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sfluegel05 merged 3 commits into from
Aug 5, 2026
Merged

Update dependencies in pyproject.toml #29

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a0bd00b
Update dependencies in pyproject.toml
sfluegel05 Feb 17, 2026
4037e63
add models extra
sfluegel05 Aug 5, 2026
d305409
update readme
sfluegel05 Aug 5, 2026
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19 changes: 11 additions & 8 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,6 @@ A web application for Chebifier is available at https://chebifier.hastingslab.or

## Installation

Not all models can be installed automatically at the moment:
- `chebai-graph` and its dependencies. To install them, follow
the instructions in the [chebai-graph repository](https://github.com/ChEB-AI/python-chebai-graph).
- `chemlog-extra` can be installed with `pip install git+https://github.com/ChEB-AI/chemlog-extra.git`
- The automatically installed version of `c3p` may not work under Windows. If you want to run chebifier on Windows, we
recommend using this forked version: `pip install git+https://github.com/sfluegel05/c3p.git`


You can get the package from PyPI:
```bash
pip install chebifier
Expand All @@ -29,6 +21,17 @@ cd python-chebifier
pip install -e .
```

By default, the models of the ensemble are not installed.
You can install them with the `[models]` extra:
```bash
pip install chebifier[models]
```

The Graph Neural Networks depend on `torch_geometric` and `torch_scatter` which you need to install separately ([depending on your CUDA version](https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html)). E.g.
```bash
pip install torch==2.12.0 torch_scatter torch_geometric -f https://data.pyg.org/whl/torch-2.12.0+cpu.html
```

## Usage

### Command Line Interface
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23 changes: 12 additions & 11 deletions pyproject.toml
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Expand Up @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"

[project]
name = "chebifier"
version = "1.2.1"
version = "1.2.2"
description = "An AI ensemble model for predicting chemical classes"
readme = "README.md"
requires-python = ">=3.9"
Expand All @@ -22,18 +22,10 @@ dependencies = [
"pyyaml",
"tqdm",
"rdkit",
# Package to install manually if required
#"chebai>=1.0.1",
#"chemlog>=1.0.4",

# pypi does not support git dependencies
#"chemlog_extra @ git+https://github.com/ChEB-AI/chemlog-extra.git",

# forked version of c3p is windows-compatible
#"c3p @ git+https://github.com/sfluegel05/c3p.git"
"jsonargparse[signatures]==4.27.7",
"scikit-learn"
]


[tool.setuptools]
packages = ["chebifier", "chebifier.ensemble", "chebifier.prediction_models"]

Expand All @@ -42,3 +34,12 @@ chebifier = ["*.yml"]

[project.optional-dependencies]
dev = ["black", "isort", "pre-commit"]

models = [
"chebai_graph==1.0.0",
"chebai==1.2.0",
"chemlog-extra==1.0.1",
"c3p"
# forked version of c3p is windows-compatible
#"c3p @ git+https://github.com/sfluegel05/c3p.git"
]
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