| Name | nomad-neb-workflows JSON |
| Version |
1.0.2
JSON |
| download |
| home_page | None |
| Summary | A NOMAD plugin containing the section definitions of a standard Nudged Elastic Band (NEB) workflow. |
| upload_time | 2025-10-09 07:33:10 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| license | Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
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|
| keywords |
nomad
neb
materials-science
workflows
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
[](https://nomad-lab.eu/prod/v1/staging/gui/)
<!-- Add when the repo is published in pypi
-->
# nomad-neb-workflows
A NOMAD plugin containing the section definitions of a standard Nudged Elastic Band (NEB) workflow.
----
This `nomad`_ plugin was generated with `Cookiecutter`_ along with `@nomad`_'s `cookiecutter-nomad-plugin`_ template.
## Getting started
### Install the dependencies
Clone the project and in the workspace folder, create a virtual environment (note this project uses Python 3.9):
```sh
git clone https://github.com/FAIRmat-NFDI/nomad-neb-workflows.git
cd nomad-neb-workflows
python3.9 -m venv .pyenv
. .pyenv/bin/activate
```
Make sure to have `pip` upgraded:
```sh
pip install --upgrade pip
```
We recommend installing `uv` for fast pip installation of the packages:
```sh
pip install uv
```
Install the `nomad-lab` package:
```sh
uv pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
```
**Note!**
Until we have an official pypi NOMAD release with the plugins functionality. Make
sure to include NOMAD's internal package registry (via `--index-url` in the above command).
The plugin is still under development. If you would like to contribute, install the package in editable mode (with the added `-e` flag) with the development dependencies:
```sh
uv pip install -e '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
```
### Run the tests
You can run local tests using the `pytest` package:
```sh
python -m pytest -sv tests
```
where the `-s` and `-v` options toggle the output verbosity.
Our CI/CD pipeline produces a more comprehensive test report using `coverage` and `coveralls` packages. We suggest you to generate your own coverage reports locally by doing:
```sh
uv pip install pytest-cov
python -m pytest --cov=src tests
```
### Setting up plugin on your local installation
Read the [NOMAD plugin documentation](https://nomad-lab.eu/prod/v1/staging/docs/howto/oasis/plugins_install.html) for all details on how to deploy the plugin on your NOMAD instance.
### Run linting and auto-formatting
```sh
ruff check .
ruff format . --check
```
Ruff auto-formatting is also a part of the GitHub workflow actions. Make sure that before you make a Pull Request, `ruff format . --check` runs in your local without any errors otherwise the workflow action will fail.
### Debugging
For interactive debugging of the tests, use `pytest` with the `--pdb` flag.
We recommend using an IDE for debugging, e.g., _VSCode_.
If using VSCode, you can add the following snippet to your `.vscode/launch.json`:
```json
{
"configurations": [
{
"name": "<descriptive tag>",
"type": "debugpy",
"request": "launch",
"cwd": "${workspaceFolder}",
"program": "${workspaceFolder}/.pyenv/bin/pytest",
"justMyCode": true,
"env": {
"_PYTEST_RAISE": "1"
},
"args": [
"-sv",
"--pdb",
"<path to plugin tests>",
]
}
]
}
```
where `${workspaceFolder}` refers to the NOMAD root.
The settings configuration file `.vscode/settings.json` performs automatically applies the linting upon saving the file progress.
### Build the python package
The `pyproject.toml` file contains everything that is necessary to turn the project
into a pip installable python package. Run the python build tool to create a package distribution:
```
uv pip install build
python -m build --sdist
```
You can install the package with pip:
```
uv pip install dist/nomad-neb-workflows-0.1.0
```
Read more about python packages, `pyproject.toml`, and how to upload packages to PyPI
on the [PyPI documentation](https://packaging.python.org/en/latest/tutorials/packaging-projects/).
### Documentation on Github pages
To deploy documentation on Github pages, make sure to [enable GitHub pages via the repo settings](https://docs.github.com/en/pages/getting-started-with-github-pages/configuring-a-publishing-source-for-your-github-pages-site#publishing-from-a-branch).
To view the documentation locally, install the documentation related packages using:
```sh
uv pip install -r requirements_docs.txt
```
Run the documentation server:
```sh
mkdocs serve
```
### Template update
We use cruft to update the project based on template changes. A `cruft-update.yml` is included in Github workflows to automatically check for updates and create pull requests to apply updates. Follow the [instructions](https://github.blog/changelog/2022-05-03-github-actions-prevent-github-actions-from-creating-and-approving-pull-requests/) on how to enable Github Actions to create pull requests.
To run the check for updates locally, follow the instructions on [`cruft` website](https://cruft.github.io/cruft/#updating-a-project).
### License
Distributed under the terms of the `Apache Software License 2.0`_ license, "nomad-neb-workflows" is free and open source software
Raw data
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"home_page": null,
"name": "nomad-neb-workflows",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.10",
"maintainer_email": "Julia Schumann <julia.schumann@physik.hu-berlin.de>, Uday Gajera <uday.gajera@physik.hu-berlin.de>, Hampus N\u00e4sstr\u00f6m <hampus.naesstroem@physik.hu-berlin.de>",
"keywords": "NOMAD, NEB, materials-science, workflows",
"author": null,
"author_email": "Julia Schumann <julia.schumann@physik.hu-berlin.de>, Uday Gajera <uday.gajera@physik.hu-berlin.de>, \"Jose M. Pizarro\" <jose.pizarro@physik.hu-berlin.de>, Hampus N\u00e4sstr\u00f6m <hampus.naesstroem@physik.hu-berlin.de>",
"download_url": "https://files.pythonhosted.org/packages/9a/36/f431ca2a9e3dc638c879c8689f2e47576fef51c509b87c29dab130516aff/nomad_neb_workflows-1.0.2.tar.gz",
"platform": null,
"description": "[](https://nomad-lab.eu/prod/v1/staging/gui/)\n\n\n<!-- Add when the repo is published in pypi\n\n\n\n-->\n\n# nomad-neb-workflows\n\nA NOMAD plugin containing the section definitions of a standard Nudged Elastic Band (NEB) workflow.\n\n----\n\nThis `nomad`_ plugin was generated with `Cookiecutter`_ along with `@nomad`_'s `cookiecutter-nomad-plugin`_ template.\n\n\n## Getting started\n\n### Install the dependencies\n\nClone the project and in the workspace folder, create a virtual environment (note this project uses Python 3.9):\n\n```sh\ngit clone https://github.com/FAIRmat-NFDI/nomad-neb-workflows.git\ncd nomad-neb-workflows\npython3.9 -m venv .pyenv\n. .pyenv/bin/activate\n```\n\nMake sure to have `pip` upgraded:\n```sh\npip install --upgrade pip\n```\n\nWe recommend installing `uv` for fast pip installation of the packages:\n```sh\npip install uv\n```\n\nInstall the `nomad-lab` package:\n\n```sh\nuv pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple\n```\n\n**Note!**\nUntil we have an official pypi NOMAD release with the plugins functionality. Make\nsure to include NOMAD's internal package registry (via `--index-url` in the above command).\n\nThe plugin is still under development. If you would like to contribute, install the package in editable mode (with the added `-e` flag) with the development dependencies:\n\n```sh\nuv pip install -e '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple\n```\n\n### Run the tests\n\nYou can run local tests using the `pytest` package:\n\n```sh\npython -m pytest -sv tests\n```\n\nwhere the `-s` and `-v` options toggle the output verbosity.\n\nOur CI/CD pipeline produces a more comprehensive test report using `coverage` and `coveralls` packages. We suggest you to generate your own coverage reports locally by doing:\n\n```sh\nuv pip install pytest-cov\npython -m pytest --cov=src tests\n```\n\n### Setting up plugin on your local installation\n\nRead the [NOMAD plugin documentation](https://nomad-lab.eu/prod/v1/staging/docs/howto/oasis/plugins_install.html) for all details on how to deploy the plugin on your NOMAD instance.\n\n### Run linting and auto-formatting\n\n```sh\nruff check .\nruff format . --check\n```\n\nRuff auto-formatting is also a part of the GitHub workflow actions. Make sure that before you make a Pull Request, `ruff format . --check` runs in your local without any errors otherwise the workflow action will fail.\n\n### Debugging\n\nFor interactive debugging of the tests, use `pytest` with the `--pdb` flag.\nWe recommend using an IDE for debugging, e.g., _VSCode_.\nIf using VSCode, you can add the following snippet to your `.vscode/launch.json`:\n\n```json\n{\n \"configurations\": [\n {\n \"name\": \"<descriptive tag>\",\n \"type\": \"debugpy\",\n \"request\": \"launch\",\n \"cwd\": \"${workspaceFolder}\",\n \"program\": \"${workspaceFolder}/.pyenv/bin/pytest\",\n \"justMyCode\": true,\n \"env\": {\n \"_PYTEST_RAISE\": \"1\"\n },\n \"args\": [\n \"-sv\",\n \"--pdb\",\n \"<path to plugin tests>\",\n ]\n }\n ]\n}\n```\n\nwhere `${workspaceFolder}` refers to the NOMAD root.\n\nThe settings configuration file `.vscode/settings.json` performs automatically applies the linting upon saving the file progress.\n\n### Build the python package\n\nThe `pyproject.toml` file contains everything that is necessary to turn the project\ninto a pip installable python package. Run the python build tool to create a package distribution:\n\n```\nuv pip install build\npython -m build --sdist\n```\n\nYou can install the package with pip:\n\n```\nuv pip install dist/nomad-neb-workflows-0.1.0\n```\n\nRead more about python packages, `pyproject.toml`, and how to upload packages to PyPI\non the [PyPI documentation](https://packaging.python.org/en/latest/tutorials/packaging-projects/).\n\n### Documentation on Github pages\n\nTo deploy documentation on Github pages, make sure to [enable GitHub pages via the repo settings](https://docs.github.com/en/pages/getting-started-with-github-pages/configuring-a-publishing-source-for-your-github-pages-site#publishing-from-a-branch).\n\nTo view the documentation locally, install the documentation related packages using:\n\n```sh\nuv pip install -r requirements_docs.txt\n```\n\nRun the documentation server:\n```sh\nmkdocs serve\n```\n\n### Template update\n\nWe use cruft to update the project based on template changes. A `cruft-update.yml` is included in Github workflows to automatically check for updates and create pull requests to apply updates. Follow the [instructions](https://github.blog/changelog/2022-05-03-github-actions-prevent-github-actions-from-creating-and-approving-pull-requests/) on how to enable Github Actions to create pull requests.\n\nTo run the check for updates locally, follow the instructions on [`cruft` website](https://cruft.github.io/cruft/#updating-a-project).\n\n### License\nDistributed under the terms of the `Apache Software License 2.0`_ license, \"nomad-neb-workflows\" is free and open source software\n",
"bugtrack_url": null,
"license": "Apache License\n Version 2.0, January 2004\n http://www.apache.org/licenses/\n \n TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION\n \n 1. Definitions.\n \n \"License\" shall mean the terms and conditions for use, reproduction,\n and distribution as defined by Sections 1 through 9 of this document.\n \n \"Licensor\" shall mean the copyright owner or entity authorized by\n the copyright owner that is granting the License.\n \n \"Legal Entity\" shall mean the union of the acting entity and all\n other entities that control, are controlled by, or are under common\n control with that entity. For the purposes of this definition,\n \"control\" means (i) the power, direct or indirect, to cause the\n direction or management of such entity, whether by contract or\n otherwise, or (ii) ownership of fifty percent (50%) or more of the\n outstanding shares, or (iii) beneficial ownership of such entity.\n \n \"You\" (or \"Your\") shall mean an individual or Legal Entity\n exercising permissions granted by this License.\n \n \"Source\" form shall mean the preferred form for making modifications,\n including but not limited to software source code, documentation\n source, and configuration files.\n \n \"Object\" form shall mean any form resulting from mechanical\n transformation or translation of a Source form, including but\n not limited to compiled object code, generated documentation,\n and conversions to other media types.\n \n \"Work\" shall mean the work of authorship, whether in Source or\n Object form, made available under the License, as indicated by a\n copyright notice that is included in or attached to the work\n (an example is provided in the Appendix below).\n \n \"Derivative Works\" shall mean any work, whether in Source or Object\n form, that is based on (or derived from) the Work and for which the\n editorial revisions, annotations, elaborations, or other modifications\n represent, as a whole, an original work of authorship. For the purposes\n of this License, Derivative Works shall not include works that remain\n separable from, or merely link (or bind by name) to the interfaces of,\n the Work and Derivative Works thereof.\n \n \"Contribution\" shall mean any work of authorship, including\n the original version of the Work and any modifications or additions\n to that Work or Derivative Works thereof, that is intentionally\n submitted to Licensor for inclusion in the Work by the copyright owner\n or by an individual or Legal Entity authorized to submit on behalf of\n the copyright owner. For the purposes of this definition, \"submitted\"\n means any form of electronic, verbal, or written communication sent\n to the Licensor or its representatives, including but not limited to\n communication on electronic mailing lists, source code control systems,\n and issue tracking systems that are managed by, or on behalf of, the\n Licensor for the purpose of discussing and improving the Work, but\n excluding communication that is conspicuously marked or otherwise\n designated in writing by the copyright owner as \"Not a Contribution.\"\n \n \"Contributor\" shall mean Licensor and any individual or Legal Entity\n on behalf of whom a Contribution has been received by Licensor and\n subsequently incorporated within the Work.\n \n 2. Grant of Copyright License. Subject to the terms and conditions of\n this License, each Contributor hereby grants to You a perpetual,\n worldwide, non-exclusive, no-charge, royalty-free, irrevocable\n copyright license to reproduce, prepare Derivative Works of,\n publicly display, publicly perform, sublicense, and distribute the\n Work and such Derivative Works in Source or Object form.\n \n 3. Grant of Patent License. Subject to the terms and conditions of\n this License, each Contributor hereby grants to You a perpetual,\n worldwide, non-exclusive, no-charge, royalty-free, irrevocable\n (except as stated in this section) patent license to make, have made,\n use, offer to sell, sell, import, and otherwise transfer the Work,\n where such license applies only to those patent claims licensable\n by such Contributor that are necessarily infringed by their\n Contribution(s) alone or by combination of their Contribution(s)\n with the Work to which such Contribution(s) was submitted. If You\n institute patent litigation against any entity (including a\n cross-claim or counterclaim in a lawsuit) alleging that the Work\n or a Contribution incorporated within the Work constitutes direct\n or contributory patent infringement, then any patent licenses\n granted to You under this License for that Work shall terminate\n as of the date such litigation is filed.\n \n 4. Redistribution. You may reproduce and distribute copies of the\n Work or Derivative Works thereof in any medium, with or without\n modifications, and in Source or Object form, provided that You\n meet the following conditions:\n \n (a) You must give any other recipients of the Work or\n Derivative Works a copy of this License; and\n \n (b) You must cause any modified files to carry prominent notices\n stating that You changed the files; and\n \n (c) You must retain, in the Source form of any Derivative Works\n that You distribute, all copyright, patent, trademark, and\n attribution notices from the Source form of the Work,\n excluding those notices that do not pertain to any part of\n the Derivative Works; and\n \n (d) If the Work includes a \"NOTICE\" text file as part of its\n distribution, then any Derivative Works that You distribute must\n include a readable copy of the attribution notices contained\n within such NOTICE file, excluding those notices that do not\n pertain to any part of the Derivative Works, in at least one\n of the following places: within a NOTICE text file distributed\n as part of the Derivative Works; within the Source form or\n documentation, if provided along with the Derivative Works; or,\n within a display generated by the Derivative Works, if and\n wherever such third-party notices normally appear. The contents\n of the NOTICE file are for informational purposes only and\n do not modify the License. You may add Your own attribution\n notices within Derivative Works that You distribute, alongside\n or as an addendum to the NOTICE text from the Work, provided\n that such additional attribution notices cannot be construed\n as modifying the License.\n \n You may add Your own copyright statement to Your modifications and\n may provide additional or different license terms and conditions\n for use, reproduction, or distribution of Your modifications, or\n for any such Derivative Works as a whole, provided Your use,\n reproduction, and distribution of the Work otherwise complies with\n the conditions stated in this License.\n \n 5. Submission of Contributions. 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