Prepare release (#7)

* fix bug

* change rule writing format Mg++ to Mg2+

* update uncertain hydrogen handling

* fix

* update source

* update source

* clean repo

* clean notebook

* clean notebook

* start cleaning

* update data AAM comparison

* cleaning

* clean

* enhance readme

* fix readme

* fix readme

* fix bug main

* prepare release

.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

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="[email protected]"}
+]
+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"

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(