From a0bd00b2f94fcab0d0e491d5ef3759e969890d73 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Simon=20Fl=C3=BCgel?= <43573433+sfluegel05@users.noreply.github.com> Date: Tue, 17 Feb 2026 16:03:22 +0100 Subject: [PATCH 1/3] Update dependencies in pyproject.toml Updated package versions and added new dependencies. --- pyproject.toml | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 60cd4fb..e90a456 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,13 +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", - + "chebai>=1.2.0", + "chemlog-extra", + "chemlog", + "c3p" # forked version of c3p is windows-compatible #"c3p @ git+https://github.com/sfluegel05/c3p.git" ] From 4037e636ecef532527d9ef21ffc335ab60d65100 Mon Sep 17 00:00:00 2001 From: sfluegel Date: Wed, 5 Aug 2026 19:08:57 +0200 Subject: [PATCH 2/3] add models extra --- pyproject.toml | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e90a456..e6f5cb4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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" @@ -22,15 +22,10 @@ dependencies = [ "pyyaml", "tqdm", "rdkit", - "chebai>=1.2.0", - "chemlog-extra", - "chemlog", - "c3p" - # 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"] @@ -39,3 +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" +] From d305409c49f4c51113b16fe5087b55e9a46dac48 Mon Sep 17 00:00:00 2001 From: sfluegel Date: Wed, 5 Aug 2026 19:09:13 +0200 Subject: [PATCH 3/3] update readme --- README.md | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 8d75fcd..0a6ce0d 100644 --- a/README.md +++ b/README.md @@ -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 @@ -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