omnigenome 0.3.21a0__tar.gz → 0.3.23a0__tar.gz

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  1. {omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/PKG-INFO +37 -39
  2. {omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/omnigenome.egg-info/PKG-INFO +37 -39
  3. {omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/setup.py +3 -0
  4. {omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/LICENSE +0 -0
  5. {omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/omnigenome/__init__.py +0 -0
  6. {omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/omnigenome.egg-info/SOURCES.txt +0 -0
  7. {omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/omnigenome.egg-info/dependency_links.txt +0 -0
  8. {omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/omnigenome.egg-info/entry_points.txt +0 -0
  9. {omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/omnigenome.egg-info/requires.txt +0 -0
  10. {omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/omnigenome.egg-info/top_level.txt +0 -0
  11. {omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/setup.cfg +0 -0
  12. {omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/setup_omnigenome.py +0 -0
  13. {omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/tests/test_dataset_patterns.py +0 -0
  14. {omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/tests/test_examples_syntax.py +0 -0
  15. {omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/tests/test_inference_with_dataset.py +0 -0
  16. {omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/tests/test_model_loading.py +0 -0
  17. {omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/tests/test_rna_functions.py +0 -0
  18. {omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/tests/test_training_patterns.py +0 -0
{omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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- Metadata-Version: 2.4
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+ Metadata-Version: 2.1
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  Name: omnigenome
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- Version: 0.3.21a0
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+ Version: 0.3.23a0
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  Summary: OmniGenome: A comprehensive toolkit for genome analysis.
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  Home-page: https://github.com/yangheng95/OmniGenBench
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  Author: Yang, Heng
@@ -19,42 +19,12 @@ Classifier: Operating System :: OS Independent
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  Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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  Requires-Python: >=3.10
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  Description-Content-Type: text/markdown
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- License-File: LICENSE
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- Requires-Dist: omnigenbench>=0.3.3
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- Requires-Dist: findfile>=2.0.0
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- Requires-Dist: autocuda>=0.16
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- Requires-Dist: metric-visualizer>=0.9.6
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- Requires-Dist: termcolor
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- Requires-Dist: gitpython
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- Requires-Dist: torch>=2.6.0
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- Requires-Dist: pandas
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- Requires-Dist: viennarna
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- Requires-Dist: scikit-learn
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- Requires-Dist: accelerate
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- Requires-Dist: transformers>=4.46.0
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- Requires-Dist: packaging
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- Requires-Dist: peft
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- Requires-Dist: dill
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  Provides-Extra: dev
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- Requires-Dist: dill; extra == "dev"
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- Requires-Dist: pytest; extra == "dev"
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- Dynamic: author
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- Dynamic: author-email
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- Dynamic: classifier
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- Dynamic: description
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- Dynamic: description-content-type
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- Dynamic: home-page
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- Dynamic: license
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- Dynamic: license-file
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- Dynamic: platform
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- Dynamic: provides-extra
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- Dynamic: requires-dist
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- Dynamic: requires-python
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- Dynamic: summary
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-
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- ![favicon.png](asset/favicon.png)
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-
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- <h3 align="center">OmniGenBench provides an all-in-one solution for genomic foundation model finetuning, inference, deployment and automated benchmarking, designed for research and applications in genomics.</h3>
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+ License-File: LICENSE
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+
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+ [//]: # (![favicon.png]&#40;asset/favicon.png&#41;)
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+
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+ [//]: # (<h3 align="center">OmniGenBench provides an all-in-one solution for genomic foundation model finetuning, inference, deployment and automated benchmarking, designed for research and applications in genomics.</h3>)
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  <div align="center">
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@@ -124,15 +94,43 @@ pip install -e .
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  ```
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  ## Quick Start
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- `OmniGenBench is available for diverse models and benchmark suites, please refer to the following sections for more details.`
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+ `OmniGenBench is available for diverse models and benchmark suites, please refer to the following sections for more details.`
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+
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+ ### Auto-inference via CLI
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+ Run inference with fine-tuned models on genomic sequences:
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+ ```bash
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+ # Single sequence inference
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+ ogb autoinfer --model yangheng/ogb_tfb_finetuned --sequence "ATCGATCGATCGATCG" --output-file predictions.json
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+
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+ # Batch inference from file
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+ ogb autoinfer --model yangheng/ogb_te_finetuned --input-file sequences.json --batch-size 64 --output-file results.json
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+
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+ # Legacy command (still supported)
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+ autoinfer --model yangheng/ogb_tfb_finetuned --sequence "ATCGATCGATCG"
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+ ```
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+
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+ ### Auto-inference via Python API
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+ Or use the Python API for programmatic inference:
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+ ```python
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+ from omnigenbench import ModelHub
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+
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+ model = ModelHub.load("yangheng/ogb_tfb_finetuned")
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+ outputs = model.inference("ATCGATCGATCGATCGATCGATCGATCGATCG")
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+ print(outputs) # {'predictions': array([1, 0, 1, ...]), 'probabilities': array([0.92, 0.15, ...])}
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+ ```
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+ You can find more examples in the [Getting Started Guide](docs/GETTING_STARTED.md) and [AutoInfer Examples](examples/autoinfer_examples/).
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+
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  ### Auto-benchmark via CLI
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  The following command will download the model from the Hugging Face model hub and run the benchmark on the RGB benchmark:
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  ```bash
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+ # New unified command
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+ ogb autobench --model yangheng/OmniGenome-186M --benchmark RGB --trainer accelerate
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+
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+ # Legacy command (still supported)
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  autobench --model_name_or_path "yangheng/OmniGenome-186M" --benchmark "RGB" --trainer accelerate
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  ```
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  You can find a visualization of AutoBench [here](asset/AutoBench.gif).
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-
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  ### Auto-benchmark via Python API
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  Or you can use the following python code to run the auto-benchmark:
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  ```python
{omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/omnigenome.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
- Metadata-Version: 2.4
1
+ Metadata-Version: 2.1
2
2
  Name: omnigenome
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- Version: 0.3.21a0
3
+ Version: 0.3.23a0
4
4
  Summary: OmniGenome: A comprehensive toolkit for genome analysis.
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  Home-page: https://github.com/yangheng95/OmniGenBench
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  Author: Yang, Heng
@@ -19,42 +19,12 @@ Classifier: Operating System :: OS Independent
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  Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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  Requires-Python: >=3.10
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  Description-Content-Type: text/markdown
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- License-File: LICENSE
23
- Requires-Dist: omnigenbench>=0.3.3
24
- Requires-Dist: findfile>=2.0.0
25
- Requires-Dist: autocuda>=0.16
26
- Requires-Dist: metric-visualizer>=0.9.6
27
- Requires-Dist: termcolor
28
- Requires-Dist: gitpython
29
- Requires-Dist: torch>=2.6.0
30
- Requires-Dist: pandas
31
- Requires-Dist: viennarna
32
- Requires-Dist: scikit-learn
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- Requires-Dist: accelerate
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- Requires-Dist: transformers>=4.46.0
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- Requires-Dist: packaging
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- Requires-Dist: peft
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- Requires-Dist: dill
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  Provides-Extra: dev
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- Requires-Dist: dill; extra == "dev"
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- Requires-Dist: pytest; extra == "dev"
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- Dynamic: author
42
- Dynamic: author-email
43
- Dynamic: classifier
44
- Dynamic: description
45
- Dynamic: description-content-type
46
- Dynamic: home-page
47
- Dynamic: license
48
- Dynamic: license-file
49
- Dynamic: platform
50
- Dynamic: provides-extra
51
- Dynamic: requires-dist
52
- Dynamic: requires-python
53
- Dynamic: summary
54
-
55
- ![favicon.png](asset/favicon.png)
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-
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- <h3 align="center">OmniGenBench provides an all-in-one solution for genomic foundation model finetuning, inference, deployment and automated benchmarking, designed for research and applications in genomics.</h3>
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+ License-File: LICENSE
24
+
25
+ [//]: # (![favicon.png]&#40;asset/favicon.png&#41;)
26
+
27
+ [//]: # (<h3 align="center">OmniGenBench provides an all-in-one solution for genomic foundation model finetuning, inference, deployment and automated benchmarking, designed for research and applications in genomics.</h3>)
58
28
 
59
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  <div align="center">
60
30
 
@@ -124,15 +94,43 @@ pip install -e .
124
94
  ```
125
95
 
126
96
  ## Quick Start
127
- `OmniGenBench is available for diverse models and benchmark suites, please refer to the following sections for more details.`
97
+ `OmniGenBench is available for diverse models and benchmark suites, please refer to the following sections for more details.`
98
+
99
+ ### Auto-inference via CLI
100
+ Run inference with fine-tuned models on genomic sequences:
101
+ ```bash
102
+ # Single sequence inference
103
+ ogb autoinfer --model yangheng/ogb_tfb_finetuned --sequence "ATCGATCGATCGATCG" --output-file predictions.json
104
+
105
+ # Batch inference from file
106
+ ogb autoinfer --model yangheng/ogb_te_finetuned --input-file sequences.json --batch-size 64 --output-file results.json
107
+
108
+ # Legacy command (still supported)
109
+ autoinfer --model yangheng/ogb_tfb_finetuned --sequence "ATCGATCGATCG"
110
+ ```
111
+
112
+ ### Auto-inference via Python API
113
+ Or use the Python API for programmatic inference:
114
+ ```python
115
+ from omnigenbench import ModelHub
116
+
117
+ model = ModelHub.load("yangheng/ogb_tfb_finetuned")
118
+ outputs = model.inference("ATCGATCGATCGATCGATCGATCGATCGATCG")
119
+ print(outputs) # {'predictions': array([1, 0, 1, ...]), 'probabilities': array([0.92, 0.15, ...])}
120
+ ```
121
+ You can find more examples in the [Getting Started Guide](docs/GETTING_STARTED.md) and [AutoInfer Examples](examples/autoinfer_examples/).
122
+
128
123
  ### Auto-benchmark via CLI
129
124
  The following command will download the model from the Hugging Face model hub and run the benchmark on the RGB benchmark:
130
125
  ```bash
126
+ # New unified command
127
+ ogb autobench --model yangheng/OmniGenome-186M --benchmark RGB --trainer accelerate
128
+
129
+ # Legacy command (still supported)
131
130
  autobench --model_name_or_path "yangheng/OmniGenome-186M" --benchmark "RGB" --trainer accelerate
132
131
  ```
133
132
  You can find a visualization of AutoBench [here](asset/AutoBench.gif).
134
133
 
135
-
136
134
  ### Auto-benchmark via Python API
137
135
  Or you can use the following python code to run the auto-benchmark:
138
136
  ```python
{omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/setup.py RENAMED
@@ -54,8 +54,11 @@ setup(
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  packages=find_packages(include=["omnigenbench", "omnigenbench.*", "omnigenome", "omnigenome.*"]),
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  entry_points={
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  "console_scripts": [
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+ "ogb=omnigenbench.cli.ogb_cli:main",
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+ # Legacy commands for backward compatibility
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  "autobench=omnigenbench.auto.auto_bench.auto_bench_cli:run_bench",
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  "autotrain=omnigenbench.auto.auto_train.auto_train_cli:run_train",
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+ "autoinfer=omnigenbench.cli.autoinfer_cli:main",
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  ],
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  },
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  install_requires=[
{omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/LICENSE RENAMED
File without changes
{omnigenome-0.3.21a0 → omnigenome-0.3.23a0}/setup.cfg RENAMED
File without changes