From 4459a726cb7ec4abb5ad7971a84c60ca3ff13409 Mon Sep 17 00:00:00 2001 From: ThimotheeV Date: Tue, 3 Nov 2026 11:31:27 +0100 Subject: [PATCH 1/4] update --- README.md | 2 +- docusaurus.config.js | 4 +- package-lock.json | 2419 ++++++++++++++++++++++++++---------------- package.json | 10 +- 4 files changed, 1517 insertions(+), 918 deletions(-) diff --git a/README.md b/README.md index 755c159..41c859a 100644 --- a/README.md +++ b/README.md @@ -25,7 +25,7 @@ $ npm install to install all dependent packages (including the Docusaurus libraries) and ``` -$ npm run pull-treeppl-models +$ npm gen-model-docs ``` to pull model descriptions from TreePPL repository. diff --git a/docusaurus.config.js b/docusaurus.config.js index f8bb319..7beb9bb 100644 --- a/docusaurus.config.js +++ b/docusaurus.config.js @@ -8,7 +8,7 @@ const darkCodeTheme = themes.dracula; import remarkMath from 'remark-math'; import rehypeKatex from 'rehype-katex'; -const config = { +export default { title: 'TreePPL', tagline: 'Universal Probabilistic Programming for Phylogenetics', url: 'http://treeppl.org/', @@ -150,5 +150,3 @@ const config = { }, }, }; - 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"node_modules/wrappy": { - "version": "1.0.2", - "dev": true, - "license": "ISC" - }, "node_modules/write-file-atomic": { "version": "3.0.3", "license": "ISC", @@ -17867,6 +18458,8 @@ }, "node_modules/wsl-utils": { "version": "0.1.0", + "resolved": "https://registry.npmjs.org/wsl-utils/-/wsl-utils-0.1.0.tgz", + "integrity": "sha512-h3Fbisa2nKGPxCpm89Hk33lBLsnaGBvctQopaBSOW/uIs6FTe1ATyAnKFJrzVs9vpGdsTe73WF3V4lIsk4Gacw==", "license": "MIT", "dependencies": { "is-wsl": "^3.1.0" @@ -17879,7 +18472,9 @@ } }, "node_modules/wsl-utils/node_modules/is-wsl": { - "version": "3.1.0", + "version": "3.1.1", + "resolved": "https://registry.npmjs.org/is-wsl/-/is-wsl-3.1.1.tgz", + "integrity": "sha512-e6rvdUCiQCAuumZslxRJWR/Doq4VpPR82kqclvcS0efgt430SlGIk05vdCN58+VrzgtIcfNODjozVielycD4Sw==", "license": "MIT", "dependencies": { "is-inside-container": "^1.0.0" @@ -17891,6 +18486,11 @@ "url": "https://github.com/sponsors/sindresorhus" } }, + "node_modules/x-is-string": { + "version": "0.1.0", + "resolved": "https://registry.npmjs.org/x-is-string/-/x-is-string-0.1.0.tgz", + "integrity": "sha512-GojqklwG8gpzOVEVki5KudKNoq7MbbjYZCbyWzEz7tyPA7eleiE0+ePwOWQQRb5fm86rD3S8Tc0tSFf3AOv50w==" + }, "node_modules/xdg-basedir": { "version": "5.1.0", "license": "MIT", @@ -17915,7 +18515,8 @@ }, "node_modules/xtend": { "version": "4.0.2", - "dev": true, + "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz", + "integrity": "sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ==", "license": "MIT", "engines": { "node": ">=0.4" diff --git a/package.json b/package.json index c4002fa..a491f7e 100644 --- a/package.json +++ b/package.json @@ -17,19 +17,19 @@ "gen-reference-docs": "./scripts/gen-reference-docs.fish" }, "dependencies": { - "@docusaurus/core": "^3.8.1", - "@docusaurus/preset-classic": "^3.8.1", + "@docusaurus/core": "^3.10.2", + "@docusaurus/preset-classic": "^3.10.2", "@mdx-js/react": "^3.1.0", "clsx": "^2.1.1", "docusaurus-plugin-remote-content": "^4.0.0", "prism-react-renderer": "^2.4.0", "react": "^18.3.1", "react-dom": "^18.3.1", - "rehype-katex": "^7.0.1", - "remark-math": "^6.0.0" + "rehype-katex": "^1.2.0", + "remark-math": "^3.0.1" }, "devDependencies": { - "@docusaurus/module-type-aliases": "^3.8.1", + "@docusaurus/module-type-aliases": "^3.10.2", "tsconfig": "^7.0.0", "typescript": "~5.2.2" }, From a8cefecd3603206536da1dd2d67cf59faf11471c Mon Sep 17 00:00:00 2001 From: ThimotheeV Date: Tue, 3 Nov 2026 14:53:14 +0100 Subject: [PATCH 2/4] expected output --- docs/changelogs/index.md | 16 ++++++ docs/changelogs/treeppl-python.md | 40 +++++++++++++++ docs/{changelog.md => changelogs/treeppl.md} | 48 ++---------------- docs/changelogs/treepplr.md | 52 ++++++++++++++++++++ docs/index.md | 2 +- 5 files changed, 112 insertions(+), 46 deletions(-) create mode 100644 docs/changelogs/index.md create mode 100644 docs/changelogs/treeppl-python.md rename docs/{changelog.md => changelogs/treeppl.md} (59%) create mode 100644 docs/changelogs/treepplr.md diff --git a/docs/changelogs/index.md b/docs/changelogs/index.md new file mode 100644 index 0000000..c563d9a --- /dev/null +++ b/docs/changelogs/index.md @@ -0,0 +1,16 @@ +--- +id: changelog +sidebar_position: 10 +--- + +# Changelog + +All notable changes to the support projects (since 2026-02-19) are documented in these files. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/). These projects adhere to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) with the following convention: + +They use versioning in the format `v{X.Y.Z}`, where X, Y, and Z are integers: +* **X and Y** are determined by the `treeppl` version and used as-is by `treepplr` and `treeppl-python` (e.g., both `treepplr v1.2.0` and `treeppl-python v1.2.1` rely on `treeppl v1.2`). +* **Z** is unconstrained for `treepplr` and `treeppl-python` so they can track their own internal chan + +- [Miking/Miking-Dppl/TreePPL](treeppl.md) +- [treeppl-python : an Python package for TreePPL](treeppl-python.md) +- [treepplr : an R package for TreePPL](treepplr.md) diff --git a/docs/changelogs/treeppl-python.md b/docs/changelogs/treeppl-python.md new file mode 100644 index 0000000..dac9f8c --- /dev/null +++ b/docs/changelogs/treeppl-python.md @@ -0,0 +1,40 @@ +--- +id: treeppl-python +sidebar_position: 2 +--- + +# treeppl-python + +## [Unreleased] + +### Added + +### Changed + +### Deprecated + +### Removed + +### Fixed + +### Security + +## v0.4.0 + +### Added + +- ([treeppl-python#18](https://github.com/treeppl/treeppl-python/pull/18)) Python interface: Introduced `CompileArguments` and `RunArguments` classes for handling compile and run arguments. `RunArguments` can now be serialized to and deserialized from JSON files for easier reuse and reproducibility. + +### Changed + +- ([treeppl-python#18](https://github.com/treeppl/treeppl-python/pull/18)) Python interface: Compile arguments now mirrors the arguments used by `tpplc` for improved consistency and alignment between interfaces. + +### Deprecated + +### Removed + +- ([treeppl-python#18](https://github.com/treeppl/treeppl-python/pull/18)) Jupyter interface: Removed legacy syntax highlighting support that was only compatible with older Jupyter Notebook versions. + +### Fixed + +### Security diff --git a/docs/changelog.md b/docs/changelogs/treeppl.md similarity index 59% rename from docs/changelog.md rename to docs/changelogs/treeppl.md index 59d9b1f..9865d08 100644 --- a/docs/changelog.md +++ b/docs/changelogs/treeppl.md @@ -1,14 +1,9 @@ --- -id: changelog -sidebar_position: 12 +id: treeppl +sidebar_position: 1 --- -# Changelog - -All notable changes to this project (since 2026-02-19) are documented in this file. - -The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), -and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +# TreePPL ## [Unreleased] @@ -33,29 +28,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - ([dppl#245](https://github.com/miking-lang/miking-dppl/pull/245), [treeppl#163](https://github.com/treeppl/treeppl/pull/163)) Add `--max-propagations INT` to limit `smc-apf` near infinite loop (see `tpplc --help` for more details) - ([treeppl#165](https://github.com/treeppl/treeppl/pull/165)) A `tpplc --version` flag that prints a version number when given to a released compiler and `~git~` when given to a manually built compiler. - ([treeppl#169](https://github.com/treeppl/treeppl/pull/169)) Add `all` function. -- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) Add `tp_runtime_options` -- ([treepplr#13](https://github.com/treeppl/treepplr/pull/13)) `tp_run(n_runs)` to run multiple sweeps/runs -- ([treepplr#13](https://github.com/treeppl/treepplr/pull/13)) `tp_run(n_processes)` to run MCMC or SMC in parallel using n cores -- ([treepplr#13](https://github.com/treeppl/treepplr/pull/13)) `tp_compile_methods()` to find available methods -- ([treepplr#14](https://github.com/treeppl/treepplr/pull/14)) Tim and Stenio as package authors in DESCRIPTION. - ([treeppl#173](https://github.com/treeppl/treeppl/pull/173)) Add `bool2int` function - ([treeppl#173](https://github.com/treeppl/treeppl/pull/173)) Inference test suite -- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) At the end of a run, `tp_run()` now prints a summary with runtime information and output directories/files. -- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) New argument `wide` in `tp_parse_smc()` and `tp_parse_mcmc()` to choose between wide (standard in other software) and long (good for plotting) format. Default = `TRUE`. ### Changed - ([treeppl#172](https://github.com/treeppl/treeppl/pull/172)) Updated external dependencies -- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) Change "compiled_model" to "sampler" (temporary) -- ([treepplr#13](https://github.com/treeppl/treepplr/pull/13)) Updated the documentation -- ([treepplr#14](https://github.com/treeppl/treepplr/pull/14)) treepplr package installation should be done with `pak::pak` because `devtools::install_github` will soon be deprecated. -- ([treepplr#30](https://github.com/treeppl/treepplr/pull/30)) Updated roxygen documentation for `tp_parse_smc()` and `tp_parse_mcmc()`. Changed their output objects to tidy data frames. - ([miking#1006](https://github.com/miking-lang/miking/pull/1006), [dppl#246](https://github.com/miking-lang/miking-dppl/pull/246), [treeppl#165](https://github.com/treeppl/treeppl/pull/165)) Rearranged `tpplc --help` output for nicer readability -- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) `tp_run()` now returns a tidy data frame (in wide format by default) instead of a list. It automatically calls `tp_parse_smc()` or `tp_parse_mcmc()`, depending on the inference method and model passed to `tp_compile()`. For models without a parser yet (e.g., models that return trees), it returns the path to the output JSON file along with a message. -- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) `tp_parse_smc()` and `tp_parse_mcmc()` now take a character vector with the path(s) to the JSON output file(s) instead of the list returned by `tp_run()`. -- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) `tp_mcmc_convergence()` and `tp_smc_convergence()` now accept data frames in either long or wide format. ### Deprecated -- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) all references to `n_runs` have been remove ### Removed @@ -63,29 +43,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - ([treeppl#162](https://github.com/treeppl/treeppl/pull/162)) Matrix operations should no longer be compiled incorrectly when using `mcmc-graph`. - ([treeppl#166](https://github.com/treeppl/treeppl/pull/166)) Lexing errors now point at the actual problem - ([treeppl#172](https://github.com/treeppl/treeppl/pull/172)) Updated builds to work on MacOS 27 -- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) Always check if tpplc is installed before calling it -- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) `tp_compile_options` update for new `--help` format -- ([treepplr#30](https://github.com/treeppl/treepplr/pull/30)) `tp_parse_smc()` and `tp_parse_mcmc()` now parse per-particle/iteration with explicit indices and (for SMC) join weights by index using `left_join(..., by = "particle")` instead of relying on positional recycling, which is the default behavior of `data.frame()` when handling vectors of different lengths. - ([dppl#251](https://github.com/miking-lang/miking-dppl/pull/251)) Removed opportunistic redraw of 0 probability `assume`s in `mcmc`, since it does not yield correct inference in general. ### Security -## v0.4.1 - -### Added - -### Changed - -### Deprecated - -### Removed - -### Fixed - -- ([treeppl-python#23](https://github.com/treeppl/treeppl-python/pull/23)) Added missing import of `importlib.resources`, which would be implicitly imported on some machines, but not all. - -### Security - ## v0.4 ### Added @@ -95,7 +56,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - ([treeppl#138](https://github.com/treeppl/treeppl/pull/138)) Added diversification model example for the birth-death diffusion (BDD) model, version 2 (analogous to ClaDS2). - ([treeppl#138](https://github.com/treeppl/treeppl/pull/138)) Added diversification model versions with hard-coded delayed sampling. - ([treeppl#138](https://github.com/treeppl/treeppl/pull/138)) Added constant-rate birth-death (CRBD) model using weights based on analytical likelihood rather than simulation. -- ([treeppl-python#18](https://github.com/treeppl/treeppl-python/pull/18)) Python interface: Introduced `CompileArguments` and `RunArguments` classes for handling compile and run arguments. `RunArguments` can now be serialized to and deserialized from JSON files for easier reuse and reproducibility. - ([dppl#231](https://github.com/miking-lang/miking-dppl/pull/231)) Added previous weight and proposal weight to output of `--debug-mcmc` - ([miking#986](https://github.com/miking-lang/miking/pull/986), [dppl#234](https://github.com/miking-lang/miking-dppl/pull/234), [dppl#236](https://github.com/miking-lang/miking-dppl/pull/236), [treeppl#155](https://github.com/treeppl/treeppl/pull/155)) Experimental new inference method `-m mcmc-graph` - ([treeppl#149](https://github.com/treeppl/treeppl/pull/149)) Models included with the compiler can now be referenced in `import`s or as arguments to `tpplc` via, e.g., `treeppl::models/diversification/crbd.tppl` @@ -104,7 +64,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - ([dppl#229](https://github.com/miking-lang/miking-dppl/pull/229)) Inference methods using alignment now crash if no aligned `assume`s were found. - ([dppl#238](https://github.com/miking-lang/miking-dppl/pull/238)) SMC-based inference methods now refuse to compile if no `observe` or `weight`s are found. -- ([treeppl-python#18](https://github.com/treeppl/treeppl-python/pull/18)) Python interface: Compile arguments now mirrors the arguments used by `tpplc` for improved consistency and alignment between interfaces. - ([miking#984](https://github.com/miking-lang/miking/pull/984), [treeppl#135](https://github.com/treeppl/treeppl/pull/135)) Command line flags are now split into categories, and some parameters can be given to a compiled model - ([treeppl#143](https://github.com/treeppl/treeppl/pull/143)) The `debug` statement now prints literal strings as-is, while variables are pretty-printed. - ([miking#999](https://github.com/miking-lang/miking/pull/999)) Incompatible flags are reported as such, rather than unrecognized. @@ -114,7 +73,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Removed - ([treeppl#153](https://github.com/treeppl/treeppl/pull/153)) Removed the `Tree` type from the `standard.tppl` library file. An identical type, called `ClockTree`, is now in the `trees.tppl` library file. This change allows a more convenient interface, in that a user can synonymize a local custom `Tree` type with `ClockTree`, or any other tree type in the standard library that is appropriate for the model script. -- ([treeppl-python#18](https://github.com/treeppl/treeppl-python/pull/18)) Jupyter interface: Removed legacy syntax highlighting support that was only compatible with older Jupyter Notebook versions. ### Fixed diff --git a/docs/changelogs/treepplr.md b/docs/changelogs/treepplr.md new file mode 100644 index 0000000..4fe50d1 --- /dev/null +++ b/docs/changelogs/treepplr.md @@ -0,0 +1,52 @@ +--- +id: treepplr +sidebar_position: 3 +--- + +# treepplr + +## [Unreleased] + +### Added + +### Changed + +### Deprecated + +### Removed + +### Fixed + +### Security + +## v0.5.0 + +### Added +- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) Add `tp_runtime_options` +- ([treepplr#13](https://github.com/treeppl/treepplr/pull/13)) `tp_run(n_runs)` to run multiple sweeps/runs +- ([treepplr#13](https://github.com/treeppl/treepplr/pull/13)) `tp_run(n_processes)` to run MCMC or SMC in parallel using n cores +- ([treepplr#13](https://github.com/treeppl/treepplr/pull/13)) `tp_compile_methods()` to find available methods +- ([treepplr#14](https://github.com/treeppl/treepplr/pull/14)) Tim and Stenio as package authors in DESCRIPTION. +- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) At the end of a run, `tp_run()` now prints a summary with runtime information and output directories/files. +- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) New argument `wide` in `tp_parse_smc()` and `tp_parse_mcmc()` to choose between wide (standard in other software) and long (good for plotting) format. Default = `TRUE`. + +### Changed +- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) Change "compiled_model" to "sampler" (temporary) +- ([treepplr#13](https://github.com/treeppl/treepplr/pull/13)) Updated the documentation +- ([treepplr#14](https://github.com/treeppl/treepplr/pull/14)) treepplr package installation should be done with `pak::pak` because `devtools::install_github` will soon be deprecated. +- ([treepplr#30](https://github.com/treeppl/treepplr/pull/30)) Updated roxygen documentation for `tp_parse_smc()` and `tp_parse_mcmc()`. Changed their output objects to tidy data frames. +- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) `tp_run()` now returns a tidy data frame (in wide format by default) instead of a list. It automatically calls `tp_parse_smc()` or `tp_parse_mcmc()`, depending on the inference method and model passed to `tp_compile()`. For models without a parser yet (e.g., models that return trees), it returns the path to the output JSON file along with a message. +- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) `tp_parse_smc()` and `tp_parse_mcmc()` now take a character vector with the path(s) to the JSON output file(s) instead of the list returned by `tp_run()`. +- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) `tp_mcmc_convergence()` and `tp_smc_convergence()` now accept data frames in either long or wide format. + +### Deprecated +- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) all references to `n_runs` have been remove + +### Removed + +### Fixed +- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) Always check if tpplc is installed before calling it +- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) `tp_compile_options` update for new `--help` format +- ([treepplr#30](https://github.com/treeppl/treepplr/pull/30)) `tp_parse_smc()` and `tp_parse_mcmc()` now parse per-particle/iteration with explicit indices and (for SMC) join weights by index using `left_join(..., by = "particle")` instead of relying on positional recycling, which is the default behavior of `data.frame()` when handling vectors of different lengths. + +### Security \ No newline at end of file diff --git a/docs/index.md b/docs/index.md index ab8683e..4bc1be2 100644 --- a/docs/index.md +++ b/docs/index.md @@ -20,5 +20,5 @@ The TreePPL documentation consists of: - [Model library](./model-library/index.md), which contains model examples that can be used as templates, - [Troubleshooting](./troubleshooting.md), describing solutions to problems you may encounter when installing or running TreePPL, - [Contribute to TreePPL development](./for-developers/index.md), with instructions for installing the command-line version and for contributing to the TreePPL development effort, - - [Changelog](./changelog.md), listing important bug fixes, new features and official releases, + - [Changelog](./changelogs/index.md), listing important bug fixes, new features and official releases, - [How to cite](./how_to_cite.md), with information on how to cite TreePPL. From 93893612b8f41a483d2d6150236cf46194965112 Mon Sep 17 00:00:00 2001 From: ThimotheeV Date: Tue, 3 Nov 2026 17:16:21 +0100 Subject: [PATCH 3/4] final --- .gitignore | 1 + docs/changelogs/index.md | 16 --- docs/changelogs/treeppl-python.md | 40 ------ docs/changelogs/treeppl.md | 105 --------------- docs/changelogs/treepplr.md | 52 -------- scripts/check-changelog.fish | 214 ------------------------------ scripts/gen-changelog.fish | 43 ++++++ 7 files changed, 44 insertions(+), 427 deletions(-) delete mode 100644 docs/changelogs/index.md delete mode 100644 docs/changelogs/treeppl-python.md delete mode 100644 docs/changelogs/treeppl.md delete mode 100644 docs/changelogs/treepplr.md delete mode 100755 scripts/check-changelog.fish create mode 100755 scripts/gen-changelog.fish diff --git a/.gitignore b/.gitignore index 4301812..98f4c32 100644 --- a/.gitignore +++ b/.gitignore @@ -5,6 +5,7 @@ /build #Auto-generate +/docs/changelogs /docs/model-library /docs/Reference /other-repositories diff --git a/docs/changelogs/index.md b/docs/changelogs/index.md deleted file mode 100644 index c563d9a..0000000 --- a/docs/changelogs/index.md +++ /dev/null @@ -1,16 +0,0 @@ ---- -id: changelog -sidebar_position: 10 ---- - -# Changelog - -All notable changes to the support projects (since 2026-02-19) are documented in these files. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/). These projects adhere to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) with the following convention: - -They use versioning in the format `v{X.Y.Z}`, where X, Y, and Z are integers: -* **X and Y** are determined by the `treeppl` version and used as-is by `treepplr` and `treeppl-python` (e.g., both `treepplr v1.2.0` and `treeppl-python v1.2.1` rely on `treeppl v1.2`). -* **Z** is unconstrained for `treepplr` and `treeppl-python` so they can track their own internal chan - -- [Miking/Miking-Dppl/TreePPL](treeppl.md) -- [treeppl-python : an Python package for TreePPL](treeppl-python.md) -- [treepplr : an R package for TreePPL](treepplr.md) diff --git a/docs/changelogs/treeppl-python.md b/docs/changelogs/treeppl-python.md deleted file mode 100644 index dac9f8c..0000000 --- a/docs/changelogs/treeppl-python.md +++ /dev/null @@ -1,40 +0,0 @@ ---- -id: treeppl-python -sidebar_position: 2 ---- - -# treeppl-python - -## [Unreleased] - -### Added - -### Changed - -### Deprecated - -### Removed - -### Fixed - -### Security - -## v0.4.0 - -### Added - -- ([treeppl-python#18](https://github.com/treeppl/treeppl-python/pull/18)) Python interface: Introduced `CompileArguments` and `RunArguments` classes for handling compile and run arguments. `RunArguments` can now be serialized to and deserialized from JSON files for easier reuse and reproducibility. - -### Changed - -- ([treeppl-python#18](https://github.com/treeppl/treeppl-python/pull/18)) Python interface: Compile arguments now mirrors the arguments used by `tpplc` for improved consistency and alignment between interfaces. - -### Deprecated - -### Removed - -- ([treeppl-python#18](https://github.com/treeppl/treeppl-python/pull/18)) Jupyter interface: Removed legacy syntax highlighting support that was only compatible with older Jupyter Notebook versions. - -### Fixed - -### Security diff --git a/docs/changelogs/treeppl.md b/docs/changelogs/treeppl.md deleted file mode 100644 index 9865d08..0000000 --- a/docs/changelogs/treeppl.md +++ /dev/null @@ -1,105 +0,0 @@ ---- -id: treeppl -sidebar_position: 1 ---- - -# TreePPL - -## [Unreleased] - -### Added - -### Changed - -### Deprecated - -### Removed - -### Fixed - -### Security - -## v0.5 - -### Added -- ([dppl#239](https://github.com/miking-lang/miking-dppl/pull/239), [treeppl#161](https://github.com/treeppl/treeppl/pull/161)) `--debug-graph-json ` to output a json representation of the graph generated when running a model compiled with `mcmc-graph`. -- ([dppl#243](https://github.com/miking-lang/miking-dppl/pull/243), [treeppl#161](https://github.com/treeppl/treeppl/pull/161)) `--debug-idealized ` to output a pretty-printed version of the graph after the idealized transformation stage. -- ([dppl#240](https://github.com/miking-lang/miking-dppl/pull/240), [dppl#242](https://github.com/miking-lang/miking-dppl/pull/242)) Improved the graph translation performed in `-m mcmc-graph` -- ([dppl#245](https://github.com/miking-lang/miking-dppl/pull/245), [treeppl#163](https://github.com/treeppl/treeppl/pull/163)) Add `--max-propagations INT` to limit `smc-apf` near infinite loop (see `tpplc --help` for more details) -- ([treeppl#165](https://github.com/treeppl/treeppl/pull/165)) A `tpplc --version` flag that prints a version number when given to a released compiler and `~git~` when given to a manually built compiler. -- ([treeppl#169](https://github.com/treeppl/treeppl/pull/169)) Add `all` function. -- ([treeppl#173](https://github.com/treeppl/treeppl/pull/173)) Add `bool2int` function -- ([treeppl#173](https://github.com/treeppl/treeppl/pull/173)) Inference test suite - -### Changed -- ([treeppl#172](https://github.com/treeppl/treeppl/pull/172)) Updated external dependencies -- ([miking#1006](https://github.com/miking-lang/miking/pull/1006), [dppl#246](https://github.com/miking-lang/miking-dppl/pull/246), [treeppl#165](https://github.com/treeppl/treeppl/pull/165)) Rearranged `tpplc --help` output for nicer readability - -### Deprecated - -### Removed - -### Fixed -- ([treeppl#162](https://github.com/treeppl/treeppl/pull/162)) Matrix operations should no longer be compiled incorrectly when using `mcmc-graph`. -- ([treeppl#166](https://github.com/treeppl/treeppl/pull/166)) Lexing errors now point at the actual problem -- ([treeppl#172](https://github.com/treeppl/treeppl/pull/172)) Updated builds to work on MacOS 27 -- ([dppl#251](https://github.com/miking-lang/miking-dppl/pull/251)) Removed opportunistic redraw of 0 probability `assume`s in `mcmc`, since it does not yield correct inference in general. - -### Security - -## v0.4 - -### Added - -- ([dppl#223](https://github.com/miking-lang/miking-dppl/pull/223), [treeppl#147](https://github.com/treeppl/treeppl/pull/147), [dppl#230](https://github.com/miking-lang/miking-dppl/pull/230), [treeppl#150](https://github.com/treeppl/treeppl/pull/150), [treeppl#151](https://github.com/treeppl/treeppl/pull/151)) New flag ```--data-augmentation``` (see ```tpplc --help``` for details) -- ([treeppl#138](https://github.com/treeppl/treeppl/pull/138)) Added some distribution functions for manual updates via conjugate priors -- ([treeppl#138](https://github.com/treeppl/treeppl/pull/138)) Added diversification model example for the birth-death diffusion (BDD) model, version 2 (analogous to ClaDS2). -- ([treeppl#138](https://github.com/treeppl/treeppl/pull/138)) Added diversification model versions with hard-coded delayed sampling. -- ([treeppl#138](https://github.com/treeppl/treeppl/pull/138)) Added constant-rate birth-death (CRBD) model using weights based on analytical likelihood rather than simulation. -- ([dppl#231](https://github.com/miking-lang/miking-dppl/pull/231)) Added previous weight and proposal weight to output of `--debug-mcmc` -- ([miking#986](https://github.com/miking-lang/miking/pull/986), [dppl#234](https://github.com/miking-lang/miking-dppl/pull/234), [dppl#236](https://github.com/miking-lang/miking-dppl/pull/236), [treeppl#155](https://github.com/treeppl/treeppl/pull/155)) Experimental new inference method `-m mcmc-graph` -- ([treeppl#149](https://github.com/treeppl/treeppl/pull/149)) Models included with the compiler can now be referenced in `import`s or as arguments to `tpplc` via, e.g., `treeppl::models/diversification/crbd.tppl` - -### Changed - -- ([dppl#229](https://github.com/miking-lang/miking-dppl/pull/229)) Inference methods using alignment now crash if no aligned `assume`s were found. -- ([dppl#238](https://github.com/miking-lang/miking-dppl/pull/238)) SMC-based inference methods now refuse to compile if no `observe` or `weight`s are found. -- ([miking#984](https://github.com/miking-lang/miking/pull/984), [treeppl#135](https://github.com/treeppl/treeppl/pull/135)) Command line flags are now split into categories, and some parameters can be given to a compiled model -- ([treeppl#143](https://github.com/treeppl/treeppl/pull/143)) The `debug` statement now prints literal strings as-is, while variables are pretty-printed. -- ([miking#999](https://github.com/miking-lang/miking/pull/999)) Incompatible flags are reported as such, rather than unrecognized. - -### Deprecated - -### Removed - -- ([treeppl#153](https://github.com/treeppl/treeppl/pull/153)) Removed the `Tree` type from the `standard.tppl` library file. An identical type, called `ClockTree`, is now in the `trees.tppl` library file. This change allows a more convenient interface, in that a user can synonymize a local custom `Tree` type with `ClockTree`, or any other tree type in the standard library that is appropriate for the model script. - -### Fixed - -- ([treeppl#138](https://github.com/treeppl/treeppl/pull/138)) Changed the `rho` parameter (leaf sampling probability) in the data files for the diversification model scripts from `2.0` to `0.5`. -- ([dppl#228](https://github.com/miking-lang/miking-dppl/pull/228)) Running multiple sweeps with `-m mcmc` now resets state properly between the runs -- ([miking#981](https://github.com/miking-lang/miking/pull/981)) The `debug` statement now properly handles printing strings -- ([treeppl#157](https://github.com/treeppl/treeppl/pull/157)) Bug in the code generation for pigeons related flags. - -### Security - -## v0.3 - -### Added - -- New flag ```--infer-time``` (see ```tpplc --help``` for details) -- Add a changelog to the webside - -### Changed - -- The `debug` statement now accepts multiple arguments - -### Deprecated - -### Removed - -### Fixed - -- Using `debug` to print strings no longer crashes - -### Security diff --git a/docs/changelogs/treepplr.md b/docs/changelogs/treepplr.md deleted file mode 100644 index 4fe50d1..0000000 --- a/docs/changelogs/treepplr.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -id: treepplr -sidebar_position: 3 ---- - -# treepplr - -## [Unreleased] - -### Added - -### Changed - -### Deprecated - -### Removed - -### Fixed - -### Security - -## v0.5.0 - -### Added -- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) Add `tp_runtime_options` -- ([treepplr#13](https://github.com/treeppl/treepplr/pull/13)) `tp_run(n_runs)` to run multiple sweeps/runs -- ([treepplr#13](https://github.com/treeppl/treepplr/pull/13)) `tp_run(n_processes)` to run MCMC or SMC in parallel using n cores -- ([treepplr#13](https://github.com/treeppl/treepplr/pull/13)) `tp_compile_methods()` to find available methods -- ([treepplr#14](https://github.com/treeppl/treepplr/pull/14)) Tim and Stenio as package authors in DESCRIPTION. -- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) At the end of a run, `tp_run()` now prints a summary with runtime information and output directories/files. -- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) New argument `wide` in `tp_parse_smc()` and `tp_parse_mcmc()` to choose between wide (standard in other software) and long (good for plotting) format. Default = `TRUE`. - -### Changed -- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) Change "compiled_model" to "sampler" (temporary) -- ([treepplr#13](https://github.com/treeppl/treepplr/pull/13)) Updated the documentation -- ([treepplr#14](https://github.com/treeppl/treepplr/pull/14)) treepplr package installation should be done with `pak::pak` because `devtools::install_github` will soon be deprecated. -- ([treepplr#30](https://github.com/treeppl/treepplr/pull/30)) Updated roxygen documentation for `tp_parse_smc()` and `tp_parse_mcmc()`. Changed their output objects to tidy data frames. -- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) `tp_run()` now returns a tidy data frame (in wide format by default) instead of a list. It automatically calls `tp_parse_smc()` or `tp_parse_mcmc()`, depending on the inference method and model passed to `tp_compile()`. For models without a parser yet (e.g., models that return trees), it returns the path to the output JSON file along with a message. -- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) `tp_parse_smc()` and `tp_parse_mcmc()` now take a character vector with the path(s) to the JSON output file(s) instead of the list returned by `tp_run()`. -- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) `tp_mcmc_convergence()` and `tp_smc_convergence()` now accept data frames in either long or wide format. - -### Deprecated -- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) all references to `n_runs` have been remove - -### Removed - -### Fixed -- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) Always check if tpplc is installed before calling it -- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) `tp_compile_options` update for new `--help` format -- ([treepplr#30](https://github.com/treeppl/treepplr/pull/30)) `tp_parse_smc()` and `tp_parse_mcmc()` now parse per-particle/iteration with explicit indices and (for SMC) join weights by index using `left_join(..., by = "particle")` instead of relying on positional recycling, which is the default behavior of `data.frame()` when handling vectors of different lengths. - -### Security \ No newline at end of file diff --git a/scripts/check-changelog.fish b/scripts/check-changelog.fish deleted file mode 100755 index 97872b6..0000000 --- a/scripts/check-changelog.fish +++ /dev/null @@ -1,214 +0,0 @@ -#!/usr/bin/env fish - -# === Library stuff === - -source (path resolve (status dirname))/repo-utils.fish - -set -g repoNames -set -g repoUrls - -function prsSince --argument-names repoName date - set -l dir "$repoDir/other-repositories/$repoName" - cd $dir - git log --since=$date --grep="[ (]#[0-9]\+\b" --format=%s\ - | sed "s!^.*\?\(#[0-9]\+\).*!$repoName\1!" -end - -function addRepo --argument-names repoName url - set -ag repoNames $repoName - set -ag repoUrls $url - ensureRepo $repoName $url -end - -function unmentionedPRs --argument-names date - set -l files $argv[2..] - - set -l allPRs - for repoName in $repoNames - set -a allPRs (prsSince $repoName $date) - end - - set -l allPRs (string join \n -- $allPRs | sort | uniq) - set -l mentioned (grep '[a-zA-Z0-9-]\+#[0-9]\+' --only-matching --no-filename $files | sort | uniq) - comm -2 -3 (string join \n $allPRs | psub) (string join \n $mentioned | psub) -end - -function setKV --argument-names key value - if not begin; echo $value | jq -Rs fromjson &>/dev/null; end - # NOTE(vipa, 2025-07-21): Not valid json, quote it - set value '"'(string join \n -- $value | jq -Rs '.')'"' - end - set -l cache $repoDir/other-repositories/cache.json - if test -f $cache - set -l result (jq -c '.["'$key'"] = '$value < $cache) - echo $result > $cache - else - echo '{"'$key'":'$value'}' > $cache - end -end - -function getKV --argument-names key - set -l cache $repoDir/other-repositories/cache.json - jq -r '.["'$key'"]' < $cache | string collect -end - -function getBody --argument-names pr - if set -gq online - string match --entire --regex --quiet '(?[a-zA-Z0-9-]+)#(?[0-9]+)' $pr - or begin; echo "match 1 failed" >&2; exit 1; end - set -l url $repoUrls[(contains --index $repoName $repoNames)] - or begin; echo "contains failed" >&2; exit 1; end - string match --entire --regex --quiet '[a-z]://(?.*?)\.git' $url - or begin; echo "match 2 failed" >&2; exit 1; end - set -l body (gh pr view --json body --jq .body --repo $repo $prNum | tr -d '\r' | jq -Rs '.') - setKV $pr $body - string collect $body - else - getKV $pr - end -end - -set -g headings -function collectBullets --argument-names pr - set -l lines (string split \n -- (getBody $pr)) - if set -l idx (contains --index -- "## TreePPL Release Notes" $lines) - for line in $lines[(math $idx + 1)..] - switch $line - case "###*" - set -l headingVar (string escape --style=var -- $line) - if not contains $headingVar $headings - set -a headings $headingVar - end - set -f currentHeading $headingVar - case "##*" "---" - break - case "- *" "\* *" - set -f addedBullet - set -q currentHeading || continue - set -ga $currentHeading "- ($pr) $(string match --regex --groups-only '. *(.*)' -- $line)" - end - end - if not set -qf addedBullet - echo $pr\t"(had changelog with no bullets)" - end - else - echo $pr - end -end - -function showBullets - for heading in $headings - if not count $$heading >/dev/null - continue - end - string unescape --style=var $heading - string join \n -- $$heading - echo - end -end - -function splitOffBullets - for pr in $argv - collectBullets $pr - end -end - -function mkGHLinkSed --argument-names i - echo -- "-e" - echo -n "s@" - echo -n $repoNames[$i]"#\([0-9]\+\)@" - echo -n '['$repoNames[$i]'#\1]('(echo $repoUrls[$i] | sed 's/.git$//')'/pull/\1)@' - echo 'g' -end - -function formatLinks - set -l cmd - sed (for i in (seq (count $repoNames)); mkGHLinkSed $i; end) -end - - -# === Application === - -set -l startDate 2026-03-13 - -if contains -- --offline $argv - set -ge online -end - -set -l extraPRs (string match --invert --entire -- --offline $argv) - -addRepo miking https://github.com/miking-lang/miking.git -addRepo dppl https://github.com/miking-lang/miking-dppl.git -addRepo treeppl https://github.com/treeppl/treeppl.git -addRepo treeppl-python https://github.com/treeppl/treeppl-python.git -addRepo treepplr https://github.com/treeppl/treepplr.git - -splitOffBullets (begin; unmentionedPRs $startDate $repoDir/docs/changelog.md $repoDir/scripts/(status basename); string join \n -- $extraPRs; end) | formatLinks -echo -showBullets | formatLinks - - -# These are to be ignored: -# dppl#224 -# dppl#226 (changes to how tests are run. Relevant for developers, but not for users?) -# dppl#227 (flake lock) -# dppl#232 (rename to avoid conflict with hoas.mc) -# dppl#233 (debug flag in cppl only) -# dppl#235 (recognize .cppl files in loader) -# miking#975 (docgen) -# miking#980 (invariant checking in --debug-phases) -# miking#982 (javascript test fixes) -# miking#983 (filesystem utilities) -# miking#985 (test-spec.mc) -# miking#987 (update ocamlformat) -# miking#988 (eqset.mc updates) -# miking#989 (subseqFindIdx function) -# miking#990 (fix test-spec.mc with tup with _many_ arguments) -# miking#991 (bump github action) -# miking#992 (shallow.mc introduce fewer functions) -# miking#993 (effects.mc test parallelism fix) -# miking#994 (test-spec.mc --watch ignore hidden files) -# treeppl#142 (add invariants to tpplc. Maybe relevant to developers, but not for users?) -# treeppl#144 (moved documentation of hostrep into repo, same as the others) -# treeppl#145 (v0.3) -# treeppl#146 (test-spec.mc. Relevant for developers, but not for users?) -# treeppl#152 (make sure --debug-mcmc is used in tests) -# treeppl-python#17 (v0.3) -# treeppl-python#19 (add import for trees.tppl) -# treeppl-python#20 (move import to lib/trees.tppl) -# treeppl-python#21 (remove import of lib/trees.tppl) -# dppl#237 (dppl typechecker, not used for tppl stuff) -# miking#995 (backend stuff, used in the graph translation) -# miking#996 (backend stuff, used in the graph translation) -# miking#997 (ast-to-json cases) -# miking#998 (free variables bugfix, used in graph translation) -# treeppl#154 (ast-to-json cases) -# treeppl#160 (release v0.4) -# treeppl-python#22 (release v0.4) -# treepplr#1 (Not entirely sure, but before the big remake) -# treepplr#9 (Not entirely sure, but before the big remake) -# treeppl#167 (Less precise tests) -# treeppl#168 (record gnu awk dependency in tests) -# treeppl#170 miking#1005 dppl#248 (loader update, only minor internal changes) -# dppl#244 (User relative paths in includes in coreppl instead of `coreppl::`) -# dppl#247 miking#1004 (Unmatched pattern change via `never`) -# miking#1000 (new parser in miking) -# miking#1001 (more flexible running of the test suite) -# miking#1002 (`exec` in miking) -# miking#1003 (nicer runing of tup, with exec instead of xargs) -# miking#1008 (nicer printing when running tests with make) -# miking#1009 (eliminate duplicate code bug, don't remember what the impact was from tppl point of view) -# treepplr#11 (new trepplr api, I _think_ this has been talked about elsewhere) -# treepplr#29 (fix to make it run in the test suite) -# miking#1014, dppl#250 (nix flake) -# miking#1007 (new parser in miking) -# miking#1013 (new interpreter in miking) -# miking#1015 (transpose function in miking) -# miking#1018 (fix `--tag` in `make` mode) -# miking#1019 (generalize type of `mapEq`) -# treeppl-python#24 (release 0.5) - - -# == stuff for the new graph, eventually == -# miking#1016 (pass that tracks instantiations in the AST) -# miking#1017 (peval graph, v1) diff --git a/scripts/gen-changelog.fish b/scripts/gen-changelog.fish new file mode 100755 index 0000000..680e083 --- /dev/null +++ b/scripts/gen-changelog.fish @@ -0,0 +1,43 @@ +#!/usr/bin/env fish + +# Generates docs/changelog from CHANGELOG.md pulling from +# the project root. docs/changelog is +# git-ignored; run this script to (re)generate it. + +source (path resolve (status dirname))/repo-utils.fish + +ensureRepo treeppl https://github.com/treeppl/treeppl.git +ensureRepo treeppl-python https://github.com/treeppl/treeppl-python.git +ensureRepo treepplr https://github.com/treeppl/treepplr.git + +set -U modelsDir $repoDir/other-repositories/treeppl $repoDir/other-repositories/treeppl-python $repoDir/other-repositories/treepplr +set -l outDir $repoDir/docs/changelogs +set -l index $outDir/index.md + +rm -rf $outDir +mkdir -p $outDir + +echo '--- +id: changelog +sidebar_position: 10 +--- + +# Changelog + +All notable changes to the support projects (since 2026-02-19) are documented in these files. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/). +These projects adhere to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) with the following convention: + +They use versioning in the format `v{X.Y.Z}`, where X, Y, and Z are integers: +* **X and Y** are determined by the `treeppl` version and used as-is by `treepplr` and `treeppl-python` (e.g., both `treepplr v1.2.0` and `treeppl-python v1.2.1` rely on `treeppl v1.2`). +* **Z** is unconstrained for `treepplr` and `treeppl-python` so they can track their own internal change +' > $index + +for dir in $modelsDir + set -l name (path basename $dir) + set -l changelog $dir/CHANGELOG.md + test -f $changelog || continue + cp $changelog $outDir/$name.md + set -l description (awk '/^#/ {sub(/^#\s*/, ""); print; exit}' $changelog) + echo "- [$description]($name.md)" + echo "- [$description]($name.md)" >> $index +end \ No newline at end of file From 6371cecf7e7c6c0eb4d2b2512ba98175fc514c5e Mon Sep 17 00:00:00 2001 From: ThimotheeV Date: Tue, 3 Nov 2026 19:39:55 +0100 Subject: [PATCH 4/4] integration and cleanning --- package.json | 1 + scripts/gen-changelog.fish | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index a491f7e..9671b1e 100644 --- a/package.json +++ b/package.json @@ -13,6 +13,7 @@ "write-translations": "docusaurus write-translations", "write-heading-ids": "docusaurus write-heading-ids", "typecheck": "tsc", + "gen-changelog": "./scripts/gen-changelog.fish", "gen-model-docs": "./scripts/gen-model-docs.fish", "gen-reference-docs": "./scripts/gen-reference-docs.fish" }, diff --git a/scripts/gen-changelog.fish b/scripts/gen-changelog.fish index 680e083..1636a61 100755 --- a/scripts/gen-changelog.fish +++ b/scripts/gen-changelog.fish @@ -38,6 +38,5 @@ for dir in $modelsDir test -f $changelog || continue cp $changelog $outDir/$name.md set -l description (awk '/^#/ {sub(/^#\s*/, ""); print; exit}' $changelog) - echo "- [$description]($name.md)" echo "- [$description]($name.md)" >> $index end \ No newline at end of file