From 28a7daeef6ff57979ec08de62777528219976df7 Mon Sep 17 00:00:00 2001 From: peterjc Date: Thu, 9 Sep 2010 18:50:58 +0100 Subject: [PATCH] Deprecate Bio.utils, Bio.PropertyManager and Bio.Encodings (see mailing list) --- Bio/Alphabet/IUPAC.py | 4 ++++ Bio/Encodings/IUPACEncoding.py | 8 ++++++++ Bio/Encodings/__init__.py | 10 ++++++---- Bio/PropertyManager.py | 9 +++++---- Bio/utils.py | 19 +++++++++++-------- DEPRECATED | 7 ++++--- 6 files changed, 38 insertions(+), 19 deletions(-) diff --git a/Bio/Alphabet/IUPAC.py b/Bio/Alphabet/IUPAC.py index bf5a1e7debe..6b2ed4191c4 100644 --- a/Bio/Alphabet/IUPAC.py +++ b/Bio/Alphabet/IUPAC.py @@ -97,6 +97,10 @@ class IUPACUnambiguousRNA(IUPACAmbiguousRNA): # # W == wyosine +# ==================================================================== +# TODO - Remove all the following code using now deprecated modules +# Bio.PropertyManager, Bio.Encoding (all used by Bio.utils) +# # We need to load the property resolution information, but we need to # wait until after the systems have been loaded. (There's a nasty loop # where, eg, translation objects need an alphabet, which need to be diff --git a/Bio/Encodings/IUPACEncoding.py b/Bio/Encodings/IUPACEncoding.py index fedc6f70ebd..a9964248cab 100644 --- a/Bio/Encodings/IUPACEncoding.py +++ b/Bio/Encodings/IUPACEncoding.py @@ -1,3 +1,11 @@ +"""Properties once used for transcription and translation (DEPRECATED). + +This module is deprecated, and is expected to be removed in the next release. +If you use this module, please contact the Biopython developers via the +mailing lists. +""" +#NOTE - Adding a deprecation warning would affect Bio.Alphabet.IUPAC + # Set up the IUPAC alphabet properties diff --git a/Bio/Encodings/__init__.py b/Bio/Encodings/__init__.py index fdfd7421f74..7a369133207 100644 --- a/Bio/Encodings/__init__.py +++ b/Bio/Encodings/__init__.py @@ -1,7 +1,9 @@ # This is a Python module. -"""Properties for functionality such as transcription and translation (OBSOLETE). +"""Properties once used for transcription and translation (DEPRECATED). -This module is obsolete, and is likely to be deprecated in a future version -of Biopython, and to be removed after that. If you use this module, please -contact the Biopython developers at biopython-dev@biopython.org. +This module is deprecated, and is expected to be removed in the next release. +If you use this module, please contact the Biopython developers via the +mailing lists. """ + +#NOTE - Adding a deprecation warning would affect Bio.Alphabet.IUPAC diff --git a/Bio/PropertyManager.py b/Bio/PropertyManager.py index 881e5e8ee28..cf7678fd19e 100644 --- a/Bio/PropertyManager.py +++ b/Bio/PropertyManager.py @@ -1,9 +1,10 @@ -"""Stores properties associated with the class of an object (OBSOLETE). +"""Stores properties associated with the class of an object (DEPRECATED). -This module is obsolete, and is likely to be deprecated in a future version -of Biopython, and to be removed after that. If you use this module, please -contact the Biopython developers at biopython-dev@biopython.org. +This module is deprecated, and is expected to be removed in the next release. +If you use this module, please contact the Biopython developers via the +mailing lists. """ +#NOTE - Adding a deprecation warning would affect Bio.Alphabet.IUPAC # Would it be nice to have support for more than one resolver per diff --git a/Bio/utils.py b/Bio/utils.py index 7ed60d20c1e..630d0d77705 100644 --- a/Bio/utils.py +++ b/Bio/utils.py @@ -4,13 +4,16 @@ # license. Please see the LICENSE file that should have been included # as part of this package. -"""Miscellaneous functions for dealing with sequences (OBSOLETE). +"""Miscellaneous functions for dealing with sequences (DEPRECATED). -This module is obsolete, and is likely to be deprecated in a future version -of Biopython, and to be removed after that. If you use this module, please -contact the Biopython developers at biopython-dev@biopython.org. +This module is deprecated, and is expected to be removed in the next release. +If you use this module, please contact the Biopython developers via the +mailing lists. """ +import warnings +warnings.warn("Bio.utils has been deprecated, and we intend to remove it in " + "the next release of Biopython.", DeprecationWarning) import Seq @@ -23,10 +26,10 @@ def ungap(seq): #TODO - Fix this? It currently assumes the outmost AlphabetEncoder #is for the gap. Consider HasStopCodon(Gapped(Protein())) as a test case. import warnings - warnings.warn("Bio.utils.ungap() has been deprecated, and we" - " intend to remove it in a future release of Biopython." - " Instead, please use the ungap method of the Seq object " - " (added in Biopython 1.53).", + warnings.warn("Bio.utils has been deprecated, and we intend to remove it " + "in the next release of Biopython. Instead of function " + "Bio.utils.ungap please use the ungap method of the Seq " + "object (added in Biopython 1.53).", DeprecationWarning) gap = seq.gap_char letters = [] diff --git a/DEPRECATED b/DEPRECATED index ebb1eba8652..4e437befbb1 100644 --- a/DEPRECATED +++ b/DEPRECATED @@ -18,11 +18,11 @@ An explicit warning was added to setup.py for Biopython 1.55. Bio.Encodings ============= -Declared obsolete in Release 1.55. +Explicitly declared obsolete in Release 1.55, and deprecated in Release 1.56. Bio.PropertyManager =================== -Declared obsolete in Biopython 1.55. +Explicitly declared obsolete in Release 1.55, and deprecated in Release 1.56. Bio.InterPro ============ @@ -423,7 +423,8 @@ Bio.utils Functions 'translate', 'translate_to_stop', 'back_translate', 'transcribe', and 'back_transcribe' were deprecated in Release 1.49, and removed in Release 1.53. Function 'ungap' was deprecated in Release 1.53. Use Bio.Seq instead. -The whole of Bio.utils was declared obsolete in Release 1.55. +The whole of Bio.utils was declared obsolete in Release 1.55, and deprecated +in Biopython 1.56. Bio.Motif =========