synkit 1.6.1__tar.gz → 1.6.2b1__tar.gz

{synkit-1.6.1 → synkit-1.6.2b1}/.gitignore

@@ -106,3 +106,7 @@ Experiment/Lewis/FLOWER/replay-results*/
 # Keep generated Python bytecode ignored after directory re-inclusions above.
 **/__pycache__/
 *.py[cod]
+
+# RBL long-run checkpoints are resumable local state, not retained evidence.
+Experiment/RBL/*checkpoint*.jsonl
+request.md

{synkit-1.6.1 → synkit-1.6.2b1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: synkit
-Version: 1.6.1
+Version: 1.6.2b1
 Summary: Utility for reaction modeling using graph grammar
 Project-URL: homepage, https://github.com/TieuLongPhan/SynKit
 Project-URL: source, https://github.com/TieuLongPhan/SynKit

{synkit-1.6.1 → synkit-1.6.2b1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "synkit"
-version = "1.6.1"
+version = "1.6.2b1"
 description = "Utility for reaction modeling using graph grammar"
 readme = "README.md"
 requires-python = ">=3.11"
@@ -39,7 +39,7 @@ docs = [
   "pydata-sphinx-theme",
   "sphinx-rtd-theme",
 
-  # Your enabled extensions
+  # Sphinx extensions
   "sphinxcontrib-bibtex",
   "sphinx-design",
   "sphinx-copybutton",
@@ -49,8 +49,7 @@ docs = [
   # (still requires the system `dot` binary to render diagrams)
   "graphviz",
 
-  # Nice-to-have for markdown in docs if you ever add .md pages
-  # (safe even if unused)
+  # Markdown source support
   "myst-parser",
 ]
 
@@ -63,12 +62,14 @@ documentation = "https://tieulongphan.github.io/SynKit/"
 
 [tool.hatch.build.targets.wheel]
 packages = ["synkit"]
+core-metadata-version = "2.4"
 
 [tool.hatch.build.targets.wheel.force-include]
 "synkit/Data/aldol.json.gz" = "synkit/Data/aldol.json.gz"
 "synkit/Data/paracetamol.json.gz" = "synkit/Data/paracetamol.json.gz"
 
 [tool.hatch.build.targets.sdist]
+core-metadata-version = "2.4"
 include = [
   "/synkit",
   "/LICENSE",
@@ -80,3 +81,11 @@ include = [
 [tool.hatch.build.targets.sdist.force-include]
 "synkit/Data/aldol.json.gz" = "synkit/Data/aldol.json.gz"
 "synkit/Data/paracetamol.json.gz" = "synkit/Data/paracetamol.json.gz"
+
+[tool.coverage.run]
+source = ["synkit"]
+
+[tool.coverage.report]
+fail_under = 70
+precision = 1
+show_missing = true

{synkit-1.6.1 → synkit-1.6.2b1}/synkit/CRN/Construct/DAG/syncrn.py

@@ -8,7 +8,7 @@ from itertools import combinations
 
 import networkx as nx
 
-from synkit.Synthesis.Reactor.syn_reactor import SynReactor
+from synkit.Synthesis.Reactor import SynReactor
 
 logger = logging.getLogger(__name__)
 

{synkit-1.6.1 → synkit-1.6.2b1}/synkit/CRN/Construct/abstract.py

@@ -10,8 +10,7 @@ ReactionSides = Tuple[List[str], List[str]]
 
 
 def _split_reaction_smiles(reaction_smiles: str) -> ReactionSides:
-    """
-    Split a reaction SMILES string into reactant and product molecule lists.
+    """Split a reaction SMILES string into reactant and product molecule lists.
 
     The expected format is ``"A.B>>C.D"``. Empty left or right sides are allowed.
 
@@ -19,15 +18,15 @@ def _split_reaction_smiles(reaction_smiles: str) -> ReactionSides:
         Reaction SMILES string.
     :type reaction_smiles: str
 
-    :returns:
+    :return:
         Tuple of reactant and product molecule lists.
     :rtype: Tuple[List[str], List[str]]
 
     :raises ValueError:
         If the reaction string does not contain ``">>"``.
 
-    Example
-    -------
+    .. rubric:: Example
+
     .. code-block:: python
 
         reactants, products = _split_reaction_smiles("CCO.O>>CC=O")
@@ -43,8 +42,7 @@ def _split_reaction_smiles(reaction_smiles: str) -> ReactionSides:
 
 
 def _excel_label(index: int) -> str:
-    """
-    Convert a zero-based integer index into an Excel-style alphabetic label.
+    """Convert a zero-based integer index into an Excel-style alphabetic label.
 
     Examples include ``0 -> "A"``, ``25 -> "Z"``, and ``26 -> "AA"``.
 
@@ -52,15 +50,15 @@ def _excel_label(index: int) -> str:
         Zero-based index.
     :type index: int
 
-    :returns:
+    :return:
         Excel-style alphabetic label.
     :rtype: str
 
     :raises ValueError:
         If ``index`` is negative.
 
-    Example
-    -------
+    .. rubric:: Example
+
     .. code-block:: python
 
         label = _excel_label(27)   # "AB"
@@ -77,19 +75,18 @@ def _excel_label(index: int) -> str:
 
 
 def _normalize_abstract_side(side: str) -> List[str]:
-    """
-    Normalize one abstract reaction side by splitting on ``"+"`` and sorting tokens.
+    """Normalize one abstract reaction side by splitting on ``"+"`` and sorting tokens.
 
     :param side:
         Abstract reaction side.
     :type side: str
 
-    :returns:
+    :return:
         Sorted abstract token list.
     :rtype: List[str]
 
-    Example
-    -------
+    .. rubric:: Example
+
     .. code-block:: python
 
         tokens = _normalize_abstract_side("B+A+C")
@@ -101,8 +98,7 @@ def _first_present(
     record: Mapping[str, Any],
     keys: Sequence[str],
 ) -> Optional[Any]:
-    """
-    Return the first non-``None`` value found in a mapping for the given keys.
+    """Return the first non-``None`` value found in a mapping for the given keys.
 
     :param record:
         Input mapping.
@@ -112,12 +108,12 @@ def _first_present(
         Candidate keys to try in order.
     :type keys: Sequence[str]
 
-    :returns:
+    :return:
         First matching value, or ``None`` if none are present.
     :rtype: Optional[Any]
 
-    Example
-    -------
+    .. rubric:: Example
+
     .. code-block:: python
 
         value = _first_present(record, ["smiles", "reaction", "rxn_smiles"])
@@ -129,8 +125,7 @@ def _first_present(
 
 
 def deduplicate_abstract_reactions(reactions: Sequence[str]) -> List[str]:
-    """
-    Remove identity reactions and duplicate abstract reactions.
+    """Remove identity reactions and duplicate abstract reactions.
 
     Reactant and product order are normalized internally before comparison.
     The original retained representative is the first encountered entry.
@@ -139,12 +134,12 @@ def deduplicate_abstract_reactions(reactions: Sequence[str]) -> List[str]:
         Abstract reactions such as ``"A+B>>C+D"``.
     :type reactions: Sequence[str]
 
-    :returns:
+    :return:
         Filtered abstract reactions.
     :rtype: List[str]
 
-    Example
-    -------
+    .. rubric:: Example
+
     .. code-block:: python
 
         filtered = deduplicate_abstract_reactions(
@@ -203,15 +198,14 @@ class AbstractReactionNetwork:
     label_to_molecule: Dict[str, str] = field(default_factory=dict)
 
     def to_dict(self) -> Dict[str, Any]:
-        """
-        Convert the abstract network to a plain dictionary.
+        """Convert the abstract network to a plain dictionary.
 
-        :returns:
+        :return:
             Dictionary representation of the abstract network.
         :rtype: Dict[str, Any]
 
-        Example
-        -------
+        .. rubric:: Example
+
         .. code-block:: python
 
             payload = network.to_dict()
@@ -226,19 +220,18 @@ class AbstractReactionNetwork:
     def to_json_payload(
         self, name: str = "abstract_reaction_network"
     ) -> Dict[str, Any]:
-        """
-        Convert the abstract network into a SynKit-style JSON payload.
+        """Convert the abstract network into a SynKit-style JSON payload.
 
         :param name:
             Name stored in the metadata block.
         :type name: str
 
-        :returns:
+        :return:
             JSON-serializable payload.
         :rtype: Dict[str, Any]
 
-        Example
-        -------
+        .. rubric:: Example
+
         .. code-block:: python
 
             payload = network.to_json_payload(name="glycolysis_abstract")
@@ -256,8 +249,7 @@ class AbstractReactionNetwork:
         }
 
     def save_json(self, path: PathLike, *, name: Optional[str] = None) -> None:
-        """
-        Save the abstract network as a JSON file.
+        """Save the abstract network as a JSON file.
 
         :param path:
             Output JSON path.
@@ -267,12 +259,12 @@ class AbstractReactionNetwork:
             Optional metadata name. If omitted, the filename stem is used.
         :type name: Optional[str]
 
-        :returns:
+        :return:
             ``None``
         :rtype: None
 
-        Example
-        -------
+        .. rubric:: Example
+
         .. code-block:: python
 
             network.save_json("abstract_network.json")
@@ -286,15 +278,14 @@ class AbstractReactionNetwork:
 
 @dataclass
 class AbstractReactionExtractor:
-    """
-    Build abstract symbolic reaction networks from reaction SMILES lists or
+    """Build abstract symbolic reaction networks from reaction SMILES lists or
     SynKit-style module/pathway JSON blocks.
 
     This class supports configurable field names when extracting reactions from
     JSON-like input records.
 
-    Example
-    -------
+    .. rubric:: Example
+
     .. code-block:: python
 
         extractor = KEGGExtractor()
@@ -316,24 +307,23 @@ class AbstractReactionExtractor:
         self,
         data: Mapping[str, Any],
     ) -> Iterable[Tuple[Mapping[str, Any], str]]:
-        """
-        Iterate over reaction records from a module-like or pathway-like JSON block.
+        """Iterate over reaction records from a module-like or pathway-like JSON block.
 
         Supported structures include:
 
-        - module-like: ``{"reactions": [...]}`
+        - module-like: ``{"reactions": [...]}``
         - pathway-like: ``{"by_module": {"M00001": {"reactions": [...]}, ...}}``
 
         :param data:
             Input JSON-like mapping.
         :type data: Mapping[str, Any]
 
-        :yields:
+        :yield:
             Tuples of ``(reaction_record, module_id)``.
         :rtype: Iterable[Tuple[Mapping[str, Any], str]]
 
-        Example
-        -------
+        .. rubric:: Example
+
         .. code-block:: python
 
             abstractor = AbstractReactionExtractor()
@@ -366,8 +356,7 @@ class AbstractReactionExtractor:
         reaction_smiles_keys: Optional[Sequence[str]] = None,
         template_keys: Optional[Sequence[str]] = None,
     ) -> Tuple[List[str], Dict[str, str]]:
-        """
-        Extract reaction SMILES and rule-template mappings from raw inputs.
+        """Extract reaction SMILES and rule-template mappings from raw inputs.
 
         Either a direct list of reaction SMILES or a JSON data block may be
         provided. If both are given, the explicit ``reactions`` list takes
@@ -412,12 +401,12 @@ class AbstractReactionExtractor:
             record. The keys are tried in order.
         :type template_keys: Optional[Sequence[str]]
 
-        :returns:
+        :return:
             Tuple of reaction SMILES list and template mapping.
         :rtype: Tuple[List[str], Dict[str, str]]
 
-        Example
-        -------
+        .. rubric:: Example
+
         .. code-block:: python
 
             extractor = KEGGExtractor()
@@ -480,8 +469,7 @@ class AbstractReactionExtractor:
         *,
         order: str = "appearance",
     ) -> List[str]:
-        """
-        Build the unique molecule pool from parsed reactions.
+        """Build the unique molecule pool from parsed reactions.
 
         :param parsed_reactions:
             Parsed reaction sides as ``(reactants, products)`` tuples.
@@ -492,15 +480,15 @@ class AbstractReactionExtractor:
             ``"sorted"``.
         :type order: str
 
-        :returns:
+        :return:
             Ordered unique molecule pool.
         :rtype: List[str]
 
         :raises ValueError:
             If ``order`` is not supported.
 
-        Example
-        -------
+        .. rubric:: Example
+
         .. code-block:: python
 
             molecule_pool = abstractor.build_molecule_pool(
@@ -544,8 +532,7 @@ class AbstractReactionExtractor:
         template_keys: Optional[Sequence[str]] = None,
         save_as: Optional[PathLike] = None,
     ) -> AbstractReactionNetwork:
-        """
-        Convert full reaction SMILES into an abstract symbolic reaction network.
+        """Convert full reaction SMILES into an abstract symbolic reaction network.
 
         You may provide either a direct list of reaction SMILES or a module/pathway
         JSON block.
@@ -607,12 +594,12 @@ class AbstractReactionExtractor:
             Optional JSON output path.
         :type save_as: Optional[PathLike]
 
-        :returns:
+        :return:
             Abstract symbolic reaction network.
         :rtype: AbstractReactionNetwork
 
-        Example
-        -------
+        .. rubric:: Example
+
         .. code-block:: python
 
             extractor = KEGGExtractor()

{synkit-1.6.1 → synkit-1.6.2b1}/synkit/CRN/Construct/worker.py

@@ -2,7 +2,7 @@ from __future__ import annotations
 
 from typing import Any, List, Optional, Set, Tuple
 
-from synkit.Synthesis.Reactor.syn_reactor import SynReactor
+from synkit.Synthesis.Reactor import SynReactor
 
 
 def apply_rule_worker(

{synkit-1.6.1 → synkit-1.6.2b1}/synkit/CRN/Pathway/_adapter.py

@@ -6,8 +6,7 @@ from ..Petrinet.net import SynCRNIncidence, extract_syncrn_incidence
 
 
 def _species_token(incidence: SynCRNIncidence, sid: str, mode: str) -> str:
-    """
-    Convert an internal species identifier into an external token.
+    """Convert an internal species identifier into an external token.
 
     Supported tokenization modes are:
 
@@ -27,15 +26,15 @@ def _species_token(incidence: SynCRNIncidence, sid: str, mode: str) -> str:
         Tokenization mode. Must be one of ``"id"``, ``"label"``, or ``"source"``.
     :type mode: str
 
-    :returns:
+    :return:
         Token representing the species.
     :rtype: str
 
     :raises ValueError:
         If ``mode`` is not one of the supported values.
 
-    Examples
-    --------
+    .. rubric:: Examples
+
     .. code-block:: python
 
         tok = _species_token(incidence, "s1", mode="label")
@@ -51,8 +50,7 @@ def _species_token(incidence: SynCRNIncidence, sid: str, mode: str) -> str:
 
 
 def _reaction_token(incidence: SynCRNIncidence, rid: str, mode: str) -> str:
-    """
-    Convert an internal reaction identifier into an external token.
+    """Convert an internal reaction identifier into an external token.
 
     Supported tokenization modes are:
 
@@ -72,15 +70,15 @@ def _reaction_token(incidence: SynCRNIncidence, rid: str, mode: str) -> str:
         Tokenization mode. Must be one of ``"id"``, ``"label"``, or ``"source"``.
     :type mode: str
 
-    :returns:
+    :return:
         Token representing the reaction.
     :rtype: str
 
     :raises ValueError:
         If ``mode`` is not one of the supported values.
 
-    Examples
-    --------
+    .. rubric:: Examples
+
     .. code-block:: python
 
         tok = _reaction_token(incidence, "r1", mode="id")
@@ -96,8 +94,7 @@ def _reaction_token(incidence: SynCRNIncidence, rid: str, mode: str) -> str:
 
 
 def _assert_unique_tokens(tokens: Mapping[str, str], *, kind: str) -> None:
-    """
-    Validate that exported tokens are unique.
+    """Validate that exported tokens are unique.
 
     This prevents ambiguous reverse mapping from public tokens back to internal
     identifiers.
@@ -111,7 +108,7 @@ def _assert_unique_tokens(tokens: Mapping[str, str], *, kind: str) -> None:
         ``"reaction"``.
     :type kind: str
 
-    :returns:
+    :return:
         ``None``.
     :rtype: None
 
@@ -133,8 +130,7 @@ def _build_species_token_map(
     *,
     species: str,
 ) -> Dict[str, str]:
-    """
-    Build the mapping from internal species ids to exported species tokens.
+    """Build the mapping from internal species ids to exported species tokens.
 
     :param incidence:
         Canonical SynCRN incidence object.
@@ -144,7 +140,7 @@ def _build_species_token_map(
         Species tokenization mode.
     :type species: str
 
-    :returns:
+    :return:
         Mapping ``internal_species_id -> exported_species_token``.
     :rtype: Dict[str, str]
     """
@@ -158,8 +154,7 @@ def _build_reaction_token_map(
     *,
     reaction: str,
 ) -> Dict[str, str]:
-    """
-    Build the mapping from internal reaction ids to exported reaction tokens.
+    """Build the mapping from internal reaction ids to exported reaction tokens.
 
     :param incidence:
         Canonical SynCRN incidence object.
@@ -169,7 +164,7 @@ def _build_reaction_token_map(
         Reaction tokenization mode.
     :type reaction: str
 
-    :returns:
+    :return:
         Mapping ``internal_reaction_id -> exported_reaction_token``.
     :rtype: Dict[str, str]
     """
@@ -183,8 +178,7 @@ def _tokenize_reaction_multiset(
     coeffs: Mapping[str, int],
     species_map: Mapping[str, str],
 ) -> Dict[str, int]:
-    """
-    Convert one incidence-side multiset from internal species ids to tokens.
+    """Convert one incidence-side multiset from internal species ids to tokens.
 
     :param coeffs:
         Mapping ``internal_species_id -> stoichiometric_coefficient``.
@@ -194,7 +188,7 @@ def _tokenize_reaction_multiset(
         Mapping ``internal_species_id -> exported_species_token``.
     :type species_map: Mapping[str, str]
 
-    :returns:
+    :return:
         Mapping ``exported_species_token -> stoichiometric_coefficient``.
     :rtype: Dict[str, int]
     """
@@ -206,8 +200,7 @@ def _build_tokenized_edges(
     species_map: Mapping[str, str],
     reaction_map: Mapping[str, str],
 ) -> Dict[str, Tuple[Dict[str, int], Dict[str, int]]]:
-    """
-    Build tokenized reaction edges.
+    """Build tokenized reaction edges.
 
     Each reaction token maps to a pair ``(tail, head)``, where ``tail`` and
     ``head`` are tokenized stoichiometric multisets for reactants and products.
@@ -224,7 +217,7 @@ def _build_tokenized_edges(
         Mapping ``internal_reaction_id -> exported_reaction_token``.
     :type reaction_map: Mapping[str, str]
 
-    :returns:
+    :return:
         Mapping
         ``reaction_token -> (reactant_multiset, product_multiset)``.
     :rtype: Dict[str, Tuple[Dict[str, int], Dict[str, int]]]
@@ -239,14 +232,13 @@ def _build_tokenized_edges(
 
 
 def _invert_token_map(token_map: Mapping[str, str]) -> Dict[str, str]:
-    """
-    Invert an internal-id to token mapping.
+    """Invert an internal-id to token mapping.
 
     :param token_map:
         Mapping ``internal_id -> token``.
     :type token_map: Mapping[str, str]
 
-    :returns:
+    :return:
         Mapping ``token -> internal_id``.
     :rtype: Dict[str, str]
     """
@@ -265,8 +257,7 @@ def tokenize_syncrn_incidence(
     Dict[str, str],
     SynCRNIncidence,
 ]:
-    """
-    Convert SynCRN incidence into tokenized vertex and edge dictionaries.
+    """Convert SynCRN incidence into tokenized vertex and edge dictionaries.
 
     The returned objects are designed for downstream algorithms that prefer
     stable public-facing tokens over internal SynCRN identifiers.
@@ -285,7 +276,7 @@ def tokenize_syncrn_incidence(
         ``"source"``.
     :type reaction: str
 
-    :returns:
+    :return:
         Tuple containing:
 
         - ``vertices``:
@@ -311,8 +302,8 @@ def tokenize_syncrn_incidence(
     :raises ValueError:
         If species or reaction tokenization produces non-unique exported tokens.
 
-    Examples
-    --------
+    .. rubric:: Examples
+
     .. code-block:: python
 
         vertices, edges, s_tok2id, r_tok2id, incidence = tokenize_syncrn_incidence(