[med-svn] [Git][med-team/biojava-live][master] 26 commits: New upstream version 1.9.5

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / biojava-live


Commits:
d7e7285e by Pierre Gruet at 2022-02-26T15:24:19+01:00
New upstream version 1.9.5
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23b0edf6 by Pierre Gruet at 2022-02-26T15:24:47+01:00
Update upstream source from tag 'upstream/1.9.5'

Update to upstream version '1.9.5'
with Debian dir 0a2a07a1b7b6fc5e43b167a5cf0bbeddcf25f546
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fb2983aa by Pierre Gruet at 2022-02-26T20:53:26+01:00
Removing obsolete get-orig-source target in d/rules

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890e1a91 by Pierre Gruet at 2022-02-27T11:30:48+01:00
The previously referenced doc files have been suppressed

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26d52d7d by Pierre Gruet at 2022-02-27T14:50:09+01:00
Refreshing d/copyright

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efad86b3 by Pierre Gruet at 2022-02-27T15:30:21+01:00
Now upstream uses Maven

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af8654b3 by Pierre Gruet at 2022-02-27T15:30:46+01:00
Providing Bug and Repository fields in d/u/metadata

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cb77b114 by Pierre Gruet at 2022-02-27T15:31:28+01:00
Stripping d/rules of obsolete contents now that we use Maven

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5a083b8f by Pierre Gruet at 2022-02-27T15:32:00+01:00
Refreshing the list of (build-)dependencies and setting it up for Maven

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5d250218 by Pierre Gruet at 2022-02-27T15:32:25+01:00
Installing the javadoc built by Maven and altering paths accordingly

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03097eb0 by Pierre Gruet at 2022-02-27T15:37:21+01:00
Now the docs are installed under apidocs/ instead of api/

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c0bc02c1 by Pierre Gruet at 2022-02-27T15:37:47+01:00
Removing obsolete d/*.dirs files

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cc937561 by Pierre Gruet at 2022-02-27T15:39:01+01:00
Removing urchinTracker() in the javadoc to enhance privacy

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697165cb by Pierre Gruet at 2022-02-27T15:39:34+01:00
Setting myself as uploader

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ce462434 by Pierre Gruet at 2022-02-27T15:52:17+01:00
Raising Standards version to 4.6.0 (no change)

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3527f6db by Pierre Gruet at 2022-02-27T20:42:33+01:00
Stop shipping the -demos package, as demos are no more provided by upstream

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b8642877 by Pierre Gruet at 2022-02-27T20:43:53+01:00
html-browser does not exist anymore

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e5322419 by Pierre Gruet at 2022-02-28T18:07:04+01:00
Filling in the classpath for the built jars

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6e41d0f4 by Pierre Gruet at 2022-02-28T18:07:17+01:00
Excluding tests with problematic data

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2ecd4588 by Pierre Gruet at 2022-02-28T18:08:26+01:00
Updating changelog

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efb8c4bf by Pierre Gruet at 2022-02-28T20:51:54+01:00
Using '1.x' instead of 'debian' for the installation of Maven artifacts

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02814fb4 by Pierre Gruet at 2022-03-28T20:45:58+02:00
Now building the package libbiojava1.9-java instead of libbiojava1.7-java

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4be4d06a by Pierre Gruet at 2022-03-28T21:12:10+02:00
Expliciting that libbiojava-java is a dependency package

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0769f89c by Pierre Gruet at 2022-03-28T21:13:26+02:00
Use secure URI in Homepage field.

Changes-By: lintian-brush
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html

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5ae85cdc by Pierre Gruet at 2022-03-28T21:18:12+02:00
Marking the doc package as Multi-Arch: foreign

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7220fa8d by Pierre Gruet at 2022-03-28T23:07:05+02:00
Upload to NEW, targetting experimental

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21 changed files:

- .cvsignore → .gitignore
- + .travis.yml
- + KEYS
- − LICENSE
- − LICENSE.COMMONS
- − README
- − README.biosql
- + README.md
- + alignment/pom.xml
- src/org/biojava/bio/alignment/ARAlignment.java → alignment/src/main/java/org/biojava/bio/alignment/ARAlignment.java
- + alignment/src/main/java/org/biojava/bio/alignment/AbstractULAlignment.java
- + alignment/src/main/java/org/biojava/bio/alignment/AlignmentAlgorithm.java
- src/org/biojava/bio/alignment/AlignmentElement.java → alignment/src/main/java/org/biojava/bio/alignment/AlignmentElement.java
- + alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java
- src/org/biojava/bio/alignment/EditableAlignment.java → alignment/src/main/java/org/biojava/bio/alignment/EditableAlignment.java
- + alignment/src/main/java/org/biojava/bio/alignment/FlexibleAlignment.java
- src/org/biojava/bio/alignment/IllegalAlignmentEditException.java → alignment/src/main/java/org/biojava/bio/alignment/IllegalAlignmentEditException.java
- + alignment/src/main/java/org/biojava/bio/alignment/NeedlemanWunsch.java
- src/org/biojava/bio/alignment/QualitativeAlignment.java → alignment/src/main/java/org/biojava/bio/alignment/QualitativeAlignment.java
- src/org/biojava/bio/alignment/SimpleAlignmentElement.java → alignment/src/main/java/org/biojava/bio/alignment/SimpleAlignmentElement.java
- src/org/biojava/bio/alignment/SmithWaterman.java → alignment/src/main/java/org/biojava/bio/alignment/SmithWaterman.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/biojava-live/-/compare/66c526c486e72f8585f8636ccd074fa5c40689ee...7220fa8d880077d24388e3beb8012daccda37c9f

-- 
View it on GitLab: https://salsa.debian.org/med-team/biojava-live/-/compare/66c526c486e72f8585f8636ccd074fa5c40689ee...7220fa8d880077d24388e3beb8012daccda37c9f
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