davebridges (Dave Bridges)

Added code to output two values, depending on whether disulfide bonds are present. Also added more details to the docstring

Routes added under resource collection should be prefixed with

Fixed named prefix scope in resource member and collection actions

Ignore name_prefix unless there is an explicit name

Move base mapper methods into Base module so plugins can easily

Move name_prefix merging into Scoping concern

Cleanup resource scoping by passing down the parent resource object

named_prefix doesn't join with "_"

Allow name_prefix to be pass into scope

Allow scope to take :path and :controller options

Pass symbol in as route name when match is used with a symbol

Responder redirects to resource if destroy fails.

Make controller.flash public to be used in responders.

Deprecate recalling generation params when the defaults are nil

Ruby 1.9.2: explicitly raise NoMethodError for explicit coercion attempts

Ruby 1.9.2: explicitly raise NoMethodError for explicit coercion attempts. Calling super gives us NameErrors.

Remove assert_raises usage that only test-unit 1 supports. Breaks minitest and test-unit 2.

Update rackmount to fix some pending tests

Replace reset_counter_cache with reset_counters that has API inline with existing update_counters method

Add support for Mysql column positioning via #add_column and #change_column

Add new html5 input types to list of serializable types. Older browers handle these as type="text" so they should be consistently serialized on both old and new browsers. Fixes #5667.

Removed 'abbr' from self-closing tags list. Fixes #5167.

Default callbackContext to the $.extended ajax options for 1.3.2 compatibility, per #5654.

Reorganized param code slightly to once again define buildParams as a named function expression, as moving it outside the param closure would necessitate moving and rewriting the add function as well.

Further modified jQuery 1.4 .param() method to serialize arrays containing non-scalar values. PHP and jQuery BBQ can both deserialize these structures, while rack (as of 1.0.0) cannot.

added a couple missing semicolons and fixed a typo in the comments

Follow-up to 100ed686426b8b404b094b8c8086aefce715f91a, forgot to remove one of the tests.

Revert the changes from 65ebf57c1e5d7fa96536b66d4fcacbafad8dc1e5, they were ineffectual against IE's insanity: https://ejohn.org/files/bugs/fragment/ Used a different tactic instead (just don't return a fragment from .parent()). Fixes #5638.

Reworked some more of the selector tests as well to clean up after themselves.

Added some more tests around the name tests to catch possible regressions.

Make sure that the node exists before attempting to clone.

Stick with just getter/setters in attrFn.

Moved readyList check.

Make sure that some height/width is set for the nothiddendiv before checking.

Reverted accidental commit in 5197ac9fc8aa71c2ebc0d7217f41a3679eb1b902.

Retooled the arguments.callee-related changes in 98ce35d52b17a033822f31d8a36232222d0d365e to avoid re-declarations where possible.

No need to use jQuery's event system for binding the onunload event in IE.

Enforce that hasClass and removeClass work even with tabs and endlines in class attributes. Fixes #5505.

Disable getting values using the .attr() function shortcut until the full implications of which can be explored.

See bug #2697 on BugZilla. Allow non-integer targets, and use default values for arguments instead of module-level default values

Mention FASTQ paper, and fixed a typo

Minor docstring improvements to BioSQL/DBUtils.py

Merge branch 'master' of git@github.com:biopython/biopython

Mention FASTQ paper, and fixed a typo

See bug #2697 on BugZilla. Allow non-integer targets, and use default values for arguments instead of module-level default values

Minor docstring improvements to BioSQL/DBUtils.py

Renaming new PDB unit test (see Bug 2820)

Removing old print-and-compare PDB test (see Bug 2820)

Mention PDBList work in NEWS file

Minor correction to reference to Bio.Emboss module

Quick example using the BLAST+ wrappers

Bumping version number ready for release this afternoon

simplifying and updating MEME parser

Better solution to cross platform variations in test_ProtParam.py output

Testing BLAST+ detection on Windows works

Better BLAST+ detection for unit test

SQLite support news

Add message about in-memory SQLite not working

Merge branch 'biosql-sqlite' of git@github.com:chapmanb/biopython

Simplifying the MAST parser

Separating the MEME and MAST parsers into separate modules

Enable SQLite test for BioSQL by default, so it will run if sqlite3 is installed.

SQLite support for BioSQL database. See discussion on Bug 2866 for additional details

Added RedditGifts to "Who Uses".

Added Winding Road to "Who Uses".

Added ryszard's full name to AUTHORS.

Added initialization bits to part of the Solr test suite. Thanks to notanumber for pointing this out.

Make sure that animated show resets the display correctly. Fixes #5130.

Fix inverted 'orig' and 'fix' event in mouseenter/mouseleave special events.

added semicolons to end of 2 statements (and fixed a misspelled word in comment)

Adding in an extra check, per the comments in 25b0ba9f9612583033b902a0e40345463a3a71d0.

Make sure that the previous element is removed from the page before the next is inserted, in replaceWith. Using a variation of the patch by snaury. Fixes #2697.

Made sure that css() in IE handles negative non-px values correctly. Fixes #3331.

Minor syntactical changes to :visible and :hidden.

Made sure that a null speed doesn't get passed around. Patch from daltonlp. Fixes #5557.

Make sure that width or height don't animate to a negative value. Fixes #3881.

Retooled the native triggering code, simplifying it.

Allow the user to explicitly set a content-type header even when there's no data being sent to the server. Fixes #1900.

Fixes a bug I introduced

Added a test for bug 1095 for animations (animations don't clear check boxes)

Updating the source version to 1.4a2pre.

Tagging the 1.4a1 release.

Switched to using slice instead of join to get the correct results.

Landing Ben Alman's patch to add nextUntil, prevUntil, and parentsUntil. Also adds some tests for prevAll and nextAll, and fixes an test edge case in parents.

Added in the .delay() method for delaying the execution of queued functions and animations.

Adding in support for bubbling submit and change events, thanks to the patch by Justin Meyer. Includes a delegation test suite for manually testing to see if the events work as intended.

Make skipping test_prosite_patterns.py on Jython conditional on buffer being missing (in case they fix it)

Meant to delete test_prosite.py as part of splitting it into test_prosite1.py and test_prosite2.py

Ugly workaround in Bio.SubsMat.MatrixInfo to run on Jython within JVM limits (based on a change by Kyle Ellrott on github)

Breaking up test_prosite.py to get it to run on Jython 2.5.1 with its JVM size limits

Skip test_prosite_patterns.py on Jython which lacks the buffer function, see https://bugs.jython.org/issue1521

Move (deprecated) Bio.Prosite.Patten tests into a separate unit test

Adding a five pairwise alignments EMBOSS matcher file to the AlignIO unit tests

Adding an EMBOSS matcher output file to the AlignIO unit tests

Don't ask EMBOSS to turn proteins into GenBank format, as it (now) maps X to N since EMBOSS considers GenBank to be for nucleotides only (with a separate format for GenPept)

Fixed some MUSCLE unit test deadlocks on Windows, and avoid the PHYLIP interlaced output since MUSCLE 3.6 (latest compiled version on Windows) seems to have a bug where this gives sequential PHYLIP outout, which Bio.AlignIO can't parse at the moment

Windows specific fix in BLAST unit test

Fixes an apparent deadlock on Mac OS Leopard from subprocess wait on a large file

Fix an apparent deadlock on Mac OS Leopard by using subprocess communicate instead of wait

Mention Jan 2010 NCBI DTD files for MedLine/PubMed in our NEWS file

Slightly more gracefull handling of missing fonts in bitmap output from ReportLab

Updated EMBOSS unit test not to use the deprecated Bio.Application.generic_run function

Don't use the deprecated generic_run function in unit tests (Patch from Cymon Cox via Bug 2961)

Update MUSCLE wrapper comments now that Bio.AlignIO will accept CLUSTALW format with a MUSCLE header, and include more undocumented output switches (using patch from Cymon Cox on Bug 2961)

Updating codon tables to NCBI version 3.9 (Bug 2962)

added some doc strings to sphinx documentation. is still not displayed correctly

added custom_filters module docstring to documentation

added on sphinx documentation. modified installation documents, and added docstring/doctest to custom_filters.py

Should be rackmount 0.2

Depend on rack-mount 0.0.2

Extended and case insensitive regexp routes aren't that important.

Update routing for rackmount 0.2 api changes

Revert "Final steps toward clean rails "foo"; cd foo; gem bundle; script/server working"

Add basic nested named route support to new routing dsl. Also add a

Fix test bleed

Final steps toward clean rails "foo"; cd foo; gem bundle; script/server working

Check whether another lib has implemented ruby 1.9 string interp syntax

Extract form_authenticity_param instance method so it's overridable in subclasses

Insert generated association members in the same order they are specified when assigning to a has_many :through using the generated *_ids method

Revert "Ensure Model#destroy respects optimistic locking"

Merge remote branch 'Fingertips/master'

Make script/server work with correct application.rb

Require action_dispatch, not action_controller

Temporarily add submodules to the Rails repo for Arel and Rack::Mount. These submodules will be removed once we add proper Gemfile following to bundler

Allow explicit placement of hidden id element for nested models.

Ruby 1.9: skip pg locking test for 1.9.1 also

Add TimeZone dependency

Added an advanced setting for disabling Haystack's initialization in the event of a conflict with other apps.

Altered ``SearchForm`` to use ``.is_valid()`` instead of ``.clean()``, which is a more idiomatic/correct usage. Thanks to askfor for the suggestion.

Added MANIFEST to ignore list.

Fixed Django 1.0 compatibility when using the Solr backend.

Marked Haystack as 1.0 final.

Incorrect test result from changing the documented way the ``highlight`` template tag gets called.

Updated the Rakefile to use the correct init code.

Shortened the build messages in the Makefile and added test/qunit and src/sizzle to the cleanup.

Don't try to run the clone code if the directory already exists.

Switched from using Git Submodules to just doing a straight clone of the QUnit and Sizzle directories. Works much better for what we want.

Bringing Sizzle and QUnit up to date.

Don't do the update after the pull - forces the submodules up to date.

Use .add() to merge two test groups together for .unwrap().

Changed the style attribute test to handle hex colors (as that's what Opera returns, in this case.

Made .show(null/undefined) and .hide(null/undefined) work the same as .show() and .hide().

Fixed a problem with animations with a duration of 0 not working properly for hide and show.

Simplified a selector in the .live() tests.

Tweaked the live test to be a bit simpler.

Fixed wrap test that was looking for comment values from .text().

Merge branch 'master' of github.com:jquery/jquery

Fixed bug with singleTag matching in core.js.

Fixes $.trim for   closes #4980

Ignore diff and patch files.

Merge branch 'master' of github.com:jquery/jquery

Adding a Rakefile to build jQuery core, for those that need it.

Record date in GenBank LOCUS line (Bug 2957)

Updated GFF doctests... may want to remove test_GFF2.py

Minor work on tutorial

Updated code blocks to installation.tex

updated installation.tex and doap.rdf to add github information

Wrote installation documentation. Updated .gitignore to skip aux, out, dvi and log files generated by latex. Both tex and pdf files will be tracked

Wrote installation documentation. Updated .gitignore to skip aux, out, dvi and log files generated by latex. Both tex and pdf files will be tracked

added missing radix parameter for parseInt()

added curly braces around all if/else statements

Force endlines to be just LF (any CRLF is auto-converted to LF by Git).

Disable the X-Requested-With header to avoid preflighting remote POST requests. Fixes #4601.

Fixed spacing on the modified Ajax code.

Fixing endlines.

Re-adding zeros removed from slice calls in last commit.

Corrected RegExp to match event namespaces. Fixes #5303.

Generic jQuery.merge and safer jQuery.makeArray(nodeList).

Added documentation about the management commands that come with Haystack.

Added docs on the template tags included with Haystack.

Added docs on highlighting.

Removed some unneeded legacy code that was causing conflicts when Haystack was used with apps that load all models (such as `django-cms2`, `localemiddleware` or `django-transmeta`).

Removed old code from the `update_index` command.

Altered spelling suggestion test to something a little more consistent.

Added tests for slicing the end of a `RelatedSearchQuerySet`.

Fixed case where `SearchQuerySet.more_like_this` would fail when using deferred Models. Thanks to Alex Gaynor for the original patch.

Added default logging bits to prevent "No handlers found" message.

BACKWARD-INCOMPATIBLE: Renamed `reindex` management command to `update_index`, renamed `clear_search_index` management command to `clear_index` and added a `rebuild_index` command to both clear & reindex.

BACKWARD-INCOMPATIBLE: `SearchIndex` no longer hooks up `post_save/post_delete` signals for the model it's registered with.

Ensured that, if a `MultiValueField` is marked as `indexed=False` in Whoosh, it ought not to post-process the field.

Ensured data going into the indexes round-trips properly. Fixed `DateField`/`DateTimeField` handling for all backends and `MultiValueField` handling in Whoosh.

Added a customizable `highlight` template tag plus an underlying `Highlighter` implementation.

Added more documentation about using custom `SearchIndex.prepare_FOO` methods.

With Whoosh 0.3.5+, the number of open files is greatly reduced.

Corrected example in docs about `RelatedSearchQuerySet`. Thanks to askfor for pointing this out.

Altered `SearchResult` objects to fail gracefully when the model/object can't be found. Thanks to akrito for the report.

Fixed a bug where `auto_query` would fail to escape strings that pulled out for exact matching. Thanks to jefftriplett for the report.

Fixing a minor typo in the tutorial

Include non-SQL requiring Bio.GFF doctests in test suite

Use Bio.Entrez in the query_pubmed.py script since Bio.PubMed is removed now

Removed unused xbb_io.py from the xbbtools script

Use the Seq object's translate method in the nextorf script

Don't use the string module in the nextorf script

Don't use deprecated Bio.Fasta module in nextorf script

Use Seq object's reverse_complement() method in nextorf script

Don't use deprecated Bio.Translate module (Bug 2954)

Fix very very out of date import statement

Don't use deprecated Bio.Translate module (Bug 2954)

Using wx instead of deprecated wxPython namespace, see https://www.wxpython.org/MigrationGuide.html for details

Don't use from XXX import *

Remove extra whitespace to try and follow PEP8 style guide

Use Bio.Seq functions instead of deprecated Bio.Translate and Bio.Transcribe modules, and don't use the string module either

Removed SeqGui back-translate (used deprecated code, and didn't seem to work anyway)

Converting tabs to spaces

Adding AlignAce tests to test_Motif.py

Corrected spelling of performanace in script name

Removing Scripts/Performance/biocorba_*.py as the python BioCorba library is obsolete (and not even in our repository history)

Removing Scripts/debug/test_db_registry.py as this is obsolete and won't have worked on any recent Biopython releases

Removing Scripts/Registry/*.py as these are obsolete and won't have worked on any recent Biopython releases

Minor docstring formatting, removed some commented out code

Making Seq.data read only

Belatedly updating BioSQL test after recently moved some FASTA example files

Belatedly updating BioSQL test after recently moved some FASTA example files

Even more Seq object translation unit tests

Even more Seq object unit tests

More Seq object unit tests

Adding 1 Jan 2010 MedLine and PubMed DTD files, announced by the NCBI in Nov 2009, expected to come into use in Dec 2009

DTD files don't need to be marked as executable

Mention deprecation of Bio.utils.ungap and fixing some long lines in the DEPRECATED file (aiming for max 78 chars)

removed the deprecated functions translate, translate_to_stop, back_translate, transcribe, and back_transcribe from Bio.utils

Removed the dprecated function translate from Bio.SeqUtils

Removing the deprecated module Bio.SCOP.FileIndex

Removing the deprecated function pairlist_to_dict from Bio.InterPro

Tiding up some warnings, and deprecating Bio.utils.ungap() function

Adding Seq object ungap method developed on one of my git branches plus explicit UnknownSeq support (see mailing list)

State the the legacy BLAST wrappers in Bio.Blast.Applications are obsolete

Removing deprecated module Bio.PubMed (use Bio.Entrez instead)

Deprecating the obsolete module Bio.listfns(most of this is covered by Python itself nowadays)

Remove Bio.pairwise2.py dependency on obsolete Bio.listfns (which used a naive Python implementation anyway, not C code)

More doctests in Bio/Seq.py

Include new Bio.SeqFeature doctests in test suite

Basic doctests for Bio.SeqFeature, and checking strand and location arguments

Adding a few PMC associated DTD files, https://www.ncbi.nlm.nih.gov/pmc/pmcdoc/dtd/pmc-1.dtd and https://www.pubmedcentral.nih.gov/pmcdoc/dtd/nlm_lib/articleset/nlm-articleset-2.0.dtd