Stack tour chicago

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff

.gitignore

@@ -212,3 +212,6 @@ src/experimental_binding_data.json
 src/rbfe_results*
 src/results
 src/bace_results*
+# pixi environments
+.pixi/*
+!.pixi/config.toml

README.md

@@ -4,11 +4,21 @@ You can find the demo notebook in `src/openfe_demo.ipynb`.
 
 See the [openfe git repo](https://github.com/OpenFreeEnergy/openfe) and [documentation](https://docs.openfree.energy/en/latest/) to learn more!
 
-## Installing openfe locally
+## Running the demo locally
 
+### using `pixi` 
+
+In this directory, run:
+
+```bash
+pixi run demo
+```
+
+
+### using `micromamba`
 To run the notebook locally, you'll need to install **openfe**:
 
-Installing from conda-forge is simplest, and you can use `micromamba` (recommended), `mamba` or `conda`:
+You can instead use `micromamba` (recommended), `mamba` or `conda`:
 
 ```bash
 

env.yaml

@@ -2,15 +2,6 @@ name: openfe-demo
 channels:
   - conda-forge
 dependencies:
-  - python=3.12
-  - openfe=1.11
+  - python=3.13
+  - openfe=1.12
   - notebook 
-  - pip
-  - pip:
-    # this commit removes some warnings that are still in v1.11 but
-    # will be removed in v1.12
-    - git+https://github.com/OpenFreeEnergy/openfe@dab402be8183
-    # cinnabar v0.6.0 and openfe_analysis v0.5.0 will come packaged with openfe v1.12,
-    # but we want to show them off in this demo early!
-    - git+https://github.com/OpenFreeEnergy/cinnabar@0.6.0
-    - git+https://github.com/OpenFreeEnergy/openfe_analysis@v0.5.0