doc: Updated databases/mariadb105-server to 10.5.15

(nia)

doc: Updated databases/mariadb105-client to 10.5.15

(nia)

mariadb105: update to 10.5.15

                        MariaDB 10.5.15 Release Notes

Notable Items

  InnoDB

    * Set innodb_change_buffering=none by default (MDEV-27734)

  Security

    * Fixes for the following security vulnerabilities:
          * CVE-2021-46665
          * CVE-2021-46664
          * CVE-2021-46661
          * CVE-2021-46668
          * CVE-2021-46663

                        MariaDB 10.5.14 Release Notes

Notable Items

  InnoDB

    * --skip-symbolic-links does not disallow .isl file creation
      (MDEV-26870)
    * Indexed CHAR columns are broken with NO_PAD collations (MDEV-25440)
    * insert-intention lock conflicts with waiting ORDINARY lock
      (MDEV-27025)
    * Crash recovery improvements (MDEV-26784, MDEV-27022, MDEV-27183,
      MDEV-27610)

  Galera

    * Galera updated to 26.4.11
    * Galera SST scripts should use ssl_capath (not ssl_ca) for CA directory
      (MDEV-27181)
    * Alter Sequence do not replicate to another nodes with in Galera
      Cluster (MDEV-19353)
    * Galera crash - Assertion. Possible parallel writeset problem
      (MDEV-26803)
    * CREATE TABLE with FOREIGN KEY constraint fails to apply in parallel
      (MDEV-27276)
    * Galera cluster node consider old server_id value even after
      modification of server_id [wsrep_gtid_mode=ON] (MDEV-26223)

  Replication

    * Seconds behind master corrected from artificial spikes at relay-log
      rotation (MDEV-16091)
    * Statement rollback in binlog when transaction creates or drop
      temporary table is set right (MDEV-26833)
    * CREATE-or-REPLACE SEQUENCE is made to binlog with the DDL flag to
      stabilize its parallel execution on slave (MDEV-27365)

  Security

    * Fixes for the following security vulnerabilities:
          * CVE-2022-24052
          * CVE-2022-24051
          * CVE-2022-24050
          * CVE-2022-24048
          * CVE-2021-46659

(nia)

doc: Updated databases/mariadb106-server to 10.6.7

(nia)

doc: Updated databases/mariadb106-client to 10.6.7

(nia)

mariadb106: update to 10.6.7

                          MariaDB 10.6.7 Release Notes

  InnoDB

    * Set innodb_change_buffering=none by default (MDEV-27734)

  Security

    * Fixes for the following security vulnerabilities:
          * CVE-2021-46665
          * CVE-2021-46664
          * CVE-2021-46661
          * CVE-2021-46668
          * CVE-2021-46663

                          MariaDB 10.6.6 Release Notes

Notable Items

  InnoDB

    * --skip-symbolic-links does not disallow .isl file creation
      (MDEV-26870)
    * Indexed CHAR columns are broken with NO_PAD collations (MDEV-25440)
    * insert-intention lock conflicts with waiting ORDINARY lock
      (MDEV-27025)
    * Crash recovery improvements (MDEV-26784, MDEV-27022, MDEV-27183,
      MDEV-27610)
    * mariabackup skips valid .ibd file (MDEV-26326)
    * Allow seamless upgrade despite ROW_FORMAT=COMPRESSED (MDEV-27736)

  Galera

    * Galera updated to 26.4.11
    * Galera SST scripts should use ssl_capath (not ssl_ca) for CA directory
      (MDEV-27181)
    * Alter Sequence do not replicate to another nodes with in Galera
      Cluster (MDEV-19353)
    * Galera crash - Assertion. Possible parallel writeset problem
      (MDEV-26803)
    * CREATE TABLE with FOREIGN KEY constraint fails to apply in parallel
      (MDEV-27276)
    * Galera cluster node consider old server_id value even after
      modification of server_id [wsrep_gtid_mode=ON] (MDEV-26223)

  Replication

    * Seconds behind master corrected from artificial spikes at relay-log
      rotation (MDEV-16091)
    * Statement rollback in binlog when transaction creates or drop
      temporary table is set right (MDEV-26833)
    * CREATE-or-REPLACE SEQUENCE is made to binlog with the DDL flag to
      stabilize its parallel execution on slave (MDEV-27365)

  Security

    * Fixes for the following security vulnerabilities:
          * CVE-2022-24052
          * CVE-2022-24051
          * CVE-2022-24050
          * CVE-2022-24048
          * CVE-2021-46659

(nia)

doc: Updated emulators/mednaffe to 0.9.2

(nia)

mednaffe: update to 0.9.2

Changes:
- Added support for gamepad navigation through game list.
- Fix Gen/MD 6-buttons controller input mapping.

(nia)

doc: Updated devel/lua-luv to 1.43.0.0

(nia)

lua-luv: update to 1.43.0

                                    1.43.0-0

    * Change the call to acquire_vm_cb() in luv.new_therad() to be made
      before the thread is created in luv_new_thread().
    * simplify vm management in thread and threadpool

(nia)

py-pkginfo: fix a pasto in the COMMENT

Bumps PKGREVISION.

(khorben)

doc: Updated x11/xscreensaver to 6.02nb2

(wiz)

xscreensaver: make proper executable setuid

The authentication part was split off into a separate program in 6.x.

Bump PKGREVISION.

(wiz)

doc: Updated fonts/fntsample to 5.4

(fcambus)

fntsample: update to 5.4.

Changes in version 5.4:

* Fixed handling of PDF files with already existing outlines
  in pdfoutline.
* Added a script for extracting outlines from PDF files
  (pdf-extract-outline).
* Pango is always used to draw glyphs, options -p and --use-pango are
  accepted but ignored.
* Fixed possible outline corruption in pdfoutline with some versions
  of PDF::API2 library (Yifeng Li).
* Various code and build system cleanups.

(fcambus)

doc: Updated fonts/liberation-ttf to 2.1.5

(fcambus)

liberation-ttf: update to 2.1.5.

ChangeLog:

* Thu Sep 30 2021 Vishal Vijayraghavan <vishalvijayraghavan@gmail.com>
- Releasing liberation-fonts 2.1.5 version
- Resolves #40: More fixes to Superscript and subscript Numbers missing issues
-- fixed inconsistent weight, missing glyphs and GSUB issues

* Tue May 04 2021 Vishal Vijayraghavan <vishalvijayraghavan@gmail.com>
- Releasing liberation-fonts 2.1.4 version
- Resolves #40: Superscript and subscript Numbers missing
- Resolves #24: Gender symbol are inconsistent in Sans

(fcambus)

mk/scripts/remove_todo: support python 3.10

(wiz)

doc: Updated devel/mob to 2.5.0

(schmonz)

Update to 2.5.0. From the changelog:

- Enable git hooks with `MOB_GIT_HOOKS_ENABLED=true`. By default, this
  option is false and no git hooks such as `pre-commit` or `pre-push`
  are triggered via mob itself.

(schmonz)

wm/leftwm: fix typo in Makefile

(pin)

Deal with meson update - unused parameter no longer optional/ignored

Thanks wiz for the pointer to gentoo patch.

(pgoyette)

xscreensaver: disable pam option by default

Didn't work for me as-is, needs fixing.

Bump PKGREVISION.

(wiz)

sile 0.12.2

(joerg)

Update sile to 0.12.2

This brings native math support and feature compatibility with TeX's
paragraph layout algorithm.

(joerg)

graphics/kvantum: add update warning

(pin)

Added www/ufdbguard version 1.35.3

(sborrill)

Add ufdbguard

(sborrill)

ufdbguard: import ufdbGuard 1.35.3

ufdbGuard is a URL filter to block unwanted web content on the internet.
ufdbGuard can also enforce Google SafeSearch, detect UltraSurf, Tor, Skype
and other chat applications, proxy tunnels and enforce safer HTTPS traffic.
ufdbGuard is a redirector for the Squid web proxy with 50,000 URL
verifications/second.  ufdbGuard integrates with user authorities like LDAP,
Kerberos and Active Directory to assign different policies to different
groups of users.

(sborrill)

sysutils/cdrtools: Build fix for Darwin and SunOS

On Darwin and SunOS libiconv was not found.

(micha)

shells/zsh: Improve completions of pkg_* on Darwin

(pho)

doc: Updated textproc/asciidoc to 10.1.2

(wiz)

asciidoc: update to 10.1.2.

Version 10.1.2 (2022-02-17)
---------------------------
.Bug fixes
- DESTDIR passed to pip as part of make install
- Add number of missing files to release tarballs
- Fix parsing asciidoc_opt values with spaces for a2x

.Miscellaneous
- Cleanup unused parts of Makefile
- Website files removed from main asciidoc-py repo

Version 10.1.1 (2021-12-20)
---------------------------
.Bug fixes
- Fix RuntimeWarning when executing asciidoc or a2x within repository
- Fix index out of range error in a2x (thanks @osmith42)

Version 10.1.0 (2021-12-17)
---------------------------
.Features
- Add top-level `__version__` and `VERSION` module exports (thanks @tbpassin)

.Bug fixes
- Fix self reference errors in AsciiDocApi (thanks @tbpassin)
- Add back asciidoc execute print in a2x verbose

Version 10.0.2 (2021-11-12)
---------------------------
.Bug fixes
- Fix errors not displaying when called via a2x (thanks @osmith42)
- Fix incorrect parsing of asciidoc_opts in a2x (thanks @lmarz)

.Miscellaneous
- Fix automating homebrew release updates

Version 10.0.1 (2021-10-28)
---------------------------
.Bug fixes
- Fix running make docs
- Fix warning in music filter when using GraphicsMagick
- Fix handling escaped attributes inside of macros
- Include *.xsl and *.sty files in pip installations

Version 10.0.0 (2021-10-16)
---------------------------
.Breaking Changes
AsciiDoc.py has been rewritten to be a https://pypi.org/project/asciidoc/[proper Python package], installable via pip. Downloading and running asciidoc from the repo is not recommended, but can be done through `python3 -m asciidoc` or `python3 -m asciidoc.a2x`. CLI usage should remain the same where both `asciidoc` and `a2x` CLI commands are available after pip installation. Support for overriding the bundled *.conf files is done through CLI flags, environment variables, etc., and not through directly editing the files within the installation. Importing asciidoc should no longer require the `asciidocapi.py` script, and can be done through regular python import, e.g. `import asciidoc; asciidoc.execute(...)`.

The APIs of the asciidoc and a2x scripts are now considered "provisional" with no guarantee of BC between releases with the exception of the `asciidoc.execute` method. Please post an issue on our tracker for any method you directly rely on and would like to have BC for.

.Features
- Install using `pip install asciidoc`

.Miscellaneous
- Changed website domain to https://asciidoc-py.github.io/. The old domain will redirect for a period of time, but will be updated at some point to point at website created by the https://asciidoc-wg.eclipse.org/[AsciiDoc Working Group].

.Testing
- Test against 3.10 stable

(wiz)

collectd-grpc: revbump after net/grpc update

(adam)

Updated net/grpc, net/py-grpcio, net/py-grpcio-testing, net/py-grpcio-tools

(adam)

grpc py-grpcio py-grpcio-testing py-grpcio-tools: updated to 1.44.0

Release v1.44.0

Core

xDS: Rbac filter updates
Fix xDS client for multiple watchers.
bump C-core version for upcoming release.
Add a trace to list which filters are contained in a channel stack.
Remove grpc_httpcli_context.
xDS: Add support for RBAC HTTP filter.
API to cancel grpc_resolve_address.
Replace work serializer with a mutex in c-ares resolver.
xDS: Add graceful shutdown for old connections on listener resource update.

C++

Promote ClientContext::set_wait_for_ready to be non-experimental.

Python

Add python async example for hellostreamingworld using generator.
Disable __wrap_memcpy hack for Python builds.
Bump Bazel Python Cython dependency to 0.29.26.
Fix libatomic linking on Raspberry Pi OS Bullseye.
Allow generated proto sources in remote repositories for py_proto_library.

(adam)

doc: Updated sysutils/py-borgbackup to 1.1.17nb5

(wiz)

py-borgbackup: remove ALTERNATIVES

The current ALTERNATIVES/post-install was not enough to make this package
avoid a self-conflict (due to the man pages). Since this is an application
that which no other packages depend upon, there is no need to have it
installed for multiple python versions at the same time, so simplify
this.

Bump PKGREVISION.

(wiz)

py-borgbackup: fix typo in ALTERNATIVES

(wiz)

py-tox: PYTHON_VERSIONS_INCOMPATIBLE goes higher

(adam)

doc: Updated sysutils/hcal to 0.3.4

(pin)

sysutils/hcal: update to 0.3.4

-Upgrade clap

(pin)

doc: Updated devel/wabt to 1.0.27

(fcambus)

wabt: update to 1.0.27.

No upstream ChangeLog.

(fcambus)

digest: catch configure.ac up with configure

(gutteridge)

Bump zathura-ps PKGREVISION for zathura update

(abs)

Bump zathura-pdf-poppler PKGREVISION for zathura update

(abs)

Updated graphics/girara to 0.3.7
Updated print/zathura to 0.4.9

(abs)

doc: Updated www/webkit-gtk to 2.34.6

(leot)

webkit-gtk: Update to 2.34.6

Changes:
2.34.6
======
  - Fix accessibility not working when the Bubblewrap sandbox is enabled.
  - Fix rendering of scrollbars when overlay scrollbars are disabled.
  - Fix the build when the X11 support is disabled.
  - Fix the build in a number of situations where the main OpenGL library is
    not called libGL or libgl, as is the case on systems that use libglvnd.
  - Fix several crashes and rendering issues.

(leot)

Updated print/zathura to 0.4.9

Add '$f' and '$p' expansions to 'exec' shortcut function
Fix build with meson 0.60
Add :source command
Various fixes and improvements
Updated translations

(Fixes build issue with updated meson in pkgsrc)

(abs)

Updated graphics/girara to 0.3.7

Various fixes and improvements
Update translations

(Needed for zathura update)

(abs)

doc: Updated net/terraform-provider-vultr to 2.9.1

(tpaul)

terraform-provider-vultr: Update to 2.9.1

See upstream release notes:
  https://github.com/vultr/terraform-provider-vultr/releases/tag/v2.9.1

(tpaul)

Fix build on Darwin

(pho)

doc: Updated x11/xscreensaver to 6.02

(wiz)

x11/xAscreensaver-demo: remove, merged into xscreensaver

(wiz)

xscreensaver: update to 6.02.

Merge xscreensaver-demo into this package.

6.02    11-Oct-2021

    New hacks, marbling and binaryhorizon.
    atlantis behaviors are more random and lifelike.
    headroom is now Mask Headroom.
    X11: fontglide skips fonts that can't display ASCII.
    X11: Use asterisks in the password dialog if the system fonts
    don't have bullets in them.
    X11: ���Disable Screen Saver��� was behaving like ���Blank Screen
    Only���.
    Android: These hacks work now: antinspect, barcode, energystream,
    fliptext, fontglide, glsnake, raverhoop, starwars, unicrud.

6.01    09-Jun-2021

    X11: Properly disable the server's built-in screen saver.
    X11: The passwdTimeout option was being ignored.
    X11: The display of the unlock thermometer was weird.
    X11: Fixed password entry on old-school multi-screen setups
    (:0.1).
    X11: Worked around a KDE 5 compositor bug that caused the
    desktop to momentarily become visible when cycling.
    X11: Fixed possible high CPU usage in xscreensaver-systemd.
    X11: Fixed some spurious warnings in xscreensaver-text.
    X11: Warn when Wayland is in use, since it makes both screen
    saving and locking impossible.

6.00    01-Apr-2021

    X11: Major refactor of the xscreensaver daemon for improved
    security, dividing it into three programs: xscreensaver,
    xscreensaver-gfx and xscreensaver-auth.
    X11: Dropped support for systems older than X11R7 (2009).
    X11: Renamed xscreensaver-demo to xscreensaver-settings.
    X11: Unlock dialog has user-selectable color schemes.
    X11: Everything uses XFreeType for fonts now.
    X11: Install a few custom fonts needed by some savers.
    X11: Fading works on systems without gamma (e.g. Raspberry Pi).
    X11: Use EGL instead of GLX when available.
    X11: xscreensaver-systemd now detects when a video player has
    inhibited screen blanking and then exits without uninhibiting.
    Improved GLSL and GLES3 support: Phong shading in etruscanvenus,
    hypertorus, klein, projectiveplane,`romanboy' and sphereeversion.
    Updates to cubicgrid.
    macOS: Added a Random XScreenSaver screen saver, which implements
    cycle mode, among other things.
    iOS: Also added cycle mode.

(wiz)

doc: Updated devel/php-composer to 2.2.6

(tpaul)

php-composer: Update to 2.2.6

Upstream release notes:
  2.2.6: https://github.com/composer/composer/releases/tag/2.2.6
  2.2.5: https://github.com/composer/composer/releases/tag/2.2.5
  2.2.4: https://github.com/composer/composer/releases/tag/2.2.4
  2.2.3: https://github.com/composer/composer/releases/tag/2.2.3
  2.2.2: https://github.com/composer/composer/releases/tag/2.2.2
  2.2.1: https://github.com/composer/composer/releases/tag/2.2.1
  2.2.0: https://github.com/composer/composer/releases/tag/2.2.0

(tpaul)

TODO: - py-pip-api-0.27, done

(wiz)

doc: Updated sysutils/findutils to 4.9.0

(wiz)

findutils: update to 4.9.0.

* Noteworthy changes in release 4.9.0 (2022-02-22) [stable]

** New features in find

  find now supports the -files0-from option to be able to safely pass an
  arbitrary number of starting points to the tool.  The option requires a file
  name as argument, or "-" to read from standard input.  The entries in that
  file have to be separated by NUL characters. [#60383]

** Changes in locate / updatedb

  updatedb now skips (fuse-mounted) s3fs filesystems by default,
  i.e., unless PRUNEFS is set.

** Bug Fixes

  'find -D stat -L ...' no longer determines SELinux security information as
  if the -L option was not given.
  [Bug present since the SELinux implementation in 4.5.6]

  'find -inum' and 'find -printf %i' now also work on platforms which allow
  the inode number Zero; e.g. the GNU/Hurd uses inode number 0 for /dev/console.
  Previously, find(1) would abort when visiting such a file.
  [Bug present since FINDUTILS_4_5_4-1.]

  findutils-4.8.0 failed to build on some MacOS versions.
  Fixed by a gnulib update. [#59972, #59991]

** Documentation Changes

  The find.1 man page and the Texinfo manual now show environment variables
  in a consistent style. [#59963]

  Furthermore, both add the description of the -printf format directive '%B',
  for a file's birth time, and its limitations. [#61327]

  The description of the -delete action has been improved and aligned among
  the manual page and the Texinfo documentation. [#61774]

  Various other documentation fixes - syntax issues and typos.
  [#61303, #60823, #61341]

  The output of 'find --help' now reads better.

  The HTML online manual is using the official GNU stylesheet again.

** Changes to the build process

  The find version without FTS, oldfind, has been completely removed.  It has
  not been installed since 4.5.18 (2015), and was only still used in tests.

(wiz)

bind916: fix builds on Solaris derivates

A patch fixing SunOS builds was lost during a recent update, restore
it. (And s/SmartOS/SunOS/ in comment, this doesn't just affect SmartOS,
reproduced and fixed on OmniOS. This package also fails to build on
Linux, but that's another issue entirely.) Addresses PR pkg/56716 from
Russell Hansen.

(gutteridge)

lang/ghc92/patches: Add a tech-kern thread URL

(pho)

py-hash: remove

Old version, latest version has incomplete distfile, no users in pkgsrc.

(wiz)

py-autograd: remove

This project is not being developed any longer upstream.
No users in pkgsrc.

There is a successor project, JAX, in case anyone's interested.

(wiz)

doc: Updated cad/py-gds to 1.6.11

(wiz)

py-gds: update to 1.6.11.

Version 1.6.11 (Jan 14, 2022)

    Fix in Cell.write_svg when missing references.
    Speed improvements in Cell.remove_polygons (thanks Troy for the contribution).

Version 1.6.10 (Nov 14, 2021)

    Fix in Cell.get_polygons

Version 1.6.9 (Sep 23, 2021)

    Fix in Cell.get_polygons with specified layer and datatype.
    Raise error for duplicate cells when reading a GDSII file.

Version 1.6.8 (Aug 2, 2021)

    Fix in boolean for complex geometries that freeze the operation.

Version 1.6.7 (Jul 14, 2021)

    Fixes in boolean for bugs with self-intersecting holes and holes horizontal edges.
    Fix bug in warning message.

Version 1.6.6 (Jun 09, 2021)

    Fix error in Path.smooth not finding _hobby function.
    Allow precision specification in SVG output.

Version 1.6.5 (Jun 08, 2021)

    Support GDSII files with 0-padding at the end.
    Allow fixing and modifying GDSII file timestamps.
    Thanks Troy Tamas and Joaquin Matres for the fixes

Version 1.6.4 (Apr 23, 2021)

    Fix missing module import (thanks Troy Tamas for the fix).

Version 1.6.3 (Dec 28, 2020)

    Fix bounding box edge case (thanks Troy Tamas for the fix).

Version 1.6.2 (Dec 18, 2020)

    More efficient bounding box calculation (thanks to Troy Tamas for the contribution).
    Fix Label creation bug.

Version 1.6.1 (Oct 22, 2020)

    Fix SVG output when Label contains special characters.

(wiz)

doc: Updated biology/py-biopython to 1.79

(wiz)

py-biopython: update to 1.79.

1 June 2021: Biopython 1.79
================================

This is intended to be our final release supporting Python 3.6. It also
supports Python 3.7, 3.8 and 3.9, and has also been tested on PyPy3.6.1 v7.1.1.

The ``Seq`` and ``MutableSeq`` classes in ``Bio.Seq`` now store their sequence
contents as ``bytes` ` and ``bytearray`` objects, respectively. Previously, for
``Seq`` objects a string object was used, and a Unicode array object for
``MutableSeq`` objects. This was maintained during the transition from Python2
to Python3. However, a Python2 string object corresponds to a ``bytes`` object
in Python3, storing the string as a series of 256-bit characters. While non-
ASCII characters could be stored in Python2 strings, they were not treated as
such. For example:

In Python2::

    >>> s = "Генетика"
    >>> type(s)
    <class 'str'>
    >>> len(s)
    16

In Python3::

    >>> s = "Генетика"
    >>> type(s)
    <class 'str'>
    >>> len(s)
    8

In Python3, storing the sequence contents as ``bytes`` and ``bytearray``
objects has the further advantage that both support the buffer protocol.

Taking advantage of the similarity between ``bytes`` and ``bytearray``, the
``Seq`` and ``MutableSeq`` classes now inherit from an abstract base class
``_SeqAbstractBaseClass`` in ``Bio.Seq`` that implements most of the ``Seq``
and ``MutableSeq`` methods, ensuring their consistency with each other. For
methods that modify the sequence contents, an optional ``inplace`` argument to
specify if a new sequence object should be returned with the new sequence
contents (if ``inplace`` is ``False``, the default) or if the sequence object
itself should be modified (if ``inplace`` is ``True``). For ``Seq`` objects,
which are immutable, using ``inplace=True`` raises an exception. For
``inplace=False``, the default, ``Seq`` objects and ``MutableSeq`` behave
consistently.

As before, ``Seq`` and ``MutableSeq`` objects can be initialized using a string
object, which will be converted to a ``bytes`` or ``bytearray`` object assuming
an ASCII encoding. Alternatively, a ``bytes`` or ``bytearray`` object can be
used, or an instance of any class inheriting from the new
``SequenceDataAbstractBaseClass`` abstract base class in ``Bio.Seq``. This
requires that the class implements the ``__len__`` and ``__getitem`` methods
that return the sequence length and sequence contents on demand. Initialzing a
``Seq`` instance using an instance of a class inheriting from
``SequenceDataAbstractBaseClass`` allows the ``Seq`` object to be lazy, meaning
that its sequence is provided on demand only, without requiring to initialize
the full sequence. This feature is now used in ``BioSQL``, providing on-demand
sequence loading from an SQL database, as well as in a new parser for twoBit
(.2bit) sequence data added to ``Bio.SeqIO``. This is a lazy parser that allows
fast access to genome-size DNA sequence files by not having to read the full
genome sequence. The new ``_UndefinedSequenceData`` class in ``Bio.Seq``  also
inherits from ``SequenceDataAbstractBaseClass`` to represent sequences of known
length but unknown sequence contents. This provides an alternative to
``UnknownSeq``, which is now deprecated as its definition was ambiguous. For
example, in these examples the ``UnknownSeq`` is interpreted as a sequence with
a well-defined sequence contents::

    >>> s = UnknownSeq(3, character="A")
    >>> s.translate()
    UnknownSeq(1, character='K')
    >>> s + "A"
    Seq("AAAA")

A sequence object with an undefined sequence contents can now be created by
using ``None`` when creating the ``Seq`` object, together with the sequence
length. Trying to access its sequence contents raises an
``UndefinedSequenceError``::

    >>> s = Seq(None, length=6)
    >>> s
    Seq(None, length=6)
    >>> len(s)
    6
    >>> "A" in s
    Traceback (most recent call last):
    ...
    Bio.Seq.UndefinedSequenceError: Sequence content is undefined
    >>> print(s)
    Traceback (most recent call last):
    ....
    Bio.Seq.UndefinedSequenceError: Sequence content is undefined

Element assignment in Bio.PDB.Atom now returns "X" when the element cannot be
unambiguously guessed from the atom name, in accordance with PDB structures.

Bio.PDB entities now have a ``center_of_mass()`` method that calculates either
centers of gravity or geometry.

New method ``disordered_remove()`` implemented in Bio.PDB DisorderedAtom and
DisorderedResidue to remove children.

New module Bio.PDB.SASA implements the Shrake-Rupley algorithm to calculate
atomic solvent accessible areas without third-party tools.

Expected ``TypeError`` behaviour has been restored to the ``Seq`` object's
string like methods (fixing a regression in Biopython 1.78).

The KEGG ``KGML_Pathway`` KGML output was fixed to produce output that complies
with KGML v0.7.2.

Parsing motifs in ``pfm-four-rows`` format can now handle motifs with values
in scientific notation.

Parsing motifs in ``minimal``` MEME format will use ``nsites`` when making
the count matrix from the frequency matrix, instead of multiply the frequency
matrix by 1000000.

Bio.UniProt.GOA now parses Gene Product Information (GPI) files version 1.2,
files can be downloaded from the EBI ftp site:
ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/

4 September 2020: Biopython 1.78
================================

This release of Biopython supports Python 3.6, 3.7 and 3.8. It has also been
tested on PyPy3.6.1 v7.1.1.

The main change is that ``Bio.Alphabet`` is no longer used. In some cases you
will now have to specify expected letters, molecule type (DNA, RNA, protein),
or gap character explicitly. Please consult the updated Tutorial and API
documentation for guidance. This simplification has sped up many ``Seq``
object methods. See https://biopython.org/wiki/Alphabet for more information.

``Bio.SeqIO.parse()`` is faster with "fastq" format due to small improvements
in the ``Bio.SeqIO.QualityIO`` module.

The ``SeqFeature`` object's ``.extract()`` method can now be used for
trans-spliced locations via an optional dictionary of references.

As in recent releases, more of our code is now explicitly available under
either our original "Biopython License Agreement", or the very similar but
more commonly used "3-Clause BSD License".  See the ``LICENSE.rst`` file for
more details.

Additionally, a number of small bugs and typos have been fixed with additions
to the test suite. There has been further work to follow the Python PEP8,
PEP257 and best practice standard coding style, and all of the tests have
been reformatted with the ``black`` tool to match the main code base.

25 May 2020: Biopython 1.77
===========================

This release of Biopython supports Python 3.6, 3.7 and 3.8 It has also been
tested on PyPy3.6.1 v7.1.1-beta0.

**We have dropped support for Python 2 now.**

``pairwise2`` now allows the input of parameters with keywords and returns the
alignments as a list of ``namedtuples``.

The codon tables have been updated to NCBI genetic code table version 4.5,
which adds Cephalodiscidae mitochondrial as table 33.

Updated ``Bio.Restriction`` to the January 2020 release of REBASE.

A major contribution by Rob Miller to ``Bio.PDB`` provides new methods to
handle protein structure transformations using dihedral angles (internal
coordinates). The new framework supports lossless interconversion between
internal and cartesian coordinates, which, among other uses, simplifies the
analysis and manipulation of coordinates of proteins structures.

As in recent releases, more of our code is now explicitly available under
either our original "Biopython License Agreement", or the very similar but
more commonly used "3-Clause BSD License".  See the ``LICENSE.rst`` file for
more details.

Additionally, a number of small bugs and typos have been fixed with further
additions to the test suite. There has been further work to follow the Python
PEP8, PEP257 and best practice standard coding style, and all the main code
base has been reformatted with the ``black`` tool.

20 December 2019: Biopython 1.76
================================

This release of Biopython supports Python 2.7, 3.5, 3.6, 3.7 and 3.8. It has
also been tested on PyPy2.7.13 v7.1.1 and PyPy3.6.1 v7.1.1-beta0.

We intend this to be our final release supporting Python 2.7 and 3.5.

As in recent releases, more of our code is now explicitly available under
either our original "Biopython License Agreement", or the very similar but
more commonly used "3-Clause BSD License".  See the ``LICENSE.rst`` file for
more details.

``PDBParser`` and ``PDBIO`` now support PQR format file parsing and input/
output.

In addition to the mainstream ``x86_64`` aka ``AMD64`` CPU architecture, we
now also test every contribution on the ``ARM64``, ``ppc64le``, and ``s390x``
CPUs under Linux thanks to Travis CI. Further post-release testing done by
Debian and other packagers and distributors of Biopython also covers these
CPUs.

``Bio.motifs.PositionSpecificScoringMatrix.search()`` method has been
re-written: it now applies ``.calculate()`` to chunks of the sequence
to maintain a low memory footprint for long sequences.

Additionally, a number of small bugs and typos have been fixed with further
additions to the test suite. There has been further work to follow the Python
PEP8, PEP257 and best practice standard coding style, and more of the code
style has been reformatted with the ``black`` tool.

6 November 2019: Biopython 1.75
===============================

This release of Biopython supports Python 2.7, 3.5, 3.6, 3.7 and is expected
to work on the soon to be released Python 3.8. It has also been tested on
PyPy2.7.13 v7.1.1 and PyPy3.6.1 v7.1.1-beta0.

Note we intend to drop Python 2.7 support in early 2020.

The restriction enzyme list in ``Bio.Restriction`` has been updated to the
August 2019 release of REBASE.

``Bio.SeqIO`` now supports reading and writing files in the native format of
Christian Marck's DNA Strider program ("xdna" format, also used by Serial
Cloner), as well as reading files in the native formats of GSL Biotech's
SnapGene ("snapgene") and Textco Biosoftware's Gene Construction Kit ("gck").

``Bio.AlignIO`` now supports GCG MSF multiple sequence alignments as the "msf"
format (work funded by the National Marrow Donor Program).

The main ``Seq`` object now has string-like ``.index()`` and ``.rindex()``
methods, matching the existing ``.find()`` and ``.rfind()`` implementations.
The ``MutableSeq`` object retains its more list-like ``.index()`` behaviour.

The ``MMTFIO`` class has been added that allows writing of MMTF file format
files from a Biopython structure object. ``MMTFIO`` has a similar interface to
``PDBIO`` and ``MMCIFIO``, including the use of a ``Select`` class to write
out a specified selection. This final addition to read/write support for
PDB/mmCIF/MMTF in Biopython allows conversion between all three file formats.

Values from mmCIF files are now read in as a list even when they consist of a
single value. This change improves consistency and reduces the likelihood of
making an error, but will require user code to be updated accordingly.

`Bio.motifs.meme` has been updated to parse XML output files from MEME over
the plain-text output file. The goal of this change is to parse a more
structured data source with minimal loss of functionality upon future MEME
releases.

``Bio.PDB`` has been updated to support parsing REMARK 99 header entries from
PDB-style Astral files.

A new keyword parameter ``full_sequences`` was added to ``Bio.pairwise2``'s
pretty print method ``format_alignment`` to restore the output of local
alignments to the 'old' format (showing the whole sequences including the
un-aligned parts instead of only showing the aligned parts).

A new function ``charge_at_pH(pH)`` has been added to ``ProtParam`` and
``IsoelectricPoint`` in ``Bio.SeqUtils``.

The ``PairwiseAligner`` in ``Bio.Align`` was extended to allow generalized
pairwise alignments, i.e. alignments of any Python object, for example
three-letter amino acid sequences, three-nucleotide codons, and arrays of
integers.

A new module ``substitution_matrices`` was added to ``Bio.Align``, which
includes an ``Array`` class that can be used as a substitution matrix. As
the ``Array`` class is a subclass of a numpy array, mathematical operations
can be applied to it directly, and C code that makes use of substitution
matrices can directly access the numerical values stored in the substitution
matrices. This module is intended as a replacement of ``Bio.SubsMat``,
which is currently unmaintained.

As in recent releases, more of our code is now explicitly available under
either our original "Biopython License Agreement", or the very similar but
more commonly used "3-Clause BSD License".  See the ``LICENSE.rst`` file for
more details.

Additionally, a number of small bugs and typos have been fixed with further
additions to the test suite, and there has been further work to follow the
Python PEP8, PEP257 and best practice standard coding style. We have also
started to use the ``black`` Python code formatting tool.

(wiz)

py-quadprog: mark as only for Python 3.x per upstream classification

(wiz)

Updated devel/py-filelock, devel/py-tox

(adam)

py-tox: updated to 3.24.5

v3.24.5 (2021-12-29)

Bugfixes
- Fixed an issue where ``usedevelop`` would cause an invocation error if setup.py does not exist. -- by :user:`VincentVanlaer`

v3.24.4 (2021-09-16)
--------------------

Bugfixes
- Fixed handling of ``-e ALL`` in parallel mode by ignoring the ``ALL`` in subprocesses -- by :user:`guahki`.
- Prevent tox from using a truncated interpreter when using
  ``TOX_LIMITED_SHEBANG`` -- by :user:`jdknight`.

Documentation
- Enabled the use of the favicon in the Sphinx docs first
  introduced in :pull:`764` but not integrated fully

v3.24.3 (2021-08-21)
--------------------

Bugfixes
- ``--parallel`` reports now show ASCII OK/FAIL/SKIP lines when full Unicode output is not available

Miscellaneous
- Started enforcing valid references in Sphinx docs -- :user:`webknjaz`

v3.24.2 (2021-08-18)
--------------------

Bugfixes
- include ``LC_ALL`` to implicit list of passenv variables

v3.24.1 (2021-07-31)
--------------------

Bugfixes
- ``get_requires_for_build_sdist`` hook (PEP 517) is assumed to return an empty list if left unimplemented by the backend build system

Documentation
- The documentation of ``install_command`` now also mentions that you can provide arbitrary commands

v3.24.0 (2021-07-14)
--------------------

Bugfixes
- ``--devenv`` no longer modifies the directory in which the ``.tox`` environment is provisioned
- Fix show config when the package names are not in canonical form

Documentation
- Extended environment variables section

Miscellaneous
- ``tox`` no longer shows deprecation warnings for ``distutils.sysconfig`` on
  Python 3.10

v3.23.1 (2021-05-05)
--------------------

Bugfixes
- Distinguish between normal Windows Python and MSYS2 Python when looking for
  virtualenv executable path.  Adds os.sep to :class:`~tox.interpreters.InterpreterInfo`
- Fix a ``tox-conda`` isolation build bug

Documentation
- Update examples in the documentation to use ``setenv`` in the ``[testenv]`` sections, not wrongly in the ``[tox]`` main section.

Miscellaneous
- Enable building tox with ``setuptools_scm`` 6+ by :user:`hroncok`

v3.23.0 (2021-03-03)
--------------------

Features
- tox can now be invoked with a new ``--no-provision`` flag that prevents provision,
  if :conf:`requires` or :conf:`minversion` are not satisfied,
  tox will fail;
  if a path is specified as an argument to the flag
  (e.g. as ``tox --no-provision missing.json``) and provision is prevented,
  provision metadata are written as JSON to that path
- Unicode support in ``pyproject.toml``

v3.22.0 (2021-02-16)
--------------------

Features
- The value of the :conf:`requires` configuration option is now exposed via
  the :class:`tox.config.Config` object

v3.21.4 (2021-02-02)
--------------------

Bugfixes
- Adapt tests not to assume the ``easy_install`` command exists, as it was removed from ``setuptools`` 52.0.0+

v3.21.3 (2021-01-28)
--------------------

Bugfixes
- Fix a killed tox (via SIGTERM) leaving the commands subprocesses running
  by handling it as if it were a KeyboardInterrupt

v3.21.2 (2021-01-19)
--------------------

Bugfixes
- Newer coverage tools update the ``COV_CORE_CONTEXT`` environment variable, add it to the list of environment variables
  that can change in our pytest plugin

v3.21.1 (2021-01-13)
--------------------

Bugfixes
- Fix regression that broke using install_command in config replacements
- Fix regression parsing posargs default containing colon.

Features
- Prevent .tox in envlist

Miscellaneous
- Enable building tox with ``setuptools_scm`` 4 and 5 by :user:`hroncok`

v3.21.0 (2021-01-08)
--------------------

Bugfixes
- Fix the false ``congratulations`` message that appears when a ``KeyboardInterrupt`` occurs during package installation.
- Fix ``platform`` support for ``install_command``.
- Fixed regression in v3.20.0 that caused escaped curly braces in setenv
  to break usage of the variable elsewhere in tox.ini.
- Prevent ``{}`` and require ``{:`` is only followed by ``}``.
- Raise ``MissingSubstitution`` on access of broken ini setting.

Features
- Allow \{ and \} in default of {env:key:default}.
- Allow {posargs} in setenv.
- Allow {/} to refer to os.sep.
- Make parsing [testenv] sections in setup.cfg official.
- Relax importlib requirement to allow 3.0.0 or any newer version

Documentation
- Document more info about using ``platform`` setting.
- Replace ``indexserver`` in documentation with environment variables
- Document that the ``passenv`` environment setting is case insensitive.

(adam)

Correct wrong checksums for the Darwin/x86_64 bootkit

(pho)

Correct wrong checksums for the Darwin/x86_64 bootkit

(pho)

py-filelock: updated to 3.5.1

v3.5.1 (2022-02-16)
-------------------
- Use ``time.monotonic`` instead of ``time.time`` for calculating timeouts.

v3.5.0 (2022-02-15)
-------------------
- Enable use as context decorator

v3.4.2 (2021-12-16)
-------------------
- Drop support for python ``3.6``

v3.4.1 (2021-12-16)
-------------------
- Add ``stacklevel`` to deprecation warnings for argument name change

v3.4.0 (2021-11-16)
-------------------
- Add correct spelling of poll interval parameter for :meth:`acquire <filelock.BaseFileLock.acquire>` method, raise
  deprecation warning when using the misspelled form :pr:`119`

v3.3.2 (2021-10-29)
-------------------
- Accept path types (like ``pathlib.Path`` and ``pathlib.PurePath``) in the constructor for ``FileLock`` objects.

v3.3.1 (2021-10-15)
-------------------
- Add changelog to the documentation :pr:`108`
- Leave the log level of the ``filelock`` logger as not set (previously was set to warning) :pr:`108` - by
  :user:`gaborbernat`

v3.3.0 (2021-10-03)
-------------------
- Drop python 2.7 and 3.5 support, add type hints :pr:`100`
- Document asyncio support
- fix typo :pr:`98`

(adam)

py-mol: remove

This package is from 2012, the current version is from 2020.
A replacement candidate is in wip/py-mol but needs more work.

One of the last users of py-numpy16 in pkgsrc.

(wiz)

py-fftw: remove

Last release in 2010, was beta, no upstream, not used in pkgsrc.

(wiz)

lang/ghc92: Work around an issue where GHCi sometimes crashes on NetBSD

(pho)

xfce4-notifyd: update homepage

(gutteridge)

xfce4-notifyd: no need for outdated URL in DESCR

(gutteridge)

xfce4-notifyd: adjust a couple of lintish things

(gutteridge)

doc: Updated x11/xfce4-notifyd to 0.6.3

(gutteridge)

xfce4-notifyd: update to 0.6.3

Change log:

0.6.3
======
- Fix compilation warnings
- autoconf: Some updates
- Update `.gitignore`
- Remove GSourceFunc casts
- Fix missing-prototypes
- Bump required GLib version to 2.56
- Implement ISO 8601 time format to avoid post-2.56 GLib functions
- settings: Drop subtitle
- Fix multiple memory issues (!11)
- Translation Updates:
  Albanian, Arabic, Armenian (Armenia), Basque, Belarusian, Bulgarian,
  Catalan, Chinese (China), Chinese (Taiwan), Croatian, Czech, Danish,
  Dutch, Eastern Armenian, English (Australia), Estonian, Finnish,
  French, Galician, Georgian, German, Greek, Hebrew, Hungarian,
  Icelandic, Indonesian, Interlingue, Italian, Japanese, Kazakh,
  Korean, Lithuanian, Malay, Norwegian Bokm奪l, Polish, Portuguese,
  Portuguese (Brazil), Russian, Serbian, Slovak, Slovenian, Spanish,
  Swedish, Thai, Turkish, Ukrainian

(gutteridge)

doc: Updated fonts/harfbuzz to 3.4.0

(wiz)

harfbuzz{,-icu}: update to 3.4.0

Overview of changes leading to 3.4.0
Sunday, February 13, 2022
====================================
- Perform sanity checks on shaping results is now part of 窶徂arfbuzz窶� library
  and can be enabled by setting the buffer flag HB_BUFFER_FLAG_VERIFY.
  (Behdad Esfahbod)
- Arabic Mark Transient Reordering Algorithm have been updated to revision 6.
  (Khaled Hosny)
- ISO 15924 code for mathematical notation, 窶六mth窶�, now maps to the OpenType
  窶藁ath窶� tag. (Alexis King)
- It is now possible to get at once all math kerning values for a given glyph
  at a given corner. (Alexis King)
- Fix locale_t portability issues on systems the typdef窶冱 it to a void pointer.
  (Behdad Esfahbod)

- New API:
+HB_BUFFER_FLAG_VERIFY
+HB_OT_TAG_MATH_SCRIPT
+HB_SCRIPT_MATH
+hb_ot_math_kern_entry_t
+hb_ot_math_get_glyph_kernings

- Deprecated API
+HB_OT_MATH_SCRIPT

(wiz)

doc: Updated textproc/csview to 1.0.1

(pin)

textproc/csview: update to 1.0.1

-implement table writer
-replace prettytable-rs
-skip title sep when there is no data
-tweak cli options
-remove unnecessary buffer
-remove compleation sub-command
-remove unstable features

(pin)

doc: Updated comms/tio to 1.34

(fcambus)

tio: update to 1.34.

Changes since tio v1.33:

* Fix setspeed2 compilation

* Only apply color formatting when using color option

  To help the color blind who may use custom terminal foreground /
  background colors.

* Update README

* Add '-c, --color' option

  Allow user to select which ANSI color code to use to colorize the tio
  text. To successfully set the color the color code must be in the range
  0..255.

  If color code is negative tio will print all available ANSI colors.

  The default color is changed to bold white to make tio defaults usable
  for most users, including color blind users.

* Fix setspeed2 check

* Fix meson header check string

* Reintroduce long timestamp format

  But make the timestamp format RFC3339 compliant instead. The RFC states:

  NOTE: ISO 8601 defines date and time separated by "T".
        Applications using this syntax may choose, for the sake of
        readability, to specify a full-date and full-time separated by
        (say) a space character.

  This way we keep the information specified by ISO 8601 but make it more
  human readable which is better for the console output.

* Update version year

Sylvain LAFRASSE:

* Fix TTY device listing on Darwin. (#136)

* Fix TCGETS2 search on Darwin.

(fcambus)

doc: Updated textproc/py-prettytable to 3.1.1

(fcambus)