(devel/R-pak) Updated 0.8.0.1 to 0.9.5
# pak 0.9.5
* Vector valued library path now works correctly in `lockfile_create()`
(#864, #868).
* pak now handles better PPM binaries on private PPM instances (#863).
# pak 0.9.4
* pak now works again with custom HTTPS certificates (#647, @tl-hbk).
# pak 0.9.3
* Setting `use_bioconductor = FALSE` (i.e. the `PKG_USE_BIOCONDUCTOR`
env var, or the `pkg.use_bioconductor` option) now truly prevents
any network contact with Bioconductor.
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textproc/treemd: update to 0.5.12
[0.5.12] - 2026-06-06
Added
Toggle mouse capture for text selection - New M shortcut and :toggle mouse capture palette command release the mouse so the terminal's native click-drag selection works for copying arbitrary text; toggle back to restore scroll-wheel navigation. The README also documents the Shift+drag bypass supported by most terminals
Toggle heading markers in outline - New outline_heading_markers config option, # keyboard shortcut, and :toggle heading markers palette command to show/hide #/##/### level prefixes in the outline sidebar (default: true) (#57) — thanks to @alisaifee
Fixed
Table copy keys did nothing useful - In interactive table mode y/Y/r had been silently rebound to generic copy/raw-source actions during the action-dispatch refactor, so cell, row, and copy-as-markdown copy were inoperative. Restored via dedicated CopyTableCell/CopyTableRow/CopyTableMarkdown actions wired to the existing handlers, with a regression test
Inline backticks render as plain text - Inline code in table cells/headers, headings, and blockquotes now renders as styled inline code via format_inline_markdown() instead of literal backticks (#51, #53). Resolves the known issue carried in 0.5.11; requires turbovault-parser 1.5.0
Navigation to duplicate headings - Selecting an outline entry whose text appears multiple times always jumped to the first occurrence. HeadingNode/OutlineItem now carry a position index, and all content-extraction, selection-restore, and rendering paths resolve by index. extract_section(text) is preserved for the CLI --section flag, delegating to a new extract_section_at_index() (#56) — thanks to @alisaifee
snake_case corruption in subscript rendering - Terms like i_am_a_snake were mangled because _x was always treated as a LaTeX subscript. Subscript conversion now applies to _{x} unconditionally and to bare _x only when not mid-identifier (#58) — thanks to @alisaifee
Mermaid image sizing and scrolling - Mermaid diagrams now expand to fit terminal width and scroll correctly (#53)
Changed
Trimmed image format dependencies - ratatui-image 10 → 11 (dropped image-defaults) and image now opts into only the needed decoders (png, jpeg, gif, webp, bmp, ico, tiff), substantially shrinking the dependency tree
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devel/gitpane: update to 0.7.13
[0.7.13] - 2026-06-07
Fixed
Adding a git submodule or linked worktree with the A key no longer removes it from the list almost immediately. A submodule stores its .git as a pointer file (gitdir: <path>) instead of a directory, so repository discovery did not recognize it as a real repo and pruned the pinned entry on the next filesystem rescan. Discovery now resolves the gitdir: pointer (absolute, or relative to the working tree) and looks for HEAD at the referenced git directory, so pinned submodules and worktrees persist.
textproc/doxx: update to 0.1.4
[0.1.4] - 2026-05-26
Added
SourceCode paragraph style renders as a distinct code block in all export formats and the TUI (#76)
Text inside wps:txbx shape text boxes is now extracted and rendered with box-drawing borders instead of being silently dropped (#76)
Fixed
Numbered list items sharing the same abstract numbering definition now count sequentially instead of both restarting at 1 (#76)
Bullet-format list levels (numFmt="bullet") no longer render as lettered sequences (#76)
w:br line break elements inside a run are now preserved, fixing multi-line code blocks concatenated into a single line (#76)
[0.1.3] - 2026-05-24
Added
Configurable keymap presets (default, vim, less) with per-user TOML overrides in ~/.config/doxx/config.toml (#26)
Search result highlighting: current match in yellow, other matches in gray
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(print/R-knitr) Updated 1.49 to 1.51
(cat Downloads/Release-yihui-knitr.nhtml| w3m -dump -T text/html)
knitr 1.51
------------------
NEW FEATURES
• Added support for OpenTelemetry observability. When the otel and otelsdk
packages are installed and tracing is enabled, spans are automatically
created for all knit operations. See otelsdk's Collecting Telemetry Data
for more details on configuring OpenTelemetry (thanks, @shikokuchuo, #2422
).
□ knit() produces 'knitr processing' and 'knitr output' spans when
starting and finishing an operation
□ knit() produces 'knit' spans for each chunk, recording attributes such
as the label and knit engine
• Added support for hooks that get executed before and after knitting
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py-owslib: updated to 0.36.0
0.36.0
1013 fix csapi failing tests
Remove legacy setuptools.command.text
remove comments from xml, because it may fail parsing it
Fix FutureWarning when truth-testing XML element
docs: update WMS example
capture dct:spatial as bbox, if it contains a box
use only pyproject configuration
delegate HTTP 401 and 403 to Python requests
Update dev setup docs to pyproject.toml
Handle WFS version mismatch
py-cbor2: updated to 6.1.2
6.1.2
- Fixed incorrect tracking of string references for definite-length text strings of length greater
than 65536
- Fixed ``cbor2.load()`` crash caused by incorrect handling
of internal read buffer extension during stream deserialization.
py-aiohttp: updated to 3.14.1
3.14.1 (2026-06-07)
Bug fixes
- Fixed a race condition in :py:class:`~aiohttp.TCPConnector` where closing the connector while a DNS resolution was in-flight could raise :py:exc:`AttributeError` instead of :py:exc:`~aiohttp.ClientConnectionError` -- by :user:`goingforstudying-ctrl`.
- Fixed ``CancelledError`` not closing a connection -- by :user:`aiolibsbot`.
- Tightened up some websocket parser checks -- by :user:`Dreamsorcerer`.
- Fixed :class:`~aiohttp.CookieJar` dropping the host-only flag of cookies when persisted with :meth:`~aiohttp.CookieJar.save` and reloaded with :meth:`~aiohttp.CookieJar.load`, so a cookie set without a ``Domain`` attribute is again scoped to the exact host that set it after a reload; the absolute expiration deadline is now persisted as well, so a reloaded cookie keeps its original lifetime instead of being rescheduled from the load time. :meth:`~aiohttp.CookieJar.load` now replaces the jar contents rather than merging onto prior state, and loaded cookies pass through the same acceptance rules as :meth:`~aiohttp.CookieJar.update_cookies`, so a cookie for an IP-address host is dropped when loaded into a jar created without ``unsafe=True`` -- by :user:`bdraco`.
- Scoped :class:`~aiohttp.DigestAuthMiddleware` credentials to the origin of the first request it handles, so a redirect to a different origin no longer triggers a digest response computed from the configured credentials; a challenge from another origin is only answered when that origin falls within a protection space advertised by the anchor origin through the RFC 7616 ``domain`` directive -- by :user:`bdraco`.
- Fixed the C HTTP parser not enforcing ``max_line_size`` on a request target or response reason phrase that is split across multiple reads; each fragment was checked on its own, so an accumulated line could exceed the limit without raising ``LineTooLong``. The accumulated length is now checked, matching the pure-Python parser -- by :user:`bdraco`.
- Changed :class:`~aiohttp.TCPConnector` to reject legacy non-canonical numeric IPv4 host forms such as ``2130706433``, ``017700000001`` and ``127.1`` with :exc:`~aiohttp.InvalidUrlClientError`; only canonical dotted-quad IPv4 literals are now treated as IP address literals, while every other host is sent through the configured resolver -- by :user:`bdraco`.
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py-jupyter_server: updated to 2.19.0
2.19.0
Enhancements made
- Return `unresolved` stanza when kernel scope is unavailable for `resolvePath` (instead of failing with 404)
Bugs fixed
- Recreate notary store on failure to prevent save deadlock and data loss
Maintenance and upkeep improvements
- Restore the test skip marks with updated compatibility reason
- Drop Python 3.9
- Bump minimatch from 3.1.2 to 3.1.5
py-jupyter_client: updated to 8.9.0
8.9.0
Enhancements made
- Add ZMQ Curve for transport encryption
Maintenance and upkeep improvements
- Temporarily pin Python to 3.14 in pre-releases test
- CI: fix testing of nbconvert
- Update pre-commit, and fix issues
- Remove `3.14t` testing until `msgpack` supports it
- Log environment information for docs build on CI, update comment on workaround
Documentation improvements
- Update status terminology from 'abort' to 'aborted'
- Added documentation for the handshake pattern
