synkit 0.0.10__tar.gz → 0.0.12__tar.gz

synkit-0.0.12/.github/dependabot.yml

@@ -0,0 +1,10 @@
+# .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+    rebase-strategy: "auto"       # auto-rebase PRs when they fall out of date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-0.0.12/.github/workflows/conda-forge-publish.yml

@@ -0,0 +1,109 @@
+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-0.0.12/.github/workflows/docker-publish.yml

@@ -0,0 +1,46 @@
+# .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-0.0.10 → synkit-0.0.12}/.github/workflows/test-and-lint.yml

@@ -2,7 +2,7 @@ name: Test & Lint
 
 on:
   push:
-    branches: [ "main", "dev", "maintain", "refractor" ]
+    branches: [ "main", "dev", "staging", "refractor" ]
   pull_request:
     branches: [ "main" ]
 

synkit-0.0.12/.github/workflows/verify-pypi-install.yml

@@ -0,0 +1,59 @@
+# .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-0.0.10 → synkit-0.0.12}/.gitignore

@@ -21,3 +21,4 @@ Data/Benchmark/*
 run.sh
 docs/*
 run_rdcanon.py
+Data/Fragment/*

synkit-0.0.12/Dockerfile

@@ -0,0 +1,45 @@
+############################################
+# 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-0.0.10 → synkit-0.0.12}/PKG-INFO

@@ -1,12 +1,13 @@
 Metadata-Version: 2.4
 Name: synkit
-Version: 0.0.10
+Version: 0.0.12
 Summary: Utility for reaction modeling using graph grammar
 Project-URL: homepage, https://github.com/TieuLongPhan/SynKit
 Project-URL: source, https://github.com/TieuLongPhan/SynKit
 Project-URL: issues, https://github.com/TieuLongPhan/SynKit/issues
 Project-URL: documentation, https://tieulongphan.github.io/SynKit/
 Author-email: Tieu Long Phan <tieu@bioinf.uni-leipzig.de>
+License: MIT
 License-File: LICENSE
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
@@ -40,7 +41,14 @@ Our tools are tailored to assist researchers and chemists in navigating complex
 
 For more details on each utility within the repository, please refer to the documentation provided in the respective folders.
 
-## Step-by-Step Installation Guide
+## Table of Contents
+- [Installation](#installation)
+- [Contribute to `SynKit`](#contribute)
+- [Contributing](#contributing)
+- [License](#license)
+- [Acknowledgments](#acknowledgments)
+
+## Installation
 
 1. **Python Installation:**
   Ensure that Python 3.11 or later is installed on your system. You can download it from [python.org](https://www.python.org/downloads/).
@@ -71,7 +79,20 @@ For more details on each utility within the repository, please refer to the docu
   pip install synkit[all]
   ```
 
-## For contributors
+4. **Install via Docker**  
+   Pull the image: 
+
+   ```bash
+   docker pull tieulongphan/synkit:latest
+   # or a specific version:
+   docker pull tieulongphan/synkit:0.1.0
+   ```
+   Run a container (sanity check):
+   ```
+   docker run --rm tieulongphan/synkit:latest
+   ```
+
+## Contribute
 
 We're welcoming new contributors to build this project better. Please not hesitate to inquire me via [email][tieu@bioinf.uni-leipzig.de].
 
@@ -82,7 +103,7 @@ git checkout main
 git pull
 ```
 
-## Working on New Features
+### Working on New Features
 
 1. **Create a New Branch**:  
    For every new feature or bug fix, create a new branch from the `main` branch. Name your branch meaningfully, related to the feature or fix you are working on.
@@ -108,7 +129,7 @@ git pull
 
    Fix any issues or errors highlighted by these checks.
 
-## Integrating Changes
+### Integrating Changes
 
 1. **Rebase onto Staging**:  
    Once your feature is complete and tests pass, rebase your changes onto the `staging` branch to prepare for integration.
@@ -128,16 +149,16 @@ git pull
    ```
 
 3. **Create a Pull Request**:
-   Open a pull request from your feature branch to the `stagging` branch. Ensure the pull request description clearly describes the changes and any additional context necessary for review.
+   Open a pull request from your feature branch to the `staging` branch. Ensure the pull request description clearly describes the changes and any additional context necessary for review.
 
 ## Contributing
 - [Tieu-Long Phan](https://tieulongphan.github.io/)
 - [Klaus Weinbauer](https://github.com/klausweinbauer)
 - [Phuoc-Chung Nguyen Van](https://github.com/phuocchung123)
 
-## Deployment timeline
+## Publication
 
-We plan to update new version quarterly.
+[**SynKit**: An Advanced Cheminformatics Python Library for Efficient Manipulation and Analysis of Chemical Reaction Data]()
 
 
 ## License

{synkit-0.0.10 → synkit-0.0.12}/README.md

@@ -10,7 +10,14 @@ Our tools are tailored to assist researchers and chemists in navigating complex
 
 For more details on each utility within the repository, please refer to the documentation provided in the respective folders.
 
-## Step-by-Step Installation Guide
+## Table of Contents
+- [Installation](#installation)
+- [Contribute to `SynKit`](#contribute)
+- [Contributing](#contributing)
+- [License](#license)
+- [Acknowledgments](#acknowledgments)
+
+## Installation
 
 1. **Python Installation:**
   Ensure that Python 3.11 or later is installed on your system. You can download it from [python.org](https://www.python.org/downloads/).
@@ -41,7 +48,20 @@ For more details on each utility within the repository, please refer to the docu
   pip install synkit[all]
   ```
 
-## For contributors
+4. **Install via Docker**  
+   Pull the image: 
+
+   ```bash
+   docker pull tieulongphan/synkit:latest
+   # or a specific version:
+   docker pull tieulongphan/synkit:0.1.0
+   ```
+   Run a container (sanity check):
+   ```
+   docker run --rm tieulongphan/synkit:latest
+   ```
+
+## Contribute
 
 We're welcoming new contributors to build this project better. Please not hesitate to inquire me via [email][tieu@bioinf.uni-leipzig.de].
 
@@ -52,7 +72,7 @@ git checkout main
 git pull
 ```
 
-## Working on New Features
+### Working on New Features
 
 1. **Create a New Branch**:  
    For every new feature or bug fix, create a new branch from the `main` branch. Name your branch meaningfully, related to the feature or fix you are working on.
@@ -78,7 +98,7 @@ git pull
 
    Fix any issues or errors highlighted by these checks.
 
-## Integrating Changes
+### Integrating Changes
 
 1. **Rebase onto Staging**:  
    Once your feature is complete and tests pass, rebase your changes onto the `staging` branch to prepare for integration.
@@ -98,16 +118,16 @@ git pull
    ```
 
 3. **Create a Pull Request**:
-   Open a pull request from your feature branch to the `stagging` branch. Ensure the pull request description clearly describes the changes and any additional context necessary for review.
+   Open a pull request from your feature branch to the `staging` branch. Ensure the pull request description clearly describes the changes and any additional context necessary for review.
 
 ## Contributing
 - [Tieu-Long Phan](https://tieulongphan.github.io/)
 - [Klaus Weinbauer](https://github.com/klausweinbauer)
 - [Phuoc-Chung Nguyen Van](https://github.com/phuocchung123)
 
-## Deployment timeline
+## Publication
 
-We plan to update new version quarterly.
+[**SynKit**: An Advanced Cheminformatics Python Library for Efficient Manipulation and Analysis of Chemical Reaction Data]()
 
 
 ## License

synkit-0.0.12/Test/Chem/Fingerprint/test_fp_calculator.py

@@ -0,0 +1,69 @@
+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()

{synkit-0.0.10 → synkit-0.0.12}/Test/Chem/Fingerprint/test_transformation_fp.py

@@ -22,13 +22,13 @@ class TestTransformationFP(unittest.TestCase):
         abs_val = True
 
         # Test with return_array=True
-        reaction_fp_array = TransformationFP.fit(
+        reaction_fp_array = TransformationFP().fit(
             reaction_smiles, symbols, fp_type, abs_val
         )
         self.assertIsInstance(reaction_fp_array, np.ndarray)
 
         # Test with return_array=False
-        reaction_fp_bitvect = TransformationFP.fit(
+        reaction_fp_bitvect = TransformationFP().fit(
             reaction_smiles, symbols, fp_type, abs_val, return_array=False
         )
         self.assertIsInstance(reaction_fp_bitvect, cDataStructs.ExplicitBitVect)
@@ -40,7 +40,7 @@ class TestTransformationFP(unittest.TestCase):
         fp_type = "maccs"
         abs_val = True
         with self.assertRaises(Exception):
-            _ = TransformationFP.fit(reaction_smiles, symbols, fp_type, abs_val)
+            _ = TransformationFP().fit(reaction_smiles, symbols, fp_type, abs_val)
 
     def test_fit_reaction_split(self):
         """Test handling of SMILES split by symbols and impact on results"""
@@ -48,7 +48,7 @@ class TestTransformationFP(unittest.TestCase):
         symbols = ">>"
         fp_type = "maccs"
         abs_val = False  # without taking absolute values
-        reaction_fp = TransformationFP.fit(reaction_smiles, symbols, fp_type, abs_val)
+        reaction_fp = TransformationFP().fit(reaction_smiles, symbols, fp_type, abs_val)
         self.assertIsInstance(reaction_fp, np.ndarray)
 
 

{synkit-0.0.10 → synkit-0.0.12}/Test/Chem/Reaction/test_cleanning.py

@@ -1,11 +1,11 @@
 import unittest
-from synkit.Chem.Reaction.cleanning import Cleanning
+from synkit.Chem.Reaction.cleaning import Cleaning
 
 
 class TestCleaning(unittest.TestCase):
 
     def setUp(self):
-        self.cleaner = Cleanning()
+        self.cleaner = Cleaning()
 
     def test_remove_duplicates(self):
         input_smiles = ["CC>>CC", "CC>>CC"]

synkit-0.0.10/Test/Chem/Reaction/test_rsmi_utils.py → synkit-0.0.12/Test/Chem/test_utils.py

@@ -1,5 +1,8 @@
 import unittest
-from synkit.Chem.Reaction.rsmi_utils import (
+from rdkit import Chem
+from synkit.Chem.utils import (
+    enumerate_tautomers,
+    mapping_success_rate,
     remove_common_reagents,
     reverse_reaction,
     remove_duplicates,
@@ -8,7 +11,49 @@ from synkit.Chem.Reaction.rsmi_utils import (
 )
 
 
-class TestChemicalReactions(unittest.TestCase):
+class TestChemUtils(unittest.TestCase):
+    def test_enumerate_tautomers_simple(self):
+        # A simple keto-enol tautomerism: acetylacetone (CC(=O)CC=O) -> same product
+        reaction = "CC(=O)CC=O>>O"
+        tautomers = enumerate_tautomers(reaction)
+        # Should return a list with at least the original reaction
+        self.assertIsInstance(tautomers, list)
+        self.assertIn(reaction, tautomers)
+        # Each entry should be a valid reaction SMILES
+        for rsmi in tautomers:
+            self.assertIsInstance(rsmi, str)
+            parts = rsmi.split(">>")
+            self.assertEqual(len(parts), 2)
+            # Reactant and product part parseable by RDKit
+            self.assertIsNotNone(Chem.MolFromSmiles(parts[0]))
+            self.assertIsNotNone(Chem.MolFromSmiles(parts[1]))
+
+    def test_enumerate_tautomers_invalid(self):
+        # Invalid SMILES input should raise ValueError
+        bad = "INVALID>>SMILES"
+        with self.assertRaises(ValueError) as cm:
+            enumerate_tautomers(bad)
+        self.assertIn("Invalid reactant or product SMILES", str(cm.exception))
+
+    def test_mapping_success_rate_normal(self):
+        data = ["C:1CC", "CCC", "O:3=O", ":5", "N"]
+        rate = mapping_success_rate(data)
+        # Entries with mapping: 'C:1CC', 'O:3=O', ':5' => 3/5 = 60.0%
+        self.assertEqual(rate, 60.0)
+
+    def test_mapping_success_rate_empty(self):
+        with self.assertRaises(ValueError):
+            mapping_success_rate([])
+
+    def test_mapping_success_rate_all(self):
+        data = [":1C", ":2", "N:3"]
+        rate = mapping_success_rate(data)
+        self.assertEqual(rate, 100.0)
+
+    def test_mapping_success_rate_none(self):
+        data = ["C", "O", "N"]
+        rate = mapping_success_rate(data)
+        self.assertEqual(rate, 0.0)
 
     def test_remove_common_reagents_no_common(self):
         reaction = "A.B.C>>D.E.F"

{synkit-0.0.10 → synkit-0.0.12}/doc/api.rst

@@ -21,6 +21,22 @@ The `Chem` module provides tools for handling input and output operations relate
    :undoc-members:
    :show-inheritance:  
 
+.. automodule:: synkit.Chem.Reaction.balance_check
+   :members:
+   :undoc-members:
+   :show-inheritance:  
+
+.. automodule:: synkit.Chem.Fingerprint.fp_calculator
+   :members:
+   :undoc-members:
+   :show-inheritance:  
+
+.. automodule:: synkit.Chem.Cluster.butina
+   :members:
+   :undoc-members:
+   :show-inheritance:  
+
+
 Synthesis Module
 ================
 

{synkit-0.0.10 → synkit-0.0.12}/doc/conf.py

@@ -1,5 +1,6 @@
 import os
 import sys
+import importlib.metadata as m
 from importlib.metadata import version as _get_version, PackageNotFoundError
 
 # -- Path setup --------------------------------------------------------------
@@ -15,12 +16,10 @@ try:
     release = _get_version("synkit")
 except PackageNotFoundError:
     try:
-        import synkit
-
-        release = synkit.__version__
+        release = m.version("synkit")
     except (ImportError, AttributeError):
         # Fallback default
-        release = "0.0.10"
+        release = "0.0.11"
 # Use only major.minor for short version
 version = ".".join(release.split(".")[:2])