Fix for CDS reader requiring at least two description characters

CHANGES.rst

@@ -134,6 +134,9 @@ Bug fixes
 
 - ``astropy.io.ascii``
 
+  - Fixed handling of CDS data file when no description is given and also
+    included stripping out of markup for missing value from description. [#4437]
+
 - ``astropy.io.fits``
 
 - ``astropy.io.misc``

astropy/io/ascii/cds.py

@@ -103,8 +103,8 @@ def get_cols(self, lines):
                                     (?P<end>   \d+)        \s+
                                     (?P<format> [\w.]+)     \s+
                                     (?P<units> \S+)        \s+
-                                    (?P<name>  \S+)        \s+
-                                    (?P<descr> \S.+)""",
+                                    (?P<name>  \S+)
+                                    (\s+ (?P<descr> \S.*))?""",
                                 re.VERBOSE)
 
         cols = []
@@ -120,13 +120,14 @@ def get_cols(self, lines):
                 col.unit = match.group('units')
                 if col.unit == '---':
                     col.unit = None  # "---" is the marker for no unit in CDS table
-                col.description = match.group('descr').strip()
+                col.description = (match.group('descr') or '').strip()
                 col.raw_type = match.group('format')
                 col.type = self.get_col_type(col)
 
                 match = re.match(
-                    r'\? (?P<equal> =)? (?P<nullval> \S*)', col.description, re.VERBOSE)
+                    r'\? (?P<equal> =)? (?P<nullval> \S*) (\s+ (?P<descriptiontext> \S.*))?', col.description, re.VERBOSE)
                 if match:
+                    col.description=(match.group('descriptiontext') or '').strip()
                     if issubclass(col.type, core.FloatType):
                         fillval = 'nan'
                     else:

astropy/io/ascii/setup_package.py

@@ -80,6 +80,8 @@ def get_package_data():
                                    't/simple_csv.csv',
                                    't/simple_csv_missing.csv',
                                    't/fixed_width_2_line.txt',
+                                   't/cds/description/ReadMe',
+                                   't/cds/description/table.dat',
                                    ]
     }
 

astropy/io/ascii/tests/t/cds/description/ReadMe

@@ -0,0 +1,67 @@
+J/A+A/511/A56       Abundances of five open clusters            (Pancino+, 2010)
+================================================================================
+Chemical abundance analysis of the open clusters Cr 110, NGC 2420, NGC 7789,
+and M 67 (NGC 2682).
+    Pancino E., Carrera R., Rossetti, E., Gallart C.
+   <Astron. Astrophys. 511, A56 (2010)>
+   =2010A&A...511A..56P
+================================================================================
+ADC_Keywords: Clusters, open ; Stars, giant ; Equivalent widths ; Spectroscopy
+Keywords: stars: abundances - Galaxy: disk -
+          open clusters and associations: general
+
+Abstract:
+    The present number of Galactic open clusters that have high resolution
+    abundance determinations, not only of [Fe/H], but also of other key
+    elements, is largely insufficient to enable a clear modeling of the
+    Galactic disk chemical evolution. To increase the number of Galactic
+    open clusters with high quality measurements, we obtained high
+    resolution (R~30000), high quality (S/N~50-100 per pixel), echelle
+    spectra with the fiber spectrograph FOCES, at Calar Alto, Spain, for
+    three red clump stars in each of five Open Clusters. We used the
+    classical equivalent width analysis method to obtain accurate
+    abundances of sixteen elements: Al, Ba, Ca, Co, Cr, Fe, La, Mg, Na,
+    Nd, Ni, Sc, Si, Ti, V, and Y. We also derived the oxygen abundance
+    using spectral synthesis of the 6300{AA} forbidden line.
+
+Description:
+    Atomic data and equivalent widths for 15 red clump giants in 5 open
+    clusters: Cr 110, NGC 2099, NGC 2420, M 67, NGC 7789.
+
+File Summary:
+--------------------------------------------------------------------------------
+ FileName   Lrecl  Records   Explanations
+--------------------------------------------------------------------------------
+ReadMe         80        .   This file
+table1.dat    103       15   Observing logs and programme stars information
+table5.dat     56     5265   Atomic data and equivalent widths
+--------------------------------------------------------------------------------
+
+See also:
+ J/A+A/455/271 : Abundances of red giants in NGC 6441 (Gratton+, 2006)
+ J/A+A/464/953 : Abundances of red giants in NGC 6441 (Gratton+, 2007)
+ J/A+A/505/117 : Abund. of red giants in 15 globular clusters (Carretta+, 2009)
+
+Byte-by-byte Description of file: table.dat
+--------------------------------------------------------------------------------
+   Bytes Format Units     Label     Explanations
+--------------------------------------------------------------------------------
+   1-  7  A7    ---       Cluster   Cluster name
+   9- 12  I4    ---       Star      
+  14- 20  F7.2  0.1nm     Wave      wave
+                                    ? Wavelength in Angstroms
+  22- 23  A2    ---       El        a
+      24  I1    ---       ion       ?=0
+                                    - Ionization stage (1 for neutral element)
+  26- 30  F5.2  eV        chiEx     Excitation potential
+  32- 37  F6.2  ---       loggf     Logarithm of the oscillator strength
+  39- 43  F5.1  0.1pm     EW        ?=-9.9 Equivalent width (in mA)
+  46- 49  F4.1  0.1pm   e_EW        ?=-9.9 rms uncertainty on EW
+  51- 56  F6.3  ---       Q         ?=-9.999 DAOSPEC quality parameter Q
+                                     (large values are bad)
+--------------------------------------------------------------------------------
+
+Acknowledgements:
+    Elena Pancino, elena.pancino(at)oabo.inaf.it
+================================================================================
+(End)    Elena Pancino [INAF-OABo, Italy], Patricia Vannier [CDS]    23-Nov-2009

astropy/io/ascii/tests/t/cds/description/table.dat

@@ -0,0 +1,2 @@
+Cr110   2108 6696.79 Al1  4.02  -1.42  29.5   2.2  0.289
+Cr110   2108 6698.67 Al1  3.14  -1.65  58.0   2.0  0.325

astropy/io/ascii/tests/test_cds_header_from_readme.py

@@ -21,6 +21,21 @@ def read_table3(readme, data):
     return ascii.read(data, readme=readme)
 
 
+def test_description():
+    readme = 't/cds/description/ReadMe'
+    data = 't/cds/description/table.dat'
+    for read_table in (read_table1, read_table2, read_table3):
+        table = read_table(readme, data)
+        assert_equal(len(table), 2)
+        assert_equal(table['Cluster'].description, 'Cluster name')
+        assert_equal(table['Star'].description, '')
+        assert_equal(table['Wave'].description, 'wave? Wavelength in Angstroms')
+        assert_equal(table['El'].description, 'a')
+        assert_equal(table['ion'].description, '- Ionization stage (1 for neutral element)')
+        assert_equal(table['EW'].description, 'Equivalent width (in mA)')
+        assert_equal(table['Q'].description, 'DAOSPEC quality parameter Q(large values are bad)')
+
+
 def test_multi_header():
     readme = 't/cds/multi/ReadMe'
     data = 't/cds/multi/lhs2065.dat'
@@ -137,3 +152,4 @@ def test_header_from_readme():
     test_header_from_readme()
     test_multi_header()
     test_glob_header()
+    test_description()