Merge pull request #31 from fmoorhof/uv-dependency-management

Uv dependency management

Author: fmoorhof

.gitignore

@@ -7,6 +7,7 @@ __pycache__/
 .vscode/
 .idea/
 results/
+.venv/
 
 # C extensions
 *.so

Dockerfile

@@ -8,18 +8,20 @@ RUN apt-get update \
     && apt-get install -y --no-install-recommends git \
     && rm -rf /var/lib/apt/lists/*
 
-COPY requirements.txt /app/requirements.txt
+COPY pyproject.toml requirements.txt uv.lock /app/
+
 RUN \
-    pip install -r requirements.txt && \
-    pip install --no-dependencies git+https://github.com/ipb-halle/SelectZyme.git@f16adbc && \
-    python -c "from huggingface_hub import snapshot_download; snapshot_download(repo_id='davari-group/selectzyme-app-data', repo_type='dataset')"
+    pip install uv && \
+    uv sync --frozen && \
+    uv pip install --no-cache-dir --no-deps git+https://github.com/ipb-halle/SelectZyme.git@f16adbc && \
+    uv run python -c "from huggingface_hub import snapshot_download; snapshot_download(repo_id='davari-group/selectzyme-app-data', repo_type='dataset')"
 
 COPY . /app
-RUN pip install .
+RUN uv pip install .
 
 # Expose the port Dash will run on
 EXPOSE 8050
 
 # Run the Dash app [stack size (-s) in kbytes] 
-ENTRYPOINT ["bash", "-c", "ulimit -s 11040 && exec gunicorn app:server --bind 0.0.0.0:8050 --workers 1"]
+ENTRYPOINT ["bash", "-c", "ulimit -s 11040 && exec uv run gunicorn app:server --bind 0.0.0.0:8050 --workers 1"]
 # ENTRYPOINT ["bash", "-c", "ulimit -s 10240 && exec python app.py \"$@\"", "--"]  # old argparsing

README.md

@@ -1,6 +1,8 @@
 # SelectZyme-app
 Web application to host the pre calculated analyses by SelectZyme.
 
+![SelectZyme](assets/selectzyme_logo.png)
+
 ## Install
 Prerequisite for all installs is to clone the repository.
 ```
@@ -19,9 +21,14 @@ Access the server from your browser at: `localhost/`
 ### Local install to run a single case study
 Install dependencies defined in the `pyproject.toml` and SelectZyme without dependencies.
 ```
-pip install .
-pip install --no-dependencies git+https://github.com/ipb-halle/SelectZyme.git
+uv sync
+uv pip install --no-deps git+https://github.com/ipb-halle/SelectZyme.git
+```
+Troubleshooting install:
 ```
+uv pip install .
+```
+
 Usage: 
 ```
 python app.py  # runs example analysis 'demo' by default
@@ -88,4 +95,16 @@ http://ocean_ip/selectzyme/demo/
 
 
 # License
-MIT License
+MIT License
+
+## Citation
+
+This repository contains the source code for the application hosted at [https://selectzyme.app.ipb-halle.de/](https://selectzyme.app.ipb-halle.de/), showing selected pre-calculated case studies for the manuscript:<br>
+
+Felix Moorhoff<sup>*1*</sup>, David Medina-Ortiz<sup>*1*</sup>, Alicja Kotnis<sup>*1*</sup>, Ahmed Hassanin<sup>*1,2*</sup>, Mehdi D. Davari<sup>*1,\**</sup>, <br>“Visualize, Explore, and Select”: A protein Language Model-Based Approach Enabling Navigation of Protein Sequence Space for Enzyme Discovery and Mining<br>
+*Journal* 2026, 61, 3463-3476 <br>
+https://doi.org/10.64898/2026.03.23.712833 <br>
+
+<sup>*1*</sup><sub>Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany</sub> <br>
+<sup>*2*</sup><sub>Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, 71526 Assiut, Egypt</sub> <br>
+<sup>*\**</sup><sub>Corresponding author</sub> <br>