https://github.com/helmholtz-ai-energy/hackasaurus-rex

https://github.com/helmholtz-ai-energy/hackasaurus-rex

Last synced: 5 months ago
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• Host: GitHub
• URL: https://github.com/helmholtz-ai-energy/hackasaurus-rex
• Owner: Helmholtz-AI-Energy
• License: bsd-3-clause
• Created: 2023-06-16T09:14:15.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2023-06-21T11:56:24.000Z (over 2 years ago)
• Last Synced: 2023-08-27T11:26:06.180Z (about 2 years ago)
• Language: Python
• Size: 198 KB
• Stars: 0
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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README

          
# hackasaurus-rex

Zenodo URL: https://zenodo.org/record/8063997

## Prediction

To run the prediction:

1. Adjust the config file `configs/detr_prot_predict.yml` and update the `data_root` to point to your data directory.

2. Once the config is updated, check to make sure that the data location is included in the `TOMOUNT` list of paths in `scripts/launch_job.sbatch`.

   The `TOMOUNT` variable is composed of paths which WHICH ARE SEPERATED BY COMMAS!

3. Run `scripts/predict.sh` to initialize the container and run the testing. The logs should end up in `/hkfs/work/workspace/scratch/ih5525-E2/slurm_logs`.

## Installation

In order to set up the necessary environment:

1. install in a container

   ```

   enroot create -n pyxis_torch PATH

   ```

2. To run code, use `scripts/launch_job.sbatch` This will launch a new sbatch job with the specified python job.

## Running a Testing job

1. Make sure that the script in `scripts/launch_job.sbatch` is the target python script

2. Ensure that the config selected in `scripts/launch_job.sbatch` is what you want to run (if you want to run on

   a different dataset, change the target parameter). If you want to train on the entire dataset you are giving it, make sure to

   set `split_data` in the config to `False`

3. launch the job with `sbatch scripts/launch_job.sbatch`

## Project Organization

```

├── AUTHORS.md              <- List of developers and maintainers.

├── CHANGELOG.md            <- Changelog to keep track of new features and fixes.

├── CONTRIBUTING.md         <- Guidelines for contributing to this project.

├── Dockerfile              <- Build a docker container with `docker build .`.

├── LICENSE.txt             <- License as chosen on the command-line.

├── README.md               <- The top-level README for developers.

├── configs                 <- Directory for configurations of model & application.

├── data

│   ├── external            <- Data from third party sources.

│   ├── interim             <- Intermediate data that has been transformed.

│   ├── processed           <- The final, canonical data sets for modeling.

│   └── raw                 <- The original, immutable data dump.

├── docs                    <- Directory for Sphinx documentation in rst or md.

├── environment.yml         <- The conda environment file for reproducibility.

├── models                  <- Trained and serialized models, model predictions,

│                              or model summaries.

├── notebooks               <- Jupyter notebooks. Naming convention is a number (for

│                              ordering), the creator's initials and a description,

│                              e.g. `1.0-fw-initial-data-exploration`.

├── pyproject.toml          <- Build configuration. Don't change! Use `pip install -e .`

│                              to install for development or to build `tox -e build`.

├── references              <- Data dictionaries, manuals, and all other materials.

├── reports                 <- Generated analysis as HTML, PDF, LaTeX, etc.

│   └── figures             <- Generated plots and figures for reports.

├── scripts                 <- Analysis and production scripts which import the

│                              actual PYTHON_PKG, e.g. train_model.

├── setup.cfg               <- Declarative configuration of your project.

├── setup.py                <- [DEPRECATED] Use `python setup.py develop` to install for

│                              development or `python setup.py bdist_wheel` to build.

├── src

│   └── hackasaurus_rex     <- Actual Python package where the main functionality goes.

├── tests                   <- Unit tests which can be run with `pytest`.

├── .coveragerc             <- Configuration for coverage reports of unit tests.

├── .isort.cfg              <- Configuration for git hook that sorts imports.

└── .pre-commit-config.yaml <- Configuration of pre-commit git hooks.

```

## Note

This project has been set up using [PyScaffold] 4.4.1 and the [dsproject extension] 0.7.2.

[conda]: https://docs.conda.io/

[pre-commit]: https://pre-commit.com/

[Jupyter]: https://jupyter.org/

[nbstripout]: https://github.com/kynan/nbstripout

[Google style]: http://google.github.io/styleguide/pyguide.html#38-comments-and-docstrings

[PyScaffold]: https://pyscaffold.org/

[dsproject extension]: https://github.com/pyscaffold/pyscaffoldext-dsproject