omnigenome 0.3.13a0__tar.gz → 0.3.15a0__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.

This version of omnigenome might be problematic. Click here for more details.

Files changed (17) hide show
  1. {omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/PKG-INFO +9 -38
  2. {omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/omnigenome/__init__.py +7 -7
  3. {omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/omnigenome.egg-info/PKG-INFO +9 -38
  4. {omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/LICENSE +0 -0
  5. {omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/omnigenome.egg-info/SOURCES.txt +0 -0
  6. {omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/omnigenome.egg-info/dependency_links.txt +0 -0
  7. {omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/omnigenome.egg-info/entry_points.txt +0 -0
  8. {omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/omnigenome.egg-info/requires.txt +0 -0
  9. {omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/omnigenome.egg-info/top_level.txt +0 -0
  10. {omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/setup.cfg +0 -0
  11. {omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/setup.py +0 -0
  12. {omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/setup_omnigenome.py +0 -0
  13. {omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/tests/test_dataset_patterns.py +0 -0
  14. {omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/tests/test_examples_syntax.py +0 -0
  15. {omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/tests/test_model_loading.py +0 -0
  16. {omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/tests/test_rna_functions.py +0 -0
  17. {omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/tests/test_training_patterns.py +0 -0
{omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
- Metadata-Version: 2.4
1
+ Metadata-Version: 2.1
2
2
  Name: omnigenome
3
- Version: 0.3.13a0
3
+ Version: 0.3.15a0
4
4
  Summary: OmniGenome: A comprehensive toolkit for genome analysis.
5
5
  Home-page: https://github.com/yangheng95/OmniGenBench
6
6
  Author: Yang, Heng
@@ -19,38 +19,8 @@ Classifier: Operating System :: OS Independent
19
19
  Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
20
20
  Requires-Python: >=3.10
21
21
  Description-Content-Type: text/markdown
22
- 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
33
- Requires-Dist: accelerate
34
- Requires-Dist: transformers>=4.46.0
35
- Requires-Dist: packaging
36
- Requires-Dist: peft
37
- Requires-Dist: dill
38
22
  Provides-Extra: dev
39
- Requires-Dist: dill; extra == "dev"
40
- Requires-Dist: pytest; extra == "dev"
41
- 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
23
+ License-File: LICENSE
54
24
 
55
25
  ![favicon.png](asset/favicon.png)
56
26
 
@@ -145,7 +115,8 @@ seeds = [0, 1, 2, 3, 4]
145
115
  bench = AutoBench(benchmark=benchmark, model_name_or_path=gfm, overwrite=False)
146
116
  bench.run(autocast=False, batch_size=bench_size, seeds=seeds)
147
117
  ```
148
- You can find an example of AutoBench via Python API [here](examples/autobench/AutoBench_Tutorial.ipynb).
118
+ You can find an example of AutoBench via Python API [here](examples/autobench_gfm_evaluation/benchmarking_with_lora.ipynb).
119
+
149
120
 
150
121
  ## Supported Models
151
122
 
@@ -187,9 +158,9 @@ RNA design is a fundamental problem in synthetic biology,
187
158
  where the goal is to design RNA sequences that fold into a target structure.
188
159
  In this demo, we show how to use OmniGenoBench to design RNA sequences
189
160
  that fold into a target structure using a pre-trained model.
190
- The tutorials of RNA Design Demo can be found in [RNA_Design_Tutorial.ipynb](examples/rna_design/RNA_Design_Tutorial.ipynb).
161
+ The tutorials of RNA Design Demo can be found in [RNA_Design_Tutorial.ipynb](examples/rna_sequence_design/RNA_Design_Tutorial.ipynb).
191
162
 
192
- You can find a visual example of RNA Design [here](asset/RNA_Design.gif).
163
+ You can find a visual example of RNA Design [here](asset/RNADesign-Demo.gif).
193
164
 
194
165
  ### RNA Secondary Structure Prediction
195
166
 
@@ -199,10 +170,10 @@ In this demo, we show how to use OmniGenoBench to predict the secondary structur
199
170
  The tutorials of RNA Secondary Structure Prediction can be found in
200
171
  [Secondary_Structure_Prediction_Tutorial.ipynb](examples/rna_secondary_structure_prediction/Secondary_Structure_Prediction_Tutorial.ipynb).
201
172
 
202
- You can find a visual example of RNA Secondary Structure Prediction [here](asset/RNA_Structure_Prediction.gif).
173
+ You can find a visual example of RNA Secondary Structure Prediction [here](asset/RNASSP-Demo.gif).
203
174
 
204
175
  ### More Tutorials
205
- Please find more usage tutorials in [examples/tutorials](examples/tutorials).
176
+ Please find more usage tutorials in [examples](examples).
206
177
 
207
178
  ## Citation
208
179
  ```bibtex
{omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/omnigenome/__init__.py RENAMED
@@ -115,23 +115,23 @@ try:
115
115
  from omnigenbench.src.trainer.accelerate_trainer import AccelerateTrainer
116
116
 
117
117
  # Import hub utilities
118
- from omnigenbench.utility.hub_utils import (
118
+ from omnigenbench.src.utility.hub_utils import (
119
119
  download_benchmark,
120
120
  download_model,
121
121
  download_pipeline,
122
122
  query_models_info,
123
123
  )
124
- from omnigenbench.utility import hub_utils
124
+ from omnigenbench.src.utility import hub_utils
125
125
 
126
126
  # Import hub classes
127
- from omnigenbench.utility.model_hub.model_hub import ModelHub
128
- from omnigenbench.utility.dataset_hub.dataset_hub import load_benchmark_datasets
129
- from omnigenbench.utility.pipeline_hub.pipeline import Pipeline
130
- from omnigenbench.utility.pipeline_hub.pipeline_hub import PipelineHub
127
+ from omnigenbench.src.utility.model_hub.model_hub import ModelHub
128
+ from omnigenbench.src.utility.dataset_hub import load_benchmark_datasets
129
+ from omnigenbench.src.utility.pipeline_hub import Pipeline
130
+ from omnigenbench.src.utility.pipeline_hub.pipeline_hub import PipelineHub
131
131
 
132
132
  # Import module utilities
133
133
  from omnigenbench.src.model.module_utils import OmniPooling
134
- from omnigenbench.utility.ensemble import VoteEnsemblePredictor
134
+ from omnigenbench.src.utility import VoteEnsemblePredictor
135
135
 
136
136
  # For backward compatibility version 0.2.7alpha and earlier
137
137
  from omnigenbench.auto.config.auto_config import AutoBenchConfig
{omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/omnigenome.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
- Metadata-Version: 2.4
1
+ Metadata-Version: 2.1
2
2
  Name: omnigenome
3
- Version: 0.3.13a0
3
+ Version: 0.3.15a0
4
4
  Summary: OmniGenome: A comprehensive toolkit for genome analysis.
5
5
  Home-page: https://github.com/yangheng95/OmniGenBench
6
6
  Author: Yang, Heng
@@ -19,38 +19,8 @@ Classifier: Operating System :: OS Independent
19
19
  Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
20
20
  Requires-Python: >=3.10
21
21
  Description-Content-Type: text/markdown
22
- 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
33
- Requires-Dist: accelerate
34
- Requires-Dist: transformers>=4.46.0
35
- Requires-Dist: packaging
36
- Requires-Dist: peft
37
- Requires-Dist: dill
38
22
  Provides-Extra: dev
39
- Requires-Dist: dill; extra == "dev"
40
- Requires-Dist: pytest; extra == "dev"
41
- 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
23
+ License-File: LICENSE
54
24
 
55
25
  ![favicon.png](asset/favicon.png)
56
26
 
@@ -145,7 +115,8 @@ seeds = [0, 1, 2, 3, 4]
145
115
  bench = AutoBench(benchmark=benchmark, model_name_or_path=gfm, overwrite=False)
146
116
  bench.run(autocast=False, batch_size=bench_size, seeds=seeds)
147
117
  ```
148
- You can find an example of AutoBench via Python API [here](examples/autobench/AutoBench_Tutorial.ipynb).
118
+ You can find an example of AutoBench via Python API [here](examples/autobench_gfm_evaluation/benchmarking_with_lora.ipynb).
119
+
149
120
 
150
121
  ## Supported Models
151
122
 
@@ -187,9 +158,9 @@ RNA design is a fundamental problem in synthetic biology,
187
158
  where the goal is to design RNA sequences that fold into a target structure.
188
159
  In this demo, we show how to use OmniGenoBench to design RNA sequences
189
160
  that fold into a target structure using a pre-trained model.
190
- The tutorials of RNA Design Demo can be found in [RNA_Design_Tutorial.ipynb](examples/rna_design/RNA_Design_Tutorial.ipynb).
161
+ The tutorials of RNA Design Demo can be found in [RNA_Design_Tutorial.ipynb](examples/rna_sequence_design/RNA_Design_Tutorial.ipynb).
191
162
 
192
- You can find a visual example of RNA Design [here](asset/RNA_Design.gif).
163
+ You can find a visual example of RNA Design [here](asset/RNADesign-Demo.gif).
193
164
 
194
165
  ### RNA Secondary Structure Prediction
195
166
 
@@ -199,10 +170,10 @@ In this demo, we show how to use OmniGenoBench to predict the secondary structur
199
170
  The tutorials of RNA Secondary Structure Prediction can be found in
200
171
  [Secondary_Structure_Prediction_Tutorial.ipynb](examples/rna_secondary_structure_prediction/Secondary_Structure_Prediction_Tutorial.ipynb).
201
172
 
202
- You can find a visual example of RNA Secondary Structure Prediction [here](asset/RNA_Structure_Prediction.gif).
173
+ You can find a visual example of RNA Secondary Structure Prediction [here](asset/RNASSP-Demo.gif).
203
174
 
204
175
  ### More Tutorials
205
- Please find more usage tutorials in [examples/tutorials](examples/tutorials).
176
+ Please find more usage tutorials in [examples](examples).
206
177
 
207
178
  ## Citation
208
179
  ```bibtex
{omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/LICENSE RENAMED
File without changes
{omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/setup.cfg RENAMED
File without changes
{omnigenome-0.3.13a0 → omnigenome-0.3.15a0}/setup.py RENAMED
File without changes