{"id":20915669,"url":"https://github.com/markovmodel/pyemma-workshop","last_synced_at":"2025-05-13T10:33:20.424Z","repository":{"id":43791610,"uuid":"121513812","full_name":"markovmodel/pyemma-workshop","owner":"markovmodel","description":null,"archived":false,"fork":false,"pushed_at":"2022-02-24T08:27:18.000Z","size":3181,"stargazers_count":31,"open_issues_count":2,"forks_count":9,"subscribers_count":19,"default_branch":"master","last_synced_at":"2025-04-01T23:05:39.817Z","etag":null,"topics":["pyemma","workshop-materials"],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"lgpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/markovmodel.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2018-02-14T13:28:56.000Z","updated_at":"2025-03-12T01:52:57.000Z","dependencies_parsed_at":"2022-07-21T05:32:35.751Z","dependency_job_id":null,"html_url":"https://github.com/markovmodel/pyemma-workshop","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markovmodel%2Fpyemma-workshop","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markovmodel%2Fpyemma-workshop/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markovmodel%2Fpyemma-workshop/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markovmodel%2Fpyemma-workshop/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/markovmodel","download_url":"https://codeload.github.com/markovmodel/pyemma-workshop/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253923125,"owners_count":21984843,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["pyemma","workshop-materials"],"created_at":"2024-11-18T16:17:15.915Z","updated_at":"2025-05-13T10:33:20.008Z","avatar_url":"https://github.com/markovmodel.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# pyemma-workshop\n\n## Installation\nWe strongly recommend to install the latest `pyemma` and `deeptime` release from the anaconda Python distribution.\n\n### step 1: Miniconda\nIf you do not have miniconda or anaconda, please follow the instructions here for Python 3.8: https://conda.io/miniconda.html\n\nWe recommend to create a separate environment for the workshop, especially if you already have a anaconda/miniconda installation:\n```\n# these steps are optional but recommended\nconda create -n workshop\nconda activate workshop\n\n# this is not optional\nconda config --env --add channels conda-forge\n```\n\n---\n**NOTE**\n\nFor Windows users it makes sense to also install GIT if it is not already available on the system: ``conda install git``\n\n---\n\n### step 2: pyemma and deeptime\nInstallation of all required software packages works by simply executing:\n\n```bash\nconda install python=3.9 pyemma_tutorials networkx black\n```\n\nYou can test your deeptime installation but running the following in your environment:\n\n```bash\npython -c \"import deeptime; print(deeptime.__version__)\" \n```\n\nThis should print the latest version of deeptime.\n\n### step 3: activate some helpers\nIn order to activate some features of the notebooks that we will be using, please also run\n```bash\njupyter contrib nbextension install --sys-prefix\njupyter nbextension enable toc2/main\njupyter nbextension enable exercise2/main\njupyter nbextension enable nglview --py --sys-prefix\n```\n\nIn case you are already a conda and jupyter notebook user with various environments, you can install your environment Python kernel via\n```bash\npython -m ipykernel install --user --name workshop\n```\n\n## Sanity check\n\nYou can check whether you installed the correct versions by calling\n```\nconda list\n```\n\nPyEMMA should show up with version `2.5.11` and deeptime with version `0.4.1`.\n\n## Usage\n### only on the first day\nPlease clone (download) this repository to get local access to the worksheets.\n\n```bash\ngit clone https://github.com/markovmodel/pyemma-workshop.git\n```\nPlease remember *where* on your local hard disk you have written it!\n\n### every morning:\n\n#### activate environment (optional) \nSkip if you don't know what a conda environment is. Only if conda environment is used; name might differ.\n``` bash\nconda activate workshop\n```\n\n#### navigate to the right folder\nPlease navigate to the folder that you cloned from our github page.\n```bash\ncd path/to/pyemma-workshop/notebooks\n```\n\n#### start the jupyter notebook server\nThis command will start the notebook server:\n```bash\njupyter notebook\n```\n\nYour 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.\n\n### getting updates\nOnce you have a local clone of this repository, you can easily obtain updates with `git pull`. \nWe'll let you know once we have published anything new.\nIf you work directly in the notebooks that we provide, you might have to use the sequence (`git pull` will raise an error):\n```bash\ngit stash\ngit pull\ngit stash pop\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarkovmodel%2Fpyemma-workshop","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmarkovmodel%2Fpyemma-workshop","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarkovmodel%2Fpyemma-workshop/lists"}