Scheduled weekly dependency update for week 17

[pyup-bot]

Update click from 7.0 to 7.1.1.

Changelog

7.1.1

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

Released 2020-03-09

-   Fix ``ClickException`` output going to stdout instead of stderr.
 :issue:`1495`

7.1

-----------

Released 2020-03-09

-   Fix PyPI package name, "click" is lowercase again.
-   Fix link in ``unicode_literals`` error message. :pr:`1151`
-   Add support for colored output on UNIX Jupyter notebooks.
 :issue:`1185`
-   Operations that strip ANSI controls will strip the cursor hide/show
 sequences. :issue:`1216`
-   Remove unused compat shim for ``bytes``. :pr:`1195`
-   Expand testing around termui, especially getchar on Windows.
 :issue:`1116`
-   Fix output on Windows Python 2.7 built with MSVC 14. :pr:`1342`
-   Fix ``OSError`` when running in MSYS2. :issue:`1338`
-   Fix ``OSError`` when redirecting to ``NUL`` stream on Windows.
 :issue:`1065`
-   Fix memory leak when parsing Unicode arguments on Windows.
 :issue:`1136`
-   Fix error in new AppEngine environments. :issue:`1462`
-   Always return one of the passed choices for ``click.Choice``
 :issue:`1277`, :pr:`1318`
-   Add ``no_args_is_help`` option to ``click.Command``, defaults to
 False :pr:`1167`
-   Add ``show_defaults`` parameter to ``Context`` to enable showing
 defaults globally. :issue:`1018`
-   Handle ``env MYPATH=''`` as though the option were not passed.
 :issue:`1196`
-   It is once again possible to call ``next(bar)`` on an active
 progress bar instance. :issue:`1125`
-   ``open_file`` with ``atomic=True`` retains permissions of existing
 files and respects the current umask for new files. :issue:`1376`
-   When using the test ``CliRunner`` with ``mix_stderr=False``, if
 ``result.stderr`` is empty it will not raise a ``ValueError``.
 :issue:`1193`
-   Remove the unused ``mix_stderr`` parameter from
 ``CliRunner.invoke``. :issue:`1435`
-   Fix ``TypeError`` raised when using bool flags and specifying
 ``type=bool``. :issue:`1287`
-   Newlines in option help text are replaced with spaces before
 re-wrapping to avoid uneven line breaks. :issue:`834`
-   ``MissingParameter`` exceptions are printable in the Python
 interpreter. :issue:`1139`
-   Fix how default values for file-type options are shown during
 prompts. :issue:`914`
-   Fix environment variable automatic generation for commands
 containing ``-``. :issue:`1253`
-   Option help text replaces newlines with spaces when rewrapping, but
 preserves paragraph breaks, fixing multiline formatting.
 :issue:`834, 1066, 1397`
-   Option help text that is wrapped adds an extra newline at the end to
 distinguish it from the next option. :issue:`1075`
-   Consider ``sensible-editor`` when determining the editor to use for
 ``click.edit()``. :pr:`1469`
-   Arguments to system calls such as the executable path passed to
 ``click.edit`` can contains spaces. :pr:`1470`
-   Add ZSH completion autoloading and error handling. :issue:`1348`
-   Add a repr to ``Command``, ``Group``, ``Option``, and ``Argument``,
 showing the name for friendlier debugging. :issue:`1267`
-   Completion doesn't consider option names if a value starts with
 ``-`` after the ``--`` separator. :issue:`1247`
-   ZSH completion escapes special characters in values. :pr:`1418`
-   Add completion support for Fish shell. :pr:`1423`
-   Decoding bytes option values falls back to UTF-8 in more cases.
 :pr:`1468`
-   Make the warning about old 2-arg parameter callbacks a deprecation
 warning, to be removed in 8.0. This has been a warning since Click
 2.0. :pr:`1492`

Links

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

Update coverage from 5.0.3 to 5.1.

Changelog

5.1

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

- The JSON report now includes counts of covered and missing branches. Thanks,
Salvatore Zagaria.

- On Python 3.8, try-finally-return reported wrong branch coverage with
decorated async functions (`issue 946`_).  This is now fixed. Thanks, Kjell
Braden.

- The :meth:`~coverage.Coverage.get_option` and
:meth:`~coverage.Coverage.set_option` methods can now manipulate the
``[paths]`` configuration setting.  Thanks to Bernát Gábor for the fix for
`issue 967`_.

.. _issue 946: https://github.com/nedbat/coveragepy/issues/946
.. _issue 967: https://github.com/nedbat/coveragepy/issues/967


.. _changes_504:

5.0.4

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

- If using the ``[run] relative_files`` setting, the XML report will use
relative files in the ``<source>`` elements indicating the location of source
code.  Closes `issue 948`_.

- The textual summary report could report missing lines with negative line
numbers on PyPy3 7.1 (`issue 943`_).  This is now fixed.

- Windows wheels for Python 3.8 were incorrectly built, but are now fixed.
(`issue 949`_)

- Updated Python 3.9 support to 3.9a4.

- HTML reports couldn't be sorted if localStorage wasn't available. This is now
fixed: sorting works even though the sorting setting isn't retained. (`issue
944`_ and `pull request 945`_). Thanks, Abdeali Kothari.

.. _issue 943: https://github.com/nedbat/coveragepy/issues/943
.. _issue 944: https://github.com/nedbat/coveragepy/issues/944
.. _pull request 945: https://github.com/nedbat/coveragepy/pull/945
.. _issue 948: https://github.com/nedbat/coveragepy/issues/948
.. _issue 949: https://github.com/nedbat/coveragepy/issues/949


.. _changes_503:

Links

• PyPI: https://pypi.org/project/coverage
• Changelog: https://pyup.io/changelogs/coverage/
• Repo: https://github.com/nedbat/coveragepy

Update importlib-metadata from 1.4.0 to 1.6.0.

The bot wasn't able to find a changelog for this release. Got an idea?

Links

• PyPI: https://pypi.org/project/importlib-metadata
• Docs: http://importlib-metadata.readthedocs.io/

Update kiwisolver from 1.1.0 to 1.2.0.

The bot wasn't able to find a changelog for this release. Got an idea?

Links

• PyPI: https://pypi.org/project/kiwisolver
• Repo: https://github.com/nucleic/kiwi

Update matplotlib from 3.1.2 to 3.2.1.

Changelog

3.2.1

This is the first bugfix release of the 3.2.x series.

This release contains several critical bug-fixes:

- fix `Quiver.set_UVC` calls with scalar inputs
- fix `bezier.get_parallels` failure from floating point rounding errors
- fix markers specified as tuples (polygons, stars, or asterisks)
- fix saving PNGs to file objects in some places
- fix saving figures using the nbAgg/notebook backend
- fix saving with tight layout using the PGF backend
- fix setting custom datapath in rcParams (note: it is still deprecated)
- fix various issues running setup.py in non-CI environments
- fix xpdf distiller
- various minor bug and documentation fixes

3.2.0rc1

This is the first release candidate from Matplotlib 3.2

Links

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

Update mock from 3.0.5 to 4.0.2.

Changelog

4.0.2

-----

- Issue 39915: Ensure :attr:`unittest.mock.AsyncMock.await_args_list` has
call objects in the order of awaited arguments instead of using
:attr:`unittest.mock.Mock.call_args` which has the last value of the call.
Patch by Karthikeyan Singaravelan.

4.0.1

-----

- Remove the universal marker from the wheel.

4.0.0

-----

- No Changes from 4.0.0b1.

4.0.0b1

-------

- The release is a fresh cut of cpython's `4a686504`__. All changes to :mod:`mock`
from that commit and before are included in this release along with the
subsequent changes listed below.

__ https://github.com/python/cpython/commit/4a686504eb2bbf69adf78077458508a7ba131667

- Issue 37972: Subscripts to the `unittest.mock.call` objects now receive
the same chaining mechanism as any other custom attributes, so that the
following usage no longer raises a `TypeError`:

call().foo().__getitem__('bar')

Patch by blhsing

- Issue 38839: Fix some unused functions in tests. Patch by Adam Johnson.

- Issue 39485: Fix a bug in :func:`unittest.mock.create_autospec` that
would complain about the wrong number of arguments for custom descriptors
defined in an extension module returning functions.

- Issue 39082: Allow AsyncMock to correctly patch static/class methods

- Issue 38093: Fixes AsyncMock so it doesn't crash when used with
AsyncContextManagers or AsyncIterators.

- Issue 38859: AsyncMock now returns StopAsyncIteration on the exaustion of
a side_effects iterable. Since PEP-479 its Impossible to raise a
StopIteration exception from a coroutine.

- Issue 38163: Child mocks will now detect their type as either synchronous
or asynchronous, asynchronous child mocks will be AsyncMocks and
synchronous child mocks will be either MagicMock or Mock (depending on
their parent type).

- Issue 38473: Use signature from inner mock for autospecced methods
attached with :func:`unittest.mock.attach_mock`. Patch by Karthikeyan
Singaravelan.

- Issue 38136: Changes AsyncMock call count and await count to be two
different counters. Now await count only counts when a coroutine has been
awaited, not when it has been called, and vice-versa. Update the
documentation around this.

- Issue 37555: Fix `NonCallableMock._call_matcher` returning tuple instead
of `_Call` object when `self._spec_signature` exists. Patch by Elizabeth
Uselton

- Issue 37251: Remove `__code__` check in AsyncMock that incorrectly
evaluated function specs as async objects but failed to evaluate classes
with `__await__` but no `__code__` attribute defined as async objects.

- Issue 38669: Raise :exc:`TypeError` when passing target as a string with
:meth:`unittest.mock.patch.object`.

- Issue 25597: Ensure, if ``wraps`` is supplied to
:class:`unittest.mock.MagicMock`, it is used to calculate return values
for the magic methods instead of using the default return values. Patch by
Karthikeyan Singaravelan.

- Issue 38108: Any synchronous magic methods on an AsyncMock now return a
MagicMock. Any asynchronous magic methods on a MagicMock now return an
AsyncMock.

- Issue 21478: Record calls to parent when autospecced object is attached
to a mock using :func:`unittest.mock.attach_mock`. Patch by Karthikeyan
Singaravelan.

- Issue 38857: AsyncMock fix for return values that are awaitable types.
This also covers side_effect iterable values that happend to be awaitable,
and wraps callables that return an awaitable type. Before these awaitables
were being awaited instead of being returned as is.

- Issue 38932: Mock fully resets child objects on reset_mock(). Patch by
Vegard Stikbakke

- Issue 37685: Fixed ``__eq__``, ``__lt__`` etc implementations in some
classes. They now return :data:`NotImplemented` for unsupported type of
the other operand. This allows the other operand to play role (for example
the equality comparison with :data:`~unittest.mock.ANY` will return
``True``).

- Issue 37212: :func:`unittest.mock.call` now preserves the order of
keyword arguments in repr output. Patch by Karthikeyan Singaravelan.

- Issue 37828: Fix default mock name in
:meth:`unittest.mock.Mock.assert_called` exceptions. Patch by Abraham
Toriz Cruz.

- Issue 36871: Improve error handling for the assert_has_calls and
assert_has_awaits methods of mocks. Fixed a bug where any errors
encountered while binding the expected calls to the mock's spec were
silently swallowed, leading to misleading error output.

- Issue 21600: Fix :func:`mock.patch.stopall` to stop active patches that
were created with :func:`mock.patch.dict`.

- Issue 38161: Removes _AwaitEvent from AsyncMock.

- Issue 36871: Ensure method signature is used instead of constructor
signature of a class while asserting mock object against method calls.
Patch by Karthikeyan Singaravelan.

Links

• PyPI: https://pypi.org/project/mock
• Changelog: https://pyup.io/changelogs/mock/
• Docs: http://mock.readthedocs.org/en/latest/

Update more-itertools from 8.1.0 to 8.2.0.

Changelog

8.2.0

See the [release notes](https://raw.githubusercontent.com/erikrose/more-itertools/0861bed72ddd4c8ebcfa3a932b7689e272c43478/docs/versions.rst) for details.

Links

• PyPI: https://pypi.org/project/more-itertools
• Changelog: https://pyup.io/changelogs/more-itertools/
• Repo: https://github.com/erikrose/more-itertools
• Docs: https://pythonhosted.org/more-itertools/

Update numpy from 1.18.1 to 1.18.3.

The bot wasn't able to find a changelog for this release. Got an idea?

Links

• PyPI: https://pypi.org/project/numpy
• Homepage: https://www.numpy.org

Update packaging from 20.1 to 20.3.

Changelog

20.3

~~~~~~~~~~~~~~~~~

* Fix changelog for 20.2.

20.2

~~~~~~~~~~~~~~~~~

* Fix a bug that caused a 32-bit OS that runs on a 64-bit ARM CPU (e.g. ARM-v8,
aarch64), to report the wrong bitness.

Links

• PyPI: https://pypi.org/project/packaging
• Changelog: https://pyup.io/changelogs/packaging/
• Repo: https://github.com/pypa/packaging

Update pandas from 0.25.3 to 1.0.3.

The bot wasn't able to find a changelog for this release. Got an idea?

Links

• PyPI: https://pypi.org/project/pandas
• Homepage: https://pandas.pydata.org

Update path.py from 12.0.2 to 12.4.0.

Changelog

12.2.0

-------

- 169: Moved project at GitHub from ``jaraco/path.py`` to
``jaraco/path``.

12.1.0

-------

- 171: Fixed exception in ``rmdir_p`` when target is not empty.
- 174: Rely on ``importlib.metadata`` on Python 3.8.

Links

• PyPI: https://pypi.org/project/path.py
• Changelog: https://pyup.io/changelogs/path.py/
• Repo: https://github.com/jaraco/path

Update pyparsing from 2.4.6 to 2.4.7.

Changelog

2.4.7

---------------------------------------------
- Backport of selected fixes from 3.0.0 work:
. Each bug with Regex expressions
. And expressions not properly constructing with generator
. Traceback abbreviation
. Bug in delta_time example
. Fix regexen in pyparsing_common.real and .sci_real
. Avoid FutureWarning on Python 3.7 or later
. Cleanup output in runTests if comments are embedded in test string

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 pytest from 5.3.4 to 5.4.1.

The bot wasn't able to find a changelog for this release. Got an idea?

Links

• PyPI: https://pypi.org/project/pytest
• Homepage: https://docs.pytest.org/en/latest/

Update pyyaml from 5.3 to 5.3.1.

The bot wasn't able to find a changelog for this release. Got an idea?

Links

• PyPI: https://pypi.org/project/pyyaml
• Repo: https://github.com/yaml/pyyaml

Update seaborn from 0.10.0 to 0.10.1.

Changelog

0.10.1

This is minor release with bug fixes for issues identified since 0.10.0.

- Fixed a bug that appeared within the bootstrapping algorithm on
 32-bit systems.
- Fixed a bug where `regplot` would crash on singleton inputs. Now a
 crash is avoided and regression estimation/plotting is skipped.
- Fixed a bug where `heatmap` would ignore user-specified
 under/over/bad values when recentering a colormap.
- Fixed a bug where `heatmap` would use values from masked cells when
 computing default colormap limits.
- Fixed a bug where `despine` would cause an error when trying to trim
 spines on a matplotlib categorical axis.
- Adapted to a change in matplotlib that caused problems with single
 swarm plots.
- Added the `showfliers` parameter to `boxenplot` to suppress plotting
 of outlier data points, matching the API of `boxplot`.
- Avoided seeing an error from statmodels when data with an IQR of 0
 is passed to `kdeplot`.
- Added the `legend.title_fontsize` to the `plotting_context`
 definition.
- Deprecated several utility functions that are no longer used
 internally (`percentiles`, `sig_stars`, `pmf_hist`, and `sort_df`).

Links

• PyPI: https://pypi.org/project/seaborn
• Changelog: https://pyup.io/changelogs/seaborn/
• Repo: https://github.com/mwaskom/seaborn/
• Homepage: https://seaborn.pydata.org

Update wcwidth from 0.1.8 to 0.1.9.

Changelog

0.1.9

- **Performance** optimization by avylove , PR 35.
- **Updated** tables to Unicode Specification 13.0.0.

Links

• PyPI: https://pypi.org/project/wcwidth
• Changelog: https://pyup.io/changelogs/wcwidth/
• Repo: https://github.com/jquast/wcwidth

Update zipp from 2.1.0 to 3.1.0.

Changelog

3.1.0

======

47: ``.open`` now raises ``FileNotFoundError`` and
``IsADirectoryError`` when appropriate.

3.0.0

======

44: Merge with v1.2.0.

2.2.1

======

43: Merge with v1.1.1.

2.2.0

======

36: Rebuild package with minimum Python version declared both
in package metadata and in the python tag.

Links

• PyPI: https://pypi.org/project/zipp
• Changelog: https://pyup.io/changelogs/zipp/
• Repo: https://github.com/jaraco/zipp

Update biopython from 1.76 to 1.76.

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 "fastq-solexa" in
Bio.SeqIO), Illumina 1.3+ FASTQ files have PHRED scores from 0 to 62 (format
name "fastq-illumina"), and Sanger FASTQ files have PHRED scores from 0 to
93 (format name "fastq" or "fastq-sanger").

Bio.Sequencing.Phd has been updated, for example to cope with missing peak
positions. The "phd" support in Bio.SeqIO has also been updated to record
the PHRED qualities (and peak positions) in the SeqRecord'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
"fastq-illumina". Biopython 1.50 supported just "fastq" (the original Sanger
style FASTQ files using PHRED scores with an ASCII offset of 33), and
"fastq-solexa" (the original Solexa/Illumina FASTQ format variant holding
Solexa scores with an ASCII offset of 64) .

For parsing the "swiss" 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'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's Entrez EFetch no longer supports rettype="genbank"
and "gb" (or "gp") should be used instead.
* Bio.SeqIO now supports "gb" as an alias for "genbank".
* 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'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'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's translate function has changed so that
ambiguous codons which could be a stop codon like "TAN" or "NNN" are now
translated as "X" (consistent with EMBOSS and BioPerl - Biopython previously
raised an exception), and a bug was fixed so that invalid codons (like "A-T")
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 "Cookbook" 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 "tab" format (simple tab separated)
- writing "nexus" files.
- reading "pir" files (NBRF/PIR)
- basic support for writing "genbank" 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 "ig" 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'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'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'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'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 >= 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 'complement' and 'reverse_complement' to Bio.Seq'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 issue 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'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 'from Bio import db' 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'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'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'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's clustering library
- Iddo'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's EUtils library
- added Michiel de Hoon'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'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's NCBIStandalone fix for long query lengths
- slew of miscellaneous fixes from George Paci
- miscellaneous cleanups and updates from Andreas Kuntzagk
- Peter Bienstman's fixes to Genbank code -- now parses whole database
- Kayte Lindner'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's patch to read T_Coffee files
- Larry Heisler's fix for primer3 output
- Bio.Medline now uses proper iterator objects
- copen now handles SIGTERM correctly
- small bugfixes and updates in Thomas Hamelryck'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'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://mailman.open-bio.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 (https://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 (https://github.com/biopython/biopython/blob/9c4785fc9eaf8a3bc436c6c0b16e7a05019cade1/LICENSE)
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're interested, please visit the web page, join the biopython
mailing list, and let us know what you think!

Jeffrey Chang <jchangsmi.stanford.edu>
Andrew Dalke <dalkebioreason.com>

Links

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

Update click_plugins from 1.1.1 to 1.1.1.

Changelog

1.1.1

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

- Fixed a version mismatch in `click_plugins/__init__.py`  See `1.1`.

1.1

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

- Fix an issue where a broken command's traceback would not be emitted - https://github.com/click-contrib/click-plugins/issues/25
- Bump required click version to `click>=4` - https://github.com/click-contrib/click-plugins/pull/28
- Runs Travis tests for the latest release of click versions 4 -> 7 - https://github.com/click-contrib/click-plugins/pull/28

1.0.4

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

- Preemptive fix for a breaking change in Click v7.  CLI command names generated from functions with underscores will have dashes instead of underscores.  See https://github.com/click-contrib/click-plugins/issues/19.

1.0.3

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

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

1.0.2

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

- General packaging and Travis-CI improvements.
- Don'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 colorama from 0.4.3 to 0.4.3.

Changelog

0.4.1

* Fix issue 196: prevent exponential number of calls when calling 'init'
 multiple times. Reported by bbayles and fixed by Delgan.

0.4.0

* Fix issue 142: reset LIGHT_EX colors with RESET_ALL. Reported by Delgan
* Fix issue 147: ignore invalid "erase" ANSI codes. Reported by shin-
* Fix issues 163 and 164: fix stream wrapping under PyCharm. Contributed
 by veleek and Delgan.
* Thanks to jdufresne for various code cleanup and updates to documentation
 and project metadata.
 (pull requests 171, 172, 173, 174, 176, 177, 189, 190, 192)
* 186: added contextlib magic methods to ansitowin32.StreamWrapper.
 Contributed by hoefling.
* Fix issue 131: don't cache stdio handles, since they might be
 closed/changed by fd redirection. This fixes an issue with pytest.
 Contributed by segevfiner.
* 146, 157: Drop support for EOL Python 2.5, 2.6, 3.1, 3.2 and 3.3,
 and add 3.6. Thanks to hugovk.

0.3.9

* Revert fix for issue 103 which causes problems for dependent applications

0.3.8

* Fix issue 121: "invalid escape sequence" deprecation fixes on Python 3.6+
* Fix issue 110: fix "set console title" when working with unicode strings
* Fix issue 103: enable color when using "input" function on Python 3.5+
* Fix issue 95: enable color when stderr is a tty but stdout is not

0.3.7

* Fix issue 84: check if stream has 'closed' attribute before testing it
* Fix issue 74: objects might become None at exit

0.3.6

* Fix issue 81: fix ValueError when a closed stream was used

0.3.5

* Bumping version to re-upload a wheel distribution

0.3.4

* Fix issue 47 and 80 - stream redirection now strips ANSI codes on Linux
* Fix issue 53 - strip readline markers
* Fix issue 32 - assign orig_stdout and orig_stderr when initialising
* Fix issue 57 - Fore.RESET did not reset style of LIGHT_EX colors.
 Fixed by Andy Neff
* Fix issue 51 - add context manager syntax. Thanks to Matt Olsen.
* Fix issue 48 - colorama didn't work on Windows when environment
 variable 'TERM' was set.
* Fix issue 54 - fix pylint errors in client code.
* Changes to readme and other improvements by Marc Abramowitz and Zearin

0.3.3

* Fix Google Code issue 13 - support changing the console title with OSC
 escape sequence
* Fix Google Code issue 16 - Add support for Windows xterm emulators
* Fix Google Code issue 30 - implement \033[nK (clear line)
* Fix Google Code issue 49 - no need to adjust for scroll when new position
 is already relative (CSI n A\B\C\D)
* Fix Google Code issue 55 - erase_data fails on Python 3.x
* Fix Google Code issue 46 - win32.COORD definition missing
* Implement \033[0J and \033[1J (clear screen options)
* Fix default ANSI parameters
* Fix position after \033[2J (clear screen)
* Add command shortcuts: colorama.Cursor, colorama.ansi.set_title,
 colorama.ansi.clear_line, colorama.ansi.clear_screen
* Fix issue 22 - Importing fails for python3 on Windows
* Thanks to John Szakmeister for adding support for light colors
* Thanks to Charles Merriam for adding documentation to demos

0.3.2

* Thanks to Marc Schlaich (schlamar) for a setup.py fix for Python2.5
* Thanks to Jurko for fix on 64-bit Windows CPython2.5 w/o ctypes
 (Google Code issue 56)
* Thanks to Remi Rampin for:
 * better github integration, incl rendered README and Travis config.
 * fixed forward slashes in README
* Thanks to Florian Bruhin for fix when stdout or stderr are None
* Thanks to Simeon Visser for:
 * closing a file handle using 'with'
 * updating classifiers to include Python 3.3 and 3.4
* Thanks to Thomas Weininger for fix ValueError on Windows
 (Google Code issue 50)

0.3.1

* Fixed crash on exit with closed stdout, with thanks to Marc Abramowitz.
* Now uses setuptools if available, and falls back to distutils if not.
* setup.py no longer imports anything from colorama source.

0.3.0

* Move repository to Git, https://github.com/tartley/colorama. (My Mercurial
 repo seemed to be corrupted, I couldn't commit nor view patches of old
 commits, even on fresh checkouts.)
* Fix always-crash on non-Windows platforms, reported by Matt McCormick.
* Fix Google Code issue 47, incompatible with pyreadline.

0.2.7

* Fix problem under 64-bit windows due to ctypes HANDLE size.
 Submitted by the rather magnificent Ben Hoyt.
 This fixes Google Code issue 43

0.2.6

* Add copyright & licensing info to every file, as requested by a large
 downstream project which has problems making sure that all 3rd party
 contributions have appropriate license.

0.2.5

* Several documentation & demo fixes.

0.2.4

* Fix to work on Windows 7.
* Python 3 compatibility in docs and demos.
* Add handling for 'cursor up' and 'get position' ANSI codes.

0.2.3

* Split changelog out into separate file.

0.2.2

* Fix bug which caused init() to raise, introduced in 0.2.1.
* Remove asserts which cause problems in various circumstances. At least
 some users saw asserts fail on 'success' returned from win32 functions,
 even though the win32 functions appear to have worked correctly.

0.2.1

* Completely broken: I added a bug which caused init() to raise.
* Added some documentation for cursor positioning and clear screen to README.
* Add 'reinit' and 'deinit' functions, as suggested by Charles FOL and
 Romanov DA.

0.2

* Merge in changes from Daniel Griffith: Add ANSI cursor positioning &
 partial support for clear screen. Patch submitted by Oscar Lester, don't
 send RESET_ALL to non-tty.
* Demos split into separate files and moved into their own directory.
* Tweak sys.path in demos so they run against local source, not installed
 version of Colorama.

0.1.18

* Fix README (no such attr as Fore.DEFAULT, etc), kindly reported by nodakai.

0.1.17

* Prevent printing of garbage ANSI codes upon installing with pip

0.1.16

* Re-upload to fix previous error. Make clean now removes old MANIFEST.

0.1.15

* Completely broken. Distribution was empty due to leftover invalid MANIFEST
 file from building on a different platform.
* Fix python3 incompatibility kindly reported by G |uumlaut| nter Kolousek

0.1.14

* Fix hard-coded reset to white-on-black colors. Fore.RESET, Back.RESET
 and Style.RESET_ALL now revert to the colors as they were when init()
 was called. Some lessons hopefully learned about testing prior to release.

0.1.13

* Completely broken: barfed when installed using pip.

0.1.12

* Completely broken: contained no source code. double oops.

0.1.11

* Completely broken: fatal import errors on Ubuntu. oops.

0.1.10

* Stop emulating 'bright' text with bright backgrounds.
* Display 'normal' text using win32 normal foreground instead of bright.
* Drop support for 'dim' text.

0.1.9

* Fix incompatibility with Python 2.5 and earlier.
* Remove setup.py dependency on setuptools, now uses stdlib distutils.

0.1.8

* Fix ghastly errors all over the place on Ubuntu.
* Add init kwargs 'convert' and 'strip', which supercede the old 'wrap'.

0.1.7

* Python 3 compatible.
* Fix: Now strips ansi on windows without necessarily converting it to
 win32 calls (eg. if output is not a tty.)
* Fix: Flaky interaction of interleaved ansi sent to stdout and stderr.
* Improved demo.sh (hg checkout only.)

0.1.6

* Fix ansi sequences with no params now default to parmlist of [0].
* Fix flaky behaviour of autoreset and reset_all atexit.
* Fix stacking of repeated atexit calls - now just called once.
* Fix ghastly import problems while running tests.
* 'demo.py' (hg checkout only) now demonstrates autoreset and reset atexit.
* Provide colorama.VERSION, used by setup.py.
* Tests defanged so they no longer actually change terminal color when run.

0.1.5

* Now works on Ubuntu.

0.1.4

* Implemented RESET_ALL on application exit

0.1.3

* Implemented init(wrap=False)

0.1.2

* Implemented init(autoreset=True)

0.1.1

* Minor tidy

0.1

* Works on Windows for foreground color, background color, bright or dim


.. |uumlaut| unicode:: U+00FC .. u with umlaut
:trim:

Links

• PyPI: https://pypi.org/project/colorama
• Changelog: https://pyup.io/changelogs/colorama/
• Repo: https://github.com/tartley/colorama

Update pyfaidx from 0.5.8 to 0.5.8.

Changelog

0.5.8

- Implemented `Fasta.__len__` (157) 
- `Sequence` instances can now be compared against strings (158 thanks Maarten-vd-Sande)

0.5.7