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Docstring changes for epydoc API documentation

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commit ccfefca109a2f9e3c7edcf6a1faffd50dac2e6f2 1 parent e297eaa
@peterjc peterjc authored
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25 Bio/ECell/__init__.py
@@ -2,10 +2,22 @@
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
+"""For reading the ECell spreadsheet format from Ecell2 (DEPRECATED).
-import warnings
-warnings.warn("Bio.ECell was deprecated, as it does not seem to have any users. If you do use this module, please contact the Biopython developers at biopython-dev@biopython.org to avoid permanent removal of this module")
+Ecell converts the ECell input from spreadsheet format to an intermediate
+format, described in http://www.e-cell.org/manual/chapter2E.html#3.2. It
+provides an alternative to the perl script supplied with the Ecell2
+distribution at http://bioinformatics.org/project/?group_id=49.
+ECell expects a spreadsheet exported in delimited text format. The file should
+be read with FilteredReader using the default filter chain to remove extraneous
+characters.
+"""
+import warnings
+warnings.warn("Bio.ECell was deprecated, as it does not seem to have any" \
+ + " users. If you do use this module, please contact the"\
+ + " Biopython developers at biopython-dev@biopython.org to"\
+ + " avoid permanent removal of this module", DeprecationWarning)
# standard library
import sys
@@ -32,15 +44,6 @@
import ecell_format
import Record
-"""
-Ecell converts the ECell input from spreadsheet format to an intermediate format, described in
-http://www.e-cell.org/manual/chapter2E.html#3.2. It provides an alternative to the perl script
-supplied with the Ecell2 distribution at http://bioinformatics.org/project/?group_id=49.
-
-ECell expects a spreadsheet exported in delimited text format. The file should be read with
-FilteredReader using the default filter chain to remove extraneous characters.
-"""
-
class Error( Exception ):
"""
"""
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4 Bio/EUtils/__init__.py
@@ -1,4 +1,6 @@
-"""EUtils is a client-side library for the Entrez databases at NCBI.
+"""A client-side library for the Entrez databases at NCBI (DEPRECATED).
+
+Please use Bio.Entrez instead.
"""
import re
import warnings
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12 Bio/FSSP/__init__.py
@@ -1,9 +1,3 @@
-import string
-import re
-import fssp_rec
-from Bio.Align import Generic
-from Bio import Alphabet
-fff_rec = fssp_rec.fff_rec
"""Parser for FSSP files, used in a database of protein fold classifications.
This is a module to handle FSSP files. For now it parses only the header,
@@ -16,6 +10,12 @@
tuple of two instances.
mult_align: returns a Biopyton alignment object
"""
+import string
+import re
+import fssp_rec
+from Bio.Align import Generic
+from Bio import Alphabet
+fff_rec = fssp_rec.fff_rec
header_records = {
'database' : re.compile('^DATABASE'),
'pdbid': re.compile('^PDBID'),
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