First version of the xmatch cli script

bin/_xmatch.py

@@ -0,0 +1,89 @@
+#!/usr/bin/env python
+from __future__ import absolute_import, print_function
+
+from xmatch import xmatch
+
+
+def open_table(filename, sep=';', columns=None):
+    import pandas
+    df = pandas.read_csv(filename, sep=sep)
+    if columns is not None and len(columns) > 0:
+        assert isinstance(columns, (list, tuple))
+        assert all(col in df.columns for col in columns)
+        df = df[columns]
+    return df
+
+
+if __name__ == '__main__':
+    import argparse
+    parser = argparse.ArgumentParser(description="Cross-Match catalogs")
+
+    parser.add_argument('catalog1', type=str,
+                        help="Target catalog (csv filename)")
+    parser.add_argument('--ra1', type=str, default='ra', required=True,
+                        help="RA column name in 'cat1'")
+    parser.add_argument('--dec1', type=str, default='dec', required=True,
+                        help="Dec column name in 'cat1'")
+    parser.add_argument('--id1', type=str, default=None,
+                        help="ID (ObjID) column name in 'cat1'")
+    parser.add_argument('--sep1', type=str, default=';',
+                        help="Column separator in 'cat1'")
+
+    parser.add_argument('catalog2', default=None, type=str,
+                        help="Ancillary catalog (csv filename)")
+    parser.add_argument('--ra2', type=str, default='ra', required=True,
+                        help="RA column name in 'cat2'")
+    parser.add_argument('--dec2', type=str, default='dec', required=True,
+                        help="Dec column name in 'cat2'")
+    parser.add_argument('--id2', type=str, default=None,
+                        help="ID (ObjID) column name in 'cat2'")
+    parser.add_argument('--sep2', type=str, default=';',
+                        help="Column separator in 'cat2'")
+
+    parser.add_argument('-r', '--radius', metavar='rs', type=float,
+                        default=None,
+                        help=("Radius (in 'arcsec' units) to search for ancillary objects."
+                              "If 'None', Nearest-Neighbour method is used."))
+
+    parser.add_argument('--method', default='gc', type=str,
+                        choices=['gc','mle','nn','filter'],
+                        help="Method for x-matching the catalogs")
+    parser.add_argument('--filter-method', default=None, type=str,
+                        help="Method for filtering catalogs")
+    parser.add_argument('--mle-column', default=None, type=str,
+                        help="Column to use from catalog2 for the likelihood")
+
+    args = parser.parse_args()
+
+    rs = args.rs
+    if rs is None:
+        method = 'nn'
+    else:
+        method = 'gc'
+        from astropy import units
+        rs = rs * units('arcsec')
+
+    # Target catalog (cat1)
+    cols1 = [args.ra1, args.dec1]
+    if args.id1 is not None:
+        cols1.append(args.id1)
+    cat1 = open_table(args.cat1, sep=args.sep1, columns=cols1)
+    if args.id1 is None:
+        cols1.append('ID')
+        cat1.index.name = 'ID'
+        cat1.reset_index(inplace=True)
+
+    # Ancillary catalog (cat2)
+    cols2 = [args.ra2, args.dec2]
+    if args.id2 is not None:
+        cols2.append(args.id2)
+    cat2 = open_table(args.cat2, sep=args.sep2, columns=cols2)
+    if args.id2 is None:
+        cols2.append('ID')
+        cat2.index.name = 'ID'
+        cat2.reset_index(inplace=True)
+
+
+    cat = xmatch(cat1, cols1,
+                 cat2, cols2,
+                 radius=rs, method=method)

bin/xmatch

@@ -0,0 +1 @@
+_xmatch.py

setup.py

@@ -1,12 +1,16 @@
-from setuptools import find_packages, setup
+from setuptools import setup
+import glob
+import os
 
 import versioneer
 
+scripts = [fname for fname in glob.glob(os.path.join('bin', '*'))]
+
 setup(name='xmatch',
       version=versioneer.get_version(),
       cmdclass=versioneer.get_cmdclass(),
       description='Astronimcal catalogs cross-matching package',
       url='http://github.com/chbrandt/xmatch',
-      packages=find_packages(),
-      zip_safe=False,
-      include_package_data=True)
+      packages=['xmatch'],
+      scripts=scripts
+      )

xmatch/__init__.py

@@ -7,11 +7,11 @@
 A maximum likelihood algorithm algorithm is provided in module `mle.py`, where
 an extra column is necessary to be used as likelihood's *data feature*.
 """
-from __future__ import absolute_import
-
-from ._xmatchi import xmatch
-from .mle import mle
+from __future__ import absolute_import, print_function
 
 from ._version import get_versions
 __version__ = get_versions()['version']
 del get_versions
+
+from ._xmatchi import xmatch
+from .mle import mle