{"id":46996112,"url":"https://github.com/pyiron/pyiron-publication-template","last_synced_at":"2026-03-11T15:17:30.208Z","repository":{"id":45886733,"uuid":"349457836","full_name":"pyiron/pyiron-publication-template","owner":"pyiron","description":"Template repository - how to publish your pyiron workflow","archived":false,"fork":false,"pushed_at":"2024-05-22T14:30:02.000Z","size":2468,"stargazers_count":0,"open_issues_count":1,"forks_count":5,"subscribers_count":9,"default_branch":"main","last_synced_at":"2024-05-22T14:56:20.622Z","etag":null,"topics":["publication","pyiron"],"latest_commit_sha":null,"homepage":"http://pyiron.org/pyiron-publication-template/","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pyiron.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2021-03-19T14:49:49.000Z","updated_at":"2023-04-20T08:56:43.000Z","dependencies_parsed_at":"2022-09-05T08:10:52.214Z","dependency_job_id":null,"html_url":"https://github.com/pyiron/pyiron-publication-template","commit_stats":null,"previous_names":[],"tags_count":0,"template":true,"template_full_name":null,"purl":"pkg:github/pyiron/pyiron-publication-template","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pyiron%2Fpyiron-publication-template","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pyiron%2Fpyiron-publication-template/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pyiron%2Fpyiron-publication-template/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pyiron%2Fpyiron-publication-template/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pyiron","download_url":"https://codeload.github.com/pyiron/pyiron-publication-template/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pyiron%2Fpyiron-publication-template/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30385500,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-11T14:10:17.325Z","status":"ssl_error","status_checked_at":"2026-03-11T14:09:37.934Z","response_time":84,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["publication","pyiron"],"created_at":"2026-03-11T15:17:29.411Z","updated_at":"2026-03-11T15:17:30.197Z","avatar_url":"https://github.com/pyiron.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# pyiron publication template\nThis is a template repository how you can publish your calculation with pyiron. It consists of the repository [itself](https://github.com/pyiron/pyiron-publication-template), a small [website](http://pyiron.org/pyiron-publication-template/) created with Jupyterbook and a [mybinder environment](https://mybinder.org/v2/gh/pyiron/pyiron-publication-template/HEAD?filepath=notebooks%2Fexample.ipynb) for testing the calculation. \n\nYou can fork this repository and populate it with your own data.\n\n## Step by step\n* Move your notebooks to the repository folder and remove the example notebook `example.ipynb`.\n* Update the conda `environment.yml` file with the conda dependencies required for your notebook. \n* Include the export of your pyiron database in the `pyiron/calculation` folder or in case no calculation are required you can remove the `pyiron/calculation/save.tar.gz` archive and the `pyiron/calculation/export.csv` database backup file. \n* Include additional pyiron resources in the `pyiron/resources` folder if required, otherwise the `pyiron/resources` folder can be deleted.\n\n## Repository structure\nIn the following the repsoitory structure is explained in more detail: \n\n### notebooks \nThe repository folder contains one or more jupyter notebooks. These notebooks are executed during the unit tests and included in the website for easy readablity. The example notebook `example.ipynb` should be removed before publication. \n\n### conda environment\nThe repository folder also includes the conda `environment.yml` file which defines the conda environment required to execute the notebooks in the repository folder. An existing environment can be exported using `conda env export \u003e environment.yml` but it is recommended to reduce the environment to the minimal requirements as a large environment is less performant. Example conda `environment.yml` file: \n\n```python\nchannels:\n- conda-forge\ndependencies:\n- python\n- pyiron_atomistics =0.2.8\n- lammps =2021.02.10=*openmpi*_4\n- nglview =2.7.7\n```\n\n### Existing calculation\nThe `pyiron/calculation` folder includes previous calculation results which are published with this repository. In this example the calculation were calculated and exported using:\n\n```\nfrom pyiron_atomistics import Project\npr = Project(\"old_calculation\")\njob = pr.create.job.Lammps(job_name=\"lmp_si\")\njob.structure = pr.create.structure.ase.bulk(\"Si\")\njob.run()\npr.pack(destination_path=\"save\")\n```\n\nThe resulting files `export.csv` and `save.tar.gz` have been copied to the `pyiron/calculation` folder.\n\n### Additional pyiron resources \nJust like the pyiron resources folder the `pyiron/resources` folder can include additional resources like links to special executables or parameter files. In this example the `pyiron/resources` folder contains a special LAMMPS potential named `Si-quip-xml` which is required for the example notebook `example.ipynb`. \n\n### Jupyterbook \nThe jupyterbook is build using the github action `.github/workflows/book.yml` and it is deployed to github pages using `.github/workflows/deploy.yml`. Both github actions internally use the conda environment defined in `.github/ci_support/environment.yml`. But there should be no need to modify these files.\n\n### mybinder\nBesides the conda environment in `environment.yml` the `.binder/postBuild` script is used to import the calculations stored in `pyiron/calculation` and install `NGLview` for both jupyter notebooks and jupyter lab. Finally the pyiron environment on mybinder is configured using the `.binder/.pyiron` file in this repository. Only the conda environment file `environment.yml` has to be updated by the user.\n\n### Continuous integration \nThe rest of the files in the repository are used to test the environment. For continuous integration the github actions are defined in `.github/workflows/notebooks.yml`. Again the conda environment file `environment.yml` is used to install all the dependencies, afterwards pyiron is configured in the test environment using `.github/ci_support/pyironconfig.py` and finally the notebooks are executed using `.github/ci_support/build_notebooks.sh`. Usually there is no need for the user to adjust any of these files other than the conda environment `environment.yml` file.\n\n### License\npyiron and also the pyiron publication template are licensed under the BSD-3-Clause license which is included in the `LICENSE` file. In addition an `CODE_OF_CONDUCT.md` file is included to foster an open and welcoming environment.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpyiron%2Fpyiron-publication-template","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpyiron%2Fpyiron-publication-template","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpyiron%2Fpyiron-publication-template/lists"}