Merge pull request #21 from CCPBioSim/jimboid-patch-1

Revise README for CCPBioSim OpenForcefield Workshop

Author: jimboid

README.md

@@ -1,15 +1,13 @@
-# 2025 CCPBioSim Training Week materials
+# CCPBioSim OpenForcefield Workshop
 
-[![CI](https://github.com/openforcefield/ccpbiosim-2025/actions/workflows/ci.yaml/badge.svg)](https://github.com/openforcefield/ccpbiosim-2025/actions/workflows/ci.yaml)
+[![ci](https://github.com/ccpbiosim/openff-workshop/actions/workflows/build.yaml/badge.svg?branch=main)](https://github.com/ccpbiosim/openff-workshop/actions/workflows/build.yaml)
+[![latest](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fccpbiosim.github.io%2Fworkshop.json&query=%24.containers.openff-workshop.latest&labelColor=grey&logo=github&logoColor=white&label=latest&color=purple)](https://github.com/ccpbiosim/openff-workshop/pkgs/container/openff-workshop) 
+[![issues](https://img.shields.io/github/issues/ccpbiosim/openff-workshop?logo=github&labelColor=grey)](https://github.com/CCPBioSim/openff-workshop/issues)
+[![pr](https://img.shields.io/github/issues-pr/ccpbiosim/openff-workshop?logo=github&labelColor=grey)](https://github.com/CCPBioSim/openff-workshop/pulls)
 
-These tutorials were delivered at the 2025 CCPBioSim training week, but are suitable for self-guided learning.
+This workshop source repository contains the build recipe for a docker container derived from the CCPBioSim JupyterHub image. This container adds the necessary software packages and notebook content to form a deployable course container.
 
-Presenters:
-
-* Danny Cole
-* Finlay Clark
-
-## Materials
+### Materials
 
 We recommend you view the materials in the following order:
 
@@ -19,17 +17,8 @@ We recommend you view the materials in the following order:
 
 Answers to most exercises are given in the [notebooks_with_solutions directory](notebooks_with_solutions).
 
-## Local installation
-
-To use these notebooks on your local machine, we recommend using [mamba](https://docs.openforcefield.org/en/latest/install.html#quick-install-guide) to create an environment from the provided YAML file:
-
-```shell
-$ mamba env create --file environment.yaml
-$ ...
-$ mamba activate openff-env
-```
 
-## More resources
+### More resources
 
 * Main [OpenFF docs](https://docs.openforcefield.org/en/latest/)
   * See "Projects" on the left for package-specific documentation
@@ -38,8 +27,32 @@ $ mamba activate openff-env
 * [Discussions](https://github.com/orgs/openforcefield/discussions) - for general usage questions
 
 
-## Acknowledgements
+### Acknowledgements
 
 Most of the material for the notebook [Parameterising small molecules with OpenFF](notebooks/small_molecule_parameterisation.ipynb) was adapted from the [2023 CCPBioSim Workshop Open Force Field Sessions](https://github.com/openforcefield/ccpbiosim-2023?) created by Matt Thompson and Jeff Wagner.
 
 Most of the material for the notebook [Parameterisation, molecular dynamics, and basic trajectory analysis for a protein-ligand complex](notebooks/protein_ligand_complex_parameterisation_and_md.ipynb) was adapted from the OpenFF [toolkit showcase](https://docs.openforcefield.org/en/latest/examples/openforcefield/openff-toolkit/toolkit_showcase/toolkit_showcase.html) and the [ProLIF Ligand-protein MD tutorial](https://prolif.readthedocs.io/en/latest/notebooks/md-ligand-protein.html#ligand-protein-md).
+
+## How to Use
+
+This training course is deployed on the [CCPBioSim](www.ccpbiosim.ac.uk) website via our cloud infrastructure, however you can deploy on your own machine with docker.
+
+Pull the container from our repository::
+
+    docker pull ghcr.io/ccpbiosim/openff-workshop:latest
+
+In our containers we are using the JupyterHub default port 8888, so you should
+forward this port when deploying locally::
+
+    docker run -p 8888:8888 ghcr.io/ccpbiosim/openff-workshop:latest
+
+## Authors
+
+Workshop Content Authors:
+
+- Danny Cole
+- Finlay Clark
+
+## Contact
+
+Please direct all questions and feedback to [Finlay Clark](mailto:finlay.clark@newcastle.ac.uk) or [Danny Cole](mailto:daniel.cole@newcastle.ac.uk)