From cecef4240ee437f9dccd21bd29604a14bf5e65cd Mon Sep 17 00:00:00 2001
From: Matthias Koenig <konigmatt@googlemail.com>
Date: Wed, 9 Sep 2026 22:33:30 +0200
Subject: [PATCH 1/2] Make streamlit optional, update sbmlutils and libsbml

Move streamlit and pandas out of the core dependencies into a new
`app` extra so that CLI and Python API users get a lightweight install.
Bump python-libsbml to >=5.21.1 and sbmlutils to >=0.10.2 (sbmlutils
0.10 moved its heavy dependencies to extras). Remove the unused
`packaging` dependency. Document the extras in the README.

Closes #7

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Ar3vD2HU6SWKcZoavQL6pz
---
 README.md        | 22 ++++++++++++++++++----
 pyproject.toml   | 12 +++++++-----
 requirements.txt |  5 ++---
 3 files changed, 27 insertions(+), 12 deletions(-)

diff --git a/README.md b/README.md
index 43d2774..2646e28 100644
--- a/README.md
+++ b/README.md
@@ -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
+```
 
 ---
 
@@ -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
 > ```
 
@@ -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)
 ```
 
diff --git a/pyproject.toml b/pyproject.toml
index 78ed5ea..ac6e8e9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -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"},
@@ -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",
diff --git a/requirements.txt b/requirements.txt
index d857aa7..fb13b25 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -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

From fe3f3de223a21386cdd7010f1435597452c3c614 Mon Sep 17 00:00:00 2001
From: Matthias Koenig <konigmatt@googlemail.com>
Date: Wed, 9 Sep 2026 22:34:02 +0200
Subject: [PATCH 2/2] Ignore uv.lock

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Ar3vD2HU6SWKcZoavQL6pz
---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 0608512..7a4d7c8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,3 +12,4 @@ notes.txt
 .mypy_cache/
 .pytest_cache/
 .coverage
+uv.lock