Scheduled weekly dependency update for week 40 #4

pyup-bot · 2018-10-08T16:47:22Z

Update click from 6.7 to 7.0.

Changelog

7.0

-----------

Released 2018-09-25

-   Drop support for Python 2.6 and 3.3. (`967`_, `976`_)
-   Wrap ``click.Choice``&#39;s missing message. (`202`_, `1000`_)
-   Add native ZSH autocompletion support. (`323`_, `865`_)
-   Document that ANSI color info isn&#39;t parsed from bytearrays in
 Python 2. (`334`_)
-   Document byte-stripping behavior of ``CliRunner``. (`334`_,
 `1010`_)
-   Usage errors now hint at the ``--help`` option. (`393`_, `557`_)
-   Implement streaming pager. (`409`_, `889`_)
-   Extract bar formatting to its own method. (`414`_)
-   Add ``DateTime`` type for converting input in given date time
 formats. (`423`_)
-   ``secho``&#39;s first argument can now be ``None``, like in ``echo``.
 (`424`_)
-   Fixes a ``ZeroDivisionError`` in ``ProgressBar.make_step``, when the
 arg passed to the first call of ``ProgressBar.update`` is 0.
 (`447`_, `1012`_)
-   Show progressbar only if total execution time is visible. (`487`_)
-   Added the ability to hide commands and options from help. (`500`_)
-   Document that options can be ``required=True``. (`514`_, `1022`_)
-   Non-standalone calls to ``Context.exit`` return the exit code,
 rather than calling ``sys.exit``. (`533`_, `667`_, `1098`_)
-   ``click.getchar()`` returns Unicode in Python 3 on Windows,
 consistent with other platforms. (`537`_, `821`_, `822`_,
 `1088`_, `1108`_)
-   Added ``FloatRange`` type. (`538`_, `553`_)
-   Added support for bash completion of ``type=click.Choice`` for
 ``Options`` and ``Arguments``. (`535`_, `681`_)
-   Only allow one positional arg for ``Argument`` parameter
 declaration. (`568`_, `574`_, `1014`_)
-   Add ``case_sensitive=False`` as an option to Choice. (`569`_)
-   ``click.getchar()`` correctly raises ``KeyboardInterrupt`` on &quot;^C&quot;
 and ``EOFError`` on &quot;^D&quot; on Linux. (`583`_, `1115`_)
-   Fix encoding issue with ``click.getchar(echo=True)`` on Linux.
 (`1115`_)
-   ``param_hint`` in errors now derived from param itself. (`598`_,
 `704`_, `709`_)
-   Add a test that ensures that when an argument is formatted into a
 usage error, its metavar is used, not its name. (`612`_)
-   Allow setting ``prog_name`` as extra in ``CliRunner.invoke``.
 (`616`_, `999`_)
-   Help text taken from docstrings truncates at the ``\f`` form feed
 character, useful for hiding Sphinx-style parameter documentation.
 (`629`_, `1091`_)
-   ``launch`` now works properly under Cygwin. (`650`_)
-   Update progress after iteration. (`651`_, `706`_)
-   ``CliRunner.invoke`` now may receive ``args`` as a string
 representing a Unix shell command. (`664`_)
-   Make ``Argument.make_metavar()`` default to type metavar. (`675`_)
-   Add documentation for ``ignore_unknown_options``. (`684`_)
-   Add bright colors support for ``click.style`` and fix the reset
 option for parameters ``fg`` and ``bg``. (`703`_, `809`_)
-   Add ``show_envvar`` for showing environment variables in help.
 (`710`_)
-   Avoid ``BrokenPipeError`` during interpreter shutdown when stdout or
 stderr is a closed pipe. (`712`_, `1106`_)
-   Document customizing option names. (`725`_, `1016`_)
-   Disable ``sys._getframes()`` on Python interpreters that don&#39;t
 support it. (`728`_)
-   Fix bug in test runner when calling ``sys.exit`` with ``None``.
 (`739`_)
-   Clarify documentation on command line options. (`741`_, `1003`_)
-   Fix crash on Windows console. (`744`_)
-   Fix bug that caused bash completion to give improper completions on
 chained commands. (`754`_, `774`_)
-   Added support for dynamic bash completion from a user-supplied
 callback. (`755`_)
-   Added support for bash completions containing spaces. (`773`_)
-   Allow autocompletion function to determine whether or not to return
 completions that start with the incomplete argument. (`790`_,
 `806`_)
-   Fix option naming routine to match documentation and be
 deterministic. (`793`_, `794`_)
-   Fix path validation bug. (`795`_, `1020`_)
-   Add test and documentation for ``Option`` naming: functionality.
 (`799`_)
-   Update doc to match arg name for ``path_type``. (`801`_)
-   Raw strings added so correct escaping occurs. (`807`_)
-   Fix 16k character limit of ``click.echo`` on Windows. (`816`_,
 `819`_)
-   Overcome 64k character limit when writing to binary stream on
 Windows 7. (`825`_, `830`_)
-   Add bool conversion for &quot;t&quot; and &quot;f&quot;. (`842`_)
-   ``NoSuchOption`` errors take ``ctx`` so that ``--help`` hint gets
 printed in error output. (`860`_)
-   Fixed the behavior of Click error messages with regards to Unicode
 on 2.x and 3.x. Message is now always Unicode and the str and
 Unicode special methods work as you expect on that platform.
 (`862`_)
-   Progress bar now uses stderr by default. (`863`_)
-   Add support for auto-completion documentation. (`866`_, `869`_)
-   Allow ``CliRunner`` to separate stdout and stderr. (`868`_)
-   Fix variable precedence. (`873`_, `874`_)
-   Fix invalid escape sequences. (`877`_)
-   Fix ``ResourceWarning`` that occurs during some tests. (`878`_)
-   When detecting a misconfigured locale, don&#39;t fail if the ``locale``
 command fails. (`880`_)
-   Add ``case_sensitive=False`` as an option to ``Choice`` types.
 (`887`_)
-   Force stdout/stderr writable. This works around issues with badly
 patched standard streams like those from Jupyter. (`918`_)
-   Fix completion of subcommand options after last argument (`919`_,
 `930`_)
-   ``_AtomicFile`` now uses the ``realpath`` of the original filename
 so that changing the working directory does not affect it.
 (`920`_)
-   Fix incorrect completions when defaults are present (`925`_,
 `930`_)
-   Add copy option attrs so that custom classes can be re-used.
 (`926`_, `994`_)
-   &quot;x&quot; and &quot;a&quot; file modes now use stdout when file is ``&quot;-&quot;``.
 (`929`_)
-   Fix missing comma in ``__all__`` list. (`935`_)
-   Clarify how parameters are named. (`949`_, `1009`_)
-   Stdout is now automatically set to non blocking. (`954`_)
-   Do not set options twice. (`962`_)
-   Move ``fcntl`` import. (`965`_)
-   Fix Google App Engine ``ImportError``. (`995`_)
-   Better handling of help text for dynamic default option values.
 (`996`_)
-   Fix ``get_winter_size()`` so it correctly returns ``(0,0)``.
 (`997`_)
-   Add test case checking for custom param type. (`1001`_)
-   Allow short width to address cmd formatting. (`1002`_)
-   Add details about Python version support. (`1004`_)
-   Added deprecation flag to commands. (`1005`_)
-   Fixed issues where ``fd`` was undefined. (`1007`_)
-   Fix formatting for short help. (`1008`_)
-   Document how ``auto_envvar_prefix`` works with command groups.
 (`1011`_)
-   Don&#39;t add newlines by default for progress bars. (`1013`_)
-   Use Python sorting order for ZSH completions. (`1047`_, `1059`_)
-   Document that parameter names are converted to lowercase by default.
 (`1055`_)
-   Subcommands that are named by the function now automatically have
 the underscore replaced with a dash. If you register a function
 named ``my_command`` it becomes ``my-command`` in the command line
 interface.
-   Hide hidden commands and options from completion. (`1058`_,
 `1061`_)
-   Fix absolute import blocking Click from being vendored into a
 project on Windows. (`1068`_, `1069`_)
-   Fix issue where a lowercase ``auto_envvar_prefix`` would not be
 converted to uppercase. (`1105`_)

.. _202: https://github.com/pallets/click/issues/202
.. _323: https://github.com/pallets/click/issues/323
.. _334: https://github.com/pallets/click/issues/334
.. _393: https://github.com/pallets/click/issues/393
.. _409: https://github.com/pallets/click/issues/409
.. _414: https://github.com/pallets/click/pull/414
.. _423: https://github.com/pallets/click/pull/423
.. _424: https://github.com/pallets/click/pull/424
.. _447: https://github.com/pallets/click/issues/447
.. _487: https://github.com/pallets/click/pull/487
.. _500: https://github.com/pallets/click/pull/500
.. _514: https://github.com/pallets/click/issues/514
.. _533: https://github.com/pallets/click/pull/533
.. _535: https://github.com/pallets/click/issues/535
.. _537: https://github.com/pallets/click/issues/537
.. _538: https://github.com/pallets/click/pull/538
.. _553: https://github.com/pallets/click/pull/553
.. _557: https://github.com/pallets/click/pull/557
.. _568: https://github.com/pallets/click/issues/568
.. _569: https://github.com/pallets/click/issues/569
.. _574: https://github.com/pallets/click/issues/574
.. _583: https://github.com/pallets/click/issues/583
.. _598: https://github.com/pallets/click/issues/598
.. _612: https://github.com/pallets/click/pull/612
.. _616: https://github.com/pallets/click/issues/616
.. _629: https://github.com/pallets/click/pull/629
.. _650: https://github.com/pallets/click/pull/650
.. _651: https://github.com/pallets/click/issues/651
.. _664: https://github.com/pallets/click/pull/664
.. _667: https://github.com/pallets/click/issues/667
.. _675: https://github.com/pallets/click/pull/675
.. _681: https://github.com/pallets/click/pull/681
.. _684: https://github.com/pallets/click/pull/684
.. _703: https://github.com/pallets/click/issues/703
.. _704: https://github.com/pallets/click/issues/704
.. _706: https://github.com/pallets/click/pull/706
.. _709: https://github.com/pallets/click/pull/709
.. _710: https://github.com/pallets/click/pull/710
.. _712: https://github.com/pallets/click/pull/712
.. _719: https://github.com/pallets/click/issues/719
.. _725: https://github.com/pallets/click/issues/725
.. _728: https://github.com/pallets/click/pull/728
.. _739: https://github.com/pallets/click/pull/739
.. _741: https://github.com/pallets/click/issues/741
.. _744: https://github.com/pallets/click/issues/744
.. _754: https://github.com/pallets/click/issues/754
.. _755: https://github.com/pallets/click/pull/755
.. _773: https://github.com/pallets/click/pull/773
.. _774: https://github.com/pallets/click/pull/774
.. _790: https://github.com/pallets/click/issues/790
.. _793: https://github.com/pallets/click/issues/793
.. _794: https://github.com/pallets/click/pull/794
.. _795: https://github.com/pallets/click/issues/795
.. _799: https://github.com/pallets/click/pull/799
.. _801: https://github.com/pallets/click/pull/801
.. _806: https://github.com/pallets/click/pull/806
.. _807: https://github.com/pallets/click/pull/807
.. _809: https://github.com/pallets/click/pull/809
.. _816: https://github.com/pallets/click/pull/816
.. _819: https://github.com/pallets/click/pull/819
.. _821: https://github.com/pallets/click/issues/821
.. _822: https://github.com/pallets/click/issues/822
.. _825: https://github.com/pallets/click/issues/825
.. _830: https://github.com/pallets/click/pull/830
.. _842: https://github.com/pallets/click/pull/842
.. _860: https://github.com/pallets/click/issues/860
.. _862: https://github.com/pallets/click/issues/862
.. _863: https://github.com/pallets/click/pull/863
.. _865: https://github.com/pallets/click/pull/865
.. _866: https://github.com/pallets/click/issues/866
.. _868: https://github.com/pallets/click/pull/868
.. _869: https://github.com/pallets/click/pull/869
.. _873: https://github.com/pallets/click/issues/873
.. _874: https://github.com/pallets/click/pull/874
.. _877: https://github.com/pallets/click/pull/877
.. _878: https://github.com/pallets/click/pull/878
.. _880: https://github.com/pallets/click/pull/880
.. _883: https://github.com/pallets/click/pull/883
.. _887: https://github.com/pallets/click/pull/887
.. _889: https://github.com/pallets/click/pull/889
.. _918: https://github.com/pallets/click/pull/918
.. _919: https://github.com/pallets/click/issues/919
.. _920: https://github.com/pallets/click/pull/920
.. _925: https://github.com/pallets/click/issues/925
.. _926: https://github.com/pallets/click/issues/926
.. _929: https://github.com/pallets/click/pull/929
.. _930: https://github.com/pallets/click/pull/930
.. _935: https://github.com/pallets/click/pull/935
.. _949: https://github.com/pallets/click/issues/949
.. _954: https://github.com/pallets/click/pull/954
.. _962: https://github.com/pallets/click/pull/962
.. _965: https://github.com/pallets/click/pull/965
.. _967: https://github.com/pallets/click/pull/967
.. _976: https://github.com/pallets/click/pull/976
.. _990: https://github.com/pallets/click/pull/990
.. _991: https://github.com/pallets/click/pull/991
.. _993: https://github.com/pallets/click/pull/993
.. _994: https://github.com/pallets/click/pull/994
.. _995: https://github.com/pallets/click/pull/995
.. _996: https://github.com/pallets/click/pull/996
.. _997: https://github.com/pallets/click/pull/997
.. _999: https://github.com/pallets/click/pull/999
.. _1000: https://github.com/pallets/click/pull/1000
.. _1001: https://github.com/pallets/click/pull/1001
.. _1002: https://github.com/pallets/click/pull/1002
.. _1003: https://github.com/pallets/click/pull/1003
.. _1004: https://github.com/pallets/click/pull/1004
.. _1005: https://github.com/pallets/click/pull/1005
.. _1007: https://github.com/pallets/click/pull/1007
.. _1008: https://github.com/pallets/click/pull/1008
.. _1009: https://github.com/pallets/click/pull/1009
.. _1010: https://github.com/pallets/click/pull/1010
.. _1011: https://github.com/pallets/click/pull/1011
.. _1012: https://github.com/pallets/click/pull/1012
.. _1013: https://github.com/pallets/click/pull/1013
.. _1014: https://github.com/pallets/click/pull/1014
.. _1016: https://github.com/pallets/click/pull/1016
.. _1020: https://github.com/pallets/click/pull/1020
.. _1022: https://github.com/pallets/click/pull/1022
.. _1027: https://github.com/pallets/click/pull/1027
.. _1047: https://github.com/pallets/click/pull/1047
.. _1055: https://github.com/pallets/click/pull/1055
.. _1058: https://github.com/pallets/click/pull/1058
.. _1059: https://github.com/pallets/click/pull/1059
.. _1061: https://github.com/pallets/click/pull/1061
.. _1068: https://github.com/pallets/click/issues/1068
.. _1069: https://github.com/pallets/click/pull/1069
.. _1088: https://github.com/pallets/click/issues/1088
.. _1091: https://github.com/pallets/click/pull/1091
.. _1098: https://github.com/pallets/click/pull/1098
.. _1105: https://github.com/pallets/click/pull/1105
.. _1106: https://github.com/pallets/click/pull/1106
.. _1108: https://github.com/pallets/click/pull/1108
.. _1115: https://github.com/pallets/click/pull/1115

Links

PyPI: https://pypi.org/project/click
Changelog: https://pyup.io/changelogs/click/
Homepage: https://palletsprojects.com/p/click/

Update pyparsing from 2.2.1 to 2.2.2.

Changelog

2.2.2

-------------------------------
- Fixed bug in SkipTo, if a SkipTo expression that was skipping to
an expression that returned a list (such as an And), and the 
SkipTo was saved as a named result, the named result could be 
saved as a ParseResults - should always be saved as a string.
Issue 28, reported by seron.

- Added simple_unit_tests.py, as a collection of easy-to-follow unit 
tests for various classes and features of the pyparsing library. 
Primary intent is more to be instructional than actually rigorous 
testing. Complex tests can still be added in the unitTests.py file.

- New features added to the Regex class:
- optional asGroupList parameter, returns all the capture groups as
 a list
- optional asMatch parameter, returns the raw re.match result
- new sub(repl) method, which adds a parse action calling
 re.sub(pattern, repl, parsed_result). Simplifies creating 
 Regex expressions to be used with transformString. Like re.sub,
 repl may be an ordinary string (similar to using pyparsing&#39;s 
 replaceWith), or may contain references to capture groups by group 
 number, or may be a callable that takes an re match group and 
 returns a string.
 
 For instance:
     expr = pp.Regex(r&quot;([Hh]\d):\s*(.*)&quot;).sub(r&quot;&lt;\1&gt;\2&lt;/\1&gt;&quot;)
     expr.transformString(&quot;h1: This is the title&quot;)

 will return
     &lt;h1&gt;This is the title&lt;/h1&gt;

- Fixed omission of LICENSE file in source tarball, also added 
CODE_OF_CONDUCT.md per GitHub community standards.

Links

PyPI: https://pypi.org/project/pyparsing
Changelog: https://pyup.io/changelogs/pyparsing/
Repo: https://github.com/pyparsing/pyparsing/
Docs: https://pythonhosted.org/pyparsing/

Update biopython from 1.71 to 1.71.

Changelog

1.51

the OBF mailing lists with EMBOSS, BioPerl, BioJava and BioRuby for inter-
conversion and the valid score range for each FASTQ variant. This means
Solexa FASTQ scores can be from -5 to 62 (format name &quot;fastq-solexa&quot; in
Bio.SeqIO), Illumina 1.3+ FASTQ files have PHRED scores from 0 to 62 (format
name &quot;fastq-illumina&quot;), and Sanger FASTQ files have PHRED scores from 0 to
93 (format name &quot;fastq&quot; or &quot;fastq-sanger&quot;).

Bio.Sequencing.Phd has been updated, for example to cope with missing peak
positions. The &quot;phd&quot; support in Bio.SeqIO has also been updated to record
the PHRED qualities (and peak positions) in the SeqRecord&#39;s per-letter
annotation. This allows conversion of PHD files into FASTQ or QUAL which may
be useful for meta-assembly.

See the notes below for the Biopython 1.50 beta release for changes since
Biopython 1.49 was released. This includes dropping support for Python 2.3,
removing our deprecated parsing infrastructure (Martel and Bio.Mindy), and
hence removing any dependence on mxTextTools.

Additionally, since the beta, a number of small bugs have been fixed, and
there have been further additions to the test suite and documentation.


June 23, 2009: Biopython 1.51 beta released.
============================================

Biopython no longer supports Python 2.3.  Currently we support Python 2.4,
2.5 and 2.6.

Our deprecated parsing infrastructure (Martel and Bio.Mindy) has been
removed.  This means Biopython no longer has any dependence on mxTextTools.

A few cosmetic issues in GenomeDiagram with arrow sigils and labels on
circular diagrams have been fixed.

Bio.SeqIO will now write GenBank files with the feature table (previously
omitted), and a couple of obscure errors parsing ambiguous locations have
been fixed.

Bio.SeqIO can now read and write Illumina 1.3+ style FASTQ files (which use
PHRED quality scores with an ASCII offset of 64) under the format name
&quot;fastq-illumina&quot;. Biopython 1.50 supported just &quot;fastq&quot; (the original Sanger
style FASTQ files using PHRED scores with an ASCII offset of 33), and
&quot;fastq-solexa&quot; (the original Solexa/Illumina FASTQ format variant holding
Solexa scores with an ASCII offset of 64) .

For parsing the &quot;swiss&quot; format, Bio.SeqIO now uses the new Bio.SwissProt
parser, making it about twice as fast as in Biopython 1.50, where the older
now deprecated Bio.SwissProt.SProt was used. There should be no functional
differences as a result of this change.

Our command line wrapper objects have been updated to support accessing
parameters via python properties, and setting of parameters at initiation
with keyword arguments.  Additionally Cymon Cox has contributed several new
multiple alignment wrappers under Bio.Align.Applications.

A few more issues with Biopython&#39;s BioSQL support have been fixed (mostly by
Cymon Cox). In particular, the default PostgreSQL schema includes some rules
intended for BioPerl support only, which were causing problems in Biopython
(see BioSQL bug 2839).

There have also been additions to the tutorial, such as the new alignment
wrappers, with a whole chapter for the SeqRecord object. We have also added
to the unit test coverage.


April 20, 2009: Biopython 1.50 released.
========================================

See the notes below for the Biopython 1.50 beta release for more details,
but the highlights are:

* The SeqRecord supports slicing and per-letter-annotation
* Bio.SeqIO can read and write FASTQ and QUAL files
* Bio.Seq now has an UnknownSeq object
* GenomeDiagram has been integrated into Biopython
* New module Bio.Motif will later replace Bio.AlignAce and Bio.MEME
* This will be the final release to support Python 2.3
* This will be the final release with Martel and Bio.Mindy

Since the 1.50 beta release:

* The NCBI&#39;s Entrez EFetch no longer supports rettype=&quot;genbank&quot;
and &quot;gb&quot; (or &quot;gp&quot;) should be used instead.
* Bio.SeqIO now supports &quot;gb&quot; as an alias for &quot;genbank&quot;.
* The Seq object now has string-like startswith and endswith methods
* Bio.Blast.NCBIXML now has a read function for single record files
* A few more unit tests were added
* More documentation


April 3, 2009: Biopython 1.50 beta released.
============================================

The SeqRecord object has a new dictionary attribute, letter_annotations,
which is for holding per-letter-annotation information like sequence
quality scores or secondary structure predictions.  As part of this work,
the SeqRecord object can now be sliced to give a new SeqRecord covering
just part of the sequence.  This will slice the per-letter-annotation to
match, and will also include any SeqFeature objects as appropriate.

Bio.SeqIO can now read and write FASTQ and QUAL quality files using PHRED
quality scores (Sanger style, also used for Roche 454 sequencing), and FASTQ
files using Solexa/Illumina quality scores.

The Bio.Seq module now has an UnknownSeq object, used for when we have a
sequence of known length, but unknown content.  This is used in parsing
GenBank and EMBL files where the sequence may not be present (e.g. for a
contig record) and when parsing QUAL files (which don&#39;t have the sequence)

GenomeDiagram by Leighton Pritchard has been integrated into Biopython as
the Bio.Graphics.GenomeDiagram module  If you use this code, please cite the
publication Pritchard et al. (2006), Bioinformatics 22 616-617.  Note that
like Bio.Graphics, this requires the ReportLab python library.

A new module Bio.Motif has been added, which is intended to replace the
existing Bio.AlignAce and Bio.MEME modules.

The set of NCBI DTD files included with Bio.Entrez has been updated with the
revised files the NCBI introduced on 1 Jan 2009.

Minor fix to BioSQL for retrieving references and comments.

Bio.SwissProt has a new faster parser which will be replacing the older
slower code in Bio.SwissProt.SProt (which we expect to deprecate in the next
release).

We&#39;ve also made some changes to our test framework, which is now given a
whole chapter in the tutorial.  This intended to help new developers or
contributors wanting to improve our unit test coverage.


November 21, 2008: Biopython 1.49 released.
===========================================

See the notes below for the Biopython 1.49 beta release for more details,
but the highlights are:

* Biopython has transitioned from Numeric to NumPy
* Martel and Bio.Mindy are now deprecated

Since the 1.49 beta release:

* A couple of NumPy issues have been resolved
* Further small improvements to BioSQL
* Bio.PopGen.SimCoal should now work on Windows
* A few more unit tests were added


November 7, 2008: Biopython 1.49 beta released.
===============================================

Biopython has transitioned from Numeric to NumPy.  Please move to NumPy.

A number of small changes have been made to support Python 2.6 (mostly
avoiding deprecated functionality), and further small changes have been
made for better compatibility with Python 3 (this work is still ongoing).
However, we intend to support Python 2.3 for only a couple more releases.

As part of the Numeric to NumPy migration, Bio.KDTree has been rewritten in
C instead of C++ which therefore simplifies building Biopython from source.

Martel and Bio.Mindy are now considered to be deprecated, meaning mxTextTools
is no longer required to use Biopython.  See the DEPRECATED file for details
of other deprecations.

The Seq object now supports more string like methods (gaining find, rfind,
split, rsplit, strip, lstrip and rstrip in addition to previously supported
methods like count).  Also, biological methods transcribe, back_transcribe
and translate have been added, joining the pre-existing reverse_complement
and complement methods.  Together these changes allow a more object
orientated programming style using the Seq object.

The behaviour of the Bio.Seq module&#39;s translate function has changed so that
ambiguous codons which could be a stop codon like &quot;TAN&quot; or &quot;NNN&quot; are now
translated as &quot;X&quot; (consistent with EMBOSS and BioPerl - Biopython previously
raised an exception), and a bug was fixed so that invalid codons (like &quot;A-T&quot;)
now raise an exception (previously these were translated as stop codons).

BioSQL had a few bugs fixed, and can now optionally fetch the NCBI taxonomy
on demand when loading sequences (via Bio.Entrez) allowing you to populate
the taxon/taxon_name tables gradually.  This has been tested in combination
with the BioSQL load_ncbi_taxonomy.pl script used to populate or update the
taxon/taxon_name tables.  BioSQL should also now work with the psycopg2
driver for PostgreSQL as well as the older psycopg driver.

The PDB and PopGen sections of the Tutorial have been promoted to full
chapters, and a new chapter has been added on supervised learning methods
like logistic regression.  The &quot;Cookbook&quot; section now has a few graphical
examples using Biopython to calculate sequence properties, and matplotlib
(pylab) to plot them.

The input functions in Bio.SeqIO and Bio.AlignIO now accept an optional
argument to specify the expected sequence alphabet.

The somewhat quirky unit test GUI has been removed, the unit tests are now
run via the command line by default.


September 8, 2008: Biopython 1.48 released.
===========================================

The SeqRecord and Alignment objects have a new method to format the object as
a string in a requested file format (handled via Bio.SeqIO and Bio.AlignIO).

Additional file formats supported in Bio.SeqIO and Bio.AlignIO:

- reading and writing &quot;tab&quot; format (simple tab separated)
- writing &quot;nexus&quot; files.
- reading &quot;pir&quot; files (NBRF/PIR)
- basic support for writing &quot;genbank&quot; files (GenBank plain text)

Fixed some problems reading Clustal alignments (introduced in Biopython 1.46
when consolidating Bio.AlignIO and Bio.Clustalw).

Updates to the Bio.Sequencing parsers.

Bio.PubMed and the online code in Bio.GenBank are now considered obsolete,
and we intend to deprecate them after the next release. For accessing PubMed
and GenBank, please use Bio.Entrez instead.

Bio.Fasta is now considered to be obsolete, please use Bio.SeqIO instead. We
do intend to deprecate this module eventually, however, for several years
this was the primary FASTA parsing module in Biopython and is likely to be in
use in many existing scripts.

Martel and Bio.Mindy are now considered to be obsolete, and are likely to be
deprecated and removed in a future release.

In addition a number of other modules have been deprecated, including:
Bio.MetaTool, Bio.EUtils, Bio.Saf, Bio.NBRF, and Bio.IntelliGenetics
See the DEPRECATED file for full details.


July 5, 2008: Biopython 1.47 released.
======================================

Improved handling of ambiguous nucleotides in Bio.Seq.Translate().
Better handling of stop codons in the alphabet from a translation.
Fixed some codon tables (problem introduced in Biopython 1.46).

Updated Nexus file handling.

Fixed a bug in Bio.Cluster potentially causing segfaults in the
single-linkage hierarchical clustering library.

Added some DTDs to be able to parse EFetch results from the
nucleotide database.

Added IntelliGenetics/MASE parsing to Bio.SeqIO (as the &quot;ig&quot; format).


June 29, 2008: Biopython 1.46 released.
=======================================

Bio.Entrez now has several Entrez format XML parsers, and a chapter
in the tutorial.

Addition of new Bio.AlignIO module for working with sequence alignments
in the style introduced with Bio.SeqIO in recent releases, with a whole
chapter in the tutorial.

A problem parsing certain EMBL files was fixed.

Several minor fixes were made to the NCBI BLAST XML parser, including
support for the online version 2.2.18+ introduced in May 2008.

The NCBIWWW.qblast() function now allows other programs (blastx, tblastn,
tblastx) in addition to just blastn and blastp.

Bio.EUtils has been updated to explicitly enforce the NCBI&#39;s rule of at
most one query every 3 seconds, rather than assuming the user would obey
this.

Iterators in Bio.Medline, Bio.SCOP, Bio.Prosite, Bio.Prosite.Prodoc,
Bio.SwissProt, and others to make them more generally usable.

Phylip export added to Bio.Nexus.

Improved handling of ambiguous nucleotides and stop codons in
Bio.Seq.Translate (plus introduced a regression fixed in Biopython 1.47).


March 22, 2008: Biopython 1.45 released.
========================================

The Seq and MutableSeq objects act more like python strings, in particular
str(object) now returns the full sequence as a plain string.  The existing
tostring() method is preserved for backwards compatibility.

BioSQL has had some bugs fixed, and has an additional unit test which loads
records into a database using Bio.SeqIO and then checks the records can be
retrieved correctly.  The DBSeq and DBSeqRecord classes now subclass the
Seq and SeqRecord classes, which provides more functionality.

The modules under Bio.WWW are being deprecated.
Functionality in Bio.WWW.NCBI, Bio.WWW.SCOP, Bio.WWW.InterPro and
Bio.WWW.ExPASy is now available from Bio.Entrez, Bio.SCOP, Bio.InterPro and
Bio.ExPASy instead. Bio.Entrez was used to fix a nasty bug in Bio.GenBank.

Tiago Antao has included more functionality in the Population Genetics
module, Bio.PopGen.

The Bio.Cluster module has been updated to be more consistent with other
Biopython code.

The tutorial has been updated, including devoting a whole chapter to
Swiss-Prot, Prosite, Prodoc, and ExPASy. There is also a new chapter on
Bio.Entrez.

Bio.biblio was deprecated.


October 28, 2007: Biopython 1.44 released.
==========================================

NOTE: This release includes some rather drastic code changes, which were
necessary to get Biopython to work with the new release of mxTextTools.

The (reverse)complement functions in Bio.Seq support ambiguous nucleotides.

Bio.Kabat, which was previously deprecated, is now removed from Biopython.

Bio.MarkupEditor was deprecated, as it does not appear to have any users.

Bio.Blast.NCBI.qblast() updated with more URL options, thanks to a patch
from Chang Soon Ong.

Several fixes to the Blast parser.

The deprecated Bio.Blast.NCBIWWW functions blast and blasturl were removed.

The standalone Blast functions blastall, blastpgp now create XML output by
default.

Bio.SeqIO.FASTA and Bio.SeqIO.generic have been deprecated in favour of
the new Bio.SeqIO module.

Bio.FormatIO has been removed (a gradual deprecation was not possible).
Please look at Bio.SeqIO for sequence input/output instead.

Fix for a bug in Bio.Cluster, which caused kcluster() to hang on some platforms.

Bio.expressions has been deprecated.

Bio.SeqUtils.CheckSum created, including new methods from Sebastian Bassi,
and functions crc32 and crc64 which were moved from Bio/crc.py.
Bio.crc is now deprecated. Bio.lcc was updated and moved to Bio.SeqUtils.lcc.

Bio.SwissProt parser updated to cope with recent file format updates.

Bio.Fasta, Bio.KEGG and Bio.Geo updated to pure python parsers which
don&#39;t rely on Martel.

Numerous fixes in the Genbank parser.

Several fixes in Bio.Nexus.

Bio.MultiProc and Bio.Medline.NLMMedlineXML were deprecating, as they failed
on some platforms, and seemed to have no users. Deprecated concurrent
behavior in Bio.config.DBRegistry and timeouts in Bio.dbdefs.swissprot,
which relies on Bio.MultiProc.

Tiago Antao has started work on a Population Genetics module, Bio.PopGen

Updates to the tutorial, including giving Bio.Seq and Bio.SeqIO a whole
chapter each.


March 17, 2007: Biopython 1.43 released.
========================================

New Bio.SeqIO module for reading and writing biological sequence files
in various formats, based on SeqRecord objects.  This includes a new fasta
parser which is much faster than Bio.Fasta, particularly for larger files.
Easier to use, too.

Various improvements in Bio.SeqRecord.

Running Blast using Bio.Blast.NCBIStandalone now generates output in XML
format by default.
The new function Bio.Blast.NCBIXML.parse can parse multiple Blast records
in XML format.

Bio.Cluster no longer uses ranlib, but uses its own random number generator
instead. Some modifications to make Bio.Cluster more compatible with the new
NumPy (we&#39;re not quite there yet though).

New Bio.UniGene parser.

Numerous improvements in Bio.PDB.

Bug fixes in Bio.SwissProt, BioSQL, Bio.Nexus, and other modules.

Faster parsing of large GenBank files.

New EMBL parser under Bio.GenBank and also integrated into (new) Bio.SeqIO

Compilation of KDTree (C++ code) is optional (setup.py asks the user if it
should be compiled). For the Windows installer, C++ code is now included.

Nominating Bio.Kabat for removal.

Believe it or not, even the documentation was updated.


July 16, 2006: Biopython 1.42 released.
=======================================

Bio.GenBank: New parser by Peter, which doesn&#39;t rely on Martel.

Numerous updates in Bio.Nexus and Bio.Geo.

Bio.Cluster became (somewhat) object-oriented.

Lots of bug fixes, and updates to the documentation.


October 28, 2005: Biopython 1.41 released.
==========================================

Major changes:

NEW: Bio.MEME -- thanks to Jason Hackney

Added transcribe, translate, and reverse_complement functions to Bio.Seq that
work both on Seq objects and plain strings.

Major code optimization in cpairwise2module.

CompareACE support added to AlignAce.

Updates to Blast parsers in Bio.Blast, in particular use of the XML parser
in NCBIXML contributed by Bertrand Frottier, and the BLAT parser by Yair
Benita.

Pairwise single-linkage hierarchical clustering in Bio.Cluster became much
faster and memory-efficient, allowing clustering of large data sets.

Bio.Emboss: Added command lines for einverted and palindrome.

Bio.Nexus: Added support for StringIO objects.

Numerous updates in Bio.PDB.

Lots of fixes in the documentation.

March 29, 2005: MEME parser added. Thanks to Jason Hackney


Feb 18, 2005: Biopython 1.40 beta
=================================
Major Changes since v1.30. For a full list of changes please see the CVS

IMPORTANT: Biopython now works with Python version &gt;= 2.3

NEW: Bio.Nexus -- thanks to Frank Kauff
Bio.Nexus is a Nexus file parser. Nexus is a common format for phylogenetic trees.

NEW: CAPS module -- Thanks to Jonathan Taylor.

NEW: Restriction enzyme package contributed by Frederic Sohm. This includes classes for
manipulating enzymes, updating from Rebase, as well as documentation and Tests.

CHANGED: Bio.PDB -- thanks to Thomas Hamelryck.

- Added atom serial number.
- Epydoc style documentation.
- Added secondary structure support (through DSSP).
- Added Accessible Surface Area support (through DSSP).
- Added Residue Depth support (through MSMS).
- Added Half Sphere Exposure.
- Added Fragment classification of the protein backbone (see Kolodny et al.,
- JMB, 2002).
- Corrected problem on Windows with PDBList (thanks to Matt Dimmic)
- Added StructureAlignment module to superimpose structures based on a FASTA
sequence alignment.
- Various additions to Polypeptide.
- Various bug corrections in Vector.
- Lots of smaller bug corrections and additional features

CHANGED: MutableSeq -- thanks to Michiel De Hoon
Added the functions &#39;complement&#39; and &#39;reverse_complement&#39; to Bio.Seq&#39;s Seq and
MutableSeq objects. Similar functions previously existed in various locations
in BioPython:

- forward_complement, reverse_complement in Bio.GFF.easy
- complement, antiparallel in Bio.SeqUtils

These functions have now been deprecated, and will generate a DeprecationWarning
when used.
The functions complement and reverse_complement, when applied to a Seq object,
will return a new Seq object. The same function applied to a MutableSeq object
will modify the MutableSeq object itself, and don&#39;t return anything.



May 14, 2004: Biopython 1.30
============================

- Affy package added for dealing with Affymetrix cel files -- thanks to Harry
Zuzan.
- Added code for parsing Blast XML output -- thanks to Bertrand Frottier.
- Added code for parsing Compass output -- thanks to James Casbon.
- New melting temperature calculation module -- thanks to Sebastian Bassi.
- Added lowess function for non-parameteric regression -- thanks to Michiel.
- Reduced protein alphabet supported added -- thanks to Iddo.

- Added documentation for Logistic Regression and Bio.PDB -- thanks to Michiel
and Thomas.
- Documentation added for converting between file formats.
- Updates to install documentation for non-root users -- thanks to Jakob
Fredslund.
- epydoc now used for automatic generation of documentation.

- Fasta parser updated to use Martel for parsing and indexing, allowing better
speed and dealing with large data files.
- Updated to Registry code. Now &#39;from Bio import db&#39; gives you a number of new
retrieval options, including embl, fasta, genbak, interpro, prodoc and swissprot.
- GenBank parser uses new Martel format. GenBank retrieval now uses EUtils instead
of the old non-working entrez scripts. GenBank indexing uses standard Mindy
indexing. Fix for valueless qualifiers in feature keys -- thanks to Leighton
Pritchard.
- Numerous updated to Bio.PDB modules -- thanks to Thomas. PDB can now parse headers
-- thanks to Kristian Rother.
- Updates to the Ace parser -- thanks to Frank Kauff and Leighton Pritchard.

- Added pgdb (PyGreSQL) support to BioSQL -- thanks to Marc Colosimo.
- Fix problems with using py2exe and Biopython -- thanks to Michael Cariaso.
- PSIBlast parser fixes -- thanks to Jer-Yee John Chuang and James Casbon.
- Fix to NCBIWWW retrieval so that HTML results are returned correctly.
- Fix to Clustalw to handle question marks in title names -- thanks to Ashleigh
Smythe.
- Fix to NBRF parsing to it accepts files produced by Clustalw -- thanks to
Ashleigh Smythe.
- Fixes to the Enyzme module -- thanks to Marc Colosimo.
- Fix for bugs in SeqUtils -- thanks to Frank Kauff.
- Fix for optional hsps in ncbiblast Martel format -- thanks to Heiko.
- Fix to Fasta parsing to allow  comment lines -- thanks to Karl Diedrich.
- Updates to the C clustering library -- thanks to Michiel.
- Fixes for breakage in the SCOP module and addition of regression tests to
framework -- thanks to Gavin.
- Various fixes to Bio.Wise -- thanks to Michael.
- Fix for bug in FastaReader -- thanks to Micheal.
- Fix EUtils bug where efetch would only return 500 sequences.
- Updates for Emboss commandlines, water and tranalign.
- Fixes to the FormatIO system of file conversion.

- C++ code (KDTree, Affy) now compiled by default on most platforms -- thanks to
Michael for some nice distutils hacks and many people for testing.
- Deprecated Bio.sequtils -- use Bio.SeqUtils instead.
- Deprecated Bio.SVM -- use libsvm instead.
- Deprecated Bio.kMeans and Bio.xkMeans -- use Bio.cluster instead.
- Deprecated RecordFile -- doesn&#39;t appear to be finished code.


Feb 16, 2004: Biopython 1.24
============================

- New parsers for Phred and Ace format files -- thanks to Frank Kauff
- New Code for dealing with NMR data -- thanks to Bob Bussell
- New SeqUtils modules for codon usage, isoelectric points and other
protein properties -- thanks to Yair Benita
- New code for dealing with Wise contributed by Michael
- EZ-Retrieve sequence retrieval now supported thanks to Jeff
- Bio.Cluster updated along with documentation by Michiel
- BioSQL fixed so it now works with the current SQL schema -- thanks to Yves
Bastide for patches
- Patches to Bio/__init__ to make it compatible with py2exe -- thanks to
Leighton Pritchard
- Added __iter__ to all Biopython Iterators to make them Python 2.2 compatible
- Fixes to NCBIWWW for retrieving from NCBI -- thanks to Chris Wroe
- Retrieval of multiple alignment objects from BLAST records -- thanks to
James Casbon
- Fixes to GenBank format for new tags by Peter
- Parsing fixes in clustalw parsed -- thanks to Greg Singer and Iddo
- Fasta Indexes can have a specified filename -- thanks to Chunlei Wu
- Fix to Prosite parser -- thanks to Mike Liang
- Fix in GenBank parsing -- mRNAs now get strand information


Oct 18, 2003: Biopython 1.23
============================

- Fixed distribution of files in Bio/Cluster
- Now distributing Bio/KDTree/_KDTree.swig.C
- minor updates in installation code
- added mmCIF support for PDB files


Oct 9, 2003: Biopython 1.22
===========================

- Added Peter Slicker&#39;s patches for speeding up modules under Python 2.3
- Fixed Martel installation.
- Does not install Bio.Cluster without Numeric.
- Distribute EUtils DTDs.
- Yves Bastide patched NCBIStandalone.Iterator to be Python 2.0 iterator
- Ashleigh&#39;s string coersion fixes in Clustalw.
- Yair Benita added precision to the protein molecular weights.
- Bartek updated AlignAce.Parser and added Motif.sim method
- bug fixes in Michiel De Hoon&#39;s clustering library
- Iddo&#39;s bug fixes to Bio.Enzyme and new RecordConsumer
- Guido Draheim added patches for fixing import path to xbb scripts
- regression tests updated to be Python 2.3 compatible
- GenBank.NCBIDictionary is smarter about guessing the format


Jul 28, 2003: Biopython 1.21
============================

- Martel added back into the released package
- new AlignACE module by Bartek Wilczynski
- Andreas Kuntzagk fix for GenBank Iterator on empty files


Jul 27, 2003: Biopython 1.20
============================

- added Andrew Dalke&#39;s EUtils library
- added Michiel de Hoon&#39;s gene expression analysis package
- updates to setup code, now smarter about dependencies
- updates to test suite, now smarter about code that is imported
- Michael Hoffman&#39;s fixes to DocSQL
- syntax fixes in triemodule.c to compile on SGI, Python 2.1 compatible
- updates in NCBIStandalone, short query error
- Sebastian Bassi submitted code to calculate LCC complexity
- Greg Kettler&#39;s NCBIStandalone fix for long query lengths
- slew of miscellaneous fixes from George Paci
- miscellaneous cleanups and updates from Andreas Kuntzagk
- Peter Bienstman&#39;s fixes to Genbank code -- now parses whole database
- Kayte Lindner&#39;s LocusLink package
- miscellaneous speedups and code cleanup in ParserSupport by Brad Chapman
- miscellaneous BLAST fixes and updates
- Iddo added new code to parse BLAST table output format
- Karl Diedrich&#39;s patch to read T_Coffee files
- Larry Heisler&#39;s fix for primer3 output
- Bio.Medline now uses proper iterator objects
- copen now handles SIGTERM correctly
- small bugfixes and updates in Thomas Hamelryck&#39;s PDB package
- bugfixes and updates to SeqIO.FASTA reader
- updates to Registry system, conforms to 2003 hackathon OBDA spec
- Yu Huang patch to support tblastn in wublast expression


Dec 17, 2002: Biopython 1.10
============================

- Python requirement bumped up to 2.2
- hierarchy reorg, many things moved upwards into Bio namespace
- pairwise2 replaces fastpairwise and pairwise
- removed deprecated Sequence.py package
- minor bug fix in File.SGMLStripper
- added Scripts/debug/debug_blast_parser.py to diagnose blast parsing errors
- IPI supported by SwissProt/SProt.py parser
- large speedup for kmeans
- new registry framework for generic access to databases and parsers
- small bug fix in stringfns.split
- scripts that access NCBI moved over to new EUtils system
- new crc module
- biblio.py supports the EBI Bibliographic database
- new CDD parser
- new Ndb parser
- new ECell parser
- new Geo parser
- access to GFF databases
- new KDTree data structure
- new LocusLink parser
- new MarkovModel algorithm
- new Saf parser
- miscellaneous sequence handling functions in sequtils
- new SVDSuperimpose algorithm

1.00a4

=============================

- minor bug fix in NCBIStandalone.blastall
- optimization in dynamic programming code
- new modules for logistic regression and maximum entropy
- minor bug fix in ParserSupport
- minor bug fixes in SCOP package
- minor updates in the kMeans cluster selection code
- minor bug fixes in SubsMat code
- support for XML-formatted MEDLINE files
- added MultiProc.run to simplify splitting code across processors
- listfns.items now supports lists with unhashable items
- new data type for pathways
- new support for intelligenetics format
- new support for metatool format
- new support for NBRF format
- new support for generalized launching of applications
- new support for genetic algorithms
- minor bug fixes in GenBank parsing
- new support for Primer in the Emboss package
- new support for chromosome graphics
- new support for HMMs
- new support for NeuralNetwork
- slew of Martel fixes (see Martel docs)

1.00a3

=============================

- added package to support KEGG
- added sequtils module for computations on sequences
- added pairwise sequence alignment algorithm
- major bug fixes in UndoHandle
- format updates in PubMed
- Tk interface to kMeans clustering

1.00a2

=============================

- deprecated old regression testing frameworks
- deprecated Sequence.py
- Swiss-Prot parser bug fixes
- GenBank parser bug fixes
- Can now output GenBank format
- can now download many sequences at a time from GenBank
- kMeans clustering algorithm
- Kabat format now supported
- FSSP format now supported
- more functionality for alignment code
- SubsMat bug fixes and updates
- fixed memory leak in listfns bug fixes
- Martel bundled and part of the install procedure
- Medline.Parser bug fixes
- PubMed.download_many handles broken IDs better


Mar 3, 2001: Biopython 1.00a1
=============================

- Refactoring of modules.  X/X.py moved to X/__init__.py.
- Can search sequences for Prosite patterns at ExPASy
- Can do BLAST searches against stable URL at NCBI
- Prosite Pattern bug fixes
- GenBank parser
- Complete Seq and SeqFeatures framework
- distutils cleanup
- compile warning cleanups
- support for UniGene
- code for working with substitution matrices
- Tools.MultiProc package for rudimentary multiprocessing stuff


Nov 10, 2000: Biopython 0.90d04
===============================

- Added support for multiple alignments, ClustalW
- BLAST updates, bug fixes, and BlastErrorParser
- Fixes for PSI-BLAST in master-slave mode
- Minor update in stringfns, split separators can be negated
- Added download_many function to PubMed
- xbbtools updates
- Prodoc parser now accepts a copyright at the end of a record
- Swiss-Prot parser now handles taxonomy ID tag


Sept 6, 2000: Biopython 0.90d03
===============================

- Blast updates:

- bug fixes in NCBIStandalone, NCBIWWW
- some __str__ methods in Record.py implemented (incomplete)

- Tests:

- new BLAST regression tests
- prosite tests fixed

- New parsers for Rebase, Gobase
- pure python implementation of C-based tools
- Thomas Sicheritz-Ponten&#39;s xbbtools
- can now generate documentation from docstrings using HappyDoc


Aug17-18, 2000: Bioinformatics Open Source Conference 2000
==========================================================

We had a very good Birds-of-a-Feather meeting:
http://www.biopython.org/pipermail/biopython/2000-August/000360.html


Aug 2, 2000: Biopython 0.90d02 is released.
===========================================

- Blast updates:
- now works with v2.0.14
- HSP.identities and HSP.positives now tuples
- HSP.gaps added
- SCOP updates:
- Lin.Iterator now works with release 50
- Starting a tutorial
- New regression tests for Prodoc


July 6, 2000: Biopython 0.90d01 is released.
============================================


February 8, 2000: Anonymous CVS made available.
===============================================


August 1999: Biopython project founded.
=======================================

Call for Participation sent out to relevant mailing lists, news
groups.

The Biopython Project (http://www.biopython.org/) is a new open
collaborative effort to develop freely available Python libraries and
applications that address the needs of current and future work in
bioinformatics, including sequence analysis, structural biology,
pathways, expression data, etc.  When available, the source code will
be released as open source (http://www.biopython.org/License.shtml)
under terms similar to Python.

This is a Call for Participation for interested people to join the
project.  We are hoping to attract people from a diverse set of
backgrounds to help with code development, site maintenance,
scientific discussion, etc.  This project is open to everyone.  If
you&#39;re interested, please visit the web page, join the biopython
mailing list, and let us know what you think!

Jeffrey Chang &lt;jchangsmi.stanford.edu&gt;
Andrew Dalke &lt;dalkebioreason.com&gt;


NEWS.rst

Links

PyPI: https://pypi.org/project/biopython
Changelog: https://pyup.io/changelogs/biopython/
Homepage: http://www.biopython.org/

Update click_plugins from 1.0.3 to 1.0.3.

Changelog

1.0.3

------------------

- Include tests in MANIFEST.in - See further discussion in 8

1.0.2

------------------

- General packaging and Travis-CI improvements.
- Don&#39;t include tests in MANIFEST.in - 8

1.0.1

------------------

- Fixed a typo in an error message - 5

1.0

----------------

- Initial release.

Links

PyPI: https://pypi.org/project/click-plugins
Changelog: https://pyup.io/changelogs/click-plugins/
Repo: https://github.com/click-contrib/click-plugins

Update coverage from 4.5.1 to 4.5.1.

Changelog

4.5.1

----------------------------

- Now that 4.5 properly separated the ``[run] omit`` and ``[report] omit``
settings, an old bug has become apparent.  If you specified a package name
for ``[run] source``, then omit patterns weren&#39;t matched inside that package.
This bug (`issue 638`_) is now fixed.

- On Python 3.7, reporting about a decorated function with no body other than a
docstring would crash coverage.py with an IndexError (`issue 640`_).  This is
now fixed.

- Configurer plugins are now reported in the output of ``--debug=sys``.

.. _issue 638: https://bitbucket.org/ned/coveragepy/issues/638/run-omit-is-ignored-since-45
.. _issue 640: https://bitbucket.org/ned/coveragepy/issues/640/indexerror-reporting-on-an-empty-decorated


.. _changes_45:

4.5

--------------------------

- A new kind of plugin is supported: configurators are invoked at start-up to
allow more complex configuration than the .coveragerc file can easily do.
See :ref:`api_plugin` for details.  This solves the complex configuration
problem described in `issue 563`_.

- The ``fail_under`` option can now be a float.  Note that you must specify the
``[report] precision`` configuration option for the fractional part to be
used.  Thanks to Lars Hupfeldt Nielsen for help with the implementation.
Fixes `issue 631`_.

- The ``include`` and ``omit`` options can be specified for both the ``[run]``
and ``[report]`` phases of execution.  4.4.2 introduced some incorrect
interactions between those phases, where the options for one were confused
for the other.  This is now corrected, fixing `issue 621`_ and `issue 622`_.
Thanks to Daniel Hahler for seeing more clearly than I could.

- The ``coverage combine`` command used to always overwrite the data file, even
when no data had been read from apparently combinable files.  Now, an error
is raised if we thought there were files to combine, but in fact none of them
could be used.  Fixes `issue 629`_.

- The ``coverage combine`` command could get confused about path separators
when combining data collected on Windows with data collected on Linux, as
described in `issue 618`_.  This is now fixed: the result path always uses
the path separator specified in the ``[paths]`` result.

- On Windows, the HTML report could fail when source trees are deeply nested,
due to attempting to create HTML filenames longer than the 250-character
maximum.  Now filenames will never get much larger than 200 characters,
fixing `issue 627`_.  Thanks to Alex Sandro for helping with the fix.

.. _issue 563: https://bitbucket.org/ned/coveragepy/issues/563/platform-specific-configuration
.. _issue 618: https://bitbucket.org/ned/coveragepy/issues/618/problem-when-combining-windows-generated
.. _issue 621: https://bitbucket.org/ned/coveragepy/issues/621/include-ignored-warning-when-using
.. _issue 622: https://bitbucket.org/ned/coveragepy/issues/622/report-omit-overwrites-run-omit
.. _issue 627: https://bitbucket.org/ned/coveragepy/issues/627/failure-generating-html-reports-when-the
.. _issue 629: https://bitbucket.org/ned/coveragepy/issues/629/multiple-use-of-combine-leads-to-empty
.. _issue 631: https://bitbucket.org/ned/coveragepy/issues/631/precise-coverage-percentage-value


.. _changes_442:

4.4.2

----------------------------

- Support for Python 3.7.  In some cases, class and module docstrings are no
longer counted in statement totals, which could slightly change your total
results.

- Specifying both ``--source`` and ``--include`` no longer silently ignores the
include setting, instead it displays a warning. Thanks, Loïc Dachary.  Closes
`issue 265`_ and `issue 101`_.

- Fixed a race condition when saving data and multiple threads are tracing
(`issue 581`_). It could produce a &quot;dictionary changed size during iteration&quot;
RuntimeError.  I believe this mostly but not entirely fixes the race
condition.  A true fix would likely be too expensive.  Thanks, Peter Baughman
for the debugging, and Olivier Grisel for the fix with tests.

- Configuration values which are file paths will now apply tilde-expansion,
closing `issue 589`_.

- Now secondary config files like tox.ini and setup.cfg can be specified
explicitly, and prefixed sections like `[coverage:run]` will be read. Fixes
`issue 588`_.

- Be more flexible about the command name displayed by help, fixing
`issue 600`_. Thanks, Ben Finney.

.. _issue 101: https://bitbucket.org/ned/coveragepy/issues/101/settings-under-report-affect-running
.. _issue 581: https://bitbucket.org/ned/coveragepy/issues/581/race-condition-when-saving-data-under
.. _issue 588: https://bitbucket.org/ned/coveragepy/issues/588/using-rcfile-path-to-toxini-uses-run
.. _issue 589: https://bitbucket.org/ned/coveragepy/issues/589/allow-expansion-in-coveragerc
.. _issue 600: https://bitbucket.org/ned/coveragepy/issues/600/get-program-name-from-command-line-when


.. _changes_441:

4.4.1

----------------------------

- No code changes: just corrected packaging for Python 2.7 Linux wheels.


.. _changes_44:

4.4

--------------------------

- Reports could produce the wrong file names for packages, reporting ``pkg.py``
instead of the correct ``pkg/__init__.py``.  This is now fixed.  Thanks, Dirk
Thomas.

- XML reports could produce ``&lt;source&gt;`` and ``&lt;class&gt;`` lines that together
didn&#39;t specify a valid source file path.  This is now fixed. (`issue 526`_)

- Namespace packages are no longer warned as having no code. (`issue 572`_)

- Code that uses ``sys.settrace(sys.gettrace())`` in a file that wasn&#39;t being
coverage-measured would prevent correct coverage measurement in following
code. An example of this was running doctests programmatically. This is now
fixed. (`issue 575`_)

- Errors printed by the ``coverage`` command now go to stderr instead of
stdout.

- Running ``coverage xml`` in a directory named with non-ASCII characters would
fail under Python 2. This is now fixed. (`issue 573`_)

.. _issue 526: https://bitbucket.org/ned/coveragepy/issues/526/generated-xml-invalid-paths-for-cobertura
.. _issue 572: https://bitbucket.org/ned/coveragepy/issues/572/no-python-source-warning-for-namespace
.. _issue 573: https://bitbucket.org/ned/coveragepy/issues/573/cant-generate-xml-report-if-some-source
.. _issue 575: https://bitbucket.org/ned/coveragepy/issues/575/running-doctest-prevents-complete-coverage

4.4b1

----------------------------

- Some warnings can now be individually disabled.  Warnings that can be
disabled have a short name appended.  The ``[run] disable_warnings`` setting
takes a list of these warning names to disable. Closes both `issue 96`_ and
`issue 355`_.

- The XML report now includes attributes from version 4 of the Cobertura XML
format, fixing `issue 570`_.

- In previous versions, calling a method that used collected data would prevent
further collection.  For example, `save()`, `report()`, `html_report()`, and
others would all stop collection.  An explicit `start()` was needed to get it
going again.  This is no longer true.  Now you can use the collected data and
also continue measurement. Both `issue 79`_ and `issue 448`_ described this
problem, and have been fixed.

- Plugins can now find unexecuted files if they choose, by implementing the
`find_executable_files` method.  Thanks, Emil Madsen.

- Minimal IronPython support. You should be able to run IronPython programs
under ``coverage run``, though you will still have to do the reporting phase
with CPython.

- Coverage.py has long had a special hack to support CPython&#39;s need to measure
the coverage of the standard library tests. This code was not installed by
kitted versions of coverage.py.  Now it is.

.. _issue 79: https://bitbucket.org/ned/coveragepy/issues/79/save-prevents-harvesting-on-stop
.. _issue 96: https://bitbucket.org/ned/coveragepy/issues/96/unhelpful-warnings-produced-when-using
.. _issue 355: https://bitbucket.org/ned/coveragepy/issues/355/warnings-should-be-suppressable
.. _issue 448: https://bitbucket.org/ned/coveragepy/issues/448/save-and-html_report-prevent-further
.. _issue 570: https://bitbucket.org/ned/coveragepy/issues/570/cobertura-coverage-04dtd-support


.. _changes_434:

4.3.4

----------------------------

- Fixing 2.6 in version 4.3.3 broke other things, because the too-tricky
exception wasn&#39;t properly derived from Exception, described in `issue 556`_.
A newb mistake; it hasn&#39;t been a good few days.

.. _issue 556: https://bitbucket.org/ned/coveragepy/issues/556/43-fails-if-there-are-html-files-in-the


.. _changes_433:

4.3.3

----------------------------

- Python 2.6 support was broken due to a testing exception imported for the
benefit of the coverage.py test suite.  Properly conditionalizing it fixed
`issue 554`_ so that Python 2.6 works again.

.. _issue 554: https://bitbucket.org/ned/coveragepy/issues/554/traceback-on-python-26-starting-with-432


.. _changes_432:

4.3.2

----------------------------

- Using the ``--skip-covered`` option on an HTML report with 100% coverage
would cause a &quot;No data to report&quot; error, as reported in `issue 549`_. This is
now fixed; thanks, Loïc Dachary.

- If-statements can be optimized away during compilation, for example, `if 0:`
or `if __debug__:`.  Coverage.py had problems properly understanding these
statements which existed in the source, but not in the compiled bytecode.
This problem, reported in `issue 522`_, is now fixed.

- If you specified ``--source`` as a directory, then coverage.py would look for
importable Python files in that directory, and could identify ones that had
never been executed at all.  But if you specified it as a package name, that
detection wasn&#39;t performed.  Now it is, closing `issue 426`_. Thanks to Loïc
Dachary for the fix.

- If you started and stopped coverage measurement thousands of times in your
process, you could crash Python with a &quot;Fatal Python error: deallocating
None&quot; error.  This is now fixed.  Thanks to Alex Groce for the bug report.

- On PyPy, measuring coverage in subprocesses could produce a warning: &quot;Trace
function changed, measurement is likely wrong: None&quot;.  This was spurious, and
has been suppressed.

- Previously, coverage.py couldn&#39;t start on Jython, due to that implementation
missing the multiprocessing module (`issue 551`_). This problem has now been
fixed. Also, `issue 322`_ about not being able to invoke coverage
conveniently, seems much better: ``jython -m coverage run myprog.py`` works
properly.

- Let&#39;s say you ran the HTML report over and over again in the same output
directory, with ``--skip-covered``. And imagine due to your heroic
test-writing efforts, a file just achieved the goal of 100% coverage. With
coverage.py 4.3, the old HTML file with the less-than-100% coverage would be
left behind.  This file is now properly deleted.

.. _issue 322: https://bitbucket.org/ned/coveragepy/issues/322/cannot-use-coverage-with-jython
.. _issue 426: https://bitbucket.org/ned/coveragepy/issues/426/difference-between-coverage-results-with
.. _issue 522: https://bitbucket.org/ned/coveragepy/issues/522/incorrect-branch-reporting-with-__debug__
.. _issue 549: https://bitbucket.org/ned/coveragepy/issues/549/skip-covered-with-100-coverage-throws-a-no
.. _issue 551: https://bitbucket.org/ned/coveragepy/issues/551/coveragepy-cannot-be-imported-in-jython27


.. _changes_431:

4.3.1

----------------------------

- Some environments couldn&#39;t install 4.3, as described in `issue 540`_. This is
now fixed.

- The check for conflicting ``--source`` and ``--include`` was too simple in a
few different ways, breaking a few perfectly reasonable use cases, described
in `issue 541`_.  The check has been reverted while we re-think the fix for
`issue 265`_.

.. _issue 540: https://bitbucket.org/ned/coveragepy/issues/540/cant-install-coverage-v43-into-under
.. _issue 541: https://bitbucket.org/ned/coveragepy/issues/541/coverage-43-breaks-nosetest-with-coverage


.. _changes_43:

4.3

--------------------------

Special thanks to **Loïc Dachary**, who took an extraordinary interest in
coverage.py and contributed a number of improvements in this release.

- Subprocesses that are measured with `automatic subprocess measurement`_ used
to read in any pre-existing data file.  This meant data would be incorrectly
carried forward from run to run.  Now those files are not read, so each
subprocess only writes its own data. Fixes `issue 510`_.

- The ``coverage combine`` command will now fail if there are no data files to
combine. The combine changes in 4.2 meant that multiple combines could lose
data, leaving you with an empty .coverage data file. Fixes
`issue 525`_, `issue 412`_, `issue 516`_, and probably `issue 511`_.

- Coverage.py wouldn&#39;t execute `sys.excepthook`_ when an exception happened in
your program.  Now it does, thanks to Andrew Hoos.  Closes `issue 535`_.

- Branch coverage fixes:

- Branch coverage could misunderstand a finally clause on a try block that
 never continued on to the following statement, as described in `issue
 493`_.  This is now fixed. Thanks to Joe Doherty for the report and Loïc
 Dachary for the fix.

- A while loop with a constant condition (while True) and a continue
 statement would be mis-analyzed, as described in `issue 496`_. This is now
 fixed, thanks to a bug report by Eli Skeggs and a fix by Loïc Dachary.

- While loops with constant conditions that were never executed could result
 in a non-zero coverage report.  Artem Dayneko reported this in `issue
 502`_, and Loïc Dachary provided the fix.

- The HTML report now supports a ``--skip-covered`` option like the other
reporting commands.  Thanks, Loïc Dachary for the implementation, closing
`issue 433`_.

- Options can now be read from a tox.ini file, if any. Like set

pyup-bot · 2018-10-15T16:45:30Z

Closing this in favor of #5

pyup-bot added 10 commits October 8, 2018 10:47

Update click from 6.7 to 7.0

45106ac

Update pyparsing from 2.2.1 to 2.2.2

6449972

Pin biopython to latest version 1.71

fc5e4a5

Pin click_plugins to latest version 1.0.3

edb2f0b

Pin coverage to latest version 4.5.1

ce59767

Pin matplotlib to latest version 3.0.0

a2e2c07

Pin numpy to latest version 1.15.2

f2db90c

Pin pandas to latest version 0.23.4

8660e5d

Pin pyfaidx to latest version 0.5.4.2

a8ff811

Pin pyyaml to latest version 3.13

0020bd6

pyup-bot mentioned this pull request Oct 8, 2018

Scheduled weekly dependency update for week 39 #3

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pyup-bot closed this Oct 15, 2018

joelb123 deleted the pyup-scheduled-update-2018-10-08 branch October 15, 2018 16:45

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Scheduled weekly dependency update for week 40 #4

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pyup-bot commented Oct 8, 2018

Update click from 6.7 to 7.0.

7.0

Update pyparsing from 2.2.1 to 2.2.2.

2.2.2

Update biopython from 1.71 to 1.71.

1.51

1.00a4

1.00a3

1.00a2

Update click_plugins from 1.0.3 to 1.0.3.

1.0.3

1.0.2

1.0.1

1.0

Update coverage from 4.5.1 to 4.5.1.

4.5.1

4.5

4.4.2

4.4.1

4.4

4.4b1

4.3.4

4.3.3

4.3.2

4.3.1

4.3

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