synkit 0.0.15__tar.gz → 0.0.17__tar.gz

{synkit-0.0.15 → synkit-0.0.17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: synkit
-Version: 0.0.15
+Version: 0.0.17
 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-0.0.17/pyproject.toml

@@ -0,0 +1,56 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "synkit"
+version = "0.0.17"
+description = "Utility for reaction modeling using graph grammar"
+readme = "README.md"
+long-description = { file = "CHANGELOG.md" }
+long-description-content-type = "text/markdown"
+requires-python = ">=3.11"
+license = { text = "MIT" }
+license-files = ["LICENSE"]
+authors = [
+  { name = "Tieu Long Phan", email = "tieu@bioinf.uni-leipzig.de" }
+]
+classifiers = [
+  "Programming Language :: Python :: 3",
+  "License :: OSI Approved :: MIT License",
+  "Operating System :: OS Independent",
+]
+dependencies = [
+  "scikit-learn>=1.4.0",
+  "pandas>=1.5.3",
+  "rdkit>=2025.3.1",
+  "networkx>=3.3",
+  "seaborn>=0.13.2",
+  "requests>=2.32.3",
+  "regex>=2024.11.6",
+]
+
+[project.optional-dependencies]
+all = ["numpy>=2.2.0", "torch>=2.2.0"]
+docs = [
+  "sphinx>=6.0",
+  "sphinx-rtd-theme",
+  "sphinxcontrib-bibtex",
+]
+
+[project.urls]
+homepage      = "https://github.com/TieuLongPhan/SynKit"
+source        = "https://github.com/TieuLongPhan/SynKit"
+issues        = "https://github.com/TieuLongPhan/SynKit/issues"
+documentation = "https://tieulongphan.github.io/SynKit/"
+
+[tool.hatch.build]
+# ship your code as normal
+packages = ["synkit"]
+
+# Force-include the entire Data directory (recursively)
+[tool.hatch.build.targets.wheel.force-include]
+"synkit/Data" = "synkit/Data"
+
+[tool.hatch.build.targets.sdist.force-include]
+"synkit/Data" = "synkit/Data"

synkit-0.0.17/synkit/Data/aldol.json.gz

@@ -0,0 +1 @@
+[{"R-id": "Mech-1", "reaction": "[CH3:1][CH:2]=[O:3].[CH:4]([H:7])([H:8])[CH:5]=[O:6]>>[CH3:1][CH:2]=[CH:4][CH:5]=[O:6].[O:3]([H:7])([H:8])", "mechanisms": [{"mech_name": "Aldol reaction (base cat)", "steps": [{"description": "Base abstracts H from substrate", "smart_string": "[CH:4]([H:7])([H:8])[CH:5]=[O:6].[*-:9]>>[CH-:4]([H:8])[CH:5]=[O:6].[*:9][H:7]", "step": 1, "step_gml": "rule [\n   ruleID \"2\"\n   left [\n   ]\n   context [\n   ]\n   right [\n   ]\n]", "step_dfs": null, "step_smart": ">>", "step_desc": "Base abstracts H from substrate"}, {"description": "Nucleophilic addition fro substrate", "smart_string": "[CH3:1][CH:2]=[O:3].[CH-:4]([H:8])[CH:5]=[O:6]>>[CH3:1][CH:2]([O-:3])[CH:4]([H:8])[CH:5]=[O:6]", "step": 2, "step_gml": "rule [\n   ruleID \"2\"\n   left [\n      edge [ source 1 target 2 label \"=\" ]\n      node [ id 2 label \"O\" ]\n      node [ id 3 label \"C-\" ]\n   ]\n   context [\n      node [ id 1 label \"C\" ]\n   ]\n   right [\n      edge [ source 1 target 2 label \"-\" ]\n      edge [ source 1 target 3 label \"-\" ]\n      node [ id 2 label \"O-\" ]\n      node [ id 3 label \"C\" ]\n   ]\n]", "step_dfs": null, "step_smart": "[CH2:1]=[O:2].[CH3-:3]>>[CH2:1]([O-:2])[CH3:3]", "step_desc": "Nucleophilic addition fro substrate"}, {"description": "Neutralize substrate", "smart_string": "[CH3:1][CH:2]([O-:3])[CH:4]([H:8])[CH:5]=[O:6].[*:9][H:7]>>[CH3:1][CH:2]([O:3][H:7])[CH:4]([H:8])[CH:5]=[O:6].[*-:9]", "step": 3, "step_gml": "rule [\n   ruleID \"2\"\n   left [\n   ]\n   context [\n   ]\n   right [\n   ]\n]", "step_dfs": null, "step_smart": ">>", "step_desc": "Neutralize substrate"}, {"description": "Base abstracts H from substrate", "smart_string": "[CH3:1][CH:2]([O:3][H:7])[CH:4]([H:8])[CH:5]=[O:6].[*-:9]>>[CH3:1][CH:2]([O:3][H:7])[CH-:4][CH:5]=[O:6].[*:9][H:8]", "step": 4, "step_gml": "rule [\n   ruleID \"2\"\n   left [\n   ]\n   context [\n   ]\n   right [\n   ]\n]", "step_dfs": null, "step_smart": ">>", "step_desc": "Base abstracts H from substrate"}, {"description": "Elimination Unimolecular Conjugate Base", "smart_string": "[CH3:1][CH:2]([O:3][H:7])[CH-:4][CH:5]=[O:6]>>[CH3:1][CH:2]=[CH:4][CH:5]=[O:6].[O-:3][H:7]", "step": 5, "step_gml": "rule [\n   ruleID \"2\"\n   left [\n      edge [ source 1 target 2 label \"-\" ]\n      edge [ source 1 target 3 label \"-\" ]\n      node [ id 2 label \"O\" ]\n      node [ id 3 label \"C-\" ]\n   ]\n   context [\n      node [ id 1 label \"C\" ]\n   ]\n   right [\n      edge [ source 1 target 3 label \"=\" ]\n      node [ id 2 label \"O-\" ]\n      node [ id 3 label \"C\" ]\n   ]\n]", "step_dfs": null, "step_smart": "[CH2:1]([OH:2])[CH2-:3]>>[CH2:1]=[CH2:3].[OH-:2]", "step_desc": "Elimination Unimolecular Conjugate Base"}, {"description": "Neutralize Hydroxide", "smart_string": "[O-:3][H:7].[*:9][H:8]>>[O:3]([H:7])([H:8]).[*-:9]", "step": 6, "step_gml": "rule [\n   ruleID \"2\"\n   left [\n   ]\n   context [\n   ]\n   right [\n   ]\n]", "step_dfs": null, "step_smart": ">>", "step_desc": "Neutralize Hydroxide"}], "cat": "[*-]"}, {"mech_name": "Aldol reaction (neutral cat)", "steps": [{"description": "Tautomerization of substrate", "smart_string": "[CH:4]([H:7])([H:8])[CH:5]=[O:6]>>[CH:4]([H:8])=[CH:5][O:6]([H:7])", "step": 1, "step_gml": "rule [\n   ruleID \"2\"\n   left [\n      edge [ source 1 target 2 label \"-\" ]\n      edge [ source 2 target 3 label \"=\" ]\n   ]\n   context [\n      node [ id 1 label \"C\" ]\n      node [ id 2 label \"C\" ]\n      node [ id 3 label \"O\" ]\n   ]\n   right [\n      edge [ source 1 target 2 label \"=\" ]\n      edge [ source 2 target 3 label \"-\" ]\n   ]\n]", "step_dfs": null, "step_smart": "[CH3:1][CH:2]=[O:3]>>[CH2:1]=[CH:2][OH:3]", "step_desc": "Tautomerization of substrate"}, {"description": "Nucleophilic addition from substrate", "smart_string": "[CH3:1][CH:2]=[O:3].[CH:4]([H:8])=[CH:5][O:6]([H:7])>>[CH3:1][CH:2]([O:3][H:7])[CH:4]([H:8])[CH:5]=[O:6]", "step": 2, "step_gml": "rule [\n   ruleID \"2\"\n   left [\n      edge [ source 1 target 2 label \"=\" ]\n      edge [ source 3 target 4 label \"=\" ]\n      edge [ source 4 target 5 label \"-\" ]\n   ]\n   context [\n      node [ id 1 label \"C\" ]\n      node [ id 2 label \"O\" ]\n      node [ id 3 label \"C\" ]\n      node [ id 4 label \"C\" ]\n      node [ id 5 label \"O\" ]\n   ]\n   right [\n      edge [ source 1 target 2 label \"-\" ]\n      edge [ source 1 target 3 label \"-\" ]\n      edge [ source 3 target 4 label \"-\" ]\n      edge [ source 4 target 5 label \"=\" ]\n   ]\n]", "step_dfs": null, "step_smart": "[CH2:1]=[O:2].[CH2:3]=[CH:4][OH:5]>>[CH2:1]([OH:2])[CH2:3][CH:4]=[O:5]", "step_desc": "Nucleophilic addition from substrate"}, {"description": "Tautomerization of substrate", "smart_string": "[CH3:1][CH:2]([O:3][H:7])[CH:4]([H:8])[CH:5]=[O:6]>>[CH3:1][CH:2]([O:3][H:7])[CH:4]=[CH:5][O:6]([H:8])", "step": 3, "step_gml": "rule [\n   ruleID \"2\"\n   left [\n      edge [ source 1 target 2 label \"-\" ]\n      edge [ source 2 target 3 label \"=\" ]\n   ]\n   context [\n      node [ id 1 label \"C\" ]\n      node [ id 2 label \"C\" ]\n      node [ id 3 label \"O\" ]\n   ]\n   right [\n      edge [ source 1 target 2 label \"=\" ]\n      edge [ source 2 target 3 label \"-\" ]\n   ]\n]", "step_dfs": null, "step_smart": "[CH3:1][CH:2]=[O:3]>>[CH2:1]=[CH:2][OH:3]", "step_desc": "Tautomerization of substrate"}, {"description": "Elimination", "smart_string": "[CH3:1][CH:2]([O:3][H:7])[CH:4]=[CH:5][O:6]([H:8])>>[CH3:1][CH:2]=[CH:4][CH:5]=[O:6].[O:3]([H:7])([H:8])", "step": 4, "step_gml": "rule [\n   ruleID \"2\"\n   left [\n      edge [ source 1 target 2 label \"-\" ]\n      edge [ source 1 target 3 label \"-\" ]\n      edge [ source 3 target 4 label \"=\" ]\n      edge [ source 4 target 5 label \"-\" ]\n   ]\n   context [\n      node [ id 1 label \"C\" ]\n      node [ id 2 label \"O\" ]\n      node [ id 3 label \"C\" ]\n      node [ id 4 label \"C\" ]\n      node [ id 5 label \"O\" ]\n   ]\n   right [\n      edge [ source 1 target 3 label \"=\" ]\n      edge [ source 3 target 4 label \"-\" ]\n      edge [ source 4 target 5 label \"=\" ]\n   ]\n]", "step_dfs": null, "step_smart": "[CH2:1]([OH:2])[CH:3]=[CH:4][OH:5]>>[CH2:1]=[CH:3][CH:4]=[O:5].[OH2:2]", "step_desc": "Elimination"}], "cat": ""}, {"mech_name": "Aldol reaction (acid cat)", "steps": [{"description": "Tautomerization of substrate with acid cat", "smart_string": "[CH:4]([H:7])([H:8])[CH:5]=[O:6].[H+:9]>>[CH:4]([H:8])=[CH:5][O:6]([H:9]).[H+:7]", "step": 1}, {"description": "Nucleophilic addition from substrate", "smart_string": "[CH3:1][CH:2]=[O:3].[CH:4]([H:8])=[CH:5][O:6]([H:9]).[H+:7]>>[CH3:1][CH:2]([O:3][H:7])[CH:4]([H:8])[CH:5]=[O:6].[H+:9]", "step": 2}, {"description": "Tautomerization of substrate with acid cat", "smart_string": "[CH3:1][CH:2]([O:3][H:7])[CH:4]([H:8])[CH:5]=[O:6].[H+:9]>>[CH3:1][CH:2]([O:3][H:7])[CH:4]=[CH:5][O:6]([H:9]).[H+:8]", "step": 3}, {"description": "Elimination", "smart_string": "[CH3:1][CH:2]([O:3][H:7])[CH:4]=[CH:5][O:6]([H:9]).[H+:8]>>[CH3:1][CH:2]=[CH:4][CH:5]=[O:6].[H+:9].[O:3]([H:7])([H:8])", "step": 4}], "cat": "[H+]"}]}]

synkit-0.0.17/synkit/Data/paracetamol.json.gz

@@ -0,0 +1 @@
+[{"R-id": 1, "aam": "[c:4]1([H:11])[cH:5][cH:6][cH:7][cH:8][cH:9]1.[CH3:1][CH:2]([CH3:3])[Cl:10]>>[CH3:1][CH:2]([CH3:3])[c:4]1[cH:5][cH:6][cH:7][cH:8][cH:9]1.[H:11][Cl:10]"}, {"R-id": 2, "aam": "[CH3:1][C:2]([H:12])([CH3:3])[c:6]1[cH:7][cH:8][cH:9][cH:10][cH:11]1.[O:4]=[O:5]>>[CH3:1][C:2]([CH3:3])([O:4][O:5][H:12])[c:6]1[cH:7][cH:8][cH:9][cH:10][cH:11]1"}, {"R-id": 3, "aam": "[CH3:8][C:9]([CH3:11])([O:10][OH:1])[c:2]1[cH:3][cH:4][cH:5][cH:6][cH:7]1>>[OH:1][c:2]1[cH:3][cH:4][cH:5][cH:6][cH:7]1.[CH3:8][C:9](=[O:10])[CH3:11]"}, {"R-id": 4, "aam": "[H:12][O:4][c:5]1[cH:6][cH:7][cH:8][cH:9][cH:10]1.[CH3:1][C:2](=[O:3])[Cl:11]>>[CH3:1][C:2](=[O:3])[O:4][c:5]1[cH:6][cH:7][cH:8][cH:9][cH:10]1.[Cl:11][H:12]"}, {"R-id": 5, "aam": "[CH3:11][C:9](=[O:10])[O:8][c:7]1[cH:6][cH:5][c:4]([H:15])[cH:13][cH:12]1.[O:1]=[N+:2]([O-:3])[OH:14]>>[O:1]=[N+:2]([O-:3])[c:4]1[cH:5][cH:6][c:7]([O:8][C:9](=[O:10])[CH3:11])[cH:12][cH:13]1.[OH:14][H:15]"}, {"R-id": 6, "aam": "[O:12]=[N+:1]([O-:13])[c:2]1[cH:3][cH:4][c:5]([O:6][C:7](=[O:8])[CH3:9])[cH:10][cH:11]1.[H:14][H:15].[H:16][H:18].[H:17][H:19]>>[N:1]([H:18])([H:19])[c:2]1[cH:3][cH:4][c:5]([O:6][C:7](=[O:8])[CH3:9])[cH:10][cH:11]1.[H:14][O:12][H:15].[H:16][O:13][H:17]"}, {"R-id": 7, "aam": "[NH2:1][c:2]1[cH:3][cH:4][c:5]([O:6][C:10](=[O:11])[CH3:9])[cH:7][cH:8]1.[OH:12][H:13]>>[NH2:1][c:2]1[cH:3][cH:4][c:5]([O:6][H:13])[cH:7][cH:8]1.[CH3:9][C:10](=[O:11])[OH:12]"}, {"R-id": 8, "aam": "[H:13][NH:4][c:5]1[cH:6][cH:7][c:8]([OH:9])[cH:10][cH:11]1.[CH3:1][C:2](=[O:3])[Cl:12]>>[CH3:1][C:2](=[O:3])[NH:4][c:5]1[cH:6][cH:7][c:8]([OH:9])[cH:10][cH:11]1.[Cl:12][H:13]"}, {"R-id": 9, "aam": "[CH3:19][C:17](=[O:18])[NH:16][c:13]1[cH:12][cH:11][c:10]([O:9][H:21])[cH:15][cH:14]1.[CH3:1][CH2:2][N:3]([CH2:4][CH3:5])[CH2:6][C:7](=[O:8])[Cl:20]>>[CH3:1][CH2:2][N:3]([CH2:4][CH3:5])[CH2:6][C:7](=[O:8])[O:9][C:10]1=[CH:11][CH:12]=[C:13]([NH:16][C:17](=[O:18])[CH3:19])[CH:14]=[CH:15]1.[Cl:20][H:21]"}]

synkit-0.0.15/.github/dependabot.yml

@@ -1,10 +0,0 @@
-# .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
-    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

synkit-0.0.15/.github/workflows/build-doc.yml

@@ -1,35 +0,0 @@
-name: Build documentation for GitHub Pages 
-
-on:
-  push:
-    branches: 
-      - main
-
-  workflow_dispatch: # Enable manual action trigger
-
-env:
-  PYTHONPATH: .
-
-jobs:
-  build_documentation_for_github_pages:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-      - uses: actions/setup-python@v4
-        with:
-          python-version: '3.11'
-          cache: 'pip' # caching pip dependencies
-      - run: pip install -r requirements.txt
-      - run: pip install sphinx sphinx-rtd-theme
-      - run: pip install sphinxcontrib-bibtex
-      - run: python3 -m sphinx ./doc docs
-      - name: publish doc
-        shell: bash
-        run: |
-          git config user.name "GitHub Action"
-          git config user.email "no@mail.tmp"
-          git add -f docs/
-          git commit -m "Doc build"
-          git push --force "https://github.com/TieuLongPhan/SynKit.git" `git subtree split --prefix docs/ main`:gh-pages

synkit-0.0.15/.github/workflows/conda-forge-publish.yml

@@ -1,109 +0,0 @@
-name: Publish to conda-forge
-
-on:
-  release:
-    types: [published]
-  push:
-    branches: [refactor]
-
-permissions:
-  contents: read
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    outputs:
-      pkg_paths: ${{ steps.build.outputs.paths }}
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          channels: conda-forge
-          auto-update-conda: true
-          auto-activate-base: true
-
-      - name: Create & activate build env
-        shell: bash -l {0}
-        run: |
-          conda create -n build python=3.11 'conda-build>=3.21' -c conda-forge -y
-          conda activate build
-
-      - id: build
-        name: Build conda package
-        shell: bash -l {0}
-        env:
-          GITHUB_RUN_NUMBER: ${{ github.run_number }}
-        run: |
-          conda activate build
-          rm -rf conda-bld && mkdir conda-bld
-
-          conda-build recipe --output-folder ./conda-bld
-
-          echo "DEBUG: Built files:"
-          find conda-bld -type f \( -name "*.conda" -o -name "*.tar.bz2" \) -print
-
-          files=$(find conda-bld -type f \( -name "*.conda" -o -name "*.tar.bz2" \) -print | tr '\n' ' ')
-          echo "paths=$files" >> $GITHUB_OUTPUT
-
-      - name: Upload built packages as artifact
-        uses: actions/upload-artifact@v4
-        with:
-          name: conda-packages
-          path: conda-bld/
-
-  publish_release:
-    needs: build
-    if: github.event_name == 'release'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Download built packages
-        uses: actions/download-artifact@v4
-        with:
-          name: conda-packages
-          path: conda-bld
-
-      - name: Install Anaconda Client
-        run: python3 -m pip install --upgrade anaconda-client
-
-      - name: Upload to conda-forge / main
-        env:
-          ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
-        run: |
-          for pkg in ${{ needs.build.outputs.pkg_paths }}; do
-            anaconda -t "$ANACONDA_TOKEN" upload \
-              --user tieulongphan \
-              --label main \
-              --no-progress \
-              "$pkg"
-          done
-
-  publish_beta:
-    needs: build
-    if: github.event_name == 'push' && github.ref == 'refs/heads/refactor'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Download built packages
-        uses: actions/download-artifact@v4
-        with:
-          name: conda-packages
-          path: conda-bld
-
-      - name: Install Anaconda Client
-        run: python3 -m pip install --upgrade anaconda-client
-
-      - name: Upload to conda-forge / beta
-        env:
-          ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
-        run: |
-          for pkg in ${{ needs.build.outputs.pkg_paths }}; do
-            anaconda -t "$ANACONDA_TOKEN" upload \
-              --user tieulongphan \
-              --label beta \
-              --no-progress \
-              "$pkg"
-          done

synkit-0.0.15/.github/workflows/docker-publish.yml

@@ -1,46 +0,0 @@
-# .github/workflows/docker-publish.yml
-name: Publish SynKit Docker Package
-
-on:
-  push:
-    # Fire on semver tags for real releases…
-    tags:
-      - 'v*.*.*'
-    # …and on any push to the refractor branch for testing
-    branches:
-      - 'staging'
-
-jobs:
-  build-and-push:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      packages: write
-      id-token: write
-
-    steps:
-      - name: Check out repository
-        uses: actions/checkout@v3
-
-      - 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
-
-      - name: Log in to Docker Hub
-        uses: docker/login-action@v2
-        with:
-          username: ${{ secrets.DOCKERHUB_USER }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
-
-      - name: Build and push Docker image
-        uses: docker/build-push-action@v4
-        with:
-          context: .
-          file: Dockerfile
-          platforms: linux/amd64,linux/arm64
-          push: true
-          tags: |
-            tieulongphan/synkit:${{ github.ref_name }}
-            tieulongphan/synkit:latest

synkit-0.0.15/.github/workflows/publish-package.yml

@@ -1,49 +0,0 @@
-name: PyPI publish
-
-on:
-  release:
-    types: [published]
-
-permissions:
-  contents: read
-
-jobs:
-  build:
-    name: Build package
-    runs-on: ubuntu-latest
-    steps:
-    - name: Checkout
-      uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v3
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install build
-    - name: Build package
-      run: python -m build
-    - name: Upload artifact
-      uses: actions/upload-artifact@v4
-      with:
-        name: package
-        path: dist/
-      
-  publish:
-    name: Upload release to PyPI
-    needs: build
-    runs-on: ubuntu-latest
-    environment:
-      name: pypi
-      url: https://pypi.org/p/synkit
-    permissions:
-      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
-    steps:
-    - name: Download artifact
-      uses: actions/download-artifact@v4
-      with:
-        name: package
-        path: dist/
-    - name: Publish package to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1

synkit-0.0.15/.github/workflows/test-and-lint.yml

@@ -1,68 +0,0 @@
-name: Test & Lint
-
-on:
-  push:
-    branches: [ "main", "partialits", "staging", "refractor" ]
-  pull_request:
-    branches: [ "main" ]
-
-permissions:
-  contents: read
-
-jobs:
-  test-lint:
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-
-    runs-on: ${{ matrix.os }}
-
-    steps:
-      # 0) Check out the code
-      - uses: actions/checkout@v3
-
-      # 1) Install Miniconda (downloaded — the “bundled” version was removed)
-      - name: Set up Miniconda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          miniconda-version: "latest"      # <<–‑‑ mandatory or the action fails
-          python-version: "3.11"
-          auto-update-conda: true
-          environment-file: environment.yml
-          activate-environment: synkit-env
-          use-mamba: true                  # optional, just faster
-
-      # 2) Extra Linux‑only dependency: mod ≥ 0.17
-      - name: Install mod (Linux only)
-        if: matrix.os == 'ubuntu-latest'
-        run: conda run -n synkit-env conda install -c jakobandersen -c conda-forge "mod>=0.17" -y
-
-      # 3) Optional extra project deps via pip (requirements.txt)
-      - name: Install project requirements
-        if: hashFiles('requirements.txt') != ''
-        run: conda run -n synkit-env pip install -r requirements.txt
-
-      # 4a) Lint on Linux/macOS
-      - name: Lint (Unix)
-        if: matrix.os != 'windows-latest'
-        shell: bash -l {0}
-        run: |
-          conda activate synkit-env
-          bash lint.sh
-
-      # 4b) Lint on Windows
-      - name: Lint (Windows)
-        if: matrix.os == 'windows-latest'
-        shell: bash -l {0}
-        run: |
-          conda activate synkit-env
-          bash lint.sh
-
-
-      # 5) Test
-      - name: Test
-        shell: bash -l {0}
-        run: |
-          conda activate synkit-env
-          bash pytest.sh

synkit-0.0.15/.github/workflows/verify-pypi-install.yml

@@ -1,59 +0,0 @@
-# .github/workflows/verify-synkit-pypi-install.yml
-name: Verify SynKit PyPI install
-
-on:
-  workflow_dispatch:
-    inputs:
-      branches:
-        type: string
-        required: true
-        default: refractor
-
-  # Scheduled test every Monday at 03:00 UTC
-  schedule:
-    - cron: '0 3 * * 1'
-
-jobs:
-  verify:
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Setup Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.x'
-
-      - name: Create & activate virtualenv, upgrade pip, install SynKit
-        run: |
-          python -m venv venv
-          source venv/bin/activate
-          python -m pip install --upgrade pip
-          pip install synkit[all]
-
-      - name: Show installed SynKit version
-        run: |
-          source venv/bin/activate
-          python -c "import importlib.metadata as m; print('SynKit version:', m.version('synkit'))"
-
-      - name: Write smoke-test script
-        run: |
-          cat << 'EOF' > test_synkit.py
-          from synkit.IO import rsmi_to_rsmarts
-
-          template = (
-              '[C:2]=[O:3].[C:4]([H:7])[H:8]'
-              '>>'
-              '[C:2]=[C:4].[O:3]([H:7])[H:8]'
-          )
-
-          smart = rsmi_to_rsmarts(template)
-          print("Reaction SMARTS:", smart)
-          EOF
-
-      - name: Run smoke-test
-        run: |
-          source venv/bin/activate
-          python test_synkit.py
-
-      - name: Success message
-        run: echo "✅ synkit[all] installed and smoke-test passed"

synkit-0.0.15/.readthedocs.yml

@@ -1,24 +0,0 @@
-# Read the Docs configuration file
-# https://docs.readthedocs.io/en/stable/config-file/v2.html
-
-# 1) Tell RTD this is v2 of the schema
-version: 2
-
-# 2) Pick your build image and interpreter
-build:
-  os: ubuntu-22.04
-  tools:
-    python: "3.11"
-
-# 3) Install your package + any doc-only extras
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements: 
-        - docs
-
-# 4) Point Sphinx at your conf.py and choose HTML
-sphinx:
-  configuration: doc/conf.py
-  builder: html

synkit-0.0.15/Data/Testcase/Compose/SingleRule/R0/0.gml

@@ -1,17 +0,0 @@
-rule [
-   ruleID "0"
-   left [
-      edge [ source 1 target 2 label "-" ]
-      edge [ source 3 target 4 label "-" ]
-   ]
-   context [
-      node [ id 1 label "H" ]
-      node [ id 2 label "N" ]
-      node [ id 3 label "C" ]
-      node [ id 4 label "Br" ]
-   ]
-   right [
-      edge [ source 1 target 4 label "-" ]
-      edge [ source 2 target 3 label "-" ]
-   ]
-]

synkit-0.0.15/Data/Testcase/Compose/SingleRule/R0/1.gml

@@ -1,17 +0,0 @@
-rule [
-   ruleID "1"
-   left [
-      edge [ source 1 target 2 label "-" ]
-      edge [ source 3 target 4 label "-" ]
-   ]
-   context [
-      node [ id 1 label "Br" ]
-      node [ id 2 label "C" ]
-      node [ id 3 label "O" ]
-      node [ id 4 label "H" ]
-   ]
-   right [
-      edge [ source 1 target 4 label "-" ]
-      edge [ source 2 target 3 label "-" ]
-   ]
-]

synkit-0.0.15/Data/Testcase/Compose/SingleRule/R0/2.gml

@@ -1,17 +0,0 @@
-rule [
-   ruleID "2"
-   left [
-      edge [ source 1 target 2 label "-" ]
-      edge [ source 3 target 4 label "-" ]
-   ]
-   context [
-      node [ id 1 label "C" ]
-      node [ id 2 label "Cl" ]
-      node [ id 3 label "N" ]
-      node [ id 4 label "H" ]
-   ]
-   right [
-      edge [ source 1 target 3 label "-" ]
-      edge [ source 2 target 4 label "-" ]
-   ]
-]

synkit-0.0.15/Dockerfile

@@ -1,45 +0,0 @@
-############################################
-# STAGE 1: Build your package wheel
-############################################
-FROM python:3.11-slim AS builder
-
-# 1. Install system build tools (for any C extensions)
-RUN apt-get update \
-    && apt-get install -y --no-install-recommends build-essential \
-    && rm -rf /var/lib/apt/lists/*
-
-# 2. Upgrade pip/setuptools/wheel and install PEP 517 tooling + Hatchling backend
-RUN pip install --upgrade pip setuptools wheel \
-    && pip install --no-cache-dir build hatchling
-
-# 3. Set working directory inside builder
-WORKDIR /build
-
-# 4. Copy project metadata (including README so Hatchling can find it)
-COPY pyproject.toml README.md ./
-# If you have a lockfile, uncomment:
-# COPY poetry.lock ./
-
-# 5. Copy your library source
-COPY synkit/ ./synkit
-
-# 6. Build the wheel
-RUN python -m build --wheel --no-isolation
-
-############################################
-# STAGE 2: Create the “release” image
-############################################
-FROM python:3.11-slim
-
-# 7. Set a clean workdir
-WORKDIR /opt/synkit
-
-# 8. Copy in the built wheel from the builder stage
-COPY --from=builder /build/dist/*.whl ./
-
-# 9. Install your package (and its dependencies), then remove the wheel
-RUN pip install --no-cache-dir *.whl \
-    && rm *.whl
-
-# 10. Sanity check: print the installed synkit version
-CMD ["python", "-c", "import importlib.metadata as m; print(m.version('synkit'))"]

synkit-0.0.15/Test/Chem/Fingerprint/test_fp_calculator.py

@@ -1,69 +0,0 @@
-import io
-import unittest
-from contextlib import redirect_stdout
-
-from synkit.Chem.Fingerprint.fp_calculator import FPCalculator
-
-
-class TestFPCalculator(unittest.TestCase):
-    def setUp(self):
-        # Sample single reaction dict
-        self.single = {"rsmi": "CCO>>CC=O"}
-        # List of dicts for parallel
-        self.batch = [
-            {"rsmi": "CCO>>CC=O"},
-            {"rsmi": "CC(Cl)C>>CCCl"},
-        ]
-        self.rsmi_key = "rsmi"
-        self.fp_type = "ecfp4"
-        self.calc = FPCalculator(n_jobs=2, verbose=0)
-
-    def test_constructor_assigns_attributes(self):
-        self.assertEqual(self.calc.n_jobs, 2)
-        self.assertEqual(self.calc.verbose, 0)
-
-    def test_validate_fp_type_accepts_supported(self):
-        # Should not raise
-        for ft in FPCalculator.VALID_FP_TYPES:
-            self.calc._validate_fp_type(ft)
-
-    def test_validate_fp_type_rejects_unsupported(self):
-        with self.assertRaises(ValueError):
-            self.calc._validate_fp_type("invalid_fp")
-
-    def test_dict_process_missing_key_raises(self):
-        with self.assertRaises(ValueError):
-            FPCalculator.dict_process({}, self.rsmi_key, fp_type=self.fp_type)
-
-    def test_dict_process_adds_fingerprint(self):
-        data = {"rsmi": "CCO>>CC=O"}
-        out = FPCalculator.dict_process(data, "rsmi", fp_type="ecfp4")
-        self.assertIn("ecfp4", out)
-        # Check it's a list/vector (not None)
-        self.assertIsNotNone(out["ecfp4"])
-
-    def test_parallel_process_returns_list_of_dicts(self):
-        results = self.calc.parallel_process(self.batch, "rsmi", fp_type="ecfp4")
-        self.assertIsInstance(results, list)
-        self.assertEqual(len(results), 2)
-        for d in results:
-            self.assertIn("ecfp4", d)
-
-    def test_str_and_help_output(self):
-        s = str(self.calc)
-        self.assertIn("FPCalculator", s)
-        buf = io.StringIO()
-        with redirect_stdout(buf):
-            self.calc.help()
-        help_out = buf.getvalue()
-
-        # The help text starts with this exact line
-        self.assertIn(
-            "FPCalculator supports the following fingerprint types:", help_out
-        )
-        # And lists our parallel jobs config
-        self.assertIn(f"Configured for {self.calc.n_jobs} parallel jobs", help_out)
-
-
-if __name__ == "__main__":
-    unittest.main()