Deprecating Bio.GenBank.LocationParser, Bio.Parsers and Bio.Parsers.s…

…park

Bio/GenBank/LocationParser.py

@@ -3,7 +3,7 @@
 # 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.
-"""Code used for parsing GenBank/EMBL feature location strings (OBSOLETE)."""
+"""Code used for parsing GenBank/EMBL feature location strings (DEPRECATED)."""
 # Don't issue a deprecation warning here, but via Bio.Parsers instead
 # This avoids the user seeing multiple deprecation warnings.
 

Bio/Parsers/__init__.py

@@ -1,10 +1,10 @@
-"""Third party and other parsers useful internally to Biopython (OBSOLETE).
+"""Third party and other parsers useful internally to Biopython (DEPRECATED).
 """
-#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)
+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)

Bio/Parsers/spark.py

@@ -19,9 +19,9 @@
 #  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).
+"""Copy of John Aycock's SPARK parser included with Biopython (DEPRECATED).
 
-To clarify, when we say obsolete we just mean to warn you that Biopython will
+To clarify, when we say deprecated 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/

DEPRECATED

@@ -33,13 +33,13 @@ 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. Declared obsolete in Release 1.55.
+longer needed. Declared obsolete in Release 1.55, deprecated in Release 1.56.
 
 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. Declared obsolete in Release
-1.55.
+1.55, deprecated in Release 1.56.
 
 Bio.Restriction.DNAUtils and check_bases
 ========================================