Release v2.0.0

.github/workflows/tests.yml

@@ -30,11 +30,5 @@ jobs:
           python -m pip install --upgrade pip
           pip install -e .[dev]
 
-      - name: ruff lint
-        run: ruff check src
-
-      - name: ruff format check
-        run: ruff format --check src
-
       - name: run tests
         run: pytest -q

.gitignore

@@ -1,8 +1,8 @@
 .DS_Store
 .pytest_cache/
-.ruff_cache/
 .vscode/
 .idea/
 scratch/
 __pycache__/
-dist/
+dist/
+lib/

README.md

@@ -59,28 +59,15 @@ In either case a the output folder will contain a log file together with the res
 
 Any column, field, or property in the input file, either CSV, TSV, SDF, or JSON, is preserved as props in the output JSON or JSONL.
 
-Stereochemistry parsing is supported by supplying the `--matchstereochem` flag. This flag annotates the identifier of every identified monomer with R/S and E/Z annotation where applicable.
+Stereochemistry parsing is supported by supplying the `-c` flag.
 
-Result JSONs or lines from a JSONL file can be loaded into Python using RetroMol's `Result` class for further downstream analyses:
+Result JSONs or lines from a JSONL file can be loaded into Python using RetroMol's `Result` class for further downstream analyses.
 
-```python
-from retromol.io import Result
-
-result = Result.from_serialized(<json_dict>)
-
-# e.g., calculate coverage
-coverage = result.best_total_coverage()
-```
-
-Check out the [examples](https://github.com/moltools/RetroMol/tree/main/examples) folder for example scripts demonstrating how to use RetroMol as a library:
-* [Read out and align linear monomer readouts](https://github.com/moltools/RetroMol/tree/main/examples/align_compounds.py)
-* [Calculate and cluster monomer fingerprints](https://github.com/moltools/RetroMol/tree/main/examples/cluster_compounds.py)
+Check out the [examples](https://github.com/moltools/RetroMol/tree/main/examples) folder for example scripts demonstrating how to use RetroMol as a library.
 
 ### Using custom rules
 
-RetroMol comes with a default set of retrosynthetic rules for modular natural products.
-
-You can also provide your own custom rules and configurations. See [the custom rules documentation](docs/customize_rules.md) for details on the YAML formats supported.
+RetroMol comes with a default set of retrosynthetic rules for modular natural products. See [the default rules](src/retromol/data/) for examples of the included rules.
 
 ## Attribution
 
@@ -101,8 +88,6 @@ in "editable" mode with the development dependencies:
 git clone git+https://github.com/MolTools/RetroMol.git
 cd RetroMol
 pip install -e .[dev]
-pip install hatch     # if you don't have hatch installed yet; needed for building the package
-hatch env create dev  # create the development environment
 ```
 
 You can now make code changes locally and have them immediately available for testing.