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https://github.com/markovmodel/pyemma-workshop
https://github.com/markovmodel/pyemma-workshop
pyemma workshop-materials
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- Host: GitHub
- URL: https://github.com/markovmodel/pyemma-workshop
- Owner: markovmodel
- License: lgpl-3.0
- Created: 2018-02-14T13:28:56.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2022-02-24T08:27:18.000Z (almost 3 years ago)
- Last Synced: 2024-03-15T12:22:41.039Z (10 months ago)
- Topics: pyemma, workshop-materials
- Language: Jupyter Notebook
- Size: 3.03 MB
- Stars: 23
- Watchers: 20
- Forks: 9
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# pyemma-workshop
## Installation
We strongly recommend to install the latest `pyemma` and `deeptime` release from the anaconda Python distribution.
### step 1: Miniconda
If you do not have miniconda or anaconda, please follow the instructions here for Python 3.8: https://conda.io/miniconda.html
We recommend to create a separate environment for the workshop, especially if you already have a anaconda/miniconda installation:
```
# these steps are optional but recommended
conda create -n workshop
conda activate workshop
# this is not optional
conda config --env --add channels conda-forge
```
---
**NOTE**
For Windows users it makes sense to also install GIT if it is not already available on the system: ``conda install git``
---
### step 2: pyemma and deeptime
Installation of all required software packages works by simply executing:
```bash
conda install python=3.9 pyemma_tutorials networkx black
```
You can test your deeptime installation but running the following in your environment:
```bash
python -c "import deeptime; print(deeptime.__version__)"
```
This should print the latest version of deeptime.
### step 3: activate some helpers
In order to activate some features of the notebooks that we will be using, please also run
```bash
jupyter contrib nbextension install --sys-prefix
jupyter nbextension enable toc2/main
jupyter nbextension enable exercise2/main
jupyter nbextension enable nglview --py --sys-prefix
```
In case you are already a conda and jupyter notebook user with various environments, you can install your environment Python kernel via
```bash
python -m ipykernel install --user --name workshop
```
## Sanity check
You can check whether you installed the correct versions by calling
```
conda list
```
PyEMMA should show up with version `2.5.11` and deeptime with version `0.4.1`.
## Usage
### only on the first day
Please clone (download) this repository to get local access to the worksheets.
```bash
git clone https://github.com/markovmodel/pyemma-workshop.git
```
Please remember *where* on your local hard disk you have written it!
### every morning:
#### activate environment (optional)
Skip if you don't know what a conda environment is. Only if conda environment is used; name might differ.
``` bash
conda activate workshop
```
#### navigate to the right folder
Please navigate to the folder that you cloned from our github page.
```bash
cd path/to/pyemma-workshop/notebooks
```
#### start the jupyter notebook server
This command will start the notebook server:
```bash
jupyter notebook
```
Your browser should pop up pointing to a list of notebooks. If it's the wrong browser, add for example `--browser=firefox` or copy and paste the URL into the browser of your choice.
### getting updates
Once you have a local clone of this repository, you can easily obtain updates with `git pull`.
We'll let you know once we have published anything new.
If you work directly in the notebooks that we provide, you might have to use the sequence (`git pull` will raise an error):
```bash
git stash
git pull
git stash pop
```