nomad-simulations
A NOMAD plugin containing base sections for simulations.
Science Score: 77.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
1 of 7 committers (14.3%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (10.5%) to scientific vocabulary
Repository
A NOMAD plugin containing base sections for simulations.
Basic Info
- Host: GitHub
- Owner: nomad-coe
- License: apache-2.0
- Language: Python
- Default Branch: develop
- Homepage: https://nomad-coe.github.io/nomad-simulations/
- Size: 1.9 MB
Statistics
- Stars: 6
- Watchers: 3
- Forks: 2
- Open Issues: 72
- Releases: 14
Metadata Files
README.md
nomad-simulations
The nomad-simulations is an open-source Python package for managing Materials Science simulation data. It is following the plugin architechture of NOMAD. This package contains a set of section definitions (Python classes) with quantities (attributes) and methods defined to automate data extraction from different simulation codes. These section definitions can be used at any prefered level by the user, they can be modified and extended, and we welcome external collaborators.
Read more in the official documentation page.
Getting started
nomad-simulations can be installed as a PyPI package using pip:
sh
pip install nomad-simulations
Development
If you want to develop locally this package, clone the project and in the workspace folder, create a virtual environment (you can use Python 3.10, 3.11, or 3.12):
sh
git clone https://github.com/nomad-coe/nomad-simulations.git
cd nomad-simulations
python3.11 -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]'
The plugin is still under development. If you would like to contribute, install the package in editable mode (with the added -e flag):
sh
uv pip install -e '.[dev]'
Run the tests
You can run locally the tests:
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 the pytest-cov package. You can generate a local coverage report:
sh
uv pip install pytest-cov
python -m pytest --cov=src tests
You can also run the script to generate a local file coverage.txt with the same information:
sh
./scripts/generate_coverage_txt.sh
Run linting and auto-formatting
We use Ruff for linting and formatting the code. Ruff auto-formatting is also a part of the GitHub workflow actions. You can run locally:
sh
ruff check .
ruff format . --check
Debugging
For interactive debugging of the tests, use pytest with the --pdb flag. We recommend using an IDE for debugging, e.g., VSCode. If that is the case, 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 <path-to-plugin-tests> must be changed to the local path to the test module to be debugged.
The settings configuration file .vscode/settings.json automatically applies the linting and formatting upon saving the modified file.
Documentation on Github pages
To view the documentation locally, install the related packages using:
sh
uv pip install -r requirements_docs.txt
Run the documentation server:
sh
mkdocs serve
Adding this plugin to NOMAD
Currently, NOMAD has two distinct flavors that are relevant depending on your role as an user: 1. A NOMAD Oasis: any user with a NOMAD Oasis instance. 2. Local NOMAD installation and the source code of NOMAD: internal developers.
Adding this plugin in your NOMAD Oasis
Read the NOMAD plugin documentation for all details on how to deploy the plugin on your NOMAD instance.
Adding this plugin in your local NOMAD installation and the source code of NOMAD
Modify the script under /nomad/scripts/install_default_plugins.sh and add the path to this repository pointing to the @develop branch:
sh
<other-content-in-install_default_plugins.sh...>
git+https://github.com/nomad-coe/nomad-simulations.git@develop
Then, go to your NOMAD folder, activate your NOMAD virtual environment and run:
sh
deactivate
cd <route-to-NOMAD-folder>/nomad
source .pyenv/bin/activate
./scripts/setup_dev_env.sh
Alternatively and only valid for your local NOMAD installation, you can modify nomad.yaml to include this plugin:
yaml
plugins:
entry_points:
include:
- ["nomad_simulations.schema_packages:nomad_simulations_plugin"]
Note!
Once you modify your nomad.yaml file adding include, all the default plugins will be disconnected, so you will need to include them as well.
How to cite this work
Pizarro, J.M., Boydas, E.B., Daelman, N., Ladines, A.N., Mohr, B. & Rudzinski, J.F., NOMAD Simulations [Computer software]. https://zenodo.org/doi/10.5281/zenodo.13838811
Main contributors
| Name | E-mail | Topics | Github profiles | |------|------------|--------|-----------------| | Dr. Nathan Daelman | nathan.daelman@physik.hu-berlin.de | DFT, Precision | @ndaelman-hu | | Dr. Bernadette Mohr | mohrbern@physik.hu-berlin.de | MD, FF | @Bernadette-Mohr | | Dr. José M. Pizarro | jose.pizarro@physik.hu-berlin.de | GW, DMFT, BSE | @JosePizarro3 | | Dr. Esma B. Boydas | esma.boydas@physik.hu-berlin.de | Quantum Chemistry | @EBB2675 | | Dr. Joseph F. Rudzinski (Coordinator) | joseph.rudzinski@physik.hu-berlin.de | General | @JFRudzinski |
Owner
- Name: NOMAD CoE and Laboratory
- Login: nomad-coe
- Kind: organization
- Email: contact@nomad-lab.eu
- Website: https://nomad-lab.eu/
- Twitter: NoMaDCoE
- Repositories: 102
- Profile: https://github.com/nomad-coe
This organisation of the Novel Materials Discovery (NOMAD) Center of Excellence and Laboratory develops FAIR tools for materials-science data.
Citation (CITATION.cff)
cff-version: 1.2.0
title: NOMAD Simulations
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: José M.
family-names: Pizarro
orcid: 'https://orcid.org/0000-0002-6751-8192'
- given-names: Esma B.
family-names: Boydas
orcid: 'https://orcid.org/0009-0005-6729-4706'
- given-names: Nathan
family-names: Daelman
orcid: 'https://orcid.org/0000-0002-7647-1816'
- given-names: Alvin Noe
family-names: Ladines
orcid: 'https://orcid.org/0000-0003-0077-2097'
- given-names: Bernadette
family-names: Mohr
orcid: 'https://orcid.org/0000-0003-0903-0073'
- given-names: Joseph F.
family-names: Rudzinski
orcid: 'https://orcid.org/0000-0003-3403-640X'
doi: 10.5281/zenodo.13838811
repository-code: 'https://github.com/nomad-coe/nomad-simulations'
url: 'https://nomad-coe.github.io/nomad-simulations/'
abstract: >-
`nomad-simulations` is a plugin for the NOMAD software (https://zenodo.org/doi/10.5281/zenodo.8366162)
providing a common data standard and analysis tools for parsed Materials Science and Quantum Chemistry
simulations. This standard is used as a template and is populated by the many available NOMAD parsers to transform their
inputs / outputs into a structured data format. This plugin is community-driven, and users are encourage to
contribute towards providing Findable, Accessible, Interoperable, and Reusable (FAIR) data.
license: Apache-2.0
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jose M. Pizarro | 1****3 | 59 |
| ndaelman-hu | 1****u | 11 |
| Joseph Rudzinski | J****i | 7 |
| Esma B. Boydas | 8****5 | 4 |
| ladinesa | 6****a | 3 |
| bernadette | b****r@u****l | 1 |
| Theodore Chang | t****m@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 78
- Total pull requests: 171
- Average time to close issues: about 2 months
- Average time to close pull requests: 19 days
- Total issue authors: 7
- Total pull request authors: 7
- Average comments per issue: 1.09
- Average comments per pull request: 2.96
- Merged pull requests: 98
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 55
- Pull requests: 103
- Average time to close issues: 16 days
- Average time to close pull requests: 12 days
- Issue authors: 7
- Pull request authors: 7
- Average comments per issue: 0.95
- Average comments per pull request: 2.24
- Merged pull requests: 52
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- JFRudzinski (30)
- JosePizarro3 (22)
- ndaelman-hu (13)
- EBB2675 (9)
- andreaa93 (2)
- ladinesa (1)
- Bernadette-Mohr (1)
Pull Request Authors
- JosePizarro3 (58)
- ndaelman-hu (40)
- JFRudzinski (37)
- EBB2675 (20)
- ladinesa (10)
- Bernadette-Mohr (4)
- TLCFEM (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 4,269 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 14
- Total maintainers: 2
pypi.org: nomad-simulations
A NOMAD plugin for FAIR schemas for simulation data.
- Homepage: https://github.com/nomad-coe/nomad-simulations
- Documentation: https://nomad-coe.github.io/nomad-simulations/
- License: Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 1. Definitions. "License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. "Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. "Legal Entity" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity. "You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License. "Source" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files. "Object" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types. "Work" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below). "Derivative Works" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof. "Contribution" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, "submitted" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as "Not a Contribution." "Contributor" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work. 2. Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form. 3. Grant of Patent License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer the Work, where such license applies only to those patent claims licensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You institute patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporated within the Work constitutes direct or contributory patent infringement, then any patent licenses granted to You under this License for that Work shall terminate as of the date such litigation is filed. 4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions: (a) You must give any other recipients of the Work or Derivative Works a copy of this License; and (b) You must cause any modified files to carry prominent notices stating that You changed the files; and (c) You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and (d) If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License. You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License. 5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions. 6. Trademarks. This License does not grant permission to use the trade names, trademarks, service marks, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and reproducing the content of the NOTICE file. 7. Disclaimer of Warranty. Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor provides its Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the appropriateness of using or redistributing the Work and assume any risks associated with Your exercise of permissions under this License. 8. Limitation of Liability. In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise, unless required by applicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses), even if such Contributor has been advised of the possibility of such damages. 9. Accepting Warranty or Additional Liability. While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability. END OF TERMS AND CONDITIONS APPENDIX: How to apply the Apache License to your work. To apply the Apache License to your work, attach the following boilerplate notice, with the fields enclosed by brackets "[]" replaced with your own identifying information. (Don't include the brackets!) The text should be enclosed in the appropriate comment syntax for the file format. We also recommend that a file or class name and description of purpose be included on the same "printed page" as the copyright notice for easier identification within third-party archives. Copyright [yyyy] [name of copyright owner] Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
-
Latest release: 0.4.0
published 10 months ago
Rankings
Maintainers (2)
Dependencies
- actions/checkout v3 composite
- actions/setup-python v2 composite
- chartboost/ruff-action v1 composite
- nomad-lab [infrastructure]@git+https://github.com/nomad-coe/nomad.git@develop
- actions/checkout v4 composite
- actions/setup-python v4 composite
- actions/checkout v4 composite
- actions/setup-python v4 composite
- sigstore/gh-action-sigstore-python v1.2.3 composite
- gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair latest build