Switch to colab (#69)

* first pass on getting onto colab

* fix key error

* few updates from code review

* final pass on notebook

* see if updating pins fix CI

* missing a python 3.9 ref

Author: mikemhenry

.binder/environment.yml

@@ -16,17 +16,17 @@ dependencies:
   - notebook
   - openff-forcefields
   - openmm
-  - openmmtools
+  - openmmtools>=0.23.0
   - pip
   - plugcli
   - pymbar
   - pytest
   - pytest-cov
   - pytest-xdist
   - pydantic
-  - python==3.9.*
+  - python==3.10.*
   - rdkit
   - typing_extensions
   - gufe>=0.7.1
-  - openfe>=0.7.1
-  - py3dmol
+  - openfe>=0.10.1
+  - py3dmol

.github/workflows/CI.yml

@@ -32,7 +32,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.9",]
+        python-version: ["3.10",]
 
     steps:
     - uses: actions/checkout@v2.4.0

README.md

@@ -1,7 +1,7 @@
 [![Logo](https://img.shields.io/badge/OSMF-OpenFreeEnergy-%23002f4a)](https://openfree.energy/)
 [![full_tests](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/CI.yml/badge.svg)](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/CI.yml)
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/OpenFreeEnergy/ExampleNotebooks/master.svg)](https://results.pre-commit.ci/latest/github/OpenFreeEnergy/ExampleNotebooks/main)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/OpenFreeEnergy/ExampleNotebooks/HEAD)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/OpenFreeEnergy/ExampleNotebooks/blob/main/openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb)
 
 # OpenFE Notebooks
 
@@ -10,8 +10,9 @@ These can be ran in the browser via the Binder links.
 
 | Binder link | Description |
 | --- | --- |
-| [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/OpenFreeEnergy/ExampleNotebooks/HEAD?labpath=openmm-rbfe%2FOpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb) | Start here.  This notebook demonstrates how a free energy calculation can be defined, executed and analyzed using the `openfe` package. |
-| [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/OpenFreeEnergy/ExampleNotebooks/HEAD?labpath=openmm-rbfe%2FApplyingProtocolToNetworkQuickrunDemo.ipynb) | Demonstrating how to plan a free energy network and apply a protocol |
+| [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/OpenFreeEnergy/ExampleNotebooks/blob/main/openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb)
+ | Start here.  This notebook demonstrates how a free energy calculation can be defined, executed and analyzed using the `openfe` package. |
+| [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/OpenFreeEnergy/ExampleNotebooks/HEAD?labpath=openmm-rbfe%2FApplyingProtocolToNetworkQuickrunDemo.ipynb) | Demonstrating how to plan a free energy network and apply a protocol Note: This notebook might not load if Binder is experiencing heavy usage. |
 
 ## Running these notebooks locally