input files', default='', required=False)
-    parser.add_argument('-outdir', dest='output_dir', help='path where the result file will be written. Default ./',
-                        default='./', required=False)
-    parser.add_argument('-download_url', dest='download_url', help='path to the download_url_prefix',
-                        default='', required=False)
-    parser.add_argument('-opendap_url', dest='opendap_url', help='path to the opendap_url_prefix',
-                        default='', required=False)
+    parser.add_argument('site_code', help='site code, like NRSMAI')
+    parser.add_argument('filenames',
+                        help='path of file listing the source URLs (relative to input_dir, if given)')
+    parser.add_argument('-i', '--input_dir', help='base path of input files', default='')
+    parser.add_argument('-o', '--output_dir', help='path where the result file will be written. Default ./',
+                        default='./')
+    parser.add_argument('--download_url', help='path to the download_url_prefix', default='')
+    parser.add_argument('--opendap_url', help='path to the opendap_url_prefix', default='')
 
     args = parser.parse_args()
 

aodntools/timeseries_products/velocity_hourly_timeseries.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import argparse
 import json
 import os
@@ -319,15 +321,14 @@ def velocity_hourly_aggregated(files_to_agg, site_code, input_dir='', output_dir
 if __name__ == "__main__":
 
     parser = argparse.ArgumentParser(description="Concatenate X,Y,Z velocity variables from ALL instruments from ALL deployments from ONE site")
-    parser.add_argument('-site', dest='site_code', help='site code, like NRMMAI',  required=True)
-    parser.add_argument('-files', dest='filenames', help='name of the file that contains the source URLs', required=True)
-    parser.add_argument('-indir', dest='input_dir', help='base path of input files', default='', required=False)
-    parser.add_argument('-outdir', dest='output_dir', help='path where the result file will be written. Default ./',
-                        default='./', required=False)
-    parser.add_argument('-download_url', dest='download_url', help='path to the download_url_prefix',
-                        default='', required=False)
-    parser.add_argument('-opendap_url', dest='opendap_url', help='path to the opendap_url_prefix',
-                        default='', required=False)
+    parser.add_argument('site_code', help='site code, like NRSMAI')
+    parser.add_argument('filenames',
+                        help='path of file listing the source URLs (relative to input_dir, if given)')
+    parser.add_argument('-i', '--input_dir', help='base path of input files', default='')
+    parser.add_argument('-o', '--output_dir', help='path where the result file will be written. Default ./',
+                        default='./')
+    parser.add_argument('--download_url', help='path to the download_url_prefix', default='')
+    parser.add_argument('--opendap_url', help='path to the opendap_url_prefix', default='')
 
     args = parser.parse_args()