Introduce LSG

.github/dependabot.yml

@@ -1,10 +1,79 @@
-# .github/dependabot.yml
 version: 2
+
 updates:
   - package-ecosystem: "pip"
-    directory: "/"                # location of requirements.txt or pyproject.toml
-    target-branch: "staging"      # open PRs against staging instead of main
+    directory: "/"
+    target-branch: "staging"
     schedule:
-      interval: "weekly"          # check for updates once a week
-    open-pull-requests-limit: 5   # max concurrent Dependabot PRs
-    rebase-strategy: "auto"       # auto-rebase PRs when they fall out of date
+      interval: "weekly"
+      day: "monday"
+      time: "04:00"
+      timezone: "Etc/UTC"
+    open-pull-requests-limit: 5
+    rebase-strategy: "auto"
+    labels:
+      - "dependencies"
+      - "python"
+    commit-message:
+      prefix: "deps"
+      include: "scope"
+    groups:
+      python-runtime:
+        patterns:
+          - "networkx"
+          - "pandas"
+          - "rdkit"
+          - "regex"
+          - "requests"
+          - "scikit-learn"
+          - "seaborn"
+      python-optional:
+        patterns:
+          - "numpy"
+          - "sympy"
+          - "torch"
+      docs:
+        patterns:
+          - "sphinx*"
+          - "pydata-sphinx-theme"
+          - "sphinx-rtd-theme"
+          - "graphviz"
+          - "myst-parser"
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    target-branch: "staging"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+      time: "04:30"
+      timezone: "Etc/UTC"
+    open-pull-requests-limit: 5
+    rebase-strategy: "auto"
+    labels:
+      - "dependencies"
+      - "github-actions"
+    commit-message:
+      prefix: "ci"
+      include: "scope"
+    groups:
+      github-actions:
+        patterns:
+          - "*"
+
+  - package-ecosystem: "docker"
+    directory: "/"
+    target-branch: "staging"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+      time: "05:00"
+      timezone: "Etc/UTC"
+    open-pull-requests-limit: 2
+    rebase-strategy: "auto"
+    labels:
+      - "dependencies"
+      - "docker"
+    commit-message:
+      prefix: "deps"
+      include: "scope"

.github/workflows/conda-forge-publish.yml

@@ -21,13 +21,14 @@ jobs:
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
+          miniconda-version: "latest"
           channels: conda-forge
           auto-update-conda: true
           auto-activate-base: true
@@ -53,13 +54,14 @@ jobs:
       pkg_paths: ${{ steps.build.outputs.paths }}
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
+          miniconda-version: "latest"
           channels: conda-forge
           auto-update-conda: true
           auto-activate-base: true

.github/workflows/docker-publish.yml

@@ -20,16 +20,16 @@ jobs:
 
     steps:
       - name: Check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up QEMU (optional, for multi‑arch)
         uses: docker/setup-qemu-action@v3
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
 
       - name: Log in to Docker Hub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USER }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}

.github/workflows/test-and-lint.yml

@@ -2,7 +2,7 @@ name: Test & Lint
 
 on:
   push:
-    branches: [ "main", "staging", "fix_query" ]
+    branches: [ "main", "staging", "mech" ]
   pull_request:
     branches: [ "main" ]
 
@@ -20,11 +20,11 @@ jobs:
 
     steps:
       # 0) Check out the code
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       # 1) Install Miniconda (downloaded — the “bundled” version was removed)
       - name: Set up Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniconda-version: "latest"      # <<–‑‑ mandatory or the action fails
           python-version: "3.11"

.github/workflows/verify-pypi-install.yml

@@ -1,65 +1,96 @@
-# .github/workflows/verify-synkit-pypi-install.yml
-name: Verify SynKit PyPI install
+name: Verify PyPI install
 
 on:
   workflow_dispatch:
     inputs:
-      branches:
+      package-version:
+        description: "Optional exact SynKit version to install, for example 1.4.0"
+        required: false
         type: string
-        required: true
-        default: refractor
-
-  # Scheduled test every Monday at 03:00 UTC
   schedule:
-    - cron: '0 3 * * 1'
+    - cron: "0 3 * * 1"
+
+permissions:
+  contents: read
+
+concurrency:
+  group: verify-pypi-install-${{ github.event_name }}-${{ github.event.inputs['package-version'] || 'latest' }}
+  cancel-in-progress: false
 
 jobs:
   verify:
-    name: Verify PyPI install on ${{ matrix.os }}
+    name: ${{ matrix.os }} / Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.11", "3.12"]
 
     steps:
-      - name: Setup Python
-        uses: actions/setup-python@v4
+      - name: Set up Python
+        uses: actions/setup-python@v6
         with:
-          python-version: '3.x'
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
 
-      - name: Create & activate virtualenv, upgrade pip, install SynKit
+      - name: Install SynKit from PyPI
+        shell: bash
         run: |
-          python -m venv venv
-          source venv/bin/activate
           python -m pip install --upgrade pip
-          pip install synkit[all]
 
-      - name: Show installed SynKit version
+          version="${{ github.event.inputs['package-version'] }}"
+          if [ -n "$version" ]; then
+            python -m pip install "synkit==$version"
+          else
+            python -m pip install synkit
+          fi
+          python -m pip install packaging
+
+      - name: Show installed package metadata
+        shell: bash
         run: |
-          source venv/bin/activate
-          python -c "import importlib.metadata as m; print('SynKit version:', m.version('synkit'))"
+          python - <<'PY'
+          import importlib.metadata as metadata
+          import sys
+
+          print("Python:", sys.version)
+          print("SynKit:", metadata.version("synkit"))
+          PY
 
-      - name: Write smoke-test script
+      - name: Run import and smoke tests
+        shell: bash
         run: |
-          cat << 'EOF' > test_synkit.py
-          from synkit.IO import rsmi_to_rsmarts
+          python - <<'PY'
+          import importlib.metadata as metadata
 
-          template = (
-              '[C:2]=[O:3].[C:4]([H:7])[H:8]'
-              '>>'
-              '[C:2]=[C:4].[O:3]([H:7])[H:8]'
-          )
+          from packaging.version import Version
 
-          smart = rsmi_to_rsmarts(template)
-          print("Reaction SMARTS:", smart)
-          EOF
+          from synkit.IO import rsmi_to_its, rsmi_to_rsmarts
 
-      - name: Run smoke-test
-        run: |
-          source venv/bin/activate
-          python test_synkit.py
+          rsmi = "[CH3:1][Cl:2].[NH3:3]>>[CH3:1][NH3+:3].[Cl-:2]"
+          smarts = rsmi_to_rsmarts(rsmi)
+          assert ">>" in smarts
+
+          version = Version(metadata.version("synkit"))
+          if version >= Version("1.4.0"):
+            import networkx as nx
+
+            from synkit.Graph.MTG.mtg import MTG
+
+            its = rsmi_to_its(rsmi, core=False, format="tuple")
+            assert isinstance(its, nx.Graph)
+            assert not any("typesGH" in attrs for _, attrs in its.nodes(data=True))
+
+            mtg_steps = [
+              "[CH3:1][Cl:2].[NH3:3]>>[CH3:1][NH3+:3].[Cl-:2]",
+              "[CH3:1][NH3+:3].[Cl-:2]>>[CH3:1][NH2:3].[Cl:2][H]",
+            ]
+            mtg = MTG(mtg_steps, mcs_mol=True)
+            graph = mtg.get_mtg()
+            assert mtg._tuple_its
+            assert graph.number_of_nodes() > 0
 
-      - name: Success message
-        run: echo "✅ synkit[all] installed and smoke-test passed"
+          print("PyPI SynKit smoke tests passed.")
+          PY

.gitignore

@@ -32,3 +32,8 @@ synkit/Graph/dev/*
 *.json
 *.txt
 *.log
+sprint/
+test_syn.py
+.gitignore
+measure_candidate_stages.py
+run_valid_bug_cases.py

Test/CRN/Props/test_dynamics.py

@@ -206,6 +206,9 @@ def test_jacobian_pattern_bipartite(self) -> None:
         self.assertTrue(B.has_edge("row:1", "col:1"))
 
 
+@unittest.skipUnless(
+    dynamics._SYMPY_AVAILABLE, "sympy is required for symbolic dynamics tests"
+)
 class TestDynamicsMatrices(unittest.TestCase):
     def test_symbolic_reactivity_matrix_cycle(self) -> None:
         G = make_cycle_crn()
@@ -429,6 +432,9 @@ def test_to_dict_and_str(self) -> None:
         self.assertIn("classification", text)
 
 
+@unittest.skipUnless(
+    dynamics._SYMPY_AVAILABLE, "sympy is required for exact singularity tests"
+)
 class TestStructuralSingularitySummary(unittest.TestCase):
     def test_single_step_is_singular_by_pattern(self) -> None:
         G = make_single_step_crn()

Test/Graph/FG/__init__.py

@@ -0,0 +1 @@
+

Test/Graph/FG/test_api.py

@@ -0,0 +1,24 @@
+import pytest
+
+from synkit.Graph.FG import smiles_to_graph_and_functional_groups
+
+
+def test_smiles_to_graph_and_functional_groups_supports_unmapped_smiles():
+    graph, groups = smiles_to_graph_and_functional_groups("CC(=O)O")
+
+    assert tuple(graph.nodes) == (1, 2, 3, 4)
+    assert groups == [("carboxylic_acid", (2, 3, 4))]
+
+
+def test_smiles_to_graph_and_functional_groups_preserves_atom_map_node_ids():
+    graph, groups = smiles_to_graph_and_functional_groups(
+        "[CH3:10][C:20](=[O:30])[OH:40]"
+    )
+
+    assert tuple(graph.nodes) == (10, 20, 30, 40)
+    assert groups == [("carboxylic_acid", (20, 30, 40))]
+
+
+def test_smiles_to_graph_and_functional_groups_rejects_invalid_smiles():
+    with pytest.raises(ValueError):
+        smiles_to_graph_and_functional_groups("not_smiles")

Test/Graph/FG/test_audit.py

@@ -0,0 +1,21 @@
+from synkit.Graph.FG.audit import audit_reaction_smiles
+
+
+def test_audit_reaction_smiles_summarizes_small_corpus():
+    report = audit_reaction_smiles(
+        [
+            "CCO>>CC=O",
+            "c1ncnnc1>>c1ncnnc1",
+        ]
+    )
+
+    assert report.reactions == 2
+    assert report.molecules == 4
+    assert report.parse_failures == 0
+    assert report.label_counts["primary_alcohol"] == 1
+    assert report.label_counts["aldehyde"] == 1
+    assert report.label_counts["heteroaromatic_ring"] == 2
+    assert report.label_counts["triazine"] == 2
+    assert report.heteroaromatic_systems == 2
+    assert report.named_heteroaromatic_systems == 2
+    assert report.unnamed_heteroaromatic_count == 0