move remaining commands to unified parser

orcasong/parser.py

@@ -7,6 +7,8 @@ from orcasong.tools.concatenate import concatenate
 from orcasong.tools.postproc import postproc_file
 from orcasong.tools.shuffle2 import h5shuffle2
 import orcasong.from_toml as from_toml
+import orcasong.plotting.plot_binstats as plot_binstats
+import orcasong.tools.make_data_split as make_data_split
 
 
 def _add_parser_concatenate(subparsers):
@@ -124,6 +126,8 @@ def main():
     _add_parser_concatenate(subparsers)
     _add_parser_h5shuffle(subparsers)
     _add_parser_h5shuffle2(subparsers)
+    plot_binstats.add_parser(subparsers)
+    make_data_split.add_parser(subparsers)
     _add_parser_version(subparsers)
 
     kwargs = vars(parser.parse_args())

orcasong/plotting/plot_binstats.py

@@ -218,6 +218,9 @@ def get_all_h5_files():
 
 
 def main():
+    # TODO deprecated
+    warnings.warn(
+        "plot_binstats is deprecated and has been renamed to orcasong plot_binstats")
     parser = argparse.ArgumentParser(
         description='Generate a plot with statistics of the binning. '
                     'Can only be used on files generated with the FileBinner when '
@@ -232,5 +235,20 @@ def main():
     plot_hist_of_files(**vars(parser.parse_args()))
 
 
+def add_parser(subparsers):
+    parser = subparsers.add_parser(
+        "plot_binstats",
+        description='Generate a plot with statistics of the binning. '
+                    'Can only be used on files generated with the FileBinner when '
+                    'add_bin_stats was set to true (default). ')
+    parser.add_argument(
+        '--save_as', type=str, default="bin_stats_plot.pdf",
+        help='Filename of the plot. Default: bin_stats_plot.pdf.')
+    parser.add_argument(
+        'files', type=str, nargs='*', default=None,
+        help='File(s) to plot. Default: Plot for all h5 files in current dir.')
+    parser.set_defaults(func=plot_hist_of_files)
+
+
 if __name__ == "__main__":
     main()

orcasong/tools/concatenate.py

@@ -324,6 +324,7 @@ def concatenate(file, outfile="concatenated.h5", no_used_files=False, skip_error
 
 
 def main():
+    # TODO deprecated
     warnings.warn("concatenate is deprecated and has been renamed to orcasong concatenate")
     parser = argparse.ArgumentParser(
         description='Concatenate many small h5 files to a single large one '

orcasong/tools/make_data_split.py

@@ -5,6 +5,7 @@
 __author__ = "Michael Moser, Daniel Guderian"
 
 import os
+import warnings
 import toml
 import argparse
 import h5py
@@ -13,6 +14,8 @@ import numpy as np
 
 
 def get_parser():
+    # TODO deprecated
+    warnings.warn("make_data_split is deprecated and has been renamed to orcasong make_data_split")
     parser = argparse.ArgumentParser(
         description="Create datasets based on the run_id's."
         "Use the config to add input folder and set the ranges."
@@ -26,6 +29,20 @@ def get_parser():
     return parser
 
 
+def add_parser(subparsers):
+    parser = subparsers.add_parser(
+        "make_data_split",
+        description="Create datasets based on the run_id's."
+        "Use the config to add input folder and set the ranges."
+        "Outputs a list in an txt file that can be used to "
+        "concatenate the files specfied"
+    )
+    parser.add_argument(
+        "config", type=str, help="See example config for detailed information"
+    )
+    parser.set_defaults(func=make_split)
+
+
 def get_all_ip_group_keys(cfg):
     """
     Gets the keys of all input groups in the config dict.
@@ -418,9 +435,10 @@ def main():
     # load the config
     parser = get_parser()
     parsed_args = parser.parse_args()
+    make_split(parsed_args.config)
 
-    config_file = parsed_args.config
 
+def make_split(config_file):
     # decode config
     cfg = toml.load(config_file)
     cfg["toml_filename"] = config_file

orcasong/tools/postproc.py

@@ -117,6 +117,7 @@ def get_filepath_output(input_file, shuffle=True, event_skipper=None):
 
 
 def h5shuffle():
+    # TODO deprecated
     warnings.warn("h5shuffle is deprecated and has been renamed to orcasong h5shuffle")
     parser = argparse.ArgumentParser(description='Shuffle an h5 file using km3pipe.')
     parser.add_argument('input_file', type=str, help='File to shuffle.')

orcasong/tools/shuffle2.py

@@ -337,6 +337,7 @@ def slicify(fancy_indices):
 
 
 def run_parser():
+    # TODO deprecated
     warnings.warn("h5shuffle2 is deprecated and has been renamed to orcasong h5shuffle2")
     parser = argparse.ArgumentParser(
         description="Shuffle datasets in a h5file that have the same length. "

setup.py

@@ -28,9 +28,9 @@ setup(
 
     entry_points={'console_scripts': [
         'orcasong=orcasong.parser:main',
+        # TODO all deprecated:
         'make_dsplit=orcasong.tools.make_data_split:main',
         'plot_binstats=orcasong.plotting.plot_binstats:main',
-        # deprecated:
         'concatenate=orcasong.tools.concatenate:main',
         'h5shuffle=orcasong.tools.postproc:h5shuffle',
         'h5shuffle2=orcasong.tools.shuffle2:run_parser',