eclipse-ms 0.1.2__py3-none-any.whl

eclipse_ms-0.1.2.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: eclipse-ms
+Version: 0.1.2
+Summary: Conditional spectrum autoencoder and clustering for MS/MS dark-proteome discovery
+Project-URL: Homepage, https://github.com/VilenneFrederique/ECLIPSE
+Project-URL: Repository, https://github.com/VilenneFrederique/ECLIPSE
+Project-URL: Issues, https://github.com/VilenneFrederique/ECLIPSE/issues
+Author-email: Frederique Vilenne <frederique.vilenne@uhasselt.be>
+License: MIT License
+        
+        Copyright (c) 2026 Frederique Vilenne, Piotr Prostko, Dirk Valkenborg
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+License-File: LICENSE
+Keywords: autoencoder,clustering,deep learning,mass spectrometry,proteomics
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Requires-Dist: numpy>=1.23
+Requires-Dist: pandas>=1.5
+Requires-Dist: platformdirs>=3.0
+Requires-Dist: scikit-learn>=1.2
+Requires-Dist: tensorflow>=2.13
+Requires-Dist: tqdm>=4.64
+Provides-Extra: dev
+Requires-Dist: build>=1.0; extra == 'dev'
+Requires-Dist: pytest>=7.0; extra == 'dev'
+Requires-Dist: ruff>=0.1; extra == 'dev'
+Provides-Extra: hdbscan
+Requires-Dist: hdbscan>=0.8.33; extra == 'hdbscan'
+Provides-Extra: mzml
+Requires-Dist: pyteomics>=4.6; extra == 'mzml'
+Provides-Extra: train
+Requires-Dist: joblib>=1.2; extra == 'train'
+Requires-Dist: pyteomics>=4.6; extra == 'train'
+Requires-Dist: regex>=2023.0; extra == 'train'
+Requires-Dist: tqdm>=4.64; extra == 'train'
+Provides-Extra: viz
+Requires-Dist: matplotlib>=3.6; extra == 'viz'
+Requires-Dist: umap-learn>=0.5; extra == 'viz'
+Description-Content-Type: text/markdown
+
+# ECLIPSE
+
+**ECLIPSE** embeds MS/MS spectra with a conditional transformer autoencoder
+and clusters the latent space to discover candidate novel ("dark proteome")
+peptides. Spectra are conditioned on precursor *m/z*, charge, and ion mobility,
+so same-peptide spectra land close together in latent space.
+
+The trained model is large (~650 MB), so it is **not** shipped on PyPI. The pip
+package contains the code; the weights are hosted externally and downloaded +
+cached on first use. Because embedding only needs the **encoder**, the default
+download is encoder-only — roughly half the full model.
+
+## Installation
+
+```bash
+pip install eclipse-ms                 # core: load model, embed, cluster
+pip install "eclipse-ms[hdbscan]"      # add HDBSCAN clustering
+pip install "eclipse-ms[viz]"          # add plotting (matplotlib, umap)
+pip install "eclipse-ms[mzml]"         # add pyteomics for mzML
+pip install "eclipse-ms[train]"        # everything needed to retrain
+```
+
+TensorFlow is a core dependency (the encoder needs it) but is imported lazily —
+`import eclipse_ms` does not load TensorFlow until you actually build or load a
+model.
+
+## Getting the weights
+
+`load_encoder()` resolves the model files in this order:
+
+1. `ECLIPSE_MODEL_DIR` — set this to a folder holding the weights (handy on
+   an HPC node where you already have them):
+```bash
+   export ECLIPSE_MODEL_DIR=/path/to/weights
+```
+2. the local cache (downloaded once, then reused);
+3. download from the GitHub release (the URLs are configured in
+   `eclipse_ms.modelhub.REGISTRY`).
+
+With no setup, option 3 runs automatically on first use. You can also bypass
+the registry with explicit local paths:
+
+```python
+from eclipse_ms import load_encoder
+encoder = load_encoder(weights="encoder.weights.h5", config="encoder_config.json")
+```
+
+## Quick start
+
+```python
+import numpy as np
+from eclipse_ms import load_encoder, embed_raw_spectra, cluster_latents, score_clusters
+
+encoder = load_encoder()  # downloads/caches the encoder on first call
+
+# raw peak lists + precursor info (lists aligned by index)
+latents = embed_raw_spectra(
+    encoder,
+    mz_list, intensity_list,
+    precursor_mz, charge, ion_mobility,
+)
+
+labels, info = cluster_latents(latents, method="hdbscan", min_cluster_size=5)
+scores = score_clusters(latents, labels)
+print(info["n_clusters"], "clusters")
+```
+
+Command line:
+
+```bash
+eclipse embed   -i parquet_dir/ -o latents.npy
+eclipse cluster -i latents.npy  -o clusters/ --method hdbscan
+```
+
+## Repository layout
+
+```
+src/eclipse_ms/     installable package (model, embed, cluster, consensus, CLI)
+training/           NOT installed: HPC data-prep, training, and export scripts
+  export_encoder.py   run once to create the slim encoder assets to publish
+  reference/          the original monolithic scripts, kept verbatim
+tests/              run without TensorFlow or weights (model tests auto-skip)
+```
+
+## Citation
+Publication Pending!
+
+Vilenne, Frédérique & Valkenborg Dirk. Clustering the Dark Proteome: A Deep Learning Approach to Novel Peptide Discovery in Immunopeptidomics (2026)
+
+## License
+
+MIT © 2026 Frédérique Vilenne, Dirk Valkenborg

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eclipse_ms-0.1.2.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: hatchling 1.30.1
+Root-Is-Purelib: true
+Tag: py3-none-any

eclipse_ms-0.1.2.dist-info/entry_points.txt

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+[console_scripts]
+eclipse = eclipse_ms.cli:main

eclipse_ms-0.1.2.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Frederique Vilenne, Piotr Prostko, Dirk Valkenborg
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.