Scheduled weekly dependency update for week 38 #2

pyup-bot · 2018-09-24T16:44:25Z

Update matplotlib from 2.2.3 to 3.0.0.

Changelog

Links

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

Update numpy from 1.15.1 to 1.15.2.

Changelog

1.15.2

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

This is a bugfix release for bugs and regressions reported following the 1.15.1
release.

* The matrix PendingDeprecationWarning is now suppressed in pytest 3.8.
* The new cached allocations machinery has been fixed to be thread safe.
* The boolean indexing of subclasses now works correctly.
* A small memory leak in PyArray_AdaptFlexibleDType has been fixed.

The Python versions supported by this release are 2.7, 3.4-3.7. The wheels are
linked with OpenBLAS v0.3.0, which should fix some of the linalg problems
reported for NumPy 1.14.

Compatibility Note
==================

The NumPy 1.15.x OS X wheels released on PyPI no longer contain 32-bit
binaries.  That will also be the case in future releases. See
`11625 &lt;https://github.com/numpy/numpy/issues/11625&gt;`__ for the related
discussion.  Those needing 32-bit support should look elsewhere or build
from source.

Contributors
============

A total of 4 people contributed to this release.  People with a &quot;+&quot; by their
names contributed a patch for the first time.

* Charles Harris
* Julian Taylor
* Marten van Kerkwijk
* Matti Picus

Pull requests merged
====================

A total of 4 pull requests were merged for this release.

* `11902 &lt;https://github.com/numpy/numpy/pull/11902&gt;`__: BUG: Fix matrix PendingDeprecationWarning suppression for pytest...
* `11981 &lt;https://github.com/numpy/numpy/pull/11981&gt;`__: BUG: fix cached allocations without the GIL for 1.15.x
* `11982 &lt;https://github.com/numpy/numpy/pull/11982&gt;`__: BUG: fix refcount leak in PyArray_AdaptFlexibleDType
* `11992 &lt;https://github.com/numpy/numpy/pull/11992&gt;`__: BUG: Ensure boolean indexing of subclasses sets base correctly.


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

Links

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

Update pyparsing from 2.2.0 to 2.2.1.

Changelog

2.2.1

-------------------------------
- Applied changes necessary to migrate hosting of pyparsing source
over to GitHub. Many thanks for help and contributions from hugovk,
jdufresne, and cngkaygusuz among others through this transition,
sorry it took me so long!

- Fixed import of collections.abc to address DeprecationWarnings
in Python 3.7.

- Updated oc.py example to support function calls in arithmetic
expressions; fixed regex for &#39;==&#39; operator; and added packrat
parsing. Raised on the pyparsing wiki by Boris Marin, thanks!

- Fixed bug in select_parser.py example, group_by_terms was not
reported. Reported on SF bugs by Adam Groszer, thanks Adam!

- Added &quot;Getting Started&quot; section to the module docstring, to 
guide new users to the most common starting points in pyparsing&#39;s
API.

- Fixed bug in Literal and Keyword classes, which erroneously
raised IndexError instead of ParseException.

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 setup.cfg, sections
are prefixed with &quot;coverage:&quot;, so ``[run]`` options will be read from the
``[coverage:run]`` section of tox.ini. Implements part of `issue 519`_.
Thanks, Stephen Finucane.

- Specifying both ``--source`` and ``--include`` no longer silently ignores the
include setting, instead it fails with a message. Thanks, Nathan Land and
Loïc Dachary. Closes `issue 265`_.

- The ``Coverage.combine`` method has a new parameter, ``strict=False``, to
support failing if there are no data files to combine.

- When forking subprocesses, the coverage data files would have the same random
number appended to the file name. This didn&#39;t cause problems, because the
file names had the process id also, making collisions (nearly) impossible.
But it was disconcerting.  This is now fixed.

- The text report now properly sizes headers when skipping some files, fixing
`issue 524`_. Thanks, Anthony Sottile and Loïc Dachary.

- Coverage.py can now search .pex files for source, just as it can .zip and
.egg.  Thanks, Peter Ebden.

- Data files are now about 15% smaller.

- Improvements in the ``[run] debug`` setting:

- The &quot;dataio&quot; debug setting now also logs when data files are deleted during
 combining or erasing.

- A new debug option, &quot;multiproc&quot;, for logging the behavior of
 ``concurrency=multiprocessing``.

- If you used the debug options &quot;config&quot; and &quot;callers&quot; together, you&#39;d get a
 call stack printed for every line in the multi-line config output. This is
 now fixed.

- Fixed an unusual bug involving multiple coding declarations affecting code
containing code in multi-line strings: `issue 529`_.

- Coverage.py will no longer be misled into thinking that a plain file is a
package when interpreting ``--source`` options.  Thanks, Cosimo Lupo.

- If you try to run a non-Python file with coverage.py, you will now get a more
useful error message. `Issue 514`_.

- The default pragma regex changed slightly, but this will only matter to you
if you are deranged and use mixed-case pragmas.

- Deal properly with non-ASCII file names in an ASCII-only world, `issue 533`_.

- Programs that set Unicode configuration values could cause UnicodeErrors when
generating HTML reports.  Pytest-cov is one example.  This is now fixed.

- Prevented deprecation warnings from configparser that happened in some
circumstances, closing `issue 530`_.

- Corrected the name of the jquery.ba-throttle-debounce.js library. Thanks,
Ben Finney.  Closes `issue 505`_.

- Testing against PyPy 5.6 and PyPy3 5.5.

- Switched to pytest from nose for running the coverage.py tests.

- Renamed AUTHORS.txt to CONTRIBUTORS.txt, since there are other ways to
contribute than by writing code. Also put the count of contributors into the
author string in setup.py, though this might be too cute.

.. _sys.excepthook: https://docs.python.org/3/library/sys.htmlsys.excepthook
.. _issue 265: https://bitbucket.org/ned/coveragepy/issues/265/when-using-source-include-is-silently
.. _issue 412: https://bitbucket.org/ned/coveragepy/issues/412/coverage-combine-should-error-if-no
.. _issue 433: https://bitbucket.org/ned/coveragepy/issues/433/coverage-html-does-not-suport-skip-covered
.. _issue 493: https://bitbucket.org/ned/coveragepy/issues/493/confusing-branching-failure
.. _issue 496: https://bitbucket.org/ned/coveragepy/issues/496/incorrect-coverage-with-branching-and
.. _issue 502: https://bitbucket.org/ned/coveragepy/issues/502/incorrect-coverage-report-with-cover
.. _issue 505: https://bitbucket.org/ned/coveragepy/issues/505/use-canonical-filename-for-debounce
.. _issue 514: https://bitbucket.org/ned/coveragepy/issues/514/path-to-problem-file-not-reported-when
.. _issue 510: https://bitbucket.org/ned/coveragepy/issues/510/erase-still-needed-in-42
.. _issue 511: https://bitbucket.org/ned/coveragepy/issues/511/version-42-coverage-combine-empties
.. _issue 516: https://bitbucket.org/ned/coveragepy/issues/516/running-coverage-combine-twice-deletes-all
.. _issue 519: https://bitbucket.org/ned/coveragepy/issues/519/coverage-run-sections-in-toxini-or-as
.. _issue 524: https://bitbucket.org/ned/coveragepy/issues/524/coverage-report-with-skip-covered-column
.. _issue 525: https://bitbucket.org/ned/coveragepy/issues/525/coverage-combine-when-not-in-parallel-mode
.. _issue 529: https://bitbucket.org/ned/coveragepy/issues/529/encoding-marker-may-only-appear-on-the
.. _issue 530: https://bitbucket.org/ned/coveragepy/issues/530/deprecationwarning-you-passed-a-bytestring
.. _issue 533: https://bitbucket.org/ned/coveragepy/issues/533/exception-on-unencodable-file-name
.. _issue 535: https://bitbucket.org/ned/coveragepy/issues/535/sysexcepthook-is-not-called


.. _changes_42:

4.2

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

- Since ``concurrency=multiprocessing`` uses subprocesses, options specified on
the coverage.py command line will not be communicated down to them.  Only
options in the configuration file will apply to the subprocesses.
Previously, the options didn&#39;t apply to the subprocesses, but there was no
indication.  Now it is an error to use ``--concurrency=multiprocessing`` and
other run-affecting options on the command line.  This prevents
failures like those reported in `issue 495`_.

- Filtering the HTML report is now faster, thanks to Ville Skyttä.

.. _issue 495: https://bitbucket.org/ned/coveragepy/issues/495/branch-and-concurrency-are-conflicting

4.2b1

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

Work from the PyCon 2016 Sprints!

- BACKWARD INCOMPATIBILITY: the ``coverage combine`` command now ignores an
existing ``.coverage`` data file.  It used to include that file in its
combining.  This caused confusing results, and extra tox &quot;clean&quot; steps.  If
you want the old behavior, use the new ``coverage combine --append`` option.

- The ``concurrency`` option can now take multiple values, to support programs
using multiprocessing and another library such as eventlet.  This is only
possible in the configuration file, not from the command line. The
configuration file is the only way for sub-processes to all run with the same
options.  Fixes `issue 484`_.  Thanks to Josh Williams for prototyping.

- Using a ``concurrency`` setting of ``multiprocessing`` now implies
``--parallel`` so that the main program is measured similarly to the
sub-processes.

- When using `automatic subprocess measurement`_, running coverage commands
would create spurious data files.  This is now fixed, thanks to diagnosis and
testing by Dan Riti.  Closes `issue 492`_.

- A new configuration option, ``report:sort``, controls what column of the
text report is used to sort the rows.  Thanks to Dan Wandschneider, this
closes `issue 199`_.

- The HTML report has a more-visible indicator for which column is being
sorted.  Closes `issue 298`_, thanks to Josh Williams.

- If the HTML report cannot find the source for a file, the message now
suggests using the ``-i`` flag to allow the report to continue. Closes
`issue 231`_, thanks, Nathan Land.

- When reports are ignoring errors, there&#39;s now a warning if a file cannot be
parsed, rather than being silently ignored.  Closes `issue 396`_. Thanks,
Matthew Boehm.

- A new option for ``coverage debug`` is available: ``coverage debug config``
shows the current configuration.  Closes `issue 454`_, thanks to Matthew
Boehm.

- Running coverage as a module (``python -m coverage``) no longer shows the
program name as ``__main__.py``.  Fixes `issue 478`_.  Thanks, Scott Belden.

- The `test_helpers` module has been moved into a separate pip-installable
package: `unittest-mixins`_.

.. _automatic subprocess measurement: https://coverage.readthedocs.io/en/latest/subprocess.html
.. _issue 199: https://bitbucket.org/ned/coveragepy/issues/199/add-a-way-to-sort-the-text-report
.. _issue 231: https://bitbucket.org/ned/coveragepy/issues/231/various-default-behavior-in-report-phase
.. _issue 298: https://bitbucket.org/ned/coveragepy/issues/298/show-in-html-report-that-the-columns-are
.. _issue 396: https://bitbucket.org/ned/coveragepy/issues/396/coverage-xml-shouldnt-bail-out-on-parse
.. _issue 454: https://bitbucket.org/ned/coveragepy/issues/454/coverage-debug-config-should-be
.. _issue 478: https://bitbucket.org/ned/coveragepy/issues/478/help-shows-silly-program-name-when-running
.. _issue 484: https://bitbucket.org/ned/coveragepy/issues/484/multiprocessing-greenlet-concurrency
.. _issue 492: https://bitbucket.org/ned/coveragepy/issues/492/subprocess-coverage-strange-detection-of
.. _unittest-mixins: https://pypi.org/project/unittest-mixins/


.. _changes_41:

4.1

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

- The internal attribute `Reporter.file_reporters` was removed in 4.1b3.  It
should have come has no surprise that there were third-party tools out there
using that attribute.  It has been restored, but with a deprecation warning.

4.1b3

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

- When running your program, execution can jump from an ``except X:`` line to
some other line when an exception other than ``X`` happens.  This jump is no
longer considered a branch when measuring branch coverage.

- When measuring branch coverage, ``yield`` statements that were never resumed
were incorrectly marked as missing, as reported in `issue 440`_.  This is now
fixed.

- During branch coverage of single-line callables like lambdas and generator
expressions, coverage.py can now distinguish between them never being called,
or being called but not completed.  Fixes `issue 90`_, `issue 460`_ and
`issue 475`_.

- The HTML report now has a map of the file along the rightmost edge of the
page, giving an overview of where the missed lines are.  Thanks, Dmitry
Shishov.

- The HTML report now uses different monospaced fonts, favoring Consolas over
Courier.  Along the way, `issue 472`_ about not properly handling one-space
indents was fixed.  The index page also has slightly different styling, to
try to make the clickable detail pages more apparent.

- Missing branches reported with ``coverage report -m`` will now say ``-&gt;exit``
for missed branches to the exit of a function, rather than a negative number.
Fixes `issue 469`_.

- ``coverage --help`` and ``coverage --version`` now mention which tracer is
installed, to help diagnose problems. The docs mention which features need
the C extension. (`issue 479`_)

- Officially support PyPy 5.1, which required no changes, just updates to the
docs.

- The `Coverage.report` function had two parameters with non-None defaults,
which have been changed.  `show_missing` used to default to True, but now
defaults to None.  If you had been calling `Coverage.report` without
specifying `show_missing`, you&#39;ll need to explicitly set it to True to keep
the same behavior.  `skip_covered` used to default to False. It is now None,
which doesn&#39;t change the behavior.  This fixes `issue 485`_.

- It&#39;s never been possible to pass a namespace module to one of the analysis
functions, but now at least we raise a more specific error message, rather
than getting confused. (`issue 456`_)

- The `coverage.process_startup` function now returns the `Coverage` instance
it creates, as suggested in `issue 481`_.

- Make a small tweak to how we compare threads, to avoid buggy custom
comparison code in thread classes. (`issue 245`_)

.. _issue 90: https://bitbucket.org/ned/coveragepy/issues/90/lambda-expression-confuses-branch
.. _issue 245: https://bitbucket.org/ned/coveragepy/issues/245/change-solution-for-issue-164
.. _issue 440: https://bitbucket.org/ned/coveragepy/issues/440/yielded-twisted-failure-marked-as-missed
.. _issue 456: https://bitbucket.org/ned/coveragepy/issues/456/coverage-breaks-with-implicit-namespaces
.. _issue 460: https://bitbucket.org/ned/coveragepy/issues/460/confusing-html-report-for-certain-partial
.. _issue 469: https://bitbucket.org/ned/coveragepy/issues/469/strange-1-line-number-in-branch-coverage
.. _issue 472: https://bitbucket.org/ned/coveragepy/issues/472/html-report-indents-incorrectly-for-one
.. _issue 475: https://bitbucket.org/ned/coveragepy/issues/475/generator-expression-is-marked-as-not
.. _issue 479: https://bitbucket.org/ned/coveragepy/issues/479/clarify-the-need-for-the-c-extension
.. _issue 481: https://bitbucket.org/ned/coveragepy/issues/481/asyncioprocesspoolexecutor-tracing-not
.. _issue 485: https://bitbucket.org/ned/coveragepy/issues/485/coveragereport-ignores-show_missing-and

4.1b2

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

- Problems with the new branch measurement in 4.1 beta 1 were fixed:

- Class docstrings were considered executable.  Now they no longer are.

- ``yield from`` and ``await`` were considered returns from functions, since
 they could transfer control to the caller.  This pro

codecov-io · 2018-09-24T16:46:38Z

Codecov Report

Merging #2 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master       #2   +/-   ##
=======================================
  Coverage   24.03%   24.03%           
=======================================
  Files           9        9           
  Lines        1090     1090           
=======================================
  Hits          262      262           
  Misses        828      828

Continue to review full report at Codecov.

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pyup-bot · 2018-10-01T16:47:28Z

Closing this in favor of #3

pyup-bot added 11 commits September 24, 2018 10:44

Update matplotlib from 2.2.3 to 3.0.0

409c8d4

Update numpy from 1.15.1 to 1.15.2

d005ba8

Update pyparsing from 2.2.0 to 2.2.1

c578611

Pin biopython to latest version 1.71

0f5e71d

Pin click_plugins to latest version 1.0.3

4fdb696

Pin coverage to latest version 4.5.1

11e82b2

Pin matplotlib to latest version 3.0.0

d78d625

Pin numpy to latest version 1.15.2

183487f

Pin pandas to latest version 0.23.4

28496bb

Pin pyfaidx to latest version 0.5.4.2

074df18

Pin pyyaml to latest version 3.13

2e9f03c

pyup-bot mentioned this pull request Sep 24, 2018

Scheduled weekly dependency update for week 37 #1

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joelb123 deleted the pyup-scheduled-update-2018-09-24 branch October 1, 2018 16:47

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Update matplotlib from 2.2.3 to 3.0.0.

Update numpy from 1.15.1 to 1.15.2.

1.15.2

Update pyparsing from 2.2.0 to 2.2.1.

2.2.1

Update biopython from 1.71 to 1.71.

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Update coverage from 4.5.1 to 4.5.1.

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4.4.2

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4.4b1

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