fix(deps): update dependency @stencila/schema

[renovate]

This PR contains the following updates:

Package	Change	Age	Adoption	Passing	Confidence
@stencila/schema	1.5.3 -> 1.18.0
stencila-schema	==1.6.1 -> ==1.16.1

---

Release Notes

stencila/stencila

v1.18.0

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v1.17.0

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v1.16.1

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v1.16.0

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Bug Fixes

• Codecs: Only call to_remote if file already exists (25644ca)
• Google Docs codec: Enable decoding of Parameter nodes from RPNGs (f590252)
• Google Docs codec: Use remote JSON when necessary (d6b3de0)
• HTML codec: Add size attribute for inputs (d6e40f1)
• Pandoc codec: Enable support for Tables (8fb6507)
• Pandoc codec: Make tex the default language for math (f7f4b37)
• PNG codec: Increase viewport size (920e0c8)
• PNG codec: Remove unecessary brace escapes (7425a25)
• R kernel: Improve tests for whether an output should be returned (86ee0e1)

Features

• Codecs CLI: Add RPNG related options to convert command (636b019)
• Codecs: Add a --lossy option to disable use of RPNGs (053cf0d)
• Google Docs codec: Add support for MathFragment and MathBlock (2d129c4)
• Google Docs codec: Add support for decoding CodeFragment nodes (c042c1d)
• Markdown and HTML codecs: Support LaTeX and AsciiMath MathFragments and MathBlocks (9c16019)
• Markdown codec: Add support for math blocks (ce132bc)
• Pandoc and Markdown codecs: Add initial support for bi-di conversion of Parameter nodes (12fa6c3)
• RPNG theme: Use different indicators for each node type and support Parameter (2376df1)
• Schema: Add Strikeout and Underline inline content types (c6d7753)

Performance Improvements

• RPNG codec: Use data:self dataURI to avoid duplication of image data for CodeChunk outputs (491808d)

v1.15.0

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Bug Fixes

• Cloud integration: Use node keys, rather than ids (78c9fab)
• Google Doc codec: Decode order of Lists (5efcc01)
• Google Doc codec: Fix handling of nested lists (af4ea1e)
• Google Doc codec: Remove unessary underlining of links (2184cab)
• Google Drive provider: Pull images from temporary URLs (a3ee671)
• Goolge Doc codec: Fix handling of superscripts and subscripts, and adjacent strings (15baf7f)
• Markdown codec: Ensure table cells have no newlines (a5c88cd)
• Pandoc codec: Add node id of CodeChunks and CodeExpressions (e55c05c)
• Rust: Update dependencies (5f12aa5)
• Word codec: Add fallback to decode CodeChunks and `CodeExpression`` from RPNG files (62d8dbe)

Features

• Auth: Add provider_token function (3a5d0a3)
• Cloud integration: Add auth providers subcommand (263a524)
• Cloud integration: Add functions for posting and retrieving nodes (4aab9e9)
• Cloud integration: Cache provider tokens to avoid additional requests (f993501)
• Google Doc codec: Decoding of lists including nested lists (cc0d89c)
• Google Doc codec: Implement encoding to Google Doc compatible docx (5a35a37)
• Google Docs codec: Create a new Google Doc when encoding (f151f27)
• Google Docs: Initial version of GdocCodec for decoding Google Docs to Stencila Articles (01d22c7)
• Pandoc codec: Add rpng_link encoding option (ea0bbb2)

v1.14.0

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Bug Fixes

• Archive utilities: Ensure parent directories are present (da3466b)
• Cron utilities: Sleep for each iteration of loop to avoid excessive spin (63f2647)
• Images: Do not pull and write base layers by default (1bd4213)
• R kernel: Make Cairo package optional (2a9dae2)
• Tasks: Default to run all tasks with watches or schedules; allow backgrounding (7ee173e)
• Tasks: Do not let version pass though in poetry:ensure task (7558299)
• Tasks: Improve display of task logs (c5703ac)
• Tasks: Run tasks in background as well as server (85fc569)
• Tasks: Use full path to asdf (45d42ff)

Features

• CLI: Add run command for running tasks, documents and/or server (011414d)
• CLI: Fallback to running a task if subcommand is unrecognized (934626e)
• Images CLI: Allow more than one image to be removed at a time (6668a71)
• Images: Add images save subcommand (a044147)
• Images: Add images snap subcommand (aff445f)
• Task binary: Enable installation of task (3b6fc1f)
• Tasks CLI: Add an -all flag for listing all tasks (19e1d0f)
• Tasks CLI: Allow for tasks to be hidden from lists (7f19060)
• Tasks CLI: Allow taks to be filtered by tool and action (50944bd)
• Tasks: Add clean and purge tasks (95f4ca5)
• Tasks: Add detect tasks (69b3866)
• Tasks: Add tasks run and tasks analyze commands and integrate (973ecee)
• Tasks: Add a default tasks during detection and fallback to it (d9710f1)
• Tasks: Add a tasks init subcommand and ensure a Taskfile is present for detect and run (7538713)
• Tasks: Add generation of docs and tasks (9d9244d)
• Tasks: Add support for Aptfiles (2a51604)
• Tasks: Add tasks for updating .gitignore (e6f9ae2)
• Tasks: Allow for custom detect tasks and for detect to be called in build (3df1d9c)
• Tasks: First iteration of task schedules and file watches (d62767e)
• Tasks: Improve UX for running tasks (170500a)
• Tasks: Inital versions of Taskfiles for dependency installation (200f6b4)
• Tasks: Initial iteration of a podman related tasks for handling projects with Dockerfiles (05a928f)
• Tasks: Initial support for Taskfiles (0f4f14c)
• Tasks: Initial versions of project and sources tasks (6cdb58a)

1.13.2 (2022-07-11)

Bug Fixes

• Python parser: Upgrade tree-sitter-python crate (a1ac6c0)
• R microkernel: Avoid issue with creating png graph devices in forks (267efaf)
• Rust: Update dependencies (f463faa)
• Rust: Upgrade google-drive crate (fbf5a7f)
• Rust: Upgrade once_cell and regex crates (873ac56)
• Rust: Upgrade path-slash crate (386387d)
• Rust: Upgrade transitive dependencies using cargo update (b06db74)

1.13.1 (2022-06-29)

Bug Fixes

• Rust: Update dependencies (187c3fe)

v1.13.0

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Bug Fixes

• Filesystem utils: Use create and truncate options for usual behaviour (abb38a4)
• Orgs: Add fields available in orgs show command (a0d91d9)
• Projects: Don't delete if invalid input (cfead07)

Features

• CLI utilities: Use cli-table crate for displaying tables of structs (6edf465)
• Cloud integration: Add commands for managing API access tokens (a648d12)
• Cloud integration: Add project and project members commands (15f1dd6)
• Cloud projects: Add clone, pull, and push actions for projects (15c845d)
• Cloud projects: Add ability to create projects; improve other commands (67c271f)
• Filesystem utilities: Add open_file_600 function (a81d8bb)
• Organizations: Initial iteration of orgs command for CLI (31f2556)
• Orgs: Add orgs plan command (d88a9d6)
• Orgs: Add orgs usage command (0d51cff)
• Orgs: Add org activity logs (2adb096)
• Orgs: Allow setting of default org (89d9711)
• Project members: Improve table layout (eeb0c0f)
• Projects: Allow members to be added using their username (d28afb6)
• Rust: Add cloud crate (8c8c414)
• Teams: Add teams CLI subcommand (040bab7)
• Users: Add users find CLI command (6e43872)
• Users: Add uses invite CLI command (0b2c301)

v1.12.0

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Features

• Images: Add list, pull, push and remove actions (753d814)

Reverts

• Revert "chore(Rust): Ignore clap deprecation warnings" (d418755)

v1.11.4

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v1.11.3

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v1.11.2

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v1.11.1

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v1.11.0

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Bug Fixes

• Apt buildpack: Do not add .deb suffx unecessarily (7e6534f)
• Binary: Improve parsing of sematic version strings (fc7331c)
• Buildpack image: Calculate a DiffID for layers (e000d22)
• Buildpacks: Fallback to a temporary dir if necessary (8a8e805)
• CLI utilities: Upgrade clap crate & linting (b33c9bc)
• CLI utilities: Upgrade syntect and linya (129b5b8)
• CLI: Migrate from structopt to clap v3 (e81e691)
• CLI: Upgrade various crates used in top level (0aef3d2)
• Dependencies: Update unicode-segmentation (45a5838)
• Dependencies: Upgrade thiserror (7f87bf9)
• Google Drive provider: Upgrade google-drive crate (324b124)
• Graph: Update petgraph (3d75039)
• HTML codec: Upgrade quick-xml crate (075d272)
• Image blob pulls: Use write_all instead of write; use async IO where possible (ea78cdf)
• Image distribution: Fix buffering of blob uploads so chunk length is observed (22aeda9)
• Image distribution: Use a HEAD request and avoid caching when checking for blob on registry (429d111)
• Image distribution: Use Docker media types for compatibility with registry (0a4cff0)
• Images: Add DiffIDs and descriptors for image layers (d292f84)
• Images: Add support for symlinks in images (3509ac6)
• Images: Add to PATH and LD_LIBRARY_PATH env vars for each layer (d5eaa28)
• Images: Allow for no changes in an image layer (9481722)
• Images: Do not include created and modified times in snapshot entries (0985b2a)
• Images: Ensure that paths are separated when prepended or appended (a94b203)
• Images: Fix chunked blob pushes (1ed4b08)
• Images: Fix compilation on non-unix operating systems (af3d82c)
• Images: Use amd64 arch and update digests of image so they are echod to user on CLI (e2b71be)
• Images: Use tempfile crate for better security and cleanup (701f3de)
• Images: Use u32 literal to avoid compile error on windows (3ee0bee)
• Images: Verify manifest digest and use in annotations (2cb3673)
• Language buildpacks: Link to the system-wide install if possible (dc80521)
• Microkernel: Update nix (21ac1f0)
• Node buildpack: Calculate the version number for the current LTS version (9d24133)
• Pandoc codec: Upgrade pandoc_types (96f57de)
• PNG codec: Avoid screenshot with 0 height error (f0f4b56)
• Python binary: Use python3 as name (and python as alias) (559dc90)
• Python buildpack: Use python3 explicitly (d4ff206)
• R buildpack: Add missing Renviron file (4e86ce4)
• R buildpack: Only build RenvLayer if R files present (36dbf5b)
• R buildpack: Set R_DOC_DIR env var (344b310)
• R Buildpack: Update env vars, paths and metods for new version of renv (b8ddc5b)
• Rust: Update dependencies (0cce85a)
• Server: Update axum and tower-http crates (8d10af5)
• Stencila buildpack: Do not create launch.toml if no build entry (5f6e338)
• Stencila buildpack: For non-local builds install into the layer dir (5728db4)
• Stencila buildpack: Update layer rather than always recreating (0d817da)
• UUIDs: Upgrade smartstring crate (7efb41a)
• Web clients: Update dependencies (800ae24)

Features

• Binaries: Add --into as an alias for --dest for install sub-command (aa2f858)
• Buildpack images: Compress layers (1ab95ef)
• Buildpack images: Implement OCI image layout spec (ee74cfa)
• Buildpack images: Initial implementation of image distribution (544eb20)
• Buildpack images: Use rkyv for faster serialization and deserialization of snapshots (d8d1605)
• Buildpack layers: Add layer methods for creating OCI layer descriptors for snapshots (9eeb337)
• Buildpacks: Add prebuild_all function (835eedc)
• Buildpacks: Initial iteration of image layer creation from buildpacks (9ca08b5)
• Chromium binary: Install Chromium from macchrome/linchrome releases (9646a52)
• CLI: Integrate images subcommand (eb31ccc)
• Images CLI: Initial implementation of build command (a9747d3)
• Images: Add --manifest-format option (1e5fa85)
• Images: Add --no-workspace and --layout-complete options (7c72fd2)
• Images: Add -no-diff option to allow complete replicas of layer directories (c97393c)
• Images: Add STENCILA_IMAGE_REF env var and use as default for --from (3c8330b)
• Images: Add annotations to layer descriptors (45d7989)
• Images: Add parsing of image specs (31d2926)
• Images: Allow for .dockerignore and .containerignore files in working dir (a83d30c)
• Images: Build image from source using buildpacks (b6b7dfb)
• Images: Implement pulling of images from registry (c0be491)
• Images: Implements cross-repository mounting (7cb32ea)
• Images: List up to 100 additions, modifications and deletions in each layer's annotations (2d63091)
• Images: Set images based on .image-labels file (121757c)
• Images: Set working dir and env variables in images (28d25c8)

Performance Improvements

• Images: Allow for application/vnd.oci.image.layer.v1.tar+zstd layer media type (0b95150)
• Images: Do not recalculate digest on pull of layers (0a5e0e8)
• Images: Reduces compression level for much faster image writes (bb1af3e)
• Images: Use a BufWriter when dowloading blobs and increase chunk size when uploading (413d618)

v1.10.1

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v1.10.0

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Bug Fixes

• Apt buildpack: Fix bug causing layer to be recreated (760b90a)
• Apt buildpack: Update rather than replace layer when list of packages changes (f95381b)
• CLI: Improve subcommand titles (0adc7d8)
• Stencila buildpack: Launch with --url suitable for use in container (7f1a821)

Features

• Apt buildpack: Use repository mirrors with option to turn off (98abff7), closes #​1434

1.9.2 (2022-05-16)

Bug Fixes

• PNG & PDF codecs: Wait for Web Components to be hydrated before rendering (d42c4f9)
• PNG and PDF codecs: Load themes from local files and do not load component JS (5c415c4)
• RPNG codec: Improve styling, resolution and aspect ratio of RPNGs (ef12e92)
• RPNG theme: Improve appearance in absence of components (ccd8181)

1.9.1 (2022-05-15)

Bug Fixes

• Web terminal: Handle error cases in select! to avoid infinite loops on disconnections (c36c539)

v1.9.1

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Bug Fixes

• Web terminal: Handle error cases in select! to avoid infinite loops on disconnections (c36c539)

v1.9.0

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Bug Fixes

• Cargo.toml: Correct ordering of YAML tables (1996878)
• Server: Drop read lock on WebSocket clients within ping task; improve logging (2bc3e53)
• Server: Ping WebSocket clients periodically to keep connections alive; use alternative pty crate (c2f3721)
• Web teminal: Only use pty-process on Linux (4c73ca6)
• Web terminal: Improve clean up after diconnects (8baaf70)
• Web terminal: Improve layout in browser (17f4e93)

Features

• Web terminal: Use username (and in the future project) from JWT in Bash prompt; simplify server to single project use (14bc6f2)

v1.8.1

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v1.8.0

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Bug Fixes

• GDrive provider: Parse open?id= style URLs (d492ec4)
• Key utilities: Generate key with sik identifying prefix (4a3b247)
• Server: Allow routing to more than one WebSocket path; remove need for projectId when conecting (6424fbc)
• Server: Do not warn if STENCILA_SERVER_KEY env var is set (1e3a9b2), closes #​1439
• Server: Set SameSite value for token cookie properly (d938617), closes #​1438

Features

• Server terminal: Add terminal for attaching to remote instances (1de900e)
• Server: Add --log-requests option (2a51c3a)

v1.7.3

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v1.7.2

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v1.7.1

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v1.7.0

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Bug Fixes

• Server: Update paths to web client JS and CSS (9e64615)
• Web: Set correct build target for browser packages (8bf32c7)

Features

• Server: Add Prometheus metrics and --max-inactivity and --max-duration options (c4e129c)

1.6.1 (2022-04-21)

Bug Fixes

• Client: Allow passing through Web Client options (8b47e97)
• Sources: Check for invalid destination path when creating a new Source (f023a52)

v1.6.1

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Bug Fixes

• Client: Allow passing through Web Client options (8b47e97)
• Sources: Check for invalid destination path when creating a new Source (f023a52)

v1.6.0

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Bug Fixes

• Google Drive provider: Import Google Docs as .gdoc JSON (c3f3d6a)
• RPNG: Use compact option, rather than deprecated "compact" theme (6a9eeac)

Features

• Codecs: Make all EncodeOptions available to convert CLI command (6fbfd81)

1.5.1 (2022-04-19)

Bug Fixes

• Docker: Install openssl and ca-certificates into stencila/stencila:focal (6ee52ed)
• Files: Do not panic if unable to make path relative (1c14ab5)

stencila/schema

v1.16.1

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Bug Fixes

• Executable code nodes: Make executeCount unsigned and clarify docs (1704980)
• Media objects: Make mediaType regex more permissive (e1d2c21)

v1.16.0

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Features

• Executable code nodes: Add executeCount property (56e0902)

v1.15.0

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Bug Fixes

• CodeExecutable: Remove CodeExpression variant from codeDependencies (294e606)

Features

• CodeChunk: Add executeAuto and executePure properties (16a4bd8)
• CodeExecutable: Add DependenciesFailed variant to executeRequired (3cde344)
• CodeExecutable: Add variants to executeStatus (7b01a09)

v1.14.0

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Features

• Executable nodes: Add properties summarising dependencies and execution (2cec08b)

v1.13.0

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Bug Fixes

• dependencies: update rust crate serde to 1.0.132 (b47af3d)
• dependencies: update rust crate serde_json to 1.0.73 (8dab589)
• dependencies: update rust crate serde_with to 1.11.0 (f4b789f)
• dependencies: update rust crate strum to 0.23.0 (2769bf8)
• Rust: Fix error message (a597cf8)

Features

• Executable code nodes: Add properties for execution status etc (9e3de92)
• Rust: Add Cord for use in digest, and other, properties (bcc186d)
• Rust: Add convieience functions for Date type (3d6e89d)

v1.12.0

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Bug Fixes

• Rust: Remove serde(skip) for pointer fields (d18ed5b)

Features

• Rust: Remove NodeTrait; Null as struct (976c2af)

1.11.4 (2021-09-20)

Bug Fixes

• dependencies: update rust crate serde_with to 1.10.0 (b328e96)

1.11.3 (2021-09-20)

Bug Fixes

• dependencies: update rust crate serde_json to 1.0.68 (745ee8c)

1.11.2 (2021-09-13)

Bug Fixes

• dependencies: update rust crate serde to 1.0.130 (5f9b78a)

1.11.1 (2021-08-29)

Bug Fixes

• Rust: Exclude content and parts and add title for simple versions (62ac660)
• Rust: Use strings for digests (df07e95)
• Rust bindings: Correct casing for property type overrides (586529a)

v1.11.4

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Bug Fixes

• dependencies: update rust crate serde_with to 1.10.0 (b328e96)

v1.11.3

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Bug Fixes

• dependencies: update rust crate serde_json to 1.0.68 (745ee8c)

v1.11.2

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Bug Fixes

• dependencies: update rust crate serde to 1.0.130 (5f9b78a)

v1.11.1

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Bug Fixes

• Rust: Exclude content and parts and add title for simple versions (62ac660)
• Rust: Use strings for digests (df07e95)
• Rust bindings: Correct casing for property type overrides (586529a)

v1.11.0

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Bug Fixes

• dependencies: update rust crate serde_json to 1.0.66 (819f74b)
• Dependencies: NPM audit fix (6f631c8)

Features

• Digests: Add buildDigest and other digests; refactor code types (0521783)
• Include: Add sha256 property and add to BlockContent (3e94190)
• Parameter: Add to InlineContent (74235e1)
• Rust: Use strum to provide a string representation of enum variants (1b7060a)

1.10.1 (2021-08-09)

Bug Fixes

• dependencies: update rust crate serde to 1.0.127 (4bfa1d5)

v1.10.1

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Bug Fixes

• dependencies: update rust crate serde to 1.0.127 (4bfa1d5)

v1.10.0

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Bug Fixes

• CreativeWork: Use semicolon separated items for authors, add csi for genre (56a3bb6)
• Primitves: Refer to internal schema for primitives (54a8264)

Features

• Rust: Include map of schemas in crate (4b82b26)

1.9.1 (2021-07-06)

Bug Fixes

• Array and string validators: Use integer for property types where appropriate (866423e)
• Rust: Do not box primitive properties; allow overrides (e817aaa)

v1.9.1

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Bug Fixes

• Array and string validators: Use integer for property types where appropriate (866423e)
• Rust: Do not box primitive properties; allow overrides (e817aaa)

v1.9.0

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Bug Fixes

• CreativeWork: Allow an array of nodes (a13cbfc)
• dependencies: update rust crate serde to 1.0.126 (371712e)
• dependencies: update rust crate serde_with to 1.9.4 (ac06fd3)
• InlineContent: Remove Array and Object from InlineContent (a844439), closes /github.com/stencila/schema/pull/274#pullrequestreview-687650292
• Python: Avoid generating recursive types (eceb36a)
• R bindings: Avoid type recursion (efdae5c)
• Rust bindings: Fix name for Array (e955f27)
• Types: Include Entity in Node union type (e713276)
• TypeScript: Reduce number, and simplify, type guards (d348d17)
• TypeScript bindings: Revert to using any (4d1b761)

Features

• Schema: Rename property format to mediaType (bfb10d6)

1.8.1 (2021-06-06)

Bug Fixes

• Rust: Box optional properties (be279c0)

Performance Improvements

• Rust: Do not include meta property (893de26)
• Rust: Reduce memory footprint of type deserialization discriminant (7c36200)
• Rust: Use simple structs for creative works when present as inline or block content (9a650d1)

v1.8.1

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Bug Fixes

• **

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[codecov]

Codecov Report

Merging #1173 (5e1f8b8) into master (671cccf) will decrease coverage by 0.02%.
The diff coverage is n/a.

❗ Current head 5e1f8b8 differs from pull request most recent head caeda02. Consider uploading reports for the commit caeda02 to get more accurate results

@@            Coverage Diff             @@
##           master    #1173      +/-   ##
==========================================
- Coverage   66.63%   66.60%   -0.03%     
==========================================
  Files         134      134              
  Lines        7880     7870      -10     
==========================================
- Hits         5251     5242       -9     
+ Misses       2629     2628       -1     

Impacted Files	Coverage Δ
worker/jobs/base/job.py	74.07% <0.00%> (-1.23%)	⬇️
worker/jobs/pull/elife.py	90.69% <0.00%> (-0.80%)	⬇️
worker/jobs/convert.py	95.38% <0.00%> (+1.35%)	⬆️

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