Note: This package is deprecated in favor of the Skeleton module within wk-libs (docs).
wknml
Python library for working with webKnossos skeleton annotation files (NML).
Installation
wknml requires Python 3.6+
pip install wknml
Documentation
See docs/wknml.md for an API documentation.
Examples
Some examples to get you started. Make sure to also check the examples directory:
# Load an NML file
with open("input.nml", "rb") as f:
nml = wknml.parse_nml(f)
# Access the most important properties
print(nml.parameters)
print(nml.trees)
print(nml.branchpoints)
print(nml.comments)
print(nml.groups)
# Iterate over all nodes
for tree in nml.trees:
for node in tree.nodes:
print(tree, node)
# Write a new NML file to disk
with open("out.nml", "wb") as f:
wknml.write_nml(f, nml)
# Convert an NML file with unlinked nodes to one with connected trees
python -m examples.fix_unlinked_nml <unlinked>.nml <fixed>.nml
Development
Make sure to install all the required dependencies using Poetry:
pip install poetry
poetry install
Please, format and test your code changes before merging them.
poetry run black wknml tests examples
poetry run pytest tests
PyPi releases are automatically pushed when creating a new Git tag/Github release. Make sure to bump the package version number manually:
poetry version <patch, minor, major>
If necessary, rebuild the documentation and commit to repository:
poetry run pydoc-markdown -m wknml -m wknml.nml_generation -m wknml.nml_utils --render-toc > docs/wknml.md
License
MIT License
1 maintainer
Metadata
1 maintainer
Release files for wknml 1.1.3
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
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| wknml-1.1.3.tar.gz | 12.5 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| wknml-1.1.3-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 25.3 kB
Release files / wknml-1.1.3.tar.gz
| Download URL | wknml-1.1.3.tar.gz |
|---|---|
| Size | 12.5 kB |
| Tags | Source |
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Release files / wknml-1.1.3-py3-none-any.whl
| Download URL | wknml-1.1.3-py3-none-any.whl |
|---|---|
| Size | 12.9 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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No |
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Security for wknml 1.1.3
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