prepare release

Author: TieuLongPhan

.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-    rebase-strategy: "auto"       # auto-rebase PRs when they fall out of date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/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

Test/Graph/MTG/test_mtg_tuple.py

@@ -299,6 +299,32 @@ def test_mech_fixture_round_trips_ordered_tuple_rsmi_steps(self):
         self.assertEqual(len(exported), len(steps))
         self.assertTrue(all(">>" in step for step in exported))
 
+    def test_string_sequences_default_to_lewis_state_graph(self):
+        data = load_database("./Data/Testcase/mech.json.gz")
+        mech = data[0]["mechanisms"][1]
+        steps = [step["smart_string"] for step in mech["steps"]]
+
+        mtg = MTG(steps, mcs_mol=True)
+        graph = mtg.get_mtg()
+
+        self.assertTrue(mtg._tuple_its)
+        self.assertFalse(any("typesGH" in attrs for _, attrs in graph.nodes(data=True)))
+        self.assertTrue(
+            all("sigma_order" in attrs for _, _, attrs in graph.edges(data=True))
+        )
+
+    def test_string_sequences_can_request_legacy_typesgh(self):
+        data = load_database("./Data/Testcase/mech.json.gz")
+        mech = data[0]["mechanisms"][1]
+        steps = [step["smart_string"] for step in mech["steps"][:2]]
+
+        mtg = MTG(steps, mcs_mol=True, its_format="typesGH")
+
+        self.assertFalse(mtg._tuple_its)
+        self.assertTrue(
+            any("typesGH" in attrs for _, attrs in mtg.get_mtg().nodes(data=True))
+        )
+
     def test_mech_fixture_tuple_mtg_automatic_mapping_matches_identity_mapping(self):
         data = load_database("./Data/Testcase/mech.json.gz")
         mech = data[0]["mechanisms"][1]

Test/Vis/test_mtg_drawer.py

@@ -7,7 +7,12 @@
 
 from synkit.Graph.ITS.its_construction import ITSConstruction  # noqa: E402
 from synkit.Graph.MTG.mtg import MTG  # noqa: E402
-from synkit.Vis.mtg_drawer import draw_mtg_graph, draw_mtg_steps  # noqa: E402
+from synkit.IO import load_database  # noqa: E402
+from synkit.Vis.mtg_drawer import (  # noqa: E402
+    _mtg_display_graph,
+    draw_mtg_graph,
+    draw_mtg_steps,
+)
 
 
 class TestMTGDrawer(unittest.TestCase):
@@ -88,19 +93,73 @@ def test_draw_mtg_graph_accepts_raw_graph_without_mutation(self):
         self.assertEqual(dict(graph.nodes(data=True)), before_nodes)
         self.assertEqual(list(graph.edges(data=True)), before_edges)
 
+    def test_draw_mtg_graph_supports_3d_layout(self):
+        mtg = self._mtg()
+
+        fig, ax = draw_mtg_graph(mtg, dimension="3d", layout="spring")
+
+        self.assertIs(fig, ax.figure)
+        self.assertEqual(getattr(ax, "name", None), "3d")
+
+    def test_mtg_edge_labels_compress_by_default(self):
+        graph = self._mtg().get_mtg()
+
+        compact = _mtg_display_graph(
+            graph,
+            mode="timeline",
+            show_atom_map=True,
+            show_node_badges=False,
+            hydrogen_mode="changed",
+            changed_only=True,
+            compress=True,
+        )
+        full = _mtg_display_graph(
+            graph,
+            mode="timeline",
+            show_atom_map=True,
+            show_node_badges=False,
+            hydrogen_mode="changed",
+            changed_only=True,
+            compress=False,
+        )
+
+        self.assertEqual(compact.edges[1, 2]["label"], "1→1")
+        self.assertEqual(full.edges[1, 2]["label"], "1→0→1")
+
     def test_draw_mtg_steps_draws_ordered_its_panels_and_composed_panel(self):
         mtg = self._mtg()
 
         fig, axes = draw_mtg_steps(mtg, include_composed=True, show_edge_labels=True)
 
         self.assertIs(fig, axes[0].figure)
         self.assertEqual(len(axes), 3)
-        self.assertEqual([ax.get_title() for ax in axes], ["Step 1", "Step 2", "Composed"])
+        self.assertEqual(
+            [ax.get_title() for ax in axes], ["Step 1", "Step 2", "Composed"]
+        )
 
     def test_draw_mtg_steps_validates_indices(self):
         with self.assertRaises(IndexError):
             draw_mtg_steps(self._mtg(), steps=[2])
 
+    def test_draw_mtg_graph_handles_real_neutral_mechanism(self):
+        data = load_database("Data/Testcase/mech.json.gz")[0]
+        neutral = data["mechanisms"][1]
+        steps = [step["smart_string"] for step in neutral["steps"]]
+        mtg = MTG(steps, mcs_mol=True)
+        graph = mtg.get_mtg()
+
+        fig, ax = draw_mtg_graph(
+            mtg,
+            title=neutral["mech_name"],
+            hydrogen_mode="changed",
+            show_edge_labels=True,
+        )
+
+        self.assertIs(fig, ax.figure)
+        self.assertEqual(ax.get_title(), "Aldol reaction (neutral cat)")
+        self.assertTrue(mtg._tuple_its)
+        self.assertFalse(any("typesGH" in attrs for _, attrs in graph.nodes(data=True)))
+
 
 if __name__ == "__main__":
     unittest.main()