spec2function 0.1.1__tar.gz

spec2function-0.1.1/LICENSE

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+MIT License
+
+Copyright (c) 2026 MS2Function contributors
+
+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.

spec2function-0.1.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: spec2function
+Version: 0.1.1
+Summary: Deep learning model for MS2 data annotation
+Home-page: https://huggingface.co/cgxjdzz/ms2function-assets
+Author: User
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: torch
+Requires-Dist: transformers
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: scikit-learn
+Requires-Dist: tqdm
+Requires-Dist: wandb
+Requires-Dist: huggingface_hub
+Dynamic: author
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# Spec2Function
+
+Spec2Function provides MS2 spectrum annotation and metabolite set analysis powered by
+MS2BioText models. Large model/data assets are hosted on Hugging Face Hub and are
+downloaded automatically on first use.
+
+## Install
+
+```bash
+pip install spec2function
+```
+
+Or for local development:
+
+```bash
+pip install -e .
+```
+
+## Assets (Hugging Face Hub)
+
+Default asset repo: `cgxjdzz/spec2function-assets`
+
+The package looks for the following files:
+
+- `models/best_model.pth`
+- `models/config.json`
+- `data/hmdb_subsections_WITH_NAME.jsonl`
+- `data/all_jsonl_embeddings.pt`
+
+Environment overrides:
+
+- `MS2FUNCTION_ASSET_DIR` (use local assets directory)
+- `MS2FUNCTION_ASSET_REPO` (override HF repo id)
+- `HUGGINGFACE_HUB_TOKEN` or `HF_TOKEN` (for private repos)
+
+## Quickstart (single spectrum)
+
+```python
+from pathlib import Path
+from Spec2Function import run_single
+
+json_input = {
+    "peaks": [[100.1, 200.0], [150.2, 300.0]],
+    "precursor_mz": 250.3,
+}
+
+result = run_single(json_input, project_root=Path(r"d:\NTU\Spec2Function"))
+print(result)
+```
+
+## Quickstart (metabolite set)
+
+```python
+from pathlib import Path
+from Spec2Function import run_set
+
+result = run_set(
+    r"d:\path\to\your.csv",
+    project_root=Path(r"d:\NTU\Spec2Function"),
+)
+print(result)
+```

spec2function-0.1.1/README.md

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+# Spec2Function
+
+Spec2Function provides MS2 spectrum annotation and metabolite set analysis powered by
+MS2BioText models. Large model/data assets are hosted on Hugging Face Hub and are
+downloaded automatically on first use.
+
+## Install
+
+```bash
+pip install spec2function
+```
+
+Or for local development:
+
+```bash
+pip install -e .
+```
+
+## Assets (Hugging Face Hub)
+
+Default asset repo: `cgxjdzz/spec2function-assets`
+
+The package looks for the following files:
+
+- `models/best_model.pth`
+- `models/config.json`
+- `data/hmdb_subsections_WITH_NAME.jsonl`
+- `data/all_jsonl_embeddings.pt`
+
+Environment overrides:
+
+- `MS2FUNCTION_ASSET_DIR` (use local assets directory)
+- `MS2FUNCTION_ASSET_REPO` (override HF repo id)
+- `HUGGINGFACE_HUB_TOKEN` or `HF_TOKEN` (for private repos)
+
+## Quickstart (single spectrum)
+
+```python
+from pathlib import Path
+from Spec2Function import run_single
+
+json_input = {
+    "peaks": [[100.1, 200.0], [150.2, 300.0]],
+    "precursor_mz": 250.3,
+}
+
+result = run_single(json_input, project_root=Path(r"d:\NTU\Spec2Function"))
+print(result)
+```
+
+## Quickstart (metabolite set)
+
+```python
+from pathlib import Path
+from Spec2Function import run_set
+
+result = run_set(
+    r"d:\path\to\your.csv",
+    project_root=Path(r"d:\NTU\Spec2Function"),
+)
+print(result)
+```