py-scipy: updated to 1.8.0

SciPy 1.8.0 is the culmination of 6 months of hard work. It contains
many new features, numerous bug-fixes, improved test coverage and better
documentation. There have been a number of deprecations and API changes
in this release, which are documented below. All users are encouraged to
upgrade to this release, as there are a large number of bug-fixes and
optimizations. Before upgrading, we recommend that users check that
their own code does not use deprecated SciPy functionality (to do so,
run your code with ``python -Wd`` and check for ``DeprecationWarning`` s).
Our development attention will now shift to bug-fix releases on the
1.8.x branch, and on adding new features on the master branch.

This release requires Python 3.8+ and NumPy 1.17.3 or greater.

For running on PyPy, PyPy3 6.0+ is required.

**************************
Highlights of this release
**************************

- A sparse array API has been added for early testing and feedback; this
  work is ongoing, and users should expect minor API refinements over
  the next few releases.
- The sparse SVD library PROPACK is now vendored with SciPy, and an interface
  is exposed via `scipy.sparse.svds` with ``solver='PROPACK'``. It is currently
  default-off due to potential issues on Windows that we aim to
  resolve in the next release, but can be optionally enabled at runtime for
  friendly testing with an environment variable setting of ``USE_PROPACK=1``.
- A new `scipy.stats.sampling` submodule that leverages the ``UNU.RAN`` C
  library to sample from arbitrary univariate non-uniform continuous and
  discrete distributions
- All namespaces that were private but happened to miss underscores in
  their names have been deprecated.

(adam)

py-numpy: updated to 1.22.3

The NumPy 1.22.3 is maintenance release that fixes bugs discovered after the
1.22.2 release. The most noticeable fixes may be those for DLPack. One that may
cause some problems is disallowing strings as inputs to logical ufuncs. It is
still undecided how strings should be treated in those functions and it was
thought best to simply disallow them until a decision was reached. That should
not cause problems with older code.

The NumPy 1.22.2 is maintenance release that fixes bugs discovered after the
1.22.1 release. Notable fixes are:

- Several build related fixes for downstream projects and other platforms.
- Various Annotation fixes/additions.
- Numpy wheels for Windows will use the 1.41 tool chain, fixing downstream link
  problems for projects using NumPy provided libraries on Windows.
- Deal with CVE-2021-41495 complaint.

The NumPy 1.22.1 is maintenance release that fixes bugs discovered after the
1.22.0 release. Notable fixes are:

- Fix f2PY docstring problems (SciPy)
- Fix reduction type problems (AstroPy)
- Fix various typing bugs.

NumPy 1.22.0 is a big release featuring the work of 153 contributers spread
over 609 pull requests. There have been many improvements, highlights are:

* Annotations of the main namespace are essentially complete. Upstream is a
  moving target, so there will likely be further improvements, but the major
  work is done. This is probably the most user visible enhancement in this
  release.
* A preliminary version of the proposed Array-API is provided. This is a step
  in creating a standard collection of functions that can be used across
  applications such as CuPy and JAX.
* NumPy now has a DLPack backend. DLPack provides a common interchange format
  for array (tensor) data.
* New methods for ``quantile``, ``percentile``, and related functions. The new
  methods provide a complete set of the methods commonly found in the
  literature.
* A new configurable allocator for use by downstream projects.
* The universal functions have been refactored to implement most of
  :ref:`NEP 43 <NEP43>`.  This also unlocks the ability to experiment with the
  future DType API.

(adam)

helix: remove unnecessary rust mk.

(nikita)

(ham/gnuradio-doxygen) PKGREVISION++

(mef)

(ham/gnuradio-doxygen) Regen PLIST for doxygen-1.9.3

(mef)

doc/pkgsrc.*: regen

(nia)

NetBSD magnetism: mention `priv`

(nia)

doc: Added devel/gitui version 0.20.1

(bsiegert)

New package for gitui. From Kimihiro Nonaka in PR pkg/56784.

Blazing fast terminal client for git written in Rust.

Features:
* Fast and intuitive keyboard only control
* Context based help (no need to memorize tons of hot-keys)
* Inspect, commit, and amend changes (incl. hooks: commit-msg/post-commit)
* Stage, unstage, revert and reset files and hunks
* Stashing (save, apply, drop, and inspect)
* Browse commit log, diff committed changes
* Scalable terminal UI layout
* Async input polling
* Async git API for fluid control

(bsiegert)

tex-firstaid: fix PLIST

(tnn)

tex package updates

(markd)

tex-rsfso{,-doc}: update to 1.03

changes unknown

(markd)

tex-repere{,-doc}: update to 21.11

changes unknown

(markd)

tex-readarray{,-doc}: update to 3.1

Version 3.0 of readarray introduces several new features.  Arrays can be
initialized with the \initarray command, rather than being read from a
file.  With \setvalue, the tokens of individual array cells can be revised
on demand.  The contents of one array can be merged into another by way of
the \mergearray command.  The \typesetarray command allows for versatile
ways to format your array output, including by way of tabular
environments. The way end-of-line characters can be handled on a data-read
is made more versatile with this package version.

(markd)

tex-ragged2e{,-doc}: update to 3.1

declare user macros robust

(markd)

Updated textproc/py-openapi-schema-validator, textproc/py-openapi-spec-validator

(adam)

py-openapi-spec-validator: updated to 0.4.0

0.4.0
Drop Python 2.7, 3.5 and 3.6 support
Add Python 3.10 support
Bump dependency upper bounds
Drop pyrsistent direct dependency

(adam)

py-openapi-schema-validator: updated to 0.2.3

0.2.3
readOnly and writeOnly on jsonschema4 fix

0.2.2
Validate oneOf, anyOf and allOf with discriminator (cherry-pick from 0.3.x)

0.2.1
Revert "make jsonschema4 compatible (DeprecationWarning fix)"
Drop python 3.6 support (cherry-pick from 0.3.x and part 2)
Limit jsonschema dependency

0.2.0
switch to poetry
drop python 2.7 and 3.5 support
make jsonschema4 compatible (DeprecationWarning fix)

(adam)

doc: Updated geography/py-googlemaps to 4.6.0

(kleink)

geography/py-googlemaps: Update to 4.6.0.

4.6.0 (2022-02-02)

Features
* Geocode by place id (427) (1364711)

(kleink)

cnxtview: document make-jobs failure

(wiz)

tex package updates

(markd)

tex-svninfo{,-doc}: update to 0.7.4.62157

changes unknown

(markd)

tex-sttools{,-doc}: update to 3.0

A new columns balancing algorithm and changed options
in the flushend and cuted packages.

(markd)

tex-stackengine{,-doc}: update to 4.11

changes unknown

(markd)

tex-soulpos{,-doc}: update to 1.2

This version works with luatex (at last)

(markd)

tex-skak{,-doc}: update to 1.5.3.61719

changes unknown

(markd)

tex-siunitx{,-doc}: update to 3.0.50

i3.0.50
- Spacing of sign when using "output-exponent-marker"
- Behavior of "minimum-decimal-digits" with uncertainties

3.0.45
- Include `reset-text-shape = false` in emulation of `detect-all`

3.0.44
-  Hint concerning hyphen inside `\text`
- Handling of `output-exponent-marker` in tables

3.0.43
- Printing `\ohm` with `beamer` clas

3.0.41
- Rounding to an uncertainty purely in the integer part

(markd)

tex-showlabels{,-doc}: update to 1.9.1

* Robustness fix: macros in arguments are now handled, so that (after
  \showlabel{index}), \index{Poincar\'e} doesn't cause an error.
* The \showlabel[optarg]{command} optional argument can now take a
  one-argument command.
* The macro \showlabeltype expands to the current label type, for possible
  use in \showlabelsetlabel.
* The code has moved from Bitbucket to Sourcehut: the new repository is
  https://hg.sr.ht/~nxg/showlabels.

(markd)

tex-seminar{,-doc}: update to 1.63a

changes unknown

(markd)

tex-schulschriften{,-doc}: update to 5

changes unknown

(markd)

tex-sansmathfonts{,-doc}: update to 2021

changes unknown

(markd)

mk: add show-depends-all

Previously, there was no easy way to list all dependencies of a package.
The target show-depends only lists the direct missing dependencies, the
target show-depends-dirs lists all direct dependencies, but neither
lists the indirect dependencies as well.  The newly added target
show-depends-all includes the indirect dependencies.

While here, document the existing targets since they differ subtly.

https://mail-index.netbsd.org/pkgsrc-users/2022/04/07/msg035444.html

(rillig)

lxterminal: add a note that there are some issues with GTK3

(gutteridge)

rabbitmq: add a note that the test target doesn't work as is

I tried it on NetBSD 9.2_STABLE and Fedora 35, and it doesn't work as
expected. Needs investigation.

(gutteridge)

tex packge updates

(markd)

tex-ipaex{,-doc}: update to 2021

changes unknown

(markd)

tex-incgraph{,-doc}: update to 1.2.0

### Added
- Option `overlay page number options`
- `\igrGetPageSize`
- `\igrPageWidth`
- `\igrPageHeight`
- `\igrSetPageSize`
- `\igrGetLastPage`
- `\igrLastPage`
- Adding/Guessing file name extensions
    - Option `extensions`
    - Option `extensions add`
    - Option `extensions from graphics`
    - Option `ignore on not found with extensions`
    - Option `ignore on not found with extensions*`
- Option `no existence check`

### Changed
- Changelog moved from CHANGES to CHANGES.md and adapted to
  [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
- From now on version numbers adhere to
  [Semantic Versioning](http://semver.org/spec/v2.0.0.html)
- Readme moved from README to README.md and adapted to
- Documentation code revised
- Internal package creation process modernized (invisible to the user)
- Adaption of paper size made compatible with lualatex
- Implementation of `\incgraph` and `\incmultigraph` changed (to LaTeX3)

### Fixed
- Documentation typos corrected
- `\incgraph` ignored option settings for not existing files.

(markd)

tex-iftex{,-doc}: update to 1.0f

Update to iftex package, adding tests for for TexpadTeX and
HiTeX (HINT format).

(markd)

tex-ifptex{,-doc}: update to 2.1

changes unknown

(markd)

tex-hologo{,-doc}: update to 1.15

Use PU directly for textepsilon and textchi

(markd)

tex-haranoaji-extra{,-doc}: update to 20220220

* Add glyphs by 180 and 270 (-90) degree rotation
* Add kana similar CIDs to pwid and pwidvert
* Improve adding GSUB vert substituion

(markd)

tex-haranoaji{,-doc}: update to 20220220

* Add glyphs by 180 and 270 (-90) degree rotation
* Add kana similar CIDs to pwid and pwidvert
* Improve adding GSUB vert substituion

(markd)

tex-glossaries{,-doc}: update to 4.49

- bug fix: list style with entrycounter has problematic unexpanded content

- new command \glsunexpandedfieldvalue (provided for use in
  \glslistexpandedname)

- new command \glscapitalisewords (defaults to \capitalisewords)
  provides a way to switch to \capitalisefmtwords if required

- added new files containing dummy entries for testing:
    -  example-glossaries-longchild.tex
    -  example-glossaries-childmultipar.tex

(markd)

tex-gentium-tug{,-doc}: update to 1.1.1.61719

changes unknown

(markd)

tex-garuda-c90: update to 2021

changes unknown

(markd)

lxterminal: add optional GTK3 support

Add the option of using GTK3 as the base X11 toolkit, rather than GTK2.
(No change to default build.)

(gutteridge)

tex package updates

(markd)

tex-firstaid{,-doc}: update to 1.0q

changes unknown

(markd)

tex-fdsymbol{,-doc}: update to 0.8.61719

changes unknown

(markd)

tex-fancyvrb{,-doc}: update to 4.1b

4.1a
allow again the setting "latline" without a value
4.0
added lastline=0 for no output
3.8
fix for linenumbers and reused SaveVerbatim (hv)

(markd)

tex-europecv{,-doc}: update to 2021.62684

Fix issue "Package can't find logo PDF" on XeLaTeX.
Improved Romanian translation.

(markd)

tex-etoc{,-doc}: update to 1.09e

Needed (if etoc is used without hyperref) updates to internal macros to
prepare for the upcoming LaTeX November 2021 change to \contentsline.

Related updates to the user macro \etoctoccontentsline.

(markd)

tex-erewhon{,-doc}: update to 1.119

changes unknown

(markd)

tex-enotez{,-doc}: update to 0.10d

- fix issues with the backref option
- print list local to a group

(markd)

tex-doclicense{,-doc}: update to 3.0.0

* Breaking change: Hard require package options "type", "modifier"
  and "version" now after one year in soft require migration period.
* Add Croatian translation.
* Add sections to docs about choosing a license and the REUSE specification.
* Update Spanish translation to match Creative Commons website.
* Add note to README that CC license texts and images are licensed
  themselves under CC0-1.0.
* Load csquotes after hyperref to avoid hyperref warning.
* Do not load the hyperxmp package if the silence package is loaded
  to avoid an endless loop.
* Improve warning messages generated by the package.
* Add "Dependency packages and load order" section to docs.

(markd)

tex-datenumber{,-doc}: update to 0.03

changes unknown

(markd)

tex-cutwin{,-doc}: update to 0.2

An update to the cutwin package, to avoid a clash on use of registers
with the extended picture mode in current latex releases.

(markd)

tex-csvsimple{,-doc}: update to 2.3.0

2.3.0
### Added
- Option `column names detection`
- Documentation: csvautotabular inspired example for tabularray.

### Changed
- `\csvlinetotablerow` changed to be expandable and to be
    usable inside a *Data Collection*
- Options `autotabular`, `autobooktabular`, `autolongtable`,
    `autobooklongtable` use `column names detection=false` now.

2.2.1
### Fixed
- Option `late after first line` ignored for `csvsimple-l3`

2.2.0
### Added
- Configurable usage of tabular-like environments
- Option `table centered`
- Option `generic table`
- Option `generic collected table`
- Option `generic table options`

### Changed
- The implementation of all tabular-like environments uses the new
  generic environments now internally. Should be unnoticeable for a user.

### Fixed
- documentation typo correction and small improvents
- Option `long tabularray`

(markd)

doc: Updated graphics/p5-Image-ExifTool to 12.30nb1

(gdt)

graphics/p5-Image-ExifTool: Update to 12.30

Despite repology showing 12.41, 12.30 is the latest production release.

Upstream changes are minor improvements and bugfixes.

(gdt)

Updated security/py-acme, security/py-certbot*

(adam)

py-acme py-certbot*: updated to 1.26.0

Certbot 1.26.0

Added

Added --new-key. When renewing or replacing a certificate that has --reuse-key
set, it will force a new private key to be generated, one time.

As before, --reuse-key and --no-reuse-key can be used to enable and disable key
reuse.

Changed

The default propagation timeout for the OVH DNS plugin (--dns-ovh-propagation-seconds)
has been increased from 30 seconds to 120 seconds, based on user feedback.

Fixed

Certbot for Windows has been upgraded to use Python 3.9.11, in response to
https://www.openssl.org/news/secadv/20220315.txt.
Previously, when Certbot was in the process of registering a new ACME account
and the ACME server did not present any Terms of Service, the user was asked to
agree with a non-existent Terms of Service ("None"). This bug is now fixed, so
that if an ACME server does not provide any Terms of Service to agree with, the
user is not asked to agree to a non-existent Terms of Service any longer.
If account registration fails, Certbot did not relay the error from the ACME server
back to the user. This is now fixed: the error message from the ACME server is now
presented to the user when account registration fails.

(adam)

doc: Updated editors/emacs28 to 28.1nb1

(wiz)

emacs28: enable cairo by default

cairo + harfbuzz is the default graphics backend.

Bump PKGREVISION.

(wiz)

doc: Updated mail/neomutt to 20220408

(wiz)

neomutt: update to 20220408.

2022-04-08  Richard Russon  <rich@flatcap.org>
* Features
  - Compose multipart emails
* Bug Fixes
  - Fix screen mode after attempting decryption
  - imap: increase max size of oauth2 token
  - Fix autocrypt
  - Unify Alias/Query workflow
  - Fix colours
  - Say which file exists when saving attachments
  - Force SMTP authentication if `smtp_user` is set
  - Fix selecting the right email after limiting
  - Make sure we have enough memory for a new email
  - Don't overwrite with zeroes after unlinking the file
  - Fix crash when forwarding attachments
  - Fix help reformatting on window resize
  - Fix poll to use PollFdsCount and not PollFdsLen
  - regex: range check arrays strictly
  - Fix Coverity defects
  - Fix out of bounds write with long log lines
  - Apply `fast_reply` to 'to', 'cc', or 'bcc'
  - Prevent warning on empty emails
* Changed Config
  - New default: `set rfc2047_parameters = yes`
* Translations
  - 100% German
  - 100% Lithuanian
  - 100% Serbian
  - 100% Czech
  - 100% Turkish
  - 72% Hungarian
* Docs
  - Improve header cache explanation
  - Improve description of some notmuch variables
  - Explain how timezones and `!`s work inside `%{}`, `%[]` and `%()`
  - Document config synonyms and deprecations
* Build
  - Create lots of GitHub Actions
  - Drop TravisCI
  - Add automated Fuzzing tests
  - Add automated ASAN tests
  - Create Dockers for building Centos/Fedora
  - Build fixes for Solaris 10
  - New libraries: browser, enter, envelope
  - New configure options: `--fuzzing` `--debug-color` `--debug-queue`
* Code
  - Split Index/Pager GUIs/functions
  - Add lots of function dispatchers
  - Eliminate `menu_loop()`
  - Refactor function opcodes
  - Refactor cursor setting
  - Unify Alias/Query functions
  - Refactor Compose/Envelope functions
  - Modernise the Colour handling
  - Refactor the Attachment View
  - Eliminate the global `Context`
  - Upgrade `mutt_get_field()`
  - Refactor the `color quoted` code
  - Fix lots of memory leaks
  - Refactor Index resolve code
  - Refactor PatternList parsing
  - Refactor Mailbox freeing
  - Improve key mapping
  - Factor out charset hooks
  - Expose mutt_file_seek API
  - Improve API of `strto*` wrappers
* Upstream
  - imap QRESYNC fixes
  - Allow an empty To: address prompt
  - Fix argc==0 handling
  - Don't queue IMAP close commands
  - Fix IMAP UTF-7 for code points >= U+10000
  - Don't include inactive messages in msgset generation

(wiz)

doc: Added editors/ced version 0.1.3

(pin)

Add ced

(pin)

editors/ced

Ced is not a fully featured editor, but more likely an "ed" for csv.
Ced simply prevents you from adding surplus column or invalid data type.

That's it. No searching, filtering, no nothing.

(pin)

doc: Added time/rsclock version 0.1.7

(pin)

Add rsclock

(pin)

time/rsclock

rsClock is a simple terminal clock.

(pin)

doc/TODO: + scidavis-2.7.1.

(wiz)

pan: add some missing tool dependencies

(wiz)

Updated security/libgpg-error, devel/py-jupyter_client

(adam)

py-jupyter_client: updated to 7.2.2

7.2.2

Maintenance and upkeep improvements

- Include py.typed file
- [pre-commit.ci] pre-commit autoupdate
- More Cleanup

(adam)

cnxtview: not parallel-make safe

(wiz)

libgpg-error: updated to 1.45

Noteworthy changes in version 1.45 (2022-04-07)
-----------------------------------------------

* Support the "sysopen" mode parameter for gpgrt_fopen so that file
  names longer than MAX_PATH can be supported under Windows.

* gpgrt_access and gpgrt_mkdir now support file names longer than
  MAX_PATH.

* gpgrt_fopen now maps "/dev/null" to "nul" on Windows.

* Published some internal helper functions for Windows.

* Interface changes relative to the 1.42 release:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gpgrt_free_wchar                NEW.
gpgrt_fname_to_wchar            NEW.
gpgrt_utf8_to_wchar              NEW.
gpgrt_wchar_to_utf8              NEW.

(adam)

doc: Updated archivers/xz to 5.2.5nb1

(wiz)

xz: add upstream patch to fix CVE-2022-1271

Bump PKGREVISION

(wiz)

doc: Updated archivers/gzip to 1.12

(wiz)

gzip: update to 1.12.

* Noteworthy changes in release 1.12 (2022-04-07) [stable]

** Changes in behavior

  'gzip -l' no longer misreports file lengths 4 GiB and larger.
  Previously, 'gzip -l' output the 32-bit value stored in the gzip
  header even though that is the uncompressed length modulo 2**32.
  Now, 'gzip -l' calculates the uncompressed length by decompressing
  the data and counting the resulting bytes.  Although this can take
  much more time, nowadays the correctness pros seem to outweigh the
  performance cons.

  'zless' is no longer installed on platforms lacking 'less'.

** Bug fixes

  zgrep applied to a crafted file name with two or more newlines
  can no longer overwrite an arbitrary, attacker-selected file.
  [bug introduced in gzip-1.3.10]

  zgrep now names input file on error instead of mislabeling it as
  "(standard input)", if grep supports the GNU -H and --label options.

  'zdiff -C 5' no longer misbehaves by treating '5' as a file name.
  [bug present since the beginning]

  Configure-time options like --program-prefix now work.

* Noteworthy changes in release 1.11 (2021-09-03) [stable]

** Performance improvements

  IBM Z platforms now support hardware-accelerated deflation.

(wiz)

doc: Updated x11/xdpyinfo to 1.3.3

(wiz)

xdpyinfo: update to 1.3.3.

This release includes a pair of changes to align with the xserver-21.x
release series - it prints the version without the leading "1." for 21.x
xservers, and it changes the default for building DMX support from --with-dmx
to --without-dmx as DMX is no longer included in the 21.x xservers.
(The DMX support in xdpyinfo is not removed in this release, and can be
enabled at build time with the --with-dmx flag to configure, but may be
fully removed in a future release of xdpyinfo.)

Adam Jackson (1):
      xdpyinfo: Fix printing the X.Org release version for xserver >= 21

Alan Coopersmith (10):
      Update README for gitlab migration
      Update configure.ac bug URL for gitlab migration
      Only check for XFree86 if vendor string doesn't match X.Org
      Add explicit casts to clear implicit conversion warnings
      Disable DMX support by default, leave --with-dmx to enable it
      gitlab CI: add a basic build test
      Build xz tarballs instead of bzip2
      Fix spelling/wording issues
      gitlab CI: stop requiring Signed-off-by in commits
      xdpyinfo 1.3.3

Emil Velikov (1):
      autogen.sh: use quoted string variables

Mihail Konev (1):
      autogen: add default patch prefix

Peter Hutterer (1):
      autogen.sh: use exec instead of waiting for configure to finish

Thomas Kuehne (1):
      fix -Wunused-[...] compiler warnings

(wiz)

doc: Updated time/xclock to 1.1.1

(wiz)

xclock: update to 1.1.1

Alan Coopersmith (2):
      Fall back to sin() and cos() calls on systems without sincos()
      xclock 1.1.1

Thomas Kuehne (2):
      fix -Wmissing-field-initializers warning
      fix -Wabsolute-value compiler warning

(wiz)

tex package updates

(markd)

tex-cmcyr{,-doc}: update to 2021

changes unknown

(markd)

tex-cjkutils{,-doc}: update to 4.8.5

changes unknown

(markd)

tex-cjk{,-doc}: update to 4.8.5

changes unknown

(markd)

tex-cjk-ko{,-doc}: update to 2.2

Support automatic Josa selection after Hangul syllables (U+AC00 .. U+D7A3)

(markd)

tex-cjk-gs-integrate{,-doc}: update to 20210625.0

* More database for free fonts (Google Fontworks fonts, HaranoAji).

(markd)

tex-circuitikz{,-doc}: update to 1.4.6

A nasty bug fix and some hack to avoid that some global Ti*k*Z option
spill into the shapes.

- Fix bug with legacy transmission lines in `overlay`s
- Robustify some shapes: do not let arrows option pass
  to the inner drawing
- Add warning about global draw options in the manual
- Fixes in the documentation: hyperlink the index again,
  cite new recovery point, remove some legacy construct
- Added 1.4.6 rollback point

(markd)