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hechth merged 4 commits into from
Dec 15, 2025
Merged

updated documentation #165

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updated documentation
acquayefrank Aug 25, 2025
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Delete docs/source/CHANGELOG.md
hechth Dec 15, 2025
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hechth Dec 15, 2025
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hechth Dec 15, 2025
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1 change: 1 addition & 0 deletions MSMetaEnhancer/libs/utils/ConverterBuilder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@ def validate_converters(converters):
for converter in converters:
try:
eval(converter)

except NameError:
raise UnknownConverter(f'Converter {converter} unknown.')

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9 changes: 5 additions & 4 deletions README.md
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Expand Up @@ -13,6 +13,7 @@ The app uses asynchronous implementation of annotation process allowing for opti
If you use MSMetaEnhancer in your work, please cite the following publication:

Troják et al., (2022). MSMetaEnhancer: A Python package for mass spectra metadata annotation. Journal of Open Source Software, 7(79), 4494, https://doi.org/10.21105/joss.04494

### Usage

```python
Expand All @@ -23,7 +24,7 @@ from MSMetaEnhancer import Application
app = Application()

# import your .msp file
app.load_spectra('tests/test_data/sample.msp', file_format='msp')
app.load_data('sample.msp', file_format='msp')

# curate given metadata (e.g. fix CAS numbers)
app.curate_metadata()
Expand All @@ -38,8 +39,8 @@ jobs = [('name', 'inchi', 'IDSM'), ('inchi', 'formula', 'IDSM'), ('inchi', 'inch
# run asynchronous annotations of spectra data
asyncio.run(app.annotate_spectra(services, jobs))

# export .msp file
app.save_spectra('tests/test_data/sample_out.msp', file_format='msp')
# export .msp file
app.save_data('sample_out.msp', file_format='msp')
```

### Installation
Expand All @@ -66,7 +67,7 @@ Create your development environment using the provided [script](conda/environmen

#### Contributing

We appreciate contributions - feel free to open an issue on our repository, create your own fork, work on the problem and post a PR.
We appreciate contributions - feel free to open an issue on our repository, create your own fork, work on the problem and post a PR.
Please add your contributions to the [changelog](CHANGELOG.md) and to adhere to the [versioning](https://semver.org/spec/v2.0.0.html).
For more information see [here](CONTRIBUTING.md).

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