Add p5-Text-Diff as test dependency.
1.7.2 - "Entebbe"
[Bugs]
* #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
* #245 - Code coverage fixes [zmughal,cjfields]
* #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
* #238 - Use a Travis cron job for network tests [zmughal,cjfields]
* #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
* #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
* #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
* #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
* #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
* #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
* #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
* #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
[Code changes]
* PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
Upstream changes:
1.7.1 - "Election"
[Bugs]
* Minor release to incorporate fix for CPAN indexing, which
prevented proper updates [cjfields]
* Fix problem in managing Target attribute for gff3 [Jukes34]
* Minor bug fixes related to NCBI HTTPS support [cjfields]
1.7.0 - "Disney"
[New site]
* We have migrated to Github Pages. This was actually planned, but the
recent OBF server compromise forced our hand.
Brian Osborne [bosborne] took this under his wing to move docs and has
done a tremendous amount of work formatting the site and working out some
of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul
Cantalupo and Franscison Ossandon also helped. Kudos!!
* Similarly, the official issue tracker is now Github Issues. This has
been updated in the relevant documentation bits (we hope!)
[Code changes]
* Previously deprecated modules removed
* Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
* Bio::DB::SeqHound has been removed due to the service no longer being
available
* Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
reasons due to the server no longer having a valid cert
* Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
* Bio::Coordinate, Bio::SearchIO::blastxml,
Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
added on CPAN
[New features]
* Docker instances of tagged releases are available! [hlapp]
* NCBI HTTPS support [mjohnson and others]
* Bio::SearchIO::infernal
- Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
* Bio::Search::HSP::ModelHSP
- Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
reports [pcantalupo]
* Bio::Search::Result::INFERNALResult
- Added new module to represent features of Infernal reports [pcantalupo]
* Bio::DB::Taxonomy SQLite option [cjfields]
* WrapperBase quoted option values [majensen]
* Various documentation fixes and updates [bosborne]
[Bug Fixes]
* Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
* Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
* NeXML parser fixes [fjossandon]
* Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
* RT 103272 : SeqFeature database deletion skipped features with a decimal -
Joshua Fortriede (Xenbase)
* RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
* Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
* Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
* Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
* Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
* Issue #84: EMBL format wrapping problem [nyamned]
* Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
* Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
or compiled C code (when Inline::C is installed) [rocky]
* Fix various Bio::Tools::Analysis remote server config problems [cjfields]
* Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
* Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
* For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
to be consistent with "$hit->bits" behaviour [fjossandon]
* Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
aminoacids made "next_seq" confused and broke the parser [fjossandon]
* Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
to "complement(join(A..B,C..D))" [fjossandon]
* For the many many many fixes that weren't mentioned - blame the release guy!
Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden). Existing SHA1
digests retained for now as an audit trail.
{perl>=5.16.6,p5-ExtUtils-ParseXS>=3.15}:../../devel/p5-ExtUtils-ParseXS
since pkgsrc enforces the newest perl version anyway, so they
should always pick perl, but sometimes (pkg_add) don't due to the
design of the {,} syntax.
No effective change for the above reason.
Ok joerg
Upstream changes:
1.6.924
[Significant changes]
* Bug/feature issue tracking has moved to GitHub Issues:
https://github.com/bioperl/bioperl-live/issues
* DB_File has been demoted from "required" to "recommended",
which should make easier for Windows users to install BioPerl
if they don't need that module.
[New features]
* Bio::Search::HSP::GenericHSP
- Bug #3370, added a "posterior_string" method to retrieve the
posterior probability lines (PP) from HMMER3 reports [fjossandon]
- Added a "consensus_string" method to retrieve the consensus
structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
* Bio::SearchIO::hmmer2
- The number of identical and conserved residues are now calculated
directly from the homology line [fjossandon]
- Now the Query Length and Hit Length are reported when the alignment
runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
- Implemented the capture of the consensus structure lines [fjossandon]
* Bio::SearchIO::hmmer3
- The number of identical and conserved residues are now calculated
directly from the homology line [fjossandon]
- Now the Hit Length is reported when the alignment runs until the end
of the sequence/model ('.]' or '[]') [fjossandon]
- Implemented the capture of the consensus structure lines [fjossandon]
- Implemented the capture of the posterior probability lines [fjossandon]
- Completed the development of NHMMER parsing, including alignments [fjossandon]
* Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
- Feature #2615, moved "_init_parse_params", "max_significance, "signif",
"min_score", "min_bits, and "hit_filter" methods from
'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
This means that the Bio::SearchIO->new() parameters '-signif', '-score',
'-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
besides Blast, instead of being ignored. Added tests for all moved methods
using HMMER outputs and run the full test suite and everything pass [fjossandon]
* Bio::SeqIO::MultiFile
- Autodetection of file format [fangly]
* Bio::Tools::GuessSeqFormat:
- Format detection from non-seekable filehandles such as STDIN [fangly]
[Bug fixes]
* Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
* Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
* SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
* Abstract: Fixed ActivePerl incapability of removing temporary files
because of problems closing tied filehandles [fjossandon]
* IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
because ActivePerl were producing a ".index.pag" and ".index.dir"
files instead of a single ".index" file (like Strawberry Perl).
Now those temporary files are correctly considered and deleted. [fjossandon]
* Test files: Added missing module requirements (DB_File and Data::Stag)
to several tests files that were failing because those modules were
not present. Now those test files are correctly skipped instead. [fjossandon]
* Blast: Added support to changes in bl2seq from BLAST+ output, which
now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
* Phylip: Return undef in "next_aln" at file end to avoid
an infinite loop [yschensandiego]
* HMMER3: When a hit description is too long, it is truncated in
the Scores table. In those cases, the more complete description from
the Annotation line (>>) will be used [fjossandon]
* GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
since it is now used by HMMER3 format in alignments [fjossandon]
* GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
to return undef if the query/hit length is unknown (like in some
HMMER outputs), to avoid division by 0 crashes. Also "query_length"
now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
* HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
added support to multi-query reports, reduced code redundancy,
and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
* [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
* [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
* [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
* Fixed some Bio::Root::Utilities subroutines [fjossandon]
* Double-quotes on paths are needed in some places [fjossandon]
* [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
* Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
* Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
with the latest changes made in their own repositories [fjossandon]
* General synching of files with the master branch [fjossandon]
* Fixed tests failing in Windows because of using Linux commands [fjossandon]
* Closed many open filehandles that prevented temporary files deletion [fjossandon]
* Fixed broken MeSH parser [fjossandon]
* Fixed missing detection of format in SeqIO when given a -string [fangly]
Do it for all packages that
* mention perl, or
* have a directory name starting with p5-*, or
* depend on a package starting with p5-
like last time, for 5.18, where this didn't lead to complaints.
Let me know if you have any this time.
a) refer 'perl' in their Makefile, or
b) have a directory name of p5-*, or
c) have any dependency on any p5-* package
Like last time, where this caused no complaints.
to trigger/signal a rebuild for the transition 5.10.1 -> 5.12.1.
The list of packages is computed by finding all packages which end
up having either of PERL5_USE_PACKLIST, BUILDLINK_API_DEPENDS.perl,
or PERL5_PACKLIST defined in their make setup (tested via
"make show-vars VARNAMES=..."), minus the packages updated after
the perl package update.
sno@ was right after all, obache@ kindly asked and he@ led the
way. Thanks!
to trigger/signal a rebuild for the transition 5.8.8 -> 5.10.0.
The list of packages is computed by finding all packages which end
up having either of PERL5_USE_PACKLIST, BUILDLINK_API_DEPENDS.perl,
or PERL5_PACKLIST defined in their make setup (tested via
"make show-vars VARNAMES=...").
developer is officially maintaining the package.
The rationale for changing this from "tech-pkg" to "pkgsrc-users" is
that it implies that any user can try to maintain the package (by
submitting patches to the mailing list). Since the folks most likely
to care about the package are the folks that want to use it or are
already using it, this would leverage the energy of users who aren't
developers.
Revision history for Bioperl core modules
0.7 Large number of changes, including refactoring of the
Object system, new parsers, new functionality and
all round better system. Highlights are:
o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
Bio::Root::IO for I/O and file/handle capabilities.
o Imported BPlite modules from Ian Korf for BLAST
parsing. This is considered the supported BLAST parser;
Bio::Tools::Blast.pm will eventually phase out due to lack of support.
o Improved Sequence Feature model. Added complete location
modelling (with fuzzy and compound locations). See
Bio::LocationI and the modules under Bio/Location. Added
support in Genbank/EMBL format parsing to completely parse
feature tables for complex locations.
o Moved special support for databanks etc to specialized modules under
Bio/Seq/. One of these supports very large sequences through
a temporary file as a backend.
o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
CDS retrieval and exon shuffling.
o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
DB/GDB (the latter has platform-specific limitations).
o New analysis parser framework for HT sequence annotation (see
Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
o New Alignment IO framework
o New Index modules (Swissprot)
o New modules for running Blast within perl
(Bio::Tools::Run::StandAloneBlast). Added modules for running
Multiple Sequence Alignment tools ClustalW and TCoffee
(Bio::Tools::Run::Alignment).
o New Cookbook-style tutorial (see bptutorial.pl). Improved
documentation across the package.
o Much improved cross platform support. Many known incompatibilities
have been fixed; however, NT and Mac do not work across the entire
setup (see PLATFORMS).
o Many bug fixes, code restructuring, etc. Overall stability and
maintainability benefit a lot.
o A total of 957 automatic tests
0.6.2
There are very few functionality changes but a large
number of software improvements/bug fixes across the package.
o The EMBL/GenBank parsing are improved.
o The Swissprot reading is improved. Swissprot writing
is disabled as it doesn't work at all. This needs to
wait for 0.7 release
o BLAST reports with no hits are correctly parsed.
o Several other bugs of the BLAST parser (regular expressions, ...)
fixed.
o Old syntax calls have been replaced with more modern syntax
o Modules that did not work at all, in particular the Sim4
set have been removed
o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
have improved compliance with interface specs and documentation
o Mailing list documentation updated throughout the distribution
o Most minor bug fixes have happened.
o The scripts in /examples now work and have the modern syntax
rather than the deprecated syntax
0.6.1 Sun April 2 2000
o Sequences can have Sequence Features attached to them
- The sequence features can be read from or written to
EMBL and GenBank style flat files
o Objects for Annotation, including References (but not
full medline abstracts), Database links and Comments are
provided
o A Species object to represent nodes on a taxonomy tree
is provided
o The ability to parse HMMER and Sim4 output has been added
o The Blast parsing has been improved, with better PSI-BLAST
support and better overall behaviour.
o Flat file indexed databases provide both random access
and sequential access to their component sequences.
o A CodonTable object has been written with all known
CodonTables accessible.
o A number of new lightweight analysis tools have been
added, such as molecular weight determination.
The 0.6 release also has improved software engineering
o The sequence objects have been rewritten, providing more
maintainable and easier to implement objects. These
objects are backwardly compatible with the 0.05.1 objects
o Many objects are defined in terms of interfaces and then
a Perl implementation has been provided. The interfaces
are found in the 'I' files (module names ending in 'I').
This means that it is possible to wrap C/CORBA/SQL access
as true "bioperl" objects, compatible with the rest of
bioperl.
o The SeqIO system has been overhauled to provide better
processing and perl-like automatic interpretation of <>
over arguments.
o Many more tests have been added (a total of 172 automatic
tests are now run before release).
0.05.1 Tue Jun 29 05:30:44 1999
- Central distribution now requires Perl 5.004. This was
done to get around 5.003-based problems in Bio/Index/*
and SimpleAlign.
- Various bug fixes in the Bio::Tools::Blast modules
including better exception handling and PSI-Blast
support. See Bio/Tools/Blast/CHANGES for more.
- Fixed the Parse mechanism in Seq.pm to use readseq.
Follow the instructions in README for how to install
it (basically, you have to edit Parse.pm).
- Improved documentation of Seq.pm, indicating where
objects are returned and where strings are returned.
- Fixed uninitialized warnings in Bio::Root::Object.pm
and Bio::Tools::SeqPattern.pm.
- Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
0.05 Sun Apr 25 01:14:11 1999
- Bio::Tools::Blast modules have less memory problems
and faster parsing. Webblast uses LWP and supports
more functionality. See Bio/Tools/Blast/CHANGES for more.
- The Bio::SeqIO system has been started, moving the
sequence reformatting code out of the sequence object
- The Bio::Index:: system has been started, providing
generic index capabilities and specifically works for
Fasta formatted databases and EMBL .dat formatted
databases
- The Bio::DB:: system started, providing access to
databases, both via flat file + index (see above) and
via http to NCBI
- The scripts/ directory, where industrial strength scripts
are put has been started.
- Many changes - a better distribution all round.
ones to do, and each compiled and installed/de-installed apparently
correctly.
As a side effect of the dynamic PLIST, we no longer need to have separate
-static and -shared PLISTs. It's now easier than ever to make a perl5
package for NetBSD :)
