[Biojava-dev] biojava-legacy 1.8.2 release plan

[Michael Heuer]

All,

I propose then to create a biojava-legacy 1.8.2 release shortly; the
changes since 1.8.1 will include commits

Adjustment to Entrez update to EFetch 2.0
Bug fix for one-ambiguous-symbol motif
Added new constructor for RestrictionMapper using
java.util.concurrent.ExecutorService
specifying all Date formats to either Locale.US or Locale.ENGLISH, to
avoid Arabic months names induced problems
Some fixes for Division in EMBL and GenBank formats
add some generics to biojavax
Added generic for biojavax Note
More fix with circularity
Added circularity for locations
Section parser now accepts tags not followed by white space.
Fix ordering of sublocations on complementary strand

and this diff to AbstractFastqParser.java

@@ -70,6 +70,7 @@
     /**
      * Validate the specified description.
      *
+     * @deprecated to be removed in version 1.9
      * @param builder FASTQ formatted sequence builder, will not be null
      * @param description description to validate, will not be null
      * @param lineNumber current line number in input stream
@@ -81,6 +82,7 @@
     /**
      * Validate the specified sequence.
      *
+     * @deprecated to be removed in version 1.9
      * @param builder FASTQ formatted sequence builder, will not be null
      * @param sequence sequence to validate, will not be null
      * @param lineNumber current line number in input stream
@@ -92,6 +94,7 @@
     /**
      * Validate the specified repeat description.
      *
+     * @deprecated to be removed in version 1.9
      * @param builder FASTQ formatted sequence builder, will not be null
      * @param repeatDescription repeat description to validate, will
not be null
      * @param lineNumber current line number in input stream
@@ -103,6 +106,7 @@
     /**
      * Validate the specified quality scores.
      *
+     * @deprecated to be removed in version 1.9
      * @param builder FASTQ formatted sequence builder, will not be null
      * @param quality quality scores to validate, will not be null
      * @param lineNumber current line number in input stream


After the 1.8.2 release, I will commit the remainder of my fastq
changes in preparation for a version 1.9 release.  Alternatively, if
there is no concern about the binary incompatibilities described
below, I could skip the mark as @deprecated in 1.8.2 step and commit
my changes before a 1.8.2 release.


I assume the documentation on cutting a release at

http://biojava.org/wiki/BioJava:Make_release

is still relevant?

   michael


> On Tue, Mar 6, 2012 at 6:18 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> both 1.8.1. and 1.9 are good names IMHO... Did you do the changes also
>> in the 3.X copy of this?
>>
>> Andreas
>>
>> On Tue, Mar 6, 2012 at 2:44 PM, Michael Heuer <heuermh at gmail.com> wrote:
>>> Hello,
>>>
>>> I was wondering what the policy is with regards to binary
>>> compatibility between releases.  I have some changes to FASTQ support
>>> in mind which result in the following binary incompatible changes.
>>>
>>> Is it ok to make such changes?  I would argue that it is:
>>> FastqVariant is final and an enum, so it should not possible for
>>> client code to be effected.  Likewise, IlluminaFastqReader,
>>> SangerFastqReader, SolexaFastqReader are all final classes.
>>>
>>> If ok, should the next version of biojava-legacy be 1.8.2, 1.9 or 2.0?
>>>  I would prefer marking the validateXxx methods as @deprecated in
>>> 1.8.2 and then releasing 1.9 with the new changes.
>>>
>>>   michael
>>>
>>>
>>> The results of clirr between my working directory and version 1.8.1 are
>>>
>>> Error   Added abstract modifier to
>>> class   org.biojava.bio.program.fastq.FastqVariant
>>> Error   Abstract method 'public double errorProbability(int)' has been
>>> added   org.biojava.bio.program.fastq.FastqVariant      public double
>>> errorProbability(int)
>>> Error   Abstract method 'public int maximumQualityScore()' has been
>>> added   org.biojava.bio.program.fastq.FastqVariant      public int
>>> maximumQualityScore()
>>> Error   Abstract method 'public int minimumQualityScore()' has been
>>> added   org.biojava.bio.program.fastq.FastqVariant      public int
>>> minimumQualityScore()
>>> Error   Abstract method 'public int qualityScore(char)' has been
>>> added   org.biojava.bio.program.fastq.FastqVariant      public int
>>> qualityScore(char)
>>> Error   Method 'protected void
>>> validateDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)' has been
>>> removed org.biojava.bio.program.fastq.IlluminaFastqReader       protected
>>> void validateDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)
>>> Error   Method 'protected void
>>> validateQuality(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)' has been
>>> removed org.biojava.bio.program.fastq.IlluminaFastqReader       protected
>>> void validateQuality(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)
>>> Error   Method 'protected void
>>> validateRepeatDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)' has been
>>> removed org.biojava.bio.program.fastq.IlluminaFastqReader       protected
>>> void validateRepeatDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)
>>> Error   Method 'protected void
>>> validateSequence(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)' has been
>>> removed org.biojava.bio.program.fastq.IlluminaFastqReader       protected
>>> void validateSequence(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)
>>> Error   Method 'protected void
>>> validateDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)' has been
>>> removed org.biojava.bio.program.fastq.SangerFastqReader protected void
>>> validateDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)
>>> Error   Method 'protected void
>>> validateQuality(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)' has been
>>> removed org.biojava.bio.program.fastq.SangerFastqReader protected void
>>> validateQuality(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)
>>> Error   Method 'protected void
>>> validateRepeatDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)' has been
>>> removed org.biojava.bio.program.fastq.SangerFastqReader protected void
>>> validateRepeatDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)
>>> Error   Method 'protected void
>>> validateSequence(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)' has been
>>> removed org.biojava.bio.program.fastq.SangerFastqReader protected void
>>> validateSequence(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)
>>> Error   Method 'protected void
>>> validateDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)' has been
>>> removed org.biojava.bio.program.fastq.SolexaFastqReader protected void
>>> validateDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)
>>> Error   Method 'protected void
>>> validateQuality(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)' has been
>>> removed org.biojava.bio.program.fastq.SolexaFastqReader protected void
>>> validateQuality(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)
>>> Error   Method 'protected void
>>> validateRepeatDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)' has been
>>> removed org.biojava.bio.program.fastq.SolexaFastqReader protected void
>>> validateRepeatDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)
>>> Error   Method 'protected void
>>> validateSequence(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)' has been
>>> removed org.biojava.bio.program.fastq.SolexaFastqReader protected void
>>> validateSequence(org.biojava.bio.program.fastq.FastqBuilder,
>>> java.lang.String, int)
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev