Add uv support alongside pixi

.gitignore

@@ -7,4 +7,8 @@
 
 notes.md
 
-documents
+documents
+
+# uv
+.venv/
+uv.lock

.python-version

@@ -0,0 +1 @@
+3.13

README.md

@@ -3,13 +3,30 @@ Simbio Tutorial for COMBINE 2026. To run in a browser following these links to r
 - https://marimo.app/https://github.com/dyscolab/simbio-tutorial/blob/main/tutorials/poincare_intro.py
 - https://marimo.app/https://github.com/dyscolab/simbio-tutorial/blob/main/tutorials/simbio_intro.py
 - https://marimo.app/https://github.com/dyscolab/simbio-tutorial/blob/main/tutorials/analysis.py
-
-For running it locally it is recommended to use [pixi](https://pixi.prefix.dev/latest/) to manage environments. Run 
+
+For running it locally, the dependencies are available via either pixi or uv.
+
+## pixi
+It is recommended to use [pixi](https://pixi.prefix.dev/latest/) to manage environments. Run
 
 ```pixi run open```
 
-to open landing page with all tutorial notebooks in browser or 
+to open landing page with all tutorial notebooks in browser or
 
 ```pixi run open [path to notebook]```
 
-to open a specific tutorial.
+to open a specific tutorial.
+
+## uv
+The same dependencies are also declared in `pyproject.toml` for [uv](https://docs.astral.sh/uv/). Run
+
+```uv run marimo edit tutorials```
+
+to open the landing page with all tutorial notebooks in browser or
+
+```uv run marimo edit tutorials/poincare_intro.py```
+```uv run marimo edit tutorials/simbio_intro.py```
+```uv run marimo edit tutorials/io.py```
+```uv run marimo edit tutorials/analysis.py```
+
+to open a specific tutorial. Use `uv run marimo run [path to notebook]` instead to open a tutorial as a read-only app with the code hidden.

pyproject.toml

@@ -0,0 +1,31 @@
+[project]
+name = "simbio-tutorial"
+version = "0.1.0"
+description = "Add your description here"
+readme = "README.md"
+requires-python = ">=3.13"
+dependencies = [
+    "biomodels>=0.3.2",
+    "ipykernel>=7.3.0",
+    "ipywidgets>=8.1.9",
+    "jablonski>=0.3.1",
+    "marimo>=0.20.2",
+    "matplotlib>=3.11.1",
+    "numpy>=2.4.2",
+    "poincare>=1.2.0",
+    "pylatex>=1.4.2",
+    "python-libsbml>=5.21.1",
+    "pyzmq>=27.1.0",
+    "rebop>=0.10.0",
+    "seaborn>=0.13.2",
+    "simbio>=1.2.0",
+    "symbolite>=1.1.1",
+]
+
+# marimo notebooks are not valid plain Python (top-level `async with app.setup()`),
+# so lint them with `marimo check` instead of ruff/ty.
+[tool.ruff]
+extend-exclude = ["tutorials"]
+
+[tool.ty.src]
+exclude = ["tutorials"]

tutorials/analysis.py

@@ -12,7 +12,7 @@
     if sys.executable == "/home/pyodide/this.program":
         import micropip
 
-        await micropip.install(
+        _ = await micropip.install(
             ["pint_pandas<=0.7", "typing_extensions>=4.15.0", "simbio>=1.2.0", "matplotlib"], verbose = False
         )
 

tutorials/io.py

@@ -14,7 +14,7 @@
     if sys.executable == "/home/pyodide/this.program":
         import micropip
 
-        await micropip.install(
+        _ = await micropip.install(
             ["pint_pandas<=0.7", "typing_extensions>=4.15.0", "simbio>=1.2.0", "matplotlib"], verbose = False
         )
 

tutorials/poincare_intro.py

@@ -12,7 +12,7 @@
     if sys.executable == "/home/pyodide/this.program":
         import micropip
 
-        await micropip.install(
+        _ = await micropip.install(
             ["pint_pandas<=0.7", "typing_extensions>=4.15.0", "poincare>=1.2.0", "matplotlib"], verbose = False
         )
 

tutorials/simbio_intro.py

@@ -12,7 +12,7 @@
     if sys.executable == "/home/pyodide/this.program":
         import micropip
 
-        await micropip.install(
+        _ = await micropip.install(
             ["pint_pandas<=0.7", "typing_extensions>=4.15.0", "simbio>=1.2.0", "matplotlib"], verbose = False
         )