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2022-12-12doc: Updated devel/makedepend to 1.0.8wiz1-1/+2
2022-12-12makedepend: update to 1.0.8.wiz2-6/+6
This bug fix release corrects a regression introduced in 1.0.7 that caused running makedepend on larger bodies of source to incorrectly hit the "out of space: increase MAXFILES" error, and made makedepend run measuribly slower than before. Alan Coopersmith (3): man page: add line breaks in Synopsis section Bug #2: fix regression introduced by fix for bug #1 makedepend 1.0.8
2022-12-12biology/Makefile: Add rna-seq meta-packagebacon1-1/+2
2022-12-12doc: Added biology/rna-seq version 1.0bacon1-1/+2
2022-12-12biology/rna-seq: Core tools needed for RNA-Seq analysisbacon2-0/+28
The rna-seq meta-package provides the core tools needed for performing a typical RNA-Seq differential gene expression analysis, including adapter trimming, quality control, alignment, and identification of differentially expressed genes. Researchers may want additional tools for data manipulation, gene ontology, etc.
2022-12-12biology/Makefile: Add fasdabacon1-1/+2
2022-12-12doc: Added biology/fasda version 0.1.2bacon1-1/+2
2022-12-12biology/fasda: Fast and simple differential analysisbacon4-0/+39
FASDA aims to provide a fast and simple differential analysis tool that just works and does not require any knowledge beyond basic Unix command-line skills. The code is written entirely in C to maximize efficiency and portability, and to provide a simple command-line user interface.
2022-12-12mlterm: pull an upstream change that fixes possible segfaults.tsutsui3-3/+21
Bump PKGREVISION.
2022-12-12mlterm: remove unnecessary chunk not generated by mkpatches(1).tsutsui2-14/+5
2022-12-12doc: Updated shells/tcsh to 6.24.06kim1-1/+2
2022-12-12{,standalone-,static-}tcsh: Update to 6.24.06:kim2-6/+6
Changes since 6.24.04: 16. V6.24.06 - 2022-12-12 15. V6.24.05 - 2022-12-04 14. Build and release process improvements (Luke Mewburn, Kimmo Suominen)
2022-12-12elfio: header only implies build only dependencynros1-1/+2
2022-12-12doc: Updated chat/matrix-synapse to 1.73.0gdt1-1/+2
2022-12-12chat/matrix-synapse: Update to 1.73.0gdt4-32/+28
Synapse 1.73.0 (2022-12-06) =========================== Please note that legacy Prometheus metric names have been removed in this release; see [the upgrade notes](https://github.com/matrix-org/synapse/blob/release-v1.73/docs/upgrade.md#legacy-prometheus-metric-names-have-now-been-removed) for more details. Features -------- - Speed-up `/messages` with `filter_events_for_client` optimizations. ([\#14527](https://github.com/matrix-org/synapse/issues/14527)) - Improve DB performance by reducing amount of data that gets read in `device_lists_changes_in_room`. ([\#14534](https://github.com/matrix-org/synapse/issues/14534)) - Adds support for handling avatar in SSO OIDC login. Contributed by @ashfame. ([\#13917](https://github.com/matrix-org/synapse/issues/13917)) - Move MSC3030 `/timestamp_to_event` endpoints to stable `v1` location (`/_matrix/client/v1/rooms/<roomID>/timestamp_to_event?ts=<timestamp>&dir=<direction>`, `/_matrix/federation/v1/timestamp_to_event/<roomID>?ts=<timestamp>&dir=<direction>`). ([\#14471](https://github.com/matrix-org/synapse/issues/14471)) - Reduce database load of [Client-Server endpoints](https://spec.matrix.org/v1.5/client-server-api/#aggregations) which return bundled aggregations. ([\#14491](https://github.com/matrix-org/synapse/issues/14491), [\#14508](https://github.com/matrix-org/synapse/issues/14508), [\#14510](https://github.com/matrix-org/synapse/issues/14510)) - Add unstable support for an Extensible Events room version (`org.matrix.msc1767.10`) via [MSC1767](https://github.com/matrix-org/matrix-spec-proposals/pull/1767), [MSC3931](https://github.com/matrix-org/matrix-spec-proposals/pull/3931), [MSC3932](https://github.com/matrix-org/matrix-spec-proposals/pull/3932), and [MSC3933](https://github.com/matrix-org/matrix-spec-proposals/pull/3933). ([\#14520](https://github.com/matrix-org/synapse/issues/14520), [\#14521](https://github.com/matrix-org/synapse/issues/14521), [\#14524](https://github.com/matrix-org/synapse/issues/14524)) - Prune user's old devices on login if they have too many. ([\#14038](https://github.com/matrix-org/synapse/issues/14038), [\#14580](https://github.com/matrix-org/synapse/issues/14580)) Deprecations and Removals ------------------------- - Remove legacy Prometheus metrics names. They were deprecated in Synapse v1.69.0 and disabled by default in Synapse v1.71.0. ([\#14538](https://github.com/matrix-org/synapse/issues/14538))
2022-12-12Updated textproc/py-itemadapter, textproc/py-itemloadersadam1-1/+3
2022-12-12py-itemloaders: updated to 1.0.6adam2-7/+6
1.0.6 Fixes a regression introduced in 1.0.5 that would cause the re parameter of ItemLoader.add_xpath and similar methods to be passed to lxml, which would trigger an exception when the value of re was a compiled pattern and not a string 1.0.5 Allow additional args to be passed when calling ItemLoader.add_xpath Fixed missing space in an exception message Updated company name in author and copyright sections Added official support for Python 3.9 and improved PyPy compatibility Added official support for Python 3.10
2022-12-12py-itemadapter: updated to 0.7.0adam3-8/+10
0.7.0 (2022-08-02) ItemAdapter.get_field_names_from_class 0.6.0 (2022-05-12) Slight performance improvement 0.5.0 (2022-03-18) Improve performance by removing imports inside functions 0.4.0 (2021-08-26) Added ItemAdapter.is_item_class and ItemAdapter.get_field_meta_from_class 0.3.0 (2021-07-15) Added built-in support for pydantic models
2022-12-12libtree: update to version 3.1.1nros2-6/+6
changelog: * Build system portability fixes * Fix make check exit code
2022-12-12doc: Updated ruby-gnome packages to 4.0.5tsutsui1-1/+18
2022-12-12libtree: remove unneeded dependenciesnros1-4/+1
libtree version 3 was rewitten in c99 without the need for dependencies.
2022-12-12ruby-gnome: update to 4.0.5.tsutsui18-70/+70
Upstream changes: https://github.com/ruby-gnome/ruby-gnome/releases/tag/4.0.5 Ruby-GNOME 4.0.5: 2022-12-12 This is a bug fix release of 4.0.4. Changes Ruby/GObjectIntrospection * Fixes + Fixed a memory leak that GDestroyNotify argument's metadata isn't freed. For example, this is happen with GLib::Timeout.add.
2022-12-12Updated devel/py-pathspec, comms/py-esptooladam1-1/+3
2022-12-12py-esptool: updated to 4.4adam3-11/+37
Version 4.4 New Features flasher_stub: Increased read/write speeds over USB-JTAG/Serial or USB-OTG modes, making some operations nearly twice as fast. Added detection for guru meditation errors induced by the flasher stub or ROM bootloader. Added a readable error message for serial-related failures, giving more information about possible HW issues. espsecure.py: Improved AES-XTS encryption speed. Bug Fixes ESP32-S3 v0.0: Fixed chip revision detection. bitstring: Added a workaround for breaking changes of bitstring==4 get_default_connected_device: Fixed to close unused serial ports. flash_freq: Fall back to a chip-specific default flash frequency when no flash_freq arg is specified. ESP32-C6: Fixed chip type detection and SPI flash communication.
2022-12-12py-pathspec: updated to 0.10.3adam3-7/+8
0.10.3 (2022-12-09) ------------------- New features: - Added utility function `pathspec.util.append_dir_sep()` to aid in distinguishing between directories and files on the file-system. Bug fixes: - Package not marked as py.typed. - Exports are considered private. - 'Self' string literal type is Unknown in pyright. Improvements: - Checking directories via match_file() does not work on Path objects.
2022-12-12doc: Updated devel/py-approvaltests to 7.4.0schmonz1-1/+2
2022-12-12Update to 7.4.0. From the changelog:schmonz3-8/+11
Throttling of reporters after 5: - To avoid too many diff tools being launched, ApprovalTests will stop launching after the 5th time. This is configurable in GenericDiffReporter.throttling_threshold
2022-12-12doc: Updated devel/py-approval-utilities to 7.4.0schmonz1-1/+2
2022-12-12Update to 7.4.0. Changes:schmonz2-6/+9
- Add dependency on py-typing-extensions - [pkgsrc] Add missing dependency on py-empty-files
2022-12-12Updated textproc/py-black, devel/py-test-xdistadam1-1/+3
2022-12-12py-test-xdist: updated to 3.1.0adam2-8/+8
pytest-xdist 3.1.0 (2022-12-01) =============================== Features -------- - Users can now set a default distribution mode in their configuration file: .. code-block:: ini [pytest] addopts = --dist loadscope - Python 3.11 is now officially supported. Removals -------- - Python 3.6 is no longer supported.
2022-12-12py-black: updated to 22.12.0adam2-6/+6
22.12.0 Preview style <!-- Changes that affect Black's preview style --> - Enforce empty lines before classes and functions with sticky leading comments - Reformat empty and whitespace-only files as either an empty file (if no newline is present) or as a single newline character (if a newline is present) - Implicitly concatenated strings used as function args are now wrapped inside parentheses - Correctly handle trailing commas that are inside a line's leading non-nested parens Configuration <!-- Changes to how Black can be configured --> - Fix incorrectly applied `.gitignore` rules by considering the `.gitignore` location and the relative path to the target file - Fix incorrectly ignoring `.gitignore` presence when more than one source directory is specified Parser <!-- Changes to the parser or to version autodetection --> - Parsing support has been added for walruses inside generator expression that are passed as function args (for example, `any(match := my_re.match(text) for text in texts)`) Integrations <!-- For example, Docker, GitHub Actions, pre-commit, editors --> - Vim plugin: Optionally allow using the system installation of Black via `let g:black_use_virtualenv = 0`
2022-12-12Updated security/py-acme, security/py-certbot*adam1-1/+17
2022-12-12py-acme py-certbot*: updated to 2.1.0adam17-66/+66
Certbot 2.1.0 Fixed Interfaces which plugins register themselves as implementing without inheriting from them now show up in certbot plugins output. IPluginFactory, IPlugin, IAuthenticator and IInstaller have been re-added to certbot.interfaces. This is to fix compatibility with a number of third-party DNS plugins which may have started erroring with AttributeError in Certbot v2.0.0. Plugin authors can find more information about Certbot 2.x compatibility here. A bug causing our certbot-apache tests to crash on some systems has been resolved.
2022-12-12Updated math/py-gmpy2, security/py-google-authadam1-1/+3
2022-12-12py-google-auth: updated to 2.15.0adam3-7/+10
2.15.0 (2022-12-01) Features Add api_key credentials Introduce a way to provide scopes granted by user Bug Fixes Allow mtls sts endpoint for external account token urls. CI broken by removal of py.path Ensure JWT segments have the right types Updated the lower bound of interactive timeout and fix the kwarg…
2022-12-12py-gmpy2: updated to 2.1.4adam2-6/+6
2.1.3 Latest release with minor bug fixes and support for Python 3.11
2022-12-12Updated devel/py-filelock, finance/py-eth-utilsadam1-1/+3
2022-12-12py-eth-utils: updated to 2.1.0adam2-7/+7
eth-utils v2.1.0 (2022-11-17) Features Allow a wider eth-hash dependency range Performance improvements Performance improvement of up to 65% on is_0x_prefixed Improved Documentation Fix typo in documentation: hexidecimal -> hexadecimal Internal Changes - for eth-utils Contributors Update use of @cached_property for debug2 logging. Breaking changes Remove support for Python 3.6, add Python 3.11, misc dev internal updates
2022-12-12py-filelock: updated to 3.8.2adam2-7/+7
3.8.2 Bump pypa/gh-action-pypi-publish from 1.5.1 to 1.6.1 Update the license classifier to "Unlicense" 3.8.1 fix BaseFileLock.timeout's getter/setter being obscured by itself Fix mypy fails understanding FileLock
2022-12-12Updated textproc/py-m2r, devel/py-jupyter_clientadam1-1/+3
2022-12-12py-jupyter_client: updated to 7.4.8adam2-6/+6
7.4.8 Bugs fixed - Make sure loop is marked with nest_asyncio
2022-12-12php81: Fix version upper bound.jperkin1-2/+2
2022-12-12py-m2r: updated to 0.3.1adam2-10/+9
Version 0.3.0 * Drop support for Python 2.7, 3.4, 3.5, and 3.6 * Add compatibility with docutils 0.19 * Sync up assertion with changes in argparse * Limit mistune dependency version range
2022-12-12Updated devel/py-limits, cad/py-gdsadam1-1/+3
2022-12-12py-gds: updated to 1.6.12adam2-6/+6
Release v1.6.12 Among other minor fixes: Fix in Cell.get_texttypes. Allow labels to inherit transforms through get_labels.
2022-12-12py-limits: updated to 2.7.2adam2-6/+6
v2.7.2 ------ * Compatibility Updates * Update documentation dependencies * Relax version constraint for packaging dependency * Bump CI to use python 3.11 final
2022-12-12doc: Updated x11/xfce4-settings to 4.16.5gutteridge1-1/+2
2022-12-12xfce4-settings: update to 4.16.5gutteridge2-7/+6
Change log: 4.16.5 (2022-11-12) ====== - mime-settings: Properly quote command parameters - Revert "Escape characters which do not belong into an URI/URL (Issue #390)" 4.16.4 (2022-11-07) ====== - Escape characters which do not belong into an URI/URL (Issue #390) - Prefer full command when basic command is env (Fixes #358) - Translation Updates: Japanese, Portuguese, Russian
2022-12-11doc: Updated www/gotosocial to 0.6.0nb2nikita1-1/+2
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