morphata 2.0.0__tar.gz → 2.0.1__tar.gz

{morphata-2.0.0 → morphata-2.0.1}/.claude/settings.local.json

@@ -11,7 +11,11 @@
       "Bash(just test *)",
       "Bash(rg *)",
       "Bash(uv run pytest *)",
-      "Bash(uv run mypy *)"
+      "Bash(uv run mypy *)",
+      "Bash(.venv/bin/python -m pytest *)",
+      "Skill(superpowers:writing-plans)",
+      "Skill(superpowers:subagent-driven-development)",
+      "Bash(grep -v \"AssertionError\\\\|Traceback\\\\|File \\\\|^\\\\s*$\")"
     ]
   }
 }

{morphata-2.0.0 → morphata-2.0.1}/.envrc

@@ -12,15 +12,19 @@ if [[ -z "${DEVJAIL:-}" ]] && nvidia_smi="$(type -p "nvidia-smi")" && [[ -n "$nv
   if [[ -n "${cuda_major_version:-}" ]]; then
     info "Detected CUDA version: $cuda_major_version"
     export CUDA_VERSION="$cuda_major_version"
+    PIXI_ENV="cu$CUDA_VERSION"
   fi
 else
   info "Did not detect nvidia-smi, using non-GPU environment"
+  PIXI_ENV="default"
 fi
+export PIXI_ENV
 
 dotenv_if_exists
 
-if [[ -z "${DEVJAIL:-}" ]] || [[ ! -e ".venv/bin/activate" ]]; then
-  uvx --from rust-just just dev
+watch_file pixi.lock
+eval "$(pixi shell-hook -e "$PIXI_ENV")"
+
+if [[ -d "$CONDA_PREFIX" ]]; then
+  export VIRTUAL_ENV="$CONDA_PREFIX"
 fi
-source ./.venv/bin/activate
-watch_file pyproject.toml

morphata-2.0.1/.gitattributes

@@ -0,0 +1,5 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML
+
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff

{morphata-2.0.0 → morphata-2.0.1}/.gitignore

@@ -257,3 +257,6 @@ $RECYCLE.BIN/
 *.lnk
 
 # End of https://www.toptal.com/developers/gitignore/api/macos,windows,linux
+# pixi environments
+.pixi/*
+!.pixi/config.toml

{morphata-2.0.0 → morphata-2.0.1}/AGENTS.md

@@ -4,6 +4,14 @@
 It packages structural automaton representations together with semiring-valued
 *operators* that turn an automaton into a computable interpretation.
 
+## Development Environment
+
+The development shell already has the project virtual environment activated,
+so `pytest`, `mypy`, `ruff`, `sphinx-build`, etc. are on `PATH` directly.
+**Do not** prefix commands with `uv run`, `pixi run`, `poetry run`, or similar.
+Just invoke the tool. If a tool is missing, stop and tell the user rather than
+trying to bootstrap or reinstall the environment.
+
 ## Core Architecture
 
 ### IR layer (`morphata.automaton`, `morphata.alphabet`, `morphata.acceptance`)
@@ -85,6 +93,21 @@ delta - the transition consumes the labelled graph eagerly, so STREL
 automata are not symbolically liftable.  Operators: Reach, Escape,
 Somewhere, Everywhere.  Boolean-only.
 
+**`morphata.logic.sere.sere_to_automaton(expr)`** : SERE -> alternating
+finite automaton.  Supports ``Concat``, ``Fusion``, ``Repeat`` (bounded
+and unbounded), ``Inter``, ``Alt``, and Boolean leaves over AP.
+Acceptance is always ``Finite``; the accepting-state set is exactly
+the *nullable* states (those that match the empty word).
+
+**`morphata.logic.psl.psl_to_automaton(phi, *, finite=False)`** : PSL ->
+alternating automaton.  Wraps pure-LTL subformulas in an internal
+``_LTL`` tag and dispatches to the LTL expansion rule; closure
+operators (``{r}!``, ``{r}``, ``!{r}``, ``{r}<>-> f``, ``{r}[]-> f``)
+become their own tagged states with SERE-step expansion.  Suffix
+implications follow Spot's overlapping semantics: the last symbol of
+``r`` and the first position of ``f`` coincide.  ``finite=True`` ->
+``Finite`` acceptance (PSLf); ``finite=False`` -> ``Buchi``.
+
 Hand-written automata are built with ``AutomatonBuilder``; the package
 has no separate ``constructions`` namespace.
 
@@ -211,6 +234,18 @@ is backend-agnostic via `backend=`.
   sets of transitions. The HOA parser ingests ``{n}`` markers from
   ``State:`` declarations; per-edge ``{n}`` markers are ignored. Convert
   transition-based HOA files to state-based form before loading them.
+- ``psl_to_automaton`` requires the continuation of any
+  ``SuffixImpliesExist`` / ``SuffixImpliesUniv`` to be a pure-LTL
+  formula in v1.  Nested PSL closures inside a suffix-implication
+  continuation raise ``NotImplementedError``.  Likewise, LTL temporal
+  operators wrapping a PSL closure at the top level
+  (e.g. ``Always(StrongClosure(r))``) are not yet decomposed; lift the
+  PSL fragment out of the LTL temporal operator before calling.
+- The PSL Buchi acceptance classification is the natural per-tag rule
+  (strong-closure non-accepting, weak-closure accepting, etc.).  It has
+  not been cross-checked against a published reference for every
+  combination of operators; consult ``docs/superpowers/specs/`` before
+  relying on omega-language semantics in production.
 
 ## Testing
 
@@ -334,6 +369,10 @@ matrix_product = algebraic.matmul(arr1, arr2)
 - `src/morphata/builder.py` : ``AutomatonBuilder``.
 - `src/morphata/acceptance.py` : expression-based acceptance conditions.
 - `src/morphata/logic/ltl.py` : LTL/LTLf -> AFA conversion.
+- `src/morphata/logic/sere.py` : SERE -> AFA conversion.
+- `src/morphata/logic/psl.py` : PSL -> AFA conversion.
+- `src/morphata/logic/_common.py` : shared BDD scratch-space setup used
+  by all three logic converters.
 - `src/morphata/logic/strel.py` : STREL automaton (``Step`` delta).
 - `src/morphata/hoa/` : HOA v1 parser, exporter, grammar.
 - `src/morphata/operators/matrix.py` : ``MatrixOperator``.

{morphata-2.0.0 → morphata-2.0.1}/CHANGELOG.md

@@ -1,6 +1,49 @@
 # Changelog
 
-## 2.0.0 — [Unreleased]
+## Unreleased
+
+### Added
+
+- `morphata.logic.sere.sere_to_automaton(formula)` — converts a
+  SERE expression to an alternating finite automaton. Supports
+  `Concat`, `Fusion`, `Alt`, `Inter` (length-matching), `Repeat`
+  (bounded and unbounded), and Boolean leaves (`Literal`, `Variable`,
+  `Not`, `And`, `Or`).
+- `morphata.logic.psl.psl_to_automaton(phi, *, finite=False)` —
+  converts a PSL expression to an alternating automaton, with
+  `Finite` acceptance for PSLf (`finite=True`) and `Büchi` acceptance
+  for full PSL (`finite=False`). Supports the strong / weak /
+  negated-strong closure operators and existential / universal
+  suffix implication. Suffix implications follow Spot's overlapping
+  semantics: the last symbol matched by the SERE prefix is shared
+  with the first position at which the continuation is evaluated.
+
+### Changed
+
+- `morphata.logic.ltl` factored its per-call BDD scratch-space
+  construction into a shared helper
+  `morphata.logic._common.make_logic_context`, reused by the SERE
+  and PSL converters. Two LTL helpers (`_aut_symbolic_expansion`,
+  `_empty_trace_value`) were renamed to `ltl_symbolic_expansion` /
+  `ltl_empty_trace_value` so PSL can delegate to them for pure-LTL
+  subformulas.
+
+### Known limitations
+
+- `psl_to_automaton` does not yet decompose LTL temporal operators
+  that wrap PSL closures at the top level
+  (e.g. `Always(StrongClosure(r))`). Lift the PSL fragment out of
+  the surrounding LTL temporal operator before calling.
+- The continuation of a `SuffixImpliesExist` / `SuffixImpliesUniv`
+  must be a pure-LTL formula; nested PSL closures inside a
+  continuation raise `NotImplementedError`.
+- The Büchi acceptance classification for PSL has not been
+  cross-checked against a published reference for every operator
+  combination; finite-trace (PSLf) acceptance is exercised end-to-end
+  via `SymbolicAutomaton.accepts` and is high-confidence, but Büchi
+  is currently only smoke-tested for construction.
+
+## 2.0.0 — 2026-05-23
 
 The major version bump folds the old `automatix` package into `morphata`
 and replaces the constellation automata classes with a single typed intermediate

{morphata-2.0.0 → morphata-2.0.1}/CONTRIBUTING.md

@@ -6,24 +6,30 @@ The `justfile` defines a set of build, lint, and test commands, which can direct
 run as below:
 
 
+The examples below assume the project virtual environment is activated (either
+via `direnv` and `.envrc`, or by sourcing `.venv/bin/activate` manually). With
+the venv active the tools are on `PATH` directly; no `uv run` prefix is needed.
+If you'd rather not activate, prefix each command with `uv run --dev --frozen`
+(or use the `just` recipes, which handle this for you).
+
 **Testing** :
 ```bash
 # Run all tests (uses --lf for last-failed)
 just test
 # OR
-uv run --dev --frozen pytest --lf
+pytest --lf
 
 # Run all tests verbosely without --lf
-uv run --dev --frozen pytest -v
+pytest -v
 
 # Run a single test file
-uv run --dev --frozen pytest tests/test_weights.py -v
+pytest tests/test_alphabet.py -v
 
 # Run a single test function
-uv run --dev --frozen pytest tests/test_weights.py::TestWeightFunctionBasics::test_constant_weight_function -v
+pytest tests/test_alphabet.py::TestBooleanAlphabet::test_powerset_alphabet -v
 
 # Run with coverage
-uv run --dev --frozen pytest --cov=morphata --cov-report=term
+pytest --cov=morphata --cov-report=term
 ```
 
 **Linting and Formatting** :
@@ -31,8 +37,8 @@ uv run --dev --frozen pytest --cov=morphata --cov-report=term
 # Format and lint (fixes issues automatically)
 just fmt
 # OR
-uv run --frozen ruff format
-uv run --frozen ruff check --output-format concise --fix --exit-non-zero-on-fix
+ruff format
+ruff check --output-format concise --fix --exit-non-zero-on-fix
 
 # Format + type check
 just lint
@@ -44,9 +50,9 @@ just lint
 just type-check
 
 # Run specific type checkers
-uv run --frozen mypy --strict
-uv run --frozen ty check --output-format concise
-uv run --frozen pyrefly check --output-format min-text
+mypy --strict
+ty check --output-format concise
+pyrefly check --output-format min-text
 ```
 
 **Development Setup** :

{morphata-2.0.0 → morphata-2.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: morphata
-Version: 2.0.0
+Version: 2.0.1
 Summary: Representation theory for automata, made practical.
 Project-URL: Documentation, https://docs.anandb.dev/morphata
 Project-URL: Repository, https://git.anandb.dev/morphata.git
@@ -16,7 +16,7 @@ Requires-Dist: attrs>=25.4.0
 Requires-Dist: dd>=0.6.0
 Requires-Dist: jaxtyping>=0.3
 Requires-Dist: lark>=1.3.1
-Requires-Dist: logic-asts>=1.4.1
+Requires-Dist: logic-asts>=1.6.0
 Requires-Dist: networkx
 Requires-Dist: numpy
 Requires-Dist: types-networkx

{morphata-2.0.0 → morphata-2.0.1}/docs/api/modules.rst

@@ -13,6 +13,8 @@
    morphata.acceptance
    morphata.hoa
    morphata.logic.ltl
+   morphata.logic.sere
+   morphata.logic.psl
    morphata.logic.strel
    morphata.operators
    morphata.operators.matrix

morphata-2.0.1/docs/api/morphata.logic.psl.rst

@@ -0,0 +1,15 @@
+PSL
+===
+
+Property Specification Language to Alternating Automaton conversion.
+
+Finite-trace (PSLf) and omega-trace (Büchi) acceptance are both
+supported via the ``finite`` keyword argument to
+:func:`~morphata.logic.psl.psl_to_automaton`. Suffix implications
+follow Spot's overlapping semantics: the last symbol matched by the
+SERE prefix is shared with the first position at which the
+continuation is evaluated.
+
+.. automodule:: morphata.logic.psl
+   :members:
+   :show-inheritance:

morphata-2.0.1/docs/api/morphata.logic.sere.rst

@@ -0,0 +1,9 @@
+SERE
+====
+
+Sequential Extended Regular Expression to Alternating Finite Automaton
+conversion.
+
+.. automodule:: morphata.logic.sere
+   :members:
+   :show-inheritance:

{morphata-2.0.0 → morphata-2.0.1}/docs/conf.py

@@ -27,7 +27,7 @@ extensions = [
 ]
 
 templates_path = ["_templates"]
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "superpowers"]
 
 autodoc_default_options = {
     "members": True,

{morphata-2.0.0 → morphata-2.0.1}/docs/index.rst

@@ -30,6 +30,15 @@ Features
     automata.
   - LTL/LTLf to alternating Büchi / finite automata in
     :mod:`morphata.logic.ltl`.
+  - SERE (Sequential Extended Regular Expressions) to alternating
+    finite automata in :mod:`morphata.logic.sere`. Supports
+    concatenation, fusion, alternation, length-matching intersection,
+    bounded and unbounded repetition, and Boolean leaves.
+  - PSL (Property Specification Language) to alternating automata in
+    :mod:`morphata.logic.psl`. Both finite-trace (PSLf) and Büchi
+    semantics, covering strong / weak / negated-strong closures and
+    existential / universal suffix implication (Spot overlapping
+    semantics).
   - Spatio-Temporal Reach and Escape Logic (STREL) over labelled
     graphs in :mod:`morphata.logic.strel`.
 
@@ -128,4 +137,3 @@ For alternating weighted automata in multi-agent systems:
    symbolic-transforms
    concepts/index
    api/modules
-   changelog

morphata-2.0.1/justfile

@@ -0,0 +1,70 @@
+# Set shell options for safety
+
+set shell := ["bash", "-eu", "-o", "pipefail", "-c"]
+set unstable
+
+# If we want to use CUDA, the CUDA_VERSION variable should not be empty and contain the
+# version number (either 12 or 13)
+
+CUDA_VERSION := env("CUDA_VERSION", "12")
+[private]
+_env := if which("nvidia-smi") == "" { "default" } else { "cu" + CUDA_VERSION }
+PIXI_ENV := env("PIXI_ENV", _env)
+DEFAULT_PIXI_ARGS := "--environment " + PIXI_ENV
+
+export PIXI_FROZEN := env("PIXI_FROZEN", "true")
+
+# Default: create the dev environment
+default: dev
+
+# Set up development environment
+dev: sync-venv
+
+# Format and lint code
+[no-cd]
+fmt:
+    ruff format
+    ruff check --output-format concise --fix --exit-non-zero-on-fix .
+
+# Run type checkers
+[no-cd]
+[private]
+ty-check:
+    ty check --output-format concise
+
+[no-cd]
+[private]
+pyrefly-check:
+    pyrefly check --output-format min-text
+
+[no-cd]
+[private]
+mypy-check:
+    mypy --strict
+
+[no-cd]
+[private]
+pyright-check:
+    basedpyright
+
+# [parallel]
+type-check: mypy-check
+
+# pyright-check
+# ty-check pyrefly-check
+
+# Run both formatting and type checking
+[no-cd]
+lint: fmt type-check
+
+# Run tests
+[no-cd]
+test:
+    pytest --lf
+
+docs:
+    sphinx-build -b html docs/ docs/_build/html
+
+# Sync virtual environment
+sync-venv:
+    pixi install {{ DEFAULT_PIXI_ARGS }}