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Make streamlit an optional dependency #8

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cecef42
Make streamlit optional, update sbmlutils and libsbml
matthiaskoenig Sep 9, 2026
fe3f3de
Ignore uv.lock
matthiaskoenig Sep 9, 2026
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -12,3 +12,4 @@ notes.txt
.mypy_cache/
.pytest_cache/
.coverage
uv.lock
22 changes: 18 additions & 4 deletions README.md
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Expand Up @@ -25,8 +25,20 @@ python -m pip install --upgrade pip
python -m pip install -e .
```

Python 3.11 or newer is required. For the optional FastAPI server, install
`.[api]`; for release development, install `.[test,release,api]`.
Python 3.11 or newer is required. The core package (CLI and Python API) has no
Streamlit dependency. Optional extras:

| Extra | Installs | Needed for |
|-------|----------|------------|
| `app` | streamlit, pandas | local Streamlit web app (`streamlit run app.py`) |
| `api` | fastapi, uvicorn, python-multipart | FastAPI server |
| `test` | pytest, mypy, flake8, httpx | running tests |

```bash
python -m pip install -e ".[app]" # web app
python -m pip install -e ".[app,api]" # web app + REST API
python -m pip install -e ".[test,release,api,app]" # release development
```

---

Expand All @@ -40,8 +52,10 @@ No installation required — open in your browser:

**[Launch Web App](https://tabularqual.streamlit.app/)**

> For large networks the Streamlit cloud may hit resource limits. Run locally instead:
> For large networks the Streamlit cloud may hit resource limits. Run locally instead
> (requires the `app` extra, see [Install](#install)):
> ```bash
> python -m pip install -e ".[app]"
> streamlit run app.py
> ```

Expand Down Expand Up @@ -237,7 +251,7 @@ Common ChEBI variants such as `chebi:35305` are normalized to the canonical
`CHEBI:35305` form before validation.

```bash
pip install sbmlutils>=0.9.6
pip install sbmlutils>=0.10.2
# then run without --no-validate (the default)
```

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12 changes: 7 additions & 5 deletions pyproject.toml
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Expand Up @@ -12,14 +12,11 @@ license = "MIT"
license-files = ["LICENSE"]
keywords = ["SBML", "SBML-qual", "logical models", "systems biology", "spreadsheet"]
dependencies = [
"python-libsbml>=5.21.0",
"python-libsbml>=5.21.1",
"openpyxl>=3.1.5",
"packaging>=24.0",
"click>=8.1.8",
"python-dateutil>=2.9.0",
"streamlit>=1.28.0",
"pandas>=2.0.0",
"sbmlutils>=0.9.6",
"sbmlutils>=0.10.2",
]
authors = [
{name = "Luna Li", email = "lixy@uw.edu"},
Expand All @@ -33,10 +30,15 @@ classifiers = [
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
"Programming Language :: Python :: 3.14",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]

[project.optional-dependencies]
app = [
"streamlit>=1.28.0",
"pandas>=2.2.0",
]
api = [
"fastapi>=0.115.0",
"python-multipart>=0.0.20",
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5 changes: 2 additions & 3 deletions requirements.txt
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@@ -1,11 +1,10 @@
python-libsbml>=5.21.0
python-libsbml>=5.21.1
openpyxl>=3.1.5
packaging>=24.0
click>=8.1.8
python-dateutil>=2.9.0
streamlit>=1.28.0
pandas>=2.0.0
sbmlutils>=0.9.6
sbmlutils>=0.10.2
fastapi>=0.115.0
uvicorn>=0.34.0
python-multipart>=0.0.20