Changelog script

.gitignore

@@ -1,25 +1,28 @@
-# Dependencies
-/node_modules
-
-# Production
-/build
-
-# Generated files
-.docusaurus
-.cache-loader
-
-# Misc
-.DS_Store
-.env.local
-.env.development.local
-.env.test.local
-.env.production.local
-
-npm-debug.log*
-yarn-debug.log*
-yarn-error.log*
-
-/.quarto/
-
-# vscode
-.vscode/
+# Dependencies
+/node_modules
+
+# Production
+/build
+
+# Generated files
+.docusaurus
+.cache-loader
+
+# Misc
+.DS_Store
+.env.local
+.env.development.local
+.env.test.local
+.env.production.local
+
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+
+/.quarto/
+
+# vscode
+.vscode/
+
+
+other-repositories

check-changelog.fish

@@ -0,0 +1,189 @@
+#!/usr/bin/env fish
+
+# === Library stuff ===
+
+set -g repoDir (path resolve (status dirname))
+
+set -g repoNames
+set -g repoUrls
+
+set -g online yes
+
+function ensureRepo --argument-names repoName url
+    set -l dir "$repoDir/other-repositories/$repoName"
+    if not test -d $dir
+        git clone $url $dir || exit 1
+    end
+    cd $dir
+    set -qg online && begin; git pull --force || exit 1; end
+end
+
+function prsSince --argument-names repoName date
+    set -l dir "$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 $value | jq -Rs fromjson &>/dev/null; end
+        # NOTE(vipa, 2025-07-21): Not valid json, quote it
+        set value '"'$value'"'
+    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 '(?<repoName>[a-zA-Z0-9-]+)#(?<prNum>[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]://(?<repo>.*?)\.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' | string collect)
+        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 -- --quiet $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/(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)

docs/changelog.md

@@ -14,28 +14,35 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
-- New flag ```--data-augmentation``` (see ```tpplc --help``` for details)
-- Added math functions, distribution types and functions, and tree types and functions to the library. The code is in separate library files (`math.tppl`, `distributions.tppl` and `trees.tppl`) in the `src/lib/` directory.
-- Added diversification model example for the birth-death diffusion (BDD) model, version 2 (analogous to ClaDS2).
-- Added diversification model versions with hard-coded delayed sampling.
-- Added constant-rate birth-death (CRBD) model using weights based on analytical likelihood rather than simulation.
-- 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#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.
+- ([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)) 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
 
-- Moved the functions `exp`, `log`, `sqrt`, `minInt`, `maxInt`, `floor`, `ceil`, `round` from the `standard.tppl` library file to `math.tppl`.
-- Python interface: Compile arguments now mirrors the arguments used by `tpplc` for improved consistency and alignment between interfaces.
+- ([dppl#229](https://github.com/miking-lang/miking-dppl/pull/229)) Inference methods using alignment now crash if no aligned `assume`s were 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.
 
 ### Deprecated
 
 ### Removed
 
 - 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.
-- Jupyter interface: Removed legacy syntax highlighting support that was only compatible with older Jupyter Notebook versions.
+- ([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
 
-- Changed the `rho` parameter (leaf sampling probability) in the data files for the diversification model scripts from `2.0` to `0.5`.
+- ([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
 
 ### Security
 
@@ -59,4 +66,3 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Using `debug` to print strings no longer crashes
 
 ### Security
-