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Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers…

… as obsolete (to be deprecated in the subsequent release)
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1 parent 20483f4 commit 1b7544bbb6f3707e58e7579b14a2641294987223 @peterjc peterjc committed Jun 25, 2010
Showing with 39 additions and 3 deletions.
  1. +3 −1 Bio/GenBank/LocationParser.py
  2. +1 −1 Bio/GenBank/__init__.py
  3. +9 −1 Bio/Parsers/__init__.py
  4. +14 −0 Bio/Parsers/spark.py
  5. +12 −0 DEPRECATED
@@ -3,7 +3,9 @@
# 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.
-"""Code used for parsing GenBank/EMBL feature location strings."""
+"""Code used for parsing GenBank/EMBL feature location strings (OBSOLETE)."""
+# Don't issue a deprecation warning here, but via Bio.Parsers instead
+# This avoids the user seeing multiple deprecation warnings.
# First pass at a parser for the location fields of a feature table.
# Everything likely to change.
View
@@ -51,7 +51,7 @@
from Bio import Entrez
# other Bio.GenBank stuff
-import LocationParser
+import LocationParser # Obsolete
from utils import FeatureValueCleaner
from Scanner import GenBankScanner
View
@@ -1,2 +1,10 @@
-"""Third party and other parsers useful internally to Biopython.
+"""Third party and other parsers useful internally to Biopython (OBSOLETE).
"""
+#import warnings
+#warnings.warn("Bio.Parsers (including our copy of SPARK) and the only part "
+# "of Biopython which used it, Bio.GenBank.LocationParser, are "
+# "now deprecated and will be removed in a future release of "
+# "Biopython. If you want to continue to use any of this code, "
+# "please get in contact with the Biopython developers via "
+# "the mailing lists to avoid its permanent removal from "
+# "Biopython.", DeprecationWarning)
View
@@ -19,6 +19,20 @@
# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
# SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+"""Copy of John Aycock's SPARK parser included with Biopython (OBSOLETE).
+
+To clarify, when we say obsolete we just mean to warn you that Biopython will
+in a future release no longer include this module. This does not affect the
+status of John Aycock's SPARK parser which can be installed separately from:
+http://pages.cpsc.ucalgary.ca/~aycock/spark/
+
+Biopython included this copy of SPARK purely for parsing GenBank/EMBL feature
+location strings using Bio.GenBank.LocationParser, and that code has now been
+replaced with something simpler and faster using regular expressions.
+"""
+# Don't issue a deprecation warning here, but via Bio.Parsers instead
+# This avoids the user seeing multiple deprecation warnings.
+
__version__ = 'SPARK-0.6.1'
import re
View
@@ -16,6 +16,18 @@ support for Python 2.4. This can be delayed given feedback from our users
(e.g. if this proves to be a problem in combination with other libraries).
An explicit warning was added to setup.py for Biopython 1.55.
+Bio.GenBank.LocationParser
+==========================
+This module used to be used for parsing GenBank and EMBL feature locations.
+It has been replaced with faster code using regular expressions, and is no
+longer needed. Declated obsolete in Release 1.55.
+
+Bio.Parsers and Bio.Parsers.spark
+=================================
+This module was a copy of John Aycock's SPARK parser included with Biopython
+soley for use in Bio.GenBank.LocationParser. Declated obsolete in Release
+1.55.
+
Bio.Restriction.DNAUtils and check_bases
========================================
This module (originally in C) offered complement and antiparallel functions

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