updated __all__ tags for 1.00a2 release

biopython · Jul 5, 2001 · a7a332b · a7a332b
1 parent 56eb624
commit a7a332b
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Showing 21 changed files with 99 additions and 10 deletions.
diff --git a/Bio/Align/__init__.py b/Bio/Align/__init__.py
@@ -1 +1,7 @@
 # Align directory
+
+__all__ = [
+    'AlignInfo',
+    'FormatConvert',
+    'Generic'
+    ]
diff --git a/Bio/Alphabet/__init__.py b/Bio/Alphabet/__init__.py
@@ -1,5 +1,9 @@
 import string, re
 
+__all__ = [
+    'IUPAC',
+    ]
+
 # This is used by sequences which contain a finite number of similar
 # words.
 

diff --git a/Bio/Blast/__init__.py b/Bio/Blast/__init__.py
@@ -3,4 +3,8 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 
-__all__ = ['NCBIStandalone', 'NCBIWWW', 'Record']
+__all__ = [
+    'NCBIStandalone',
+    'NCBIWWW',
+    'Record',
+    ]
diff --git a/Bio/Clustalw/__init__.py b/Bio/Clustalw/__init__.py
@@ -21,6 +21,10 @@
 o _AlignCreator
 o MultipleAlignCL"""
 
+__all__ = [
+    'clustal_format',
+    ]
+
 # standard library
 import os
 import string

diff --git a/Bio/Data/__init__.py b/Bio/Data/__init__.py
@@ -1 +1,6 @@
 # This is a Python module
+
+__all__ = [
+    'CodonTable',
+    'IUPACData'
+    ]
diff --git a/Bio/Encodings/__init__.py b/Bio/Encodings/__init__.py
@@ -1 +1,6 @@
 # This is a Python module.
+
+__all__ = [
+    'IUPACEncoding',
+    ]
+
diff --git a/Bio/Fasta/__init__.py b/Bio/Fasta/__init__.py
@@ -28,6 +28,10 @@
 import string
 import os
 
+__all__ = [
+    'FastaAlign',
+    ]
+
 
 from Bio import File
 from Bio import Index

diff --git a/Bio/GenBank/__init__.py b/Bio/GenBank/__init__.py
@@ -34,6 +34,11 @@
 download_many         Download many GenBank records.
 
 """
+__all__ = [
+    'LocationParser',
+    'Record',
+    'genbank_format',
+    ]
 # standard library
 import string
 import os

diff --git a/Bio/Kabat/__init__.py b/Bio/Kabat/__init__.py
@@ -3,6 +3,11 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 
+__all__ = [
+    'Record',
+    'kabat_format'
+    ]
+
 # standard library
 import string
 import array

diff --git a/Bio/Prosite/__init__.py b/Bio/Prosite/__init__.py
@@ -38,7 +38,10 @@
 _extract_pattern_hits Extract Prosite patterns from a web page.
 
 """
-__all__ = ['Prodoc', 'Pattern']
+__all__ = [
+    'Pattern',
+    'Prodoc',
+    ]
 from types import *
 import string
 import re

diff --git a/Bio/SCOP/__init__.py b/Bio/SCOP/__init__.py
@@ -3,4 +3,8 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 
-__all__ = ['Dom', 'Lin', 'Location']
+__all__ = [
+    'Dom',
+    'Lin',
+    'Location'
+    ]
diff --git a/Bio/SeqIO/__init__.py b/Bio/SeqIO/__init__.py
@@ -7,3 +7,6 @@
 # Note that once a parser is given an input string, it is free to read
 # as much of the data as it wants to read, unless otherwise mentioned.
 
+__all__ = [
+    'FASTA'
+    ]
diff --git a/Bio/SubsMat/__init__.py b/Bio/SubsMat/__init__.py
@@ -1,3 +1,8 @@
+__all__ = [
+   'FreqTable',
+   'MatrixInfo'
+   ]
+
 import re
 import string
 import sys

diff --git a/Bio/SwissProt/__init__.py b/Bio/SwissProt/__init__.py
@@ -3,4 +3,7 @@
 # license.  Please see the LICENSE file that should have been included
 # as part of this package.
 
-__all__ = ['SProt', 'KeyWList']
+__all__ = [
+    'KeyWList',
+    'SProt',
+    ]
diff --git a/Bio/Tools/Clustering/__init__.py b/Bio/Tools/Clustering/__init__.py
@@ -2,3 +2,7 @@
 # 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.
+
+__init__ = [
+    'kMeans',
+    ]
diff --git a/Bio/Tools/MultiProc/__init__.py b/Bio/Tools/MultiProc/__init__.py
@@ -0,0 +1,10 @@
+# Copyright 2001 by Jeffrey Chang.  All rights reserved.
+# 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.
+
+__all__ = [
+    'Scheduler',
+    'Task',
+    'copen'
+    ]
diff --git a/Bio/Tools/Parsers/__init__.py b/Bio/Tools/Parsers/__init__.py
@@ -1 +1,5 @@
 # make files in this directory importable
+
+__all__ = [
+    'spark',
+    ]
diff --git a/Bio/WWW/__init__.py b/Bio/WWW/__init__.py
@@ -1,5 +1,11 @@
 # This is a Python module
 
+__all__ = [
+    'ExPASy',
+    'NCBI,
+    'SCOP',
+    ]
+
 import time
 
 class RequestLimiter:

diff --git a/Bio/__init__.py b/Bio/__init__.py
@@ -11,17 +11,20 @@
     "Data",
     "Encodings",
     "Enzyme",
+    "FSSP",
     "Fasta",
     "File",
     "GenBank",
     "Gobase",
     "Index",
+    "Kabat",
     "Medline",
     "PDB",
     "ParserSupport",
     "PropertyManager",
     "Prosite",
     "Rebase",
+    "RecordFile",
     "SCOP",
     "Seq",
     "SeqFeature",

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -20,6 +20,13 @@ recursive-include Tests *
 global-exclude CVS
 global-exclude CVS/*
 
+# Don't include obsolete regression testing frameworks.
+exclude Tests/br_regrtest.py
+recursive-exclude Tests/UnitTests *
+
+# Don't include obsolete Sequence.py
+exclude Bio/Sequence.py
+
 exclude Tests/Amino
 exclude Tests/Blast
 exclude Tests/Enzymes
@@ -30,9 +37,6 @@ exclude Tests/Prosite
 exclude Tests/Prosite/Doc
 exclude Tests/Rebase
 exclude Tests/SwissProt
-exclude Tests/UnitTests
-exclude Tests/UnitTests/Prosite
-exclude Tests/UnitTests/Save
-exclude Tests/UnitTests/Seq
 exclude Tests/output
 exclude Tests/Blast/bt008*    # file too large
+
diff --git a/README b/README
@@ -131,8 +131,6 @@ setup.py --     Installation file.
 
 - microarray data
 
-- deprecate Sequence.py
-
 If you see something here you would like to work on, please send mail
 to biopython@biopython.org!