deepmodeling / deepmodeling/dftio
[Code scan] Clean up non-portable example notebooks and unpublished pip command
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- Jupyter Notebook
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Description
This issue comes from a Codex global repository scan.
## Problem
Some examples are not reproducible from a fresh checkout.
`example/dftio_demo.ipynb` executes `Field.from_cube("xxx.cube")`, but no `xxx.cube` fixture exists in the repository:
https://github.com/deepmodeling/dftio/blob/c9d128f24a74ef2911e1a28f5640357488beb196/example/dftio_demo.ipynb#L87
The SIESTA notebooks contain private absolute paths and stale imports, so they fail outside the author's machine:
https://github.com/deepmodeling/dftio/blob/c9d128f24a74ef2911e1a28f5640357488beb196/dftio/io/siesta/try_siesta.ipynb#L11
https://github.com/deepmodeling/dftio/blob/c9d128f24a74ef2911e1a28f5640357488beb196/dftio/io/siesta/try_siesta.ipynb#L65
https://github.com/deepmodeling/dftio/blob/c9d128f24a74ef2911e1a28f5640357488beb196/dftio/io/siesta/check_siesta.ipynb#L9-L12
The README also shows an uncommented `pip install dftio` command under a “coming soon” heading, which fails while the package is not published to PyPI:
https://github.com/deepmodeling/dftio/blob/c9d128f24a74ef2911e1a28f5640357488beb196/README.md#L42-L46
## Suggested fix
Add a small cube fixture or make that notebook cell non-executed, replace private paths/stale imports in SIESTA notebooks with repo-relative examples, and remove or comment out the PyPI install command until publication.
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