diff --git a/.github/workflows/publish-package.yml b/.github/workflows/publish-package.yml new file mode 100644 index 0000000..817b102 --- /dev/null +++ b/.github/workflows/publish-package.yml @@ -0,0 +1,49 @@ +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/syntemp + 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 \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..e596d23 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,40 @@ +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[project] +name = "syntemp" +version = "0.0.1" +authors = [ + {name="Tieu Long Phan", email="tieu@bioinf.uni-leipzig.de"} +] +description = "Test." +readme = "README.md" +requires-python = ">=3.11" +classifiers = [ + "Programming Language :: Python :: 3", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", +] +dependencies = [ + "dgl==2.1.0", + "dgllife==0.3.2", + "localmapper==0.1.3", + "rxn-chem-utils==1.5.0", + "rxn-utils==2.0.0", + "rxnmapper==0.3.0", + "chython==1.75", + "chytorch==1.60", + "chytorch-rxnmap==1.4", + "torchdata==0.7.1", + "rdkit==2023.9.5", + "networkx==3.3", + "fgutils==0.0.17", + "seaborn==0.13.2", + "joblib==1.3.2" +] + +[project.urls] +homepage = "https://github.com/TieuLongPhan/SynTemp" +source = "https://github.com/TieuLongPhan/SynTemp" +issues = "https://github.com/TieuLongPhan/SynTemp/issues" diff --git a/syntemp/__main__.py b/syntemp/__main__.py index e3dd02f..63a832d 100644 --- a/syntemp/__main__.py +++ b/syntemp/__main__.py @@ -25,7 +25,6 @@ def parse_arguments(): ) parser.add_argument( "--n_jobs", type=int, default=1, help="Number of jobs to run in parallel" - "--n_jobs", type=int, default=1, help="Number of jobs to run in parallel" ) parser.add_argument("--verbose", type=int, default=2, help="Verbosity level") parser.add_argument( @@ -83,7 +82,7 @@ def read_data(filepath): def main(): args = parse_arguments() - data = read_data(args.data_path)[0:] + data = read_data(args.data_path) try: auto = AutoTemp(