Updated comms/py-colorama, devel/py-frozenlist

(adam)

py-frozenlist: updated to 1.3.3

1.3.3 (2022-11-08)
==================
- Fixed CI runs when creating a new release, where new towncrier versions
  fail when the current version section is already present.

1.3.2 (2022-11-08)
==================

Misc
----
- Updated the CI runs to better check for test results and to avoid deprecated syntax.

(adam)

py-colorama: revert DESCR

(adam)

py-colorama: updated to 0.4.6

0.4.6 Current release
* https://github.com/tartley/colorama/pull/139 Add alternative to 'init()',
  called 'just_fix_windows_console'. This fixes many longstanding problems
  with 'init', such as working incorrectly on modern Windows terminals, and
  wonkiness when init gets called multiple times. The intention is that it
  just makes all Windows terminals treat ANSI the same way as other terminals
  do. Many thanks the njsmith for fixing our messes.
* https://github.com/tartley/colorama/pull/352 Support Windows 10's ANSI/VT
  console. This didn't exist when Colorama was created, and avoiding us
  causing havok there is long overdue. Thanks to segeviner for the initial
  approach, and to njsmith for getting it merged.
* https://github.com/tartley/colorama/pull/338 Internal overhaul of package
  metadata declaration, which abolishes our use of the now heavily
  discouraged setuptools (and hence setup.py, setup.cfg and MANIFEST.in), in
  favor of hatchling (and hence pyproject.toml), generously contributed by
  ofek (author of hatchling). This includes dropping support Python3.5 and
  3.6, which are EOL, and were already dropped from setuptools, so this
  should not affect our users.
* https://github.com/tartley/colorama/pull/353 Attention to detail award to
  LqdBcnAtWork for a spelling fix in demo06

(adam)

py-build: use correct dependencies

(adam)

shells/ksh93: fix broken build

(pin)

doc: Updated sysutils/intel-microcode-netbsd to 20221108.

(msaitoh)

intel-microcode-netbsd: Update intel-microcode-netbsd to 20221108.

### Purpose

- Update for functional issues.
  Refer to Intel(R) Xeon(R) D-2700 Processor Family Specification Update
  Refer to 13th Generation Intel(R) Core(TM) Processor Specification Update
  Refer to 12th Generation Intel(R) Core(TM) Processor Specification Update
  Refer to 11th Generation Intel(R) Core(TM) Processor Specification Update
  Refer to 10th Generation Intel(R) Core(TM) Processor Specification Update
  Refer to 8th and 9th Generation Intel(R) Core(TM) Processor Family Specification Update
  Refer to 8th Generation Intel(R) Core(TM) Processor Specification Update

### New Platforms

| Processor      | Stepping | F-M-S/PI    | Old Ver  | New Ver  | Products
|:---------------|:---------|:------------|:---------|:---------|:---------
| ICL-D          | B0      | 06-6c-01/10 |          | 01000201 | Xeon D-17xx, D-27xx
| RPL-S          | S0      | 06-b7-01/32 |          | 0000010e | Core Gen13

### Updated Platforms

| Processor      | Stepping | F-M-S/PI    | Old Ver  | New Ver  | Products
|:---------------|:---------|:------------|:---------|:---------|:---------
| ICL-U/Y        | D1      | 06-7e-05/80 | 000000b2 | 000000b6 | Core Gen10 Mobile
| TGL            | B1      | 06-8c-01/80 | 000000a4 | 000000a6 | Core Gen11 Mobile
| TGL-H          | R0      | 06-8d-01/c2 | 00000040 | 00000042 | Core Gen11 Mobile
| AML-Y42        | V0      | 06-8e-0c/94 | 000000f0 | 000000f4 | Core Gen10 Mobile
| CML-Y42        | V0      | 06-8e-0c/94 | 000000f0 | 000000f4 | Core Gen10 Mobile
| WHL-U          | V0      | 06-8e-0c/94 | 000000f0 | 000000f4 | Core Gen8 Mobile
| EHL            | B1      | 06-96-01/01 | 00000016 | 00000017 | Pentium J6426/N6415, Celeron J6412/J6413/N6210/N6211, Atom x6000E
| ADL            | C0      | 06-97-02/07 | 00000022 | 00000026 | Core Gen12
| ADL            | C0      | 06-97-05/07 | 00000022 | 00000026 | Core Gen12
| ADL            | L0      | 06-9a-03/80 | 00000421 | 00000424 | Core Gen12
| ADL            | L0      | 06-9a-04/80 | 00000421 | 00000424 | Core Gen12
| CFL-H          | R0      | 06-9e-0d/22 | 000000f0 | 000000f4 | Core Gen9 Mobile
| CML-H          | R1      | 06-a5-02/20 | 000000f0 | 000000f4 | Core Gen10 Mobile
| CML-S62        | G1      | 06-a5-03/22 | 000000f0 | 000000f4 | Core Gen10
| CML-S102      | Q0      | 06-a5-05/22 | 000000f0 | 000000f4 | Core Gen10
| CML-U62 V1    | A0      | 06-a6-00/80 | 000000f0 | 000000f4 | Core Gen10 Mobile
| CML-U62 V2    | K1      | 06-a6-01/80 | 000000f0 | 000000f4 | Core Gen10 Mobile
| RKL-S          | B0      | 06-a7-01/02 | 00000054 | 00000056 | Core Gen11
| ADL            | C0      | 06-bf-02/07 | 00000022 | 00000026 | Core Gen12
| ADL            | C0      | 06-bf-05/07 | 00000022 | 00000026 | Core Gen12

### Removed Platforms

None

(msaitoh)

doc: Updated net/sayaka to 3.5.4

(tsutsui)

sayaka: update to 3.5.4.

Upstream changes:

* 3.5.4 (2022/11/08)
- implement --force-sixel option
- fix printf bug when --progress is specified

(tsutsui)

Note bash 5.2.9 update

(kre)

Updated to bash 5.2 patch 9 (5.2.9) (from 5.2.2)

The patches fix the following bugs:

Patch 3:
Command substitutions need to preserve newlines instead of replacing
them with semicolons
Patch 4:
Bash needs to keep better track of nested brace expansions to
avoid problems with quoting and POSIX semantics.
Patch 5:
Null pattern substitution replacement strings can cause a crash
Patch 6:
In interactive shells, interrupting the shell while entering a command
substitution can inhibit alias expansion.
Patch 7:
Several problems with alias expansion inside command
substitutions when in POSIX mode
Patch 8:
Array subscript expansion can inappropriately quote brackets
if the expression contains < or >.
Patch 9:
Bash arithmetic expansion should allow `@' and `*' to be used
as associative array keys in expressions.

(kre)

net/icingaweb2: update HOMEPAGE

(taca)

doc: Updated devel/php-igbinary to 3.2.11

(taca)

devel/php-igbinary: update to 3.2.11

3.2.7 (2022-01-12)

* Update test expectations for php 8.2.0-dev.  Add
  `#[AllowDynamicProperties]` Attribute to some tests to avoid notices.

* In php 8.1+, make igbinary_unserialize check to see if an equivalent
  interned string already exists when unserializing object property names,
  array keys, and class names and use that instead of creating a brand new
  string.
  (This deliberately doesn't create a new interned string if one doesn't
  already exist.)
  (Before this change, igbinary would deduplicate strings when serializing,
  but would not check if strings were interned by PHP itself when
  unserializing)

* Avoid debug build assertion failure for `HT_ASSERT_RC1` the same way as
  PHP's unserialize - this is a case where ostensibly there are no other
  references to the array being unserialized.

3.2.8 (2022-10-17)

* Reduce excessive inlining to reduce shared library size.

* Miscellaneous optimizations.

* Update test expectations to handle changes to var_export output (fully
  qualified class names) in PHP 8.2.

* Throw an Error when igbinary_unserialize would add dynamic properties to
  class definitions that forbid them in PHP 8.0+
  (especially PHP 8.2 `readonly` classes)

* Emit a deprecation notice when igbinary_unserialize() adds dynamic
  properties to a class without `#[AllowDynamicProperties]` in PHP 8.2.
  Doing that would become an Error in PHP 9.0.

* Set up CI job to build dlls on https://github.com/igbinary/igbinary - at
  the moment, the infrastructure used by the Windows for php team has been
  broken for months.

3.2.9 (2022-10-17)

* Fix invalid release artifact name in job to build dlls for
  https://github.com/igbinary/igbinary

3.2.10 (2022-11-06)

* Add a macro that callers can use to check if igbinary will accept the
  header for data being unserialized.

* Fix bug preventing the unserialization of data containing representations
  of strings larger than 4GB.

3.2.11 (2022-11-06)

* Fix a bug that could prevent objects/arrays with reference cycles from
  being properly garbage collected.

* Fix bugs in unserializing PHP references to values found in php 7.4 typed
  properties (#363)

(taca)

Rewrite versioned Python dependency handling to deal with more than just
py27 vs py3.

(joerg)

Updated devel/py-coverage, devel/py-test-cov

(adam)

py-test-cov: updated to 4.0.0

4.0.0 (2022-09-28)
------------------

**Note that this release drops support for multiprocessing.**

* `--cov-fail-under` no longer causes `pytest --collect-only` to fail
* Dropped support for multiprocessing (mostly because `issue 82408 <https://github.com/python/cpython/issues/82408>`_). This feature was
  mostly working but very broken in certain scenarios and made the test suite very flaky and slow.

  There is builtin multiprocessing support in coverage and you can migrate to that. All you need is this in your
  ``.coveragerc``::

    [run]
    concurrency = multiprocessing
    parallel = true
    sigterm = true
* Fixed deprecation in ``setup.py`` by trying to import setuptools before distutils.
* Removed undesirable new lines that were displayed while reporting was disabled.
* Documentation fixes.
* Added support for LCOV output format via `--cov-report=lcov`. Only works with coverage 6.3+.
* Modernized pytest hook implementation.

(adam)

py-coverage: updated to 6.5.0

Version 6.5.0 — 2022-09-29
--------------------------

- The JSON report now includes details of which branches were taken, and which
  are missing for each file. Thanks, Christoph Blessing (`pull 1438`_). Closes
  `issue 1425`_.

- Starting with coverage.py 6.2, ``class`` statements were marked as a branch.
  This wasn't right, and has been reverted, fixing `issue 1449`_. Note this
  will very slightly reduce your coverage total if you are measuring branch
  coverage.

- Packaging is now compliant with `PEP 517`_, closing `issue 1395`_.

- A new debug option ``--debug=pathmap`` shows details of the remapping of
  paths that happens during combine due to the ``[paths]`` setting.

- Fix an internal problem with caching of invalid Python parsing. Found by
  OSS-Fuzz, fixing their `bug 50381`_.

.. _bug 50381: https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=50381
.. _PEP 517: https://peps.python.org/pep-0517/
.. _issue 1395: https://github.com/nedbat/coveragepy/issues/1395
.. _issue 1425: https://github.com/nedbat/coveragepy/issues/1425
.. _pull 1438: https://github.com/nedbat/coveragepy/pull/1438
.. _issue 1449: https://github.com/nedbat/coveragepy/issues/1449

(adam)

Updated textproc/pugixml

(adam)

pugixml: updated to 1.13

v1.13 2022-11-01
Maintenance release. Changes:

Improvements:

xml_attribute::set_value, xml_node::set_value and xml_text::set now have overloads that accept pointer to non-null-terminated string and size
Improve performance of tree traversal when using compact mode (PUGIXML_COMPACT)

Bug fixes:

Fix error handling in xml_document::save_file that could result in the function succeeding while running out of disk space
Fix memory leak during error handling of some out-of-memory conditions during xml_document::load

Compatibility improvements:

Fix exported symbols in CMake DLL builds when using CMake
Fix exported symbols in CMake shared object builds when using -fvisibility=hidden

(adam)

Updated databases/slony1, devel/py-setuptools

(adam)

py-setuptools: updated to 65.5.1

v65.5.1

Misc
Drop a test dependency on the mock package, always use unittest.mock
Fixed REDoS vector in package_index.

(adam)

clisp: fix module linking with X11_TYPE = native on NetBSD

X11 pkg-config files on NetBSD includes -Wl,-rpath,/usr/X11R7/lib
that can't be understood by the ld command, so use the compiler
that can understand this for linking instead.
Fixes build of x11/clisp-gtk2 with X11_TYPE = native and cwrappers.
Concerns PR pkg/57077 .

(nros)

slony1: updated to 2.2.11

2.2.11
- Add support for PG 15
- Remove standard_conforming_strings autoconf check
- Fix typo in admin guide

(adam)

orc: add upstream bug report URL

(wiz)

doc: Updated devel/orc to 0.4.33

(wiz)

orc: update to 0.4.33.

0.4.33
======

  - Add support for aarch64 (64-bit ARM) architecture (not yet enabled on Windows though)
    (Marek Vasut, Dongju Chae, Gaetan Bahl)
  - aarch32: Implement loadupdb instruction used e.g. for video pixel
    format packing/unpacking/conversions (Marek Vasut, Gaetan Bahl)
  - neon: Fix unsigned only implementation of loadoffb, loadoffw and loadoffl
    (Daniel Knobe)
  - neon: Fix testsuite not passing on arm CPUs (Gaetan Bahl)
  - orccodemem: Fix use-after-free in error paths (Bastien Nocera)
  - orccpu-powerpc: Fix build with kernel < 4.11 (Fabrice Fontaine)
  - Add support for macOS Hardened Runtime (Doug Nazar)
  - Enable only SSE and MMX backends for Windows (Seungha Yang)
  - Fix ORC_RESTRICT definition for MSVC (Tim-Philipp M端ller)
  - pkgconfig: add -DORC_STATIC_COMPILATION flag to .pc file for static-only builds
    (Steve Lhomme)

(wiz)

Updated biology/py-pydicom, devel/py-pip

(adam)

py-pip: updated to 22.3.1

22.3.1 (2022-11-05)
===================

Bug Fixes
---------

- Fix entry point generation of ``pip.X``, ``pipX.Y``, and ``easy_install-X.Y``
  to correctly account for multi-digit Python version segments (e.g. the "11"
  part of 3.11).

(adam)

py-pydicom: updated to 2.3.0

Version 2.3.0
=================================

Changes
-------
* :meth:`DataElement.description<pydicom.dataelem.DataElement.description>` is
  deprecated and will be removed in v3.0, use
  :attr:`DataElement.name<pydicom.dataelem.DataElement.name>` instead
* Updated the private dictionary
* :attr:`~pydicom.config.enforce_valid_values` is deprecated in favor of
  :attr:`~pydicom.config.settings.reading_validation_mode`
* Added `download` parameter to :func:`~pydicom.data.get_testdata_file`
  to allow skipping downloading the file if missed locally (:pr:`1617`)

Enhancements
------------
* Values are now validated for valid length, allowed character set and format
  on reading and writing. Depending on the value of
  :attr:`~pydicom.config.settings.reading_validation_mode`
  and :attr:`~pydicom.config.settings.writing_validation_mode`
  a warning is logged, an exception is raised, or the validation is skipped.
* Added :class:`~pydicom.valuerep.VR` enum (:pr:`1500`)
* UIDs for all Storage SOP Classes have been added to the ``uid`` module
  (:issue:`1498`)
* Use rle_handler as last resort handler for decoding RLE encoded data as it is
  the slowest handler (:issue:`1487`)
* Added, enhanced, or removed a number of Mitra private dictionary entries (:pr:`1588`)
* Added support for unpacking bit-packed data without using NumPy to
  :func:`~pydicom.pixel_data_handlers.utils.unpack_bits`(:pr:`1594`)
* Added :func:`~pydicom.pixel_data_handlers.util.expand_ybr422` for expanding
  uncompressed ``YBR_FULL_422`` data to ``YBR_FULL`` (:pr:`1593`)
* Replacement of ``UN`` VR with ``SQ`` VR for undefined length data elements
  (introduced in 2.2.2), can now be configured via
  :attr:`~pydicom.config.settings.infer_sq_for_un_vr`
* Updated dictionaries to DICOM 2022a

Fixes
-----
* Fixed odd-length **OB** values not being padded during write (:issue:`1511`)
* Fixed Hologic private dictionary entry (0019xx43)
* Fixed Mitra global patient ID private dictionary entry (:pr:`1588`)
* Fixed :meth:`~pydicom.dataset.Dataset.compress` not setting the correct
  encoding for the rest of the dataset (:issue:`1565`)
* Fixed `AttributeError` on deep copy of :class:`~pydicom.dataset.FileDataset`
  (:issue:`1571`)
* Fixed an exception during pixel decoding if using GDCM < 2.8.8 on Windows
  (:issue:`1581`)
* Fixed crashes on Windows and MacOS when using the GDCM plugin to compress
  into *RLE Lossless* (:issue:`1581`)
* Fixed ``dir(Dataset())`` not returning class attributes (:issue:`1599`)
* Fixed bad DICOMDIR offsets when using :meth:`FileSet.write()
  <pydicom.fileset.FileSet.write>` with a *Directory Record Sequence* using
  undefined length items (:issue:`1596`)
* Assigning a list of length one as tag value is now correctly handled as
  assigning the single value (:issue:`1606`)
* Fixed an exception with multiple deferred reads with file-like objects
  (:issue:`1609`)

(adam)

Updated devel/py-xopen, databases/py-asyncpg

(adam)

py-asyncpg: updated to 0.27.0

v0.27.0

Support Python 3.11 and PostgreSQL 15. This release also drops support
for Python 3.6.

Changes

Add arm64 mac and linux wheels
Add Python 3.11 to the test matrix
Exclude .venv from flake8
Upgrade to flake8 5.0.4 (from 3.9.2)
Show an example of a custom Record class
Use the exact type name in Record.repr
Drop Python 3.6 support
Test on Python 3.11 and PostgreSQL 15, fix workflow deprecations

(adam)

py-xopen: updated to 1.7.0

1.7.0:
Unknown changes

(adam)

Removed devel/py-typed-ast; comms/py-enrich

(adam)

py-enrich: removed; not needed anymore for ansible-lint

(adam)

py-typed-ast: removed; included in Python 3.8 - ast module

(adam)

py-astroid: no need to depend on py-typed-ast anymore

(adam)

py-black: no need to depend on py-typed-ast anymore

(adam)

Updated sysutils/py-psutil, devel/py-immutabledict, lang/py-mypy, devel/py-faker

(adam)

py-faker: updated to 15.3.1

v15.3.1

* Update the `word_list` for `pl_PL`.

v15.3.0

* Add color provider for `id_ID`.

v15.2.0

* Add banks for `en_IN` locale.

v15.1.5

* Fix type variable inside the `ElementsType`.

v15.1.4

* Remove test dependency on `random2`.

v15.1.3

*  Fix pyfloat causing ValueError.

v15.1.2

* Fix missing return in `en_US` `state_abbr`.

v15.1.1

* Fix ImportError on python <3.7.2.

v15.1.0

* Add enum provider.

v15.0.0

* Add support for Python 3.10.
* Drop support for Python 3.6.

v14.2.1

* Fix misspelled first name in `da_DK` locale.

(adam)

py-mypy: updated to 0.990

v0.990
Remove +dev from version

(adam)

py-immutabledict: updated to 2.2.3

Version 2.2.3

Fix TypeError message when using |=.
Update docstring for ImmutableOrderedDict to indicate that is not needed anymore for Python >= 3.7 but kept for compatibility purposes
Use postponed evaluation of annotations (PEP 563) for the typing

Version 2.2.2

Update classifiers, Github Actions... for Python 3.11 (no code changes)

(adam)

py-psutil: updated to 5.9.4

5.9.4
=====

2022-11-07

**Enhancements**

- 2102_: use Limited API when building wheels with CPython 3.6+ on Linux,
  macOS and Windows. This allows to use pre-built wheels in all future versions
  of cPython 3.  (patch by Matthieu Darbois)

**Bug fixes**

- 2077_, [Windows]: Use system-level values for `virtual_memory()`_. (patch by
  Daniel Widdis)
- 2156_, [Linux]: compilation may fail on very old gcc compilers due to missing
  ``SPEED_UNKNOWN`` definition.  (patch by Amir Rossert)
- 2010_, [macOS]: on MacOS, arm64 ``IFM_1000_TX`` and ``IFM_1000_T`` are the
  same value, causing a build failure.  (patch by Lawrence D'Anna)

(adam)

doc: Updated net/unison to 2.53.0

(gdt)

net/unison: Update to 2.53.0

Change to lablgkt3.
Drop MAKE_JOBS_SAFE because the issue was fixed upstream.

## Changes in 2.53.0

Released 2022-11-07

  * OCaml >= 4.08 is required to build unison.
  * unison can be built with (unreleased) OCaml 5.
  * Change GUI to use GTK3 (via lablgtk3) instead of GTK2 (via lablgtk2)
  * Add support for syncing extended attributes.
  * Add support for syncing ACLs.
  * On Windows, add the ability to build unison as a hybrid
    application (GUI application attached to a text console) by
    defining UI_WINOS=hybrid (see src/Makefile).  Add this to CI.
    (Doing this for non-Windows is unnecessary as all applications,
    both GUI and non-GUI, are always executed with a connection to
    stdout/stderr. GUI-only applications (ie, no stdout/stderr) is a
    Windows-only concept.)
  * Notable bugfixes
    - Merge results are stored in archive more accurately.
    - Windows `\\?\` paths now work correctly (including `\\?\Volume{GUID}\` paths).
  * CI changes
    - The macOS binaries are properly signed.
    - Add workaround for bugs in the github CI Windows builds, one of
      which resulted in the 2.52.1 GUI version failing, in the Windows
      CI build artifacts.  (This does not affect platforms other than
      Windows, and may not affect other Windows builds.)
  * Changes that should not affect behavior
    - Clean up a variety of unmaintained and unused bits, mainly
      build-related.
    - OCaml's Unix library is now extensively used also on
      Windows. This allowed removal of large amount of
      Windows-specific OCaml and mainly C code.

(gdt)

seamonkey: update Python 3 tool dependency

(gutteridge)

thunderbird68: update Python 3 tool dependency

(gutteridge)

doc: Updated devel/patchelf to 0.17.0

(fcambus)

patchelf: update to 0.17.0.

- fix pagesize on ia64
- write out replace sections in original order
- patchelf: correct page size for sparc64/sparc32
- update vendored elf file
- add workaround for readelf from binutils 2.30
- make objdump/objcopy/readelf configurable and respect cross-compiling

(fcambus)

Pullup ticket #6701 - requested by taca
lang/php74: security fix

Revisions pulled up:
- lang/php/phpversion.mk                                        1.380
- lang/php56/Makefile                                          1.30
- lang/php74/Makefile                                          1.17
- lang/php74/distinfo                                          1.39
- lang/php80/Makefile                                          1.10
- lang/php81/Makefile                                          1.8

---
  Module Name: pkgsrc
  Committed By: taca
  Date: Sun Oct 30 10:50:01 UTC 2022

  Modified Files:
  pkgsrc/lang/php56: Makefile
  pkgsrc/lang/php74: Makefile
  pkgsrc/lang/php80: Makefile
  pkgsrc/lang/php81: Makefile

  Log Message:
  lang/php: post-install clean up

  Do not manually install executable files and manual.
  These are already done by php's Makefile from some time ago.

---
  Module Name: pkgsrc
  Committed By: taca
  Date: Fri Nov  4 00:40:58 UTC 2022

  Modified Files:
  pkgsrc/lang/php: phpversion.mk
  pkgsrc/lang/php74: distinfo

  Log Message:
  lang/php74: update to 7.4.33

  7.4.33 (2022-11-03)

  - GD:
    . Fixed bug #81739: OOB read due to insufficient input validation in
      imageloadfont(). (CVE-2022-31630) (cmb)

  - Hash:
    . Fixed bug #81738: buffer overflow in hash_update() on long parameter.
      (CVE-2022-37454) (nicky at mouha dot be)

(bsiegert)

doc: Updated security/sudo to 1.9.12p1

(taca)

security/sudo: update to 1.9.12p1

1.9.12p1 (2022-11-07)

What's new in Sudo 1.9.12p1

* Sudo's configure script now does a better job of detecting when
  the -fstack-clash-protection compiler option does not work.
  GitHub issue #191.

* Fixed CVE-2022-43995, a potential out-of-bounds write for passwords
  smaller than 8 characters when passwd authentication is enabled.
  This does not affect configurations that use other authentication
  methods such as PAM, AIX authentication or BSD authentication.

* Fixed a build error with some configurations compiling host_port.c.

(taca)

Updated textproc/utf8-cpp, devel/py-jaraco.collections

(adam)

py-jaraco.collections: updated to 3.8.0

v3.8.0
======
Made ``DictStack`` mutable.

(adam)

utf8-cpp: updated to 3.2.2

v3.2.2
Minor changes that eliminate some conversion warnings in some cases.

(adam)

firefox52: adjust outdated comments

(gutteridge)

thunderbird: remove 37 from PYTHON_VERSIONS_ACCEPTED

(gutteridge)

devel/backports.cached-property-1.0.1: Drop 37

as this depends on things that no longer exist.
It should be removed, but this should fix the bulk scan failure.

(gdt)

devel/Makefile: comment out py-backports.cached-property

python 3.7 only and the packages it depends upon by default
do not build 3.7 versions any longer

(wiz)

biology/Makefile: Add gffread

(bacon)

doc: Added biology/gffread version 0.12.7

(bacon)

biology/gffread: GFF/GTF format conversions, filtering, etc

GFF/GTF utility providing format conversions, filtering, FASTA sequence
extraction and more.  The program gffread can be used to validate,
filter, convert and perform various other operations on GFF files.
Because the program shares the same GFF parser code with Cufflinks,
Stringtie, and gffcompare, it could be used to verify that a GFF file
from a certain annotation source is correctly "understood" by these
programs.

(bacon)

biology/Makefile: Add fastq-trim

(bacon)

doc: Added biology/fastq-trim version 0.1.1.16

(bacon)

biology/fastq-trim: Lightening fast sequence read trimmer

Fastq-trim is a lightening fast read trimming tool for QA of DNA and RNA reads
prior to analyses such as RNA-Seq.  it runs in a fraction of the time required
by popular trimmers and uses only a few megabytes of RAM, so it will run
almost entirely in cache.  The design supports adding any number of alignment
functions, so it can be easily adapted to any trimming needs.

(bacon)

doc: Updated emulators/dosbox-x to 0.84.3

(triaxx)

dosbox-x: Update to 0.84.3

pkgsrc changes:
---------------
  * Fix building of FreeBSD by adding -lpthread to LDFLAGS and by disabling
    call to X11_ErrorHandlerInstall.

upstream changes:
-----------------
  * 0.84.3: https://dosbox-x.com/release-0.84.3.html
  * 0.84.2: https://dosbox-x.com/release-0.84.2.html
  * 0.84.1: https://dosbox-x.com/release-0.84.1.html
  * 0.84.0: https://dosbox-x.com/release-0.84.0.html

(triaxx)

doc: Updated shells/zsh to 5.9nb2

(wiz)

zsh: add candidate upstream patch for bg/fg issue with shell functions

Bump PKGREVISION.

(wiz)

Updated devel/py-jaraco.itertools, www/py-websockets

(adam)

py-websockets: updated to 10.4

10.4

New features

Validated compatibility with Python 3.11.
Added the latency property to protocols.
Changed ping to return the latency of the connection.
Supported overriding or removing the User-Agent header in clients and the Server header in servers.
Added deployment guides for more Platform as a Service providers.

Improvements

Improved FAQ.

(adam)

py-jaraco.itertools: updated to 6.2.1

v6.2.1
======
Fixed broken test in ``ensure_unique``.

v6.2.0
======
Added ``accumulate`` function.

v6.1.1
======
Fixed typo in ``ensure_unique`` doctest.

v6.1.0
======
Add ``ensure_unique`` function.

v6.0.3
======
Fixed doc build errors.

v6.0.2
======
Minor fixes.

v6.0.1
======
Switch to PEP 420 for namespace package.

v6.0.0
======
Remove ``Counter.GetCount``.
Remove ``flatten`` and ``iflatten``.

(adam)

Added devel/py-jaraco.collections; Updated time/py-tempora, net/py-portend, www/py-cheroot, www/py-cherrypy, www/py-webpy

(adam)

py-webpy: updated to 0.62

0.62

* Fixed: application.load() assumes ctx.path will be a latin1 string
* Fixed: can not reset session data to same value as initialized.
* Fixed: can not set session expire time.
* Fixed: not export session store `MemoryStore`.

0.61

* setup.py: Add python_requires='>=3.5'

0.60

* Python-2 support has been completely dropped. Welcome to Python 3.
* Fixed: session store `DiskStore` doesn't return correctly if session
  directory doesn't exist.
* Fixed: incorrect str/bytes type of session data.
* Fixed: `db.query("insert... returning")` fails to commit.

(adam)

py-cherrypy: updated to 18.8.0

v18.8.0
-------

* :issue:`1974`: Dangerous characters received in a host header
  encoded using RFC 2047 are now elided by default. Currently,
  dangerous characters are defined as CR and LF. The original
  value is still available as ``cherrypy.request.headers['Host'].raw``
  if needed.

v18.7.0
-------

* :pr:`1923`: Drop support for Python 3.5.
* :pr:`1945`: Fixed compatibility on Python 3.11.

v18.6.1
-------

* :issue:`1849` via :pr:`1879`: Fixed XLF flag in gzip header
  emitted by gzip compression tool per
  :rfc:`1952#section-2.3.1` -- by :user:`webknjaz`.

* :issue:`1874`: Restricted depending on pywin32 only under
  CPython so that it won't get pulled-in under PyPy
  -- by :user:`webknjaz`.

* :issue:`1920`: Bumped minimum version of PyWin32 to 227.
  Block pywin32 install on Python 3.10 and later.

v18.6.0
-------

* :issue:`1776` via :pr:`1851`: Add support for UTF-8 encoded attachment
  file names in ``Content-Disposition`` header via :rfc:`6266#appendix-D`.

v18.5.0
-------

* :issue:`1827`: Fixed issue where bytes values in a ``HeaderMap``
  would be converted to strings.

* :pr:`1826`: Rely on
  `jaraco.collections <https://pypi.org/project/jaraco.collections>`_
  for its case-insensitive dictionary support.

v18.4.0
-------

* :pr:`1715`: Fixed issue in cpstats where the ``data/`` endpoint
  would fail with encoding errors on Python 3.

* :pr:`1821`: Simplify the passthrough of parameters to
  ``CPWebCase.getPage`` to cheroot. CherryPy now requires
  cheroot 8.2.1 or later.

(adam)

py-jaraco.collections: added version 3.7.0

Models and classes to supplement the stdlib 'collections' module.

(adam)

py-cheroot: updated to 8.6.0

v8.6.0

Significant improvements:

- :issue:`384` via :pr:`385`, :pr:`406`: Exposed type stubs with
  annotations for public API -- by :user:`kasium`.

- :pr:`401` (related to the :pr:`352` effort): Started reusing the
  the ``expriration_interval`` setting in the low-level
  :py:func:`~select.select` invocation, effectively reducing the system
  load under the Windows OS when idle, that is noticeable on low-end
  hardware systems -- by :user:`MichaIng`.

Internal changes:

- Implemented a manual-trigger-based release workflow.
- Integrated publishing GitHub Releases into the workflow.
- Migrated the docs theme to `Furo <https://pradyunsg.me/furo>`__
  (created by :user:`pradyunsg`).
- Attempted to improve the stability of testing.
- Configured the CI to test the same distribution as will be shipped.
- Improved the linting setup and contributor checklists.
- Stopped running tests under Ubuntu 16.04.
- Tweaked the distribution packages metadata to satisfy strict checks.
- Implemented distribution build reproducibility using a pip constraints
  lock-file.
- Added per-environment lock-files into the tox test environments.

v8.5.2

- :issue:`358` via :pr:`359`: Fixed a regression from
  :pr:`199` that made the worker threads exit on invalid
  connection attempts and could make the whole server
  unresponsive once there was no workers left.
  -- by :user:`cameronbrunner`.

v8.5.1

- :cp-issue:`1873` via :pr:`340`: Resurrected an
  unintentionally removed feature of interrupting a server
  main thread by externally assigning an exception to the
  :py:meth:`HTTPServer.interrupt <cheroot.server.\
  HTTPServer.interrupt>` property -- by :user:`liamstask`.

- :pr:`350`: Fixed the incarnation of an earlier regression
  of not resetting the serving state
  on :py:data:`SIGINT` originally fixed by :pr:`322` and
  :pr:`331` but reintroduced by the changes in :pr:`311`
  -- by :user:`liamstask`.

v8.5.0

- :issue:`305` via :pr:`311`: In
  :py:class:`~cheroot.connections.ConnectionManager`,
  process connections as they become active rather than
  waiting for a ``tick`` event, addressing performance
  degradation introduced in v8.1.0 -- by :user:`liamstask`.

- :issue:`341` via :pr:`342`: Suppress legitimate OS errors
  expected on shutdown -- by :user:`webknjaz`.

v8.4.8

- :issue:`317` via :pr:`337`: Fixed a regression in
  8.4.5 where the connections dictionary would change
  size during iteration, leading to a :py:exc:`RuntimeError`
  raised in the logs -- by :user:`liamstask`.

v8.4.7

- :pr:`334`: Started filtering out TLS/SSL errors when
  the version requested by the client is unsupported
  -- by :user:`sanderjo` and :user:`Safihre`.

v8.4.6

- :issue:`328` via :pr:`322` and :pr:`331`: Fixed a
  regression introduced in the earlier refactoring in v8.4.4
  via :pr:`309` that caused the :py:meth:`~cheroot.server.\
  HTTPServer.serve` method to skip setting
  ``serving=False`` on :py:data:``SIGINT`` and
  :py:data:``SIGTERM`` -- by :user:`marc1n` and
  :user:`cristicbz`.

v8.4.5

- :issue:`312` via :pr:`313`: Fixed a regression introduced
  in the earlier refactoring in v8.4.4 via :pr:`309` that
  caused the connection manager to modify the selector map
  while looping over it -- by :user:`liamstask`.

- :issue:`312` via :pr:`316`: Added a regression test for
  the error handling in :py:meth:`~cheroot.connections.\
  ConnectionManager.get_conn` to ensure more stability
  -- by :user:`cyraxjoe`.

v8.4.4

- :issue:`304` via :pr:`309`: Refactored :py:class:`~\
  cheroot.connections.ConnectionManager` to use :py:meth:`~\
  selectors.BaseSelector.get_map` and reorganized the
  readable connection tracking -- by :user:`liamstask`.

- :issue:`304` via :pr:`309`: Fixed the server shutdown
  sequence to avoid race condition resulting in accepting
  new connections while it is being terminated
  -- by :user:`liamstask`.

v8.4.3

- :pr:`282`: Fixed a race condition happening when an HTTP
  client attempts to reuse a persistent HTTP connection after
  it's been discarded on the server in :py:class:`~cheroot.\
  server.HTTPRequest` but no TCP FIN packet has been received
  yet over the wire -- by :user:`meaksh`.

  This change populates the ``Keep-Alive`` header exposing
  the timeout value for persistent HTTP/1.1 connections which
  helps mitigate such race conditions by letting the client
  know not to reuse the connection after that time interval.

v8.4.2

- Fixed a significant performance regression introduced in
  v8.1.0 (:issue:`305` via :pr:`308`) - by :user:`mar10`.

  The issue turned out to add 0.1s delay on new incoming
  connection processing. We've lowered that delay to mitigate
  the problem short-term, better fix is yet to come.

v8.4.1

- Prevent :py:exc:`ConnectionAbortedError` traceback from being
  printed out to the terminal output during the app start-up on
  Windows when built-in TLS adapter is used (:issue:`302` via
  :pr:`306`) - by :user:`mxii-ca`.

v8.4.0

- Converted management from low-level :py:func:`~select.select` to
  high-level :py:mod:`selectors` (:issue:`249` via :pr:`301`)
  - by :user:`tommilligan`.

  This change also introduces a conditional dependency on
  ``selectors2`` as a fall-back for legacy Python interpreters.

v8.3.1

- Fixed TLS socket related unclosed resource warnings
  (:pr:`291` and :pr:`298`).
- Made terminating keep-alive connections more graceful
  (:issue:`263` via :pr:`277`).

v8.3.0

- :cp-issue:`910` via :pr:`243`: Provide TLS-related
  details via WSGI environment interface.
- :pr:`248`: Fix parsing of the ``--bind`` CLI option
  for abstract UNIX sockets.

(adam)

py-portend: updated to 3.1.0

v3.1.0
======
Require Python 3.7 or later.

v3.0.0
======
Removed legacy aliases ``wait_for_occupied_port``
and ``wait_for_free_port``.

v2.7.2
======
Packaging refresh.

v2.7.1
======
Fix host/port order.

v2.7.0
======
Refresh package. Require Python 3.6 or later.

(adam)

py-tempora: updated to 5.0.2

v5.0.2
======
- Refreshed project.
- Enrolled with Tidelift.

v5.0.1
======
- Refreshed project.

v5.0.0
======
- Removed deprecated ``divide_*`` functions and ``Parser``
  class.
- Require Python 3.7 or later.
- Fixed error reporting in parse_timedelta.

v4.1.2
======
- Docs now build without warnings.

v4.1.1
======
- Fixed issue where digits were picked up in the unit when
  adjacent to the last unit.

v4.1.0
======
- Added support for more formats in ``parse_timedelta``.
- ``parse_timedelta`` now supports formats emitted by
  ``timeit``, including honoring nanoseconds at the
  microsecond resolution.

v4.0.2
======
- Refreshed package metadata.

v4.0.1
======
- Refreshed package metadata.

v4.0.0
======
- Removed ``strptime`` function in favor of
  `datetime.datetime.strptime <https://docs.python.org/3/library/datetime.html#datetime.datetime.strptime>`_. If passing
  a ``tzinfo`` parameter, instead invoke `.replace(tzinfo=...)`
  on the result.
- Deprecated ``divide_timedelta`` and ``divide_timedelta_float``
  now that Python supports this functionality natively.
- Deprecated ``Parser`` class. The
  `dateutil.parser <https://dateutil.readthedocs.io/en/stable/parser.html>`_
  provides more sophistication.

(adam)

Updated lang/py-inflect, devel/py-jaraco.functools; Added devel/py-jaraco.context, textproc/py-jaraco.text

(adam)

py-jaraco.functools: updated to 3.5.2

v3.5.2
======
Refreshed packaging.

v3.5.1
======
Packaging refresh.
Enrolled with Tidelift.

v3.5.0
======
* Add type annotations to ``method_cache``.
* Require Python 3.7.

v3.4.0
======
``apply`` now uses ``functools.wraps`` to ensure docstring
passthrough.

v3.3.0
======
In method_cache, support cache_clear before cache
is initialized.

v3.2.1
======
Refreshed package metadata.

v3.2.0
======
Switched to PEP 420 for ``jaraco`` namespace.

v3.1.0
======
Added ``except_`` decorator.

v3.0.1
======
Removed unnecessary compatibility libraries in testing.

v3.0.0
======
Require Python 3.6 or later.

(adam)

py-jaraco.text: added version 3.10.0

This package provides handy routines for dealing with text, such as wrapping,
substitution, trimming, stripping, prefix and suffix removal, line
continuation, indentation, comment processing, identifier processing, values
parsing, case insensitive comparison, and more.

(adam)

py-jaraco.context: added version 4.1.2

Context managers by jaraco

(adam)

py-inflect: updated to 6.0.2

v6.0.2
======
* Require pydantic 1.9.1 to avoid ``ValueError``.

v6.0.1
======
* Minor tweaks and packaging refresh.

v6.0.0
======
* ``compare`` methods now validate their inputs
  and will raise a more meaningful exception if an
  empty string or None is passed. This expectation is now
  documented.

* Many public methods now perform validation on arguments.
  An empty string is no longer allowed for words or text.
  Callers are expected to pass non-empty text or trap
  the validation errors that are raised. The exceptions
  raised are ``pydantic.error_wrappers.ValidationError``,
  which are currently a subclass of ``ValueError``, but since
  that
  `may change <https://pydantic-docs.helpmanual.io/usage/validation_decorator/#validation-exception>`_,
  tests check for a generic ``Exception``.

(adam)

libslirp: Fix the patch which fixed building on FreeBSD

(triaxx)

doc: Updated net/libslirp to 4.7.0nb1

(triaxx)

libslirp: Fix building on FreeBSD

pkgsrc changes:
---------------
  * Add patch to include sys/socket.h on FreeBSD.
  * Fix alignment in buildlink3.mk (thanks to pkglint).
  * Bump revision.

(triaxx)

Updated devel/hdf5, devel/hdf5-c++, math/octave

(adam)

octave: updated to 7.3.0

GNU Octave 7.3.0

This version is a bug fixing release:

Improvements and fixes

scanf: Don窶冲 set error when reaching end of stream
Fix duplicate names displayed with mixed @class/classdef classes
canonicalize_file_name: Handle symlinks to UNC network shares
canonicalize_file_name: Generalize check for mapped network drive
fortran_vec: Fix instances of method chaining that may cause dangling pointer.
Fix wrong color in PDF printout of some LaTeX strings
unpack.m: Escape backslashes in paths on Windows
canonicalize_file_name: Check root of potential mapped network drive
nextpow2.m: Fix for input between 0.5 and 1
quad2d: Fix unintended complex conjugate return
Make sure we don窶冲 pass short 8.3 path to latex on Windows
canonicalize_file_name: Trim trailing file separators from root of mapped network drive
imformats.m: Fix isa function in return value
pie3: Fix 窶弋oo many input窶� args error.
Accept negative inputs to -2^63 for dec2bin and dec2hex
Fix incorrect lambda outputs for lsqnonneg and pqpnonneg
addtodate.m: Fix wrong month returned when subtracting a month from some end-of-month dates
var.m: Fix some Inf and NaN inputs returning 0 instead of NaN
var.m: Fix automatic broadcasting error for sparse and diagonal matrix inputs with vector weighting
legend.m: Fix error with contour plot containing clabels
dec2bin.m: Fix input validation
glpk.m: Avoid using isfinite on potentially sparse input.
var.m: Use bsxfun rather than broadcasting with vector weighting
Fix out of bound indexing in in-place broadcasting operations

GUI

Respect confirmation when deleting files in file browser widget

Build system / Tests

io.tst: Add test case for scanf
nextpow2.m: Add bug number tag to regression tests
quad2d.m: Add BIST to cset b0e90ca8e679
Add test for number of methods with classdef in @folder
Use Autoconf macro to find egrep executable.

Documentation

uitable.m: Fix example code
Clarify number of processors returned by nproc with hyperthreading.
Minor wording change to hashing documentation.
lsqnonneg and pqpnonneg: Document undocumented outputs.
pqpnonneg.m: Improve docstring readability.
lsode: Make TeX and non-TeX docstrings agree.
curl: Fix error in TeX docstring.
Update text on function argument checking.
schur: Update documentation.

(adam)