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DNALLM Documentation Verification Report

Generated: 2026-05-14T09:39:35.920681+00:00Z Total code blocks: 529 Files scanned: 120 Markdown + 19 notebooks

Summary

Status Count
PASS 480
FAIL 11
SKIP 38
TIMEOUT 0

Details

CONTRIBUTING.md

Line Lang Status Error
351 python PASS
401 python PASS
35 bash PASS
41 bash PASS
49 bash PASS
67 bash PASS
77 bash PASS
104 bash PASS
116 bash PASS
129 bash PASS
147 bash PASS
153 bash PASS
172 bash PASS
181 bash PASS
190 bash PASS
196 bash PASS
205 bash PASS
220 bash PASS
238 bash PASS
436 bash PASS
478 bash PASS
494 bash PASS
500 bash PASS
624 bash PASS
253 cmd SKIP unsupported language: cmd
273 text SKIP unsupported language: text
383 SKIP unsupported language:
458 SKIP unsupported language:
514 markdown SKIP unsupported language: markdown

README.md

Line Lang Status Error
303 python SKIP requires async event loop context
229 python PASS
251 python PASS
266 python PASS
324 python PASS
15 bash PASS
69 bash PASS
100 bash PASS
128 bash PASS
172 bash PASS
185 bash PASS
289 bash PASS
298 bash PASS
354 bash PASS
369 bash PASS
381 bash PASS
435 bash PASS
473 bash PASS
406 SKIP unsupported language:

docs/concepts/biology/dna_sequences.md

Line Lang Status Error
21 SKIP unsupported language:

docs/concepts/biology/genomic_features.md

Line Lang Status Error
25 SKIP unsupported language:

docs/concepts/biology/sequence_analysis.md

Line Lang Status Error
13 python PASS
27 python PASS

docs/concepts/mcp.md

Line Lang Status Error
254 python PASS
119 SKIP unsupported language:
199 SKIP unsupported language:
211 javascript SKIP unsupported language: javascript
231 javascript SKIP unsupported language: javascript

docs/example/notebooks/overview.md

Line Lang Status Error
19 bash PASS

docs/faq/index.md

Line Lang Status Error
109 python PASS
133 python PASS
145 python PASS
35 bash PASS
51 bash PASS
56 bash PASS
69 bash PASS
171 bash PASS
176 bash PASS
270 bash PASS

docs/faq/install_troubleshooting.md

Line Lang Status Error
19 bash PASS
8 SKIP unsupported language:

docs/faq/models_troubleshooting.md

Line Lang Status Error
9 bash PASS

docs/getting_started/installation.md

Line Lang Status Error
22 bash PASS
50 bash PASS
73 bash PASS
94 bash PASS
151 bash PASS
167 bash PASS
186 bash PASS
205 bash PASS
227 bash PASS
243 bash PASS
259 bash PASS
288 bash PASS
305 bash PASS
323 bash PASS
338 bash PASS
364 bash PASS
380 bash PASS
389 bash PASS
398 bash PASS
406 bash PASS
412 bash PASS
418 bash PASS
424 bash PASS
434 bash PASS
442 bash PASS
450 bash PASS

docs/getting_started/quick_start.md

Line Lang Status Error
127 python PASS
150 python PASS
177 python PASS
210 python PASS
24 bash PASS
52 bash PASS
74 bash PASS
86 bash PASS
108 bash PASS
240 bash PASS
252 bash PASS
271 bash PASS

docs/index.md

Line Lang Status Error
129 python SKIP requires async event loop context
73 python PASS
95 python PASS
110 python PASS
45 bash PASS
144 bash PASS
156 bash PASS
180 bash PASS
206 SKIP unsupported language:

docs/resources/datahandling.md

Line Lang Status Error
30 python PASS
37 python PASS
87 python PASS

docs/resources/model_selection.md

Line Lang Status Error
66 python PASS
99 python PASS
91 yaml PASS

docs/resources/model_zoo.md

Line Lang Status Error
117 python PASS

docs/resources/models/bert_models.md

Line Lang Status Error
37 python PASS
53 python PASS
25 bash PASS

docs/resources/models/caduceus_models.md

Line Lang Status Error
37 python PASS
53 python PASS
25 bash PASS

docs/resources/models/esm_models.md

Line Lang Status Error
38 python PASS
62 python PASS
25 bash PASS

docs/resources/models/evo_models.md

Line Lang Status Error
65 python PASS
31 bash PASS
40 bash PASS
52 bash PASS

docs/resources/models/flash_attention_models.md

Line Lang Status Error
64 python PASS
40 bash PASS
53 bash PASS

docs/resources/models/hyena_models.md

Line Lang Status Error
40 python PASS
56 python PASS
25 bash PASS

docs/resources/models/llama_models.md

Line Lang Status Error
37 python PASS
53 python PASS
25 bash PASS

docs/resources/models/mamba_models.md

Line Lang Status Error
56 python PASS
85 python PASS
29 bash PASS
38 bash PASS

docs/resources/models/special_models.md

Line Lang Status Error
33 python PASS
75 python PASS
108 python PASS
23 bash PASS
66 bash PASS
100 bash PASS
130 bash PASS
147 bash PASS

docs/resources/troubleshooting_models.md

Line Lang Status Error
78 python PASS
90 python PASS
26 bash PASS
32 bash PASS
45 bash PASS
69 yaml PASS

docs/user_guide/benchmark/advanced_techniques.md

Line Lang Status Error
19 python PASS
81 python PASS
111 python PASS
166 python PASS
230 python PASS
316 python PASS
355 python PASS
395 python PASS
446 python PASS
493 python PASS
534 python PASS
556 python PASS
578 python PASS

docs/user_guide/benchmark/configuration.md

Line Lang Status Error
640 python PASS
17 yaml PASS
40 yaml PASS
50 yaml PASS
93 yaml PASS
104 yaml PASS
142 yaml PASS
155 yaml PASS
166 yaml PASS
176 yaml PASS
187 yaml PASS
219 yaml PASS
229 yaml PASS
266 yaml PASS
293 yaml PASS
306 yaml PASS
340 yaml PASS
357 yaml PASS
367 yaml PASS
406 yaml PASS
443 yaml PASS
467 yaml PASS
496 yaml PASS
527 yaml PASS
604 yaml PASS
664 yaml PASS
681 yaml PASS
695 yaml PASS

docs/user_guide/benchmark/examples.md

Line Lang Status Error
13 python PASS
43 python PASS

docs/user_guide/benchmark/getting_started.md

Line Lang Status Error
29 python PASS
81 python PASS
140 python PASS
17 bash PASS
106 bash PASS
256 bash PASS
39 yaml PASS
222 yaml PASS
230 yaml PASS
237 yaml PASS
262 yaml PASS
269 yaml PASS
204 json FAIL Expecting value: line 1 column 2 (char 1)
196 csv PASS
212 fasta PASS

docs/user_guide/benchmark/index.md

Line Lang Status Error
33 python PASS

docs/user_guide/best_practices.md

Line Lang Status Error
15 python PASS
41 yaml PASS
53 yaml PASS

docs/user_guide/case_studies/motif_detection.md

Line Lang Status Error
42 python PASS
108 bash PASS
115 bash PASS
26 yaml PASS

docs/user_guide/case_studies/multi_task_learning.md

Line Lang Status Error
69 python PASS
38 yaml PASS
28 SKIP unsupported language:

docs/user_guide/case_studies/promoter_prediction.md

Line Lang Status Error
55 python PASS
23 yaml PASS
134 SKIP unsupported language:

docs/user_guide/case_studies/sequence_generation.md

Line Lang Status Error
44 python PASS
26 yaml PASS

docs/user_guide/cli/config_generator.md

Line Lang Status Error
17 bash PASS
197 bash PASS
208 bash PASS
218 bash PASS
229 bash PASS
50 yaml PASS
86 yaml PASS
114 yaml PASS
269 yaml PASS
280 yaml PASS
295 yaml PASS

docs/user_guide/cli/index.md

Line Lang Status Error
25 bash PASS
53 bash PASS

docs/user_guide/cli/mcp_server.md

Line Lang Status Error
256 python PASS
19 bash PASS
32 bash PASS
58 bash PASS
170 bash PASS
181 bash PASS
192 bash PASS
320 bash PASS
340 bash PASS
350 bash PASS
80 yaml PASS
214 yaml PASS
276 json FAIL Expecting property name enclosed in double quotes: line 1 column 2 (char 1)
293 javascript SKIP unsupported language: javascript

docs/user_guide/cli/usage.md

Line Lang Status Error
13 bash PASS
36 bash PASS
52 bash PASS
68 bash PASS
95 bash PASS
114 bash PASS
132 bash PASS
150 bash PASS
172 bash PASS
301 bash PASS
184 yaml PASS
210 yaml PASS
226 yaml PASS
255 SKIP unsupported language:

docs/user_guide/common_workflows.md

Line Lang Status Error
21 python PASS
64 python PASS

docs/user_guide/data_processing/data_augmentation.md

Line Lang Status Error
25 python SKIP empty code block

docs/user_guide/data_processing/data_preparation.md

Line Lang Status Error
56 csv PASS
66 text SKIP unsupported language: text

docs/user_guide/data_processing/format_conversion.md

Line Lang Status Error
23 python PASS
56 python PASS
84 python PASS
102 python PASS
34 json PASS
45 text SKIP unsupported language: text

docs/user_guide/data_processing/quality_control.md

Line Lang Status Error
15 python SKIP empty code block
26 python PASS

docs/user_guide/fine_tuning/advanced_techniques.md

Line Lang Status Error
20 python PASS
82 python PASS
115 python PASS
241 python PASS
275 python PASS
330 python PASS
380 python PASS
454 python PASS
525 python PASS
581 python PASS
315 yaml PASS

docs/user_guide/fine_tuning/configuration.md

Line Lang Status Error
16 yaml PASS
52 yaml PASS
75 yaml PASS
84 yaml PASS
92 yaml PASS
101 yaml PASS
108 yaml PASS
118 yaml PASS
136 yaml PASS
158 yaml PASS
166 yaml PASS
174 yaml PASS
183 yaml PASS
193 yaml PASS
214 yaml PASS
235 yaml PASS
252 yaml PASS
267 yaml PASS
278 yaml PASS
325 yaml PASS
368 yaml PASS
414 yaml PASS
458 yaml PASS
474 yaml PASS
493 yaml PASS
512 yaml PASS
529 yaml PASS

docs/user_guide/fine_tuning/getting_started.md

Line Lang Status Error
32 python PASS
81 python PASS
100 python PASS
121 python PASS
241 python PASS
17 bash PASS
145 bash PASS
309 bash PASS
47 yaml PASS
162 yaml PASS
184 yaml PASS
328 yaml PASS
368 yaml PASS
376 yaml PASS
384 yaml PASS
222 json FAIL Expecting value: line 1 column 2 (char 1)
214 csv PASS
230 fasta PASS

docs/user_guide/fine_tuning/index.md

Line Lang Status Error
35 python PASS

docs/user_guide/fine_tuning/task_guides.md

Line Lang Status Error
51 python PASS
142 python PASS
219 python PASS
296 python PASS
374 python PASS
453 python PASS
533 python PASS
583 python PASS
606 python PASS
624 python PASS
638 python PASS
25 yaml PASS
116 yaml PASS
193 yaml PASS
271 yaml PASS
348 yaml PASS
428 yaml PASS
507 yaml PASS
42 csv PASS
133 csv PASS
210 csv PASS
287 csv PASS
365 csv PASS
444 csv PASS
524 csv PASS

docs/user_guide/getting_started.md

Line Lang Status Error
79 python PASS
28 bash PASS
35 bash PASS
45 bash PASS
57 bash PASS
65 bash PASS

docs/user_guide/inference/advanced_inference.md

Line Lang Status Error
24 python PASS
71 python PASS
112 python PASS
126 python PASS

docs/user_guide/inference/basic_inference.md

Line Lang Status Error
17 python PASS
90 bash PASS
100 json FAIL Expecting property name enclosed in double quotes: line 1 column 2 (char 1)

docs/user_guide/inference/getting_started.md

Line Lang Status Error
28 bash PASS
51 yaml PASS

docs/user_guide/inference/mutagenesis_analysis.md

Line Lang Status Error
48 python PASS
81 python PASS
121 python PASS
150 python PASS

docs/user_guide/inference/performance_optimization.md

Line Lang Status Error
73 python PASS
108 python PASS
16 yaml PASS
30 yaml PASS

docs/user_guide/inference/visualization.md

Line Lang Status Error
39 python PASS
64 python PASS
89 python PASS
114 python PASS
144 python PASS
170 bash PASS

docs/user_guide/mcp/configuration.md

Line Lang Status Error
382 bash PASS
443 bash PASS
468 bash PASS
16 yaml PASS
34 yaml PASS
48 yaml PASS
67 yaml PASS
84 yaml PASS
106 yaml PASS
128 yaml PASS
145 yaml PASS
171 yaml PASS
199 yaml PASS
267 yaml PASS
305 yaml PASS
343 yaml PASS

docs/user_guide/mcp/startserver.md

Line Lang Status Error
314 python SKIP requires async event loop and running server
20 bash PASS
30 bash PASS
36 bash PASS
228 bash PASS
241 bash PASS
255 bash PASS
283 bash PASS
295 bash PASS
303 bash PASS
366 bash PASS
381 bash PASS
398 bash PASS
433 bash PASS
53 yaml PASS
113 yaml PASS
195 yaml PASS
412 yaml PASS
421 yaml PASS
266 text SKIP unsupported language: text

docs/user_guide/mcp/usage.md

Line Lang Status Error
226 python SKIP requires async event loop and running server
276 python SKIP requires async event loop and running server
320 python SKIP requires async event loop and running server
213 python PASS
426 python PASS
449 python PASS
475 python PASS
497 python PASS
550 python PASS
398 bash PASS
405 bash PASS
412 bash PASS
419 bash PASS
24 json FAIL Expecting property name enclosed in double quotes: line 1 column 2 (char 1)
50 json FAIL Expecting property name enclosed in double quotes: line 1 column 2 (char 1)
85 json FAIL Expecting property name enclosed in double quotes: line 1 column 2 (char 1)
159 json FAIL Expecting property name enclosed in double quotes: line 1 column 2 (char 1)
527 json FAIL Expecting property name enclosed in double quotes: line 1 column 2 (char 1)
534 json FAIL Expecting property name enclosed in double quotes: line 1 column 2 (char 1)
541 json FAIL Expecting property name enclosed in double quotes: line 1 column 2 (char 1)
350 javascript SKIP unsupported language: javascript

docs/user_guide/models.md

Line Lang Status Error
54 python PASS

docs/user_guide/performance/gpu_optimization.md

Line Lang Status Error
31 bash PASS
52 bash PASS
74 bash PASS
23 yaml PASS
80 yaml PASS

docs/user_guide/performance/inference_speed.md

Line Lang Status Error
38 python PASS
68 python PASS
20 yaml PASS

docs/user_guide/performance/memory_optimization.md

Line Lang Status Error
26 bash PASS
49 bash PASS
18 yaml PASS
43 yaml PASS

docs/user_guide/performance_guide.md

Line Lang Status Error
61 python PASS
21 bash PASS
30 bash PASS
11 yaml PASS
33 yaml PASS
46 yaml PASS

docs/user_guide/troubleshooting.md

Line Lang Status Error
50 python PASS
26 bash PASS
40 yaml PASS

docs/user_guide/tutorial/end_to_end_workflow.md

Line Lang Status Error
853 python SKIP requires running server instance to connect to
899 python SKIP requires running server instance to connect to
87 python PASS
130 python PASS
209 python PASS
251 python PASS
268 python PASS
380 python PASS
465 python PASS
548 python PASS
594 python PASS
646 python PASS
674 python PASS
695 python PASS
723 python PASS
1053 python PASS
1068 python PASS
1084 python PASS
1151 python PASS
34 bash PASS
56 bash PASS
334 bash PASS
842 bash PASS
878 bash SKIP requires running server instance to connect to
999 bash PASS
821 yaml SKIP requires server configuration file and runtime environment
154 yaml PASS
362 yaml PASS
448 yaml PASS
516 yaml PASS
627 yaml PASS
758 yaml PASS
821 yaml SKIP requires server configuration file and runtime environment
1015 yaml PASS
1025 yaml PASS
1033 yaml PASS
1112 yaml PASS
1128 yaml PASS
1162 yaml PASS
112 csv PASS
352 csv PASS
441 csv PASS
967 dockerfile PASS
121 tsv SKIP unsupported language: tsv
433 txt SKIP unsupported language: txt
1138 SKIP unsupported language:

Notebooks

example/notebooks/benchmark/benchmark.ipynb

Cell Status Error
0 FAIL [NbConvertApp] Converting notebook /home/forrest/Github/DNALLM/tmpg_tjtc4z.ipynb to notebook
Traceback (most recent call last):
File "/home/forrest/Github/DNALLM/.venv/bin/jupyter-nbconvert", line 6, in 
sys.exit(main())
         ~~~~^^

File "/home/forrest/Github/DNALLM/.venv/lib/python3.13/site-packages/jupyter_core/application.py", line 284, in launch_instance super().launch_instance(argv=argv, **kwargs) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/home/for | | 1 | FAIL | Execution halted due to earlier cell failure | | 3 | FAIL | Execution halted due to earlier cell failure | | 4 | FAIL | Execution halted due to earlier cell failure | | 5 | FAIL | Execution halted due to earlier cell failure | | 6 | FAIL | Execution halted due to earlier cell failure | | 7 | FAIL | Execution halted due to earlier cell failure |

example/notebooks/data_prepare/finetune/finetune_data.ipynb

Cell Status Error
0 FAIL [NbConvertApp] Converting notebook /home/forrest/Github/DNALLM/tmpf_yn4m6i.ipynb to notebook
Traceback (most recent call last):
File "/home/forrest/Github/DNALLM/.venv/bin/jupyter-nbconvert", line 6, in 
sys.exit(main())
         ~~~~^^

File "/home/forrest/Github/DNALLM/.venv/lib/python3.13/site-packages/jupyter_core/application.py", line 284, in launch_instance super().launch_instance(argv=argv, **kwargs) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/home/for | | 2 | FAIL | Execution halted due to earlier cell failure | | 3 | FAIL | Execution halted due to earlier cell failure | | 4 | FAIL | Execution halted due to earlier cell failure | | 5 | FAIL | Execution halted due to earlier cell failure | | 6 | FAIL | Execution halted due to earlier cell failure | | 7 | FAIL | Execution halted due to earlier cell failure | | 8 | FAIL | Execution halted due to earlier cell failure | | 10 | FAIL | Execution halted due to earlier cell failure | | 11 | FAIL | Execution halted due to earlier cell failure | | 12 | FAIL | Execution halted due to earlier cell failure | | 14 | FAIL | Execution halted due to earlier cell failure | | 15 | FAIL | Execution halted due to earlier cell failure | | 17 | FAIL | Execution halted due to earlier cell failure | | 18 | FAIL | Execution halted due to earlier cell failure | | 19 | FAIL | Execution halted due to earlier cell failure | | 20 | FAIL | Execution halted due to earlier cell failure | | 21 | FAIL | Execution halted due to earlier cell failure | | 22 | FAIL | Execution halted due to earlier cell failure | | 23 | FAIL | Execution halted due to earlier cell failure | | 24 | FAIL | Execution halted due to earlier cell failure |

example/notebooks/data_prepare/predict/predict_data.ipynb

Cell Status Error

example/notebooks/embedding_attention.ipynb

Cell Status Error
0 TIMEOUT Notebook execution timed out after 180s
1 TIMEOUT Notebook execution timed out after 180s
2 TIMEOUT Notebook execution timed out after 180s
3 TIMEOUT Notebook execution timed out after 180s
4 TIMEOUT Notebook execution timed out after 180s
5 TIMEOUT Notebook execution timed out after 180s
6 TIMEOUT Notebook execution timed out after 180s
8 TIMEOUT Notebook execution timed out after 180s
9 TIMEOUT Notebook execution timed out after 180s
11 TIMEOUT Notebook execution timed out after 180s
12 TIMEOUT Notebook execution timed out after 180s
14 TIMEOUT Notebook execution timed out after 180s
15 TIMEOUT Notebook execution timed out after 180s

example/notebooks/finetune_NER_task/data_generation_and_inference.ipynb

Cell Status Error
0 FAIL [NbConvertApp] Converting notebook /home/forrest/Github/DNALLM/tmphgyh6kgr.ipynb to notebook
Traceback (most recent call last):
File "/home/forrest/Github/DNALLM/.venv/bin/jupyter-nbconvert", line 6, in 
sys.exit(main())
         ~~~~^^

File "/home/forrest/Github/DNALLM/.venv/lib/python3.13/site-packages/jupyter_core/application.py", line 284, in launch_instance super().launch_instance(argv=argv, **kwargs) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/home/for | | 1 | FAIL | Execution halted due to earlier cell failure | | 2 | FAIL | Execution halted due to earlier cell failure | | 3 | FAIL | Execution halted due to earlier cell failure | | 4 | FAIL | Execution halted due to earlier cell failure | | 5 | FAIL | Execution halted due to earlier cell failure | | 6 | FAIL | Execution halted due to earlier cell failure | | 7 | FAIL | Execution halted due to earlier cell failure | | 8 | FAIL | Execution halted due to earlier cell failure | | 9 | FAIL | Execution halted due to earlier cell failure | | 10 | FAIL | Execution halted due to earlier cell failure | | 11 | FAIL | Execution halted due to earlier cell failure | | 12 | FAIL | Execution halted due to earlier cell failure | | 13 | FAIL | Execution halted due to earlier cell failure | | 14 | FAIL | Execution halted due to earlier cell failure | | 15 | FAIL | Execution halted due to earlier cell failure | | 16 | FAIL | Execution halted due to earlier cell failure | | 17 | FAIL | Execution halted due to earlier cell failure | | 18 | FAIL | Execution halted due to earlier cell failure | | 19 | FAIL | Execution halted due to earlier cell failure |

example/notebooks/finetune_NER_task/finetune_NER_task.ipynb

Cell Status Error
0 FAIL [NbConvertApp] Converting notebook /home/forrest/Github/DNALLM/tmpumzj0xvo.ipynb to notebook
Traceback (most recent call last):
File "/home/forrest/Github/DNALLM/.venv/bin/jupyter-nbconvert", line 6, in 
sys.exit(main())
         ~~~~^^

File "/home/forrest/Github/DNALLM/.venv/lib/python3.13/site-packages/jupyter_core/application.py", line 284, in launch_instance super().launch_instance(argv=argv, **kwargs) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/home/for | | 1 | FAIL | Execution halted due to earlier cell failure | | 2 | FAIL | Execution halted due to earlier cell failure | | 3 | FAIL | Execution halted due to earlier cell failure | | 4 | FAIL | Execution halted due to earlier cell failure | | 5 | FAIL | Execution halted due to earlier cell failure | | 6 | FAIL | Execution halted due to earlier cell failure |

example/notebooks/finetune_binary/finetune_binary.ipynb

Cell Status Error
0 FAIL [NbConvertApp] Converting notebook /home/forrest/Github/DNALLM/tmpwtyqoclg.ipynb to notebook
Traceback (most recent call last):
File "/home/forrest/Github/DNALLM/.venv/bin/jupyter-nbconvert", line 6, in 
sys.exit(main())
         ~~~~^^

File "/home/forrest/Github/DNALLM/.venv/lib/python3.13/site-packages/jupyter_core/application.py", line 284, in launch_instance super().launch_instance(argv=argv, **kwargs) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/home/for | | 1 | FAIL | Execution halted due to earlier cell failure | | 2 | FAIL | Execution halted due to earlier cell failure | | 3 | FAIL | Execution halted due to earlier cell failure | | 4 | FAIL | Execution halted due to earlier cell failure | | 5 | FAIL | Execution halted due to earlier cell failure | | 6 | FAIL | Execution halted due to earlier cell failure |

example/notebooks/finetune_custom_head/finetune.ipynb

Cell Status Error
0 FAIL [NbConvertApp] Converting notebook /home/forrest/Github/DNALLM/tmpx7u8lazp.ipynb to notebook
Traceback (most recent call last):
File "/home/forrest/Github/DNALLM/.venv/bin/jupyter-nbconvert", line 6, in 
sys.exit(main())
         ~~~~^^

File "/home/forrest/Github/DNALLM/.venv/lib/python3.13/site-packages/jupyter_core/application.py", line 284, in launch_instance super().launch_instance(argv=argv, **kwargs) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/home/for | | 2 | FAIL | Execution halted due to earlier cell failure | | 3 | FAIL | Execution halted due to earlier cell failure | | 4 | FAIL | Execution halted due to earlier cell failure | | 5 | FAIL | Execution halted due to earlier cell failure | | 6 | FAIL | Execution halted due to earlier cell failure | | 7 | FAIL | Execution halted due to earlier cell failure | | 9 | FAIL | Execution halted due to earlier cell failure | | 10 | FAIL | Execution halted due to earlier cell failure | | 11 | FAIL | Execution halted due to earlier cell failure | | 12 | FAIL | Execution halted due to earlier cell failure | | 13 | FAIL | Execution halted due to earlier cell failure | | 14 | FAIL | Execution halted due to earlier cell failure |

example/notebooks/finetune_generation/finetune_generation.ipynb

Cell Status Error
1 FAIL [NbConvertApp] Converting notebook /home/forrest/Github/DNALLM/tmph0sysem6.ipynb to notebook
Traceback (most recent call last):
File "/home/forrest/Github/DNALLM/.venv/bin/jupyter-nbconvert", line 6, in 
sys.exit(main())
         ~~~~^^

File "/home/forrest/Github/DNALLM/.venv/lib/python3.13/site-packages/jupyter_core/application.py", line 284, in launch_instance super().launch_instance(argv=argv, **kwargs) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/home/for | | 2 | FAIL | Execution halted due to earlier cell failure | | 3 | FAIL | Execution halted due to earlier cell failure | | 4 | FAIL | Execution halted due to earlier cell failure | | 5 | FAIL | Execution halted due to earlier cell failure | | 7 | FAIL | Execution halted due to earlier cell failure | | 8 | FAIL | Execution halted due to earlier cell failure | | 9 | FAIL | Execution halted due to earlier cell failure | | 10 | FAIL | Execution halted due to earlier cell failure | | 11 | FAIL | Execution halted due to earlier cell failure | | 12 | FAIL | Execution halted due to earlier cell failure | | 13 | FAIL | Execution halted due to earlier cell failure | | 15 | FAIL | Execution halted due to earlier cell failure | | 16 | FAIL | Execution halted due to earlier cell failure | | 17 | FAIL | Execution halted due to earlier cell failure | | 18 | FAIL | Execution halted due to earlier cell failure | | 19 | FAIL | Execution halted due to earlier cell failure | | 20 | FAIL | Execution halted due to earlier cell failure | | 21 | FAIL | Execution halted due to earlier cell failure | | 22 | FAIL | Execution halted due to earlier cell failure | | 23 | FAIL | Execution halted due to earlier cell failure | | 24 | FAIL | Execution halted due to earlier cell failure |

example/notebooks/finetune_multi_labels/finetune_multi_labels.ipynb

Cell Status Error
0 FAIL [NbConvertApp] Converting notebook /home/forrest/Github/DNALLM/tmpj6034k1i.ipynb to notebook
Traceback (most recent call last):
File "/home/forrest/Github/DNALLM/.venv/bin/jupyter-nbconvert", line 6, in 
sys.exit(main())
         ~~~~^^

File "/home/forrest/Github/DNALLM/.venv/lib/python3.13/site-packages/jupyter_core/application.py", line 284, in launch_instance super().launch_instance(argv=argv, **kwargs) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/home/for | | 1 | FAIL | Execution halted due to earlier cell failure | | 2 | FAIL | Execution halted due to earlier cell failure | | 3 | FAIL | Execution halted due to earlier cell failure | | 4 | FAIL | Execution halted due to earlier cell failure | | 5 | FAIL | Execution halted due to earlier cell failure | | 6 | FAIL | Execution halted due to earlier cell failure |

example/notebooks/generation/inference.ipynb

Cell Status Error
0 FAIL [NbConvertApp] Converting notebook /home/forrest/Github/DNALLM/tmpxglj7fvn.ipynb to notebook
Traceback (most recent call last):
File "/home/forrest/Github/DNALLM/.venv/bin/jupyter-nbconvert", line 6, in 
sys.exit(main())
         ~~~~^^

File "/home/forrest/Github/DNALLM/.venv/lib/python3.13/site-packages/jupyter_core/application.py", line 284, in launch_instance super().launch_instance(argv=argv, **kwargs) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/home/for | | 1 | FAIL | Execution halted due to earlier cell failure | | 2 | FAIL | Execution halted due to earlier cell failure | | 3 | FAIL | Execution halted due to earlier cell failure | | 4 | FAIL | Execution halted due to earlier cell failure | | 5 | FAIL | Execution halted due to earlier cell failure |

example/notebooks/generation_evo_models/inference.ipynb

Cell Status Error
0 FAIL [NbConvertApp] Converting notebook /home/forrest/Github/DNALLM/tmp2vei3494.ipynb to notebook
Traceback (most recent call last):
File "/home/forrest/Github/DNALLM/.venv/bin/jupyter-nbconvert", line 6, in 
sys.exit(main())
         ~~~~^^

File "/home/forrest/Github/DNALLM/.venv/lib/python3.13/site-packages/jupyter_core/application.py", line 284, in launch_instance super().launch_instance(argv=argv, **kwargs) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/home/for | | 1 | FAIL | Execution halted due to earlier cell failure | | 3 | FAIL | Execution halted due to earlier cell failure | | 4 | FAIL | Execution halted due to earlier cell failure | | 5 | FAIL | Execution halted due to earlier cell failure | | 6 | FAIL | Execution halted due to earlier cell failure | | 7 | FAIL | Execution halted due to earlier cell failure | | 8 | FAIL | Execution halted due to earlier cell failure | | 10 | FAIL | Execution halted due to earlier cell failure | | 11 | FAIL | Execution halted due to earlier cell failure | | 12 | FAIL | Execution halted due to earlier cell failure | | 13 | FAIL | Execution halted due to earlier cell failure | | 14 | FAIL | Execution halted due to earlier cell failure | | 15 | FAIL | Execution halted due to earlier cell failure |

example/notebooks/generation_megaDNA/inference.ipynb

Cell Status Error
0 FAIL [NbConvertApp] Converting notebook /home/forrest/Github/DNALLM/tmpuc1di5_6.ipynb to notebook
Traceback (most recent call last):
File "/home/forrest/Github/DNALLM/.venv/bin/jupyter-nbconvert", line 6, in 
sys.exit(main())
         ~~~~^^

File "/home/forrest/Github/DNALLM/.venv/lib/python3.13/site-packages/jupyter_core/application.py", line 284, in launch_instance super().launch_instance(argv=argv, **kwargs) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/home/for | | 1 | FAIL | Execution halted due to earlier cell failure | | 2 | FAIL | Execution halted due to earlier cell failure | | 3 | FAIL | Execution halted due to earlier cell failure | | 4 | FAIL | Execution halted due to earlier cell failure | | 5 | FAIL | Execution halted due to earlier cell failure | | 6 | FAIL | Execution halted due to earlier cell failure | | 7 | FAIL | Execution halted due to earlier cell failure |

example/notebooks/in_silico_mutagenesis/in_silico_mutagenesis.ipynb

Cell Status Error
0 FAIL [NbConvertApp] Converting notebook /home/forrest/Github/DNALLM/tmpdjp2q1s3.ipynb to notebook
Traceback (most recent call last):
File "/home/forrest/Github/DNALLM/.venv/bin/jupyter-nbconvert", line 6, in 
sys.exit(main())
         ~~~~^^

File "/home/forrest/Github/DNALLM/.venv/lib/python3.13/site-packages/jupyter_core/application.py", line 284, in launch_instance super().launch_instance(argv=argv, **kwargs) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/home/for | | 1 | FAIL | Execution halted due to earlier cell failure | | 3 | FAIL | Execution halted due to earlier cell failure | | 4 | FAIL | Execution halted due to earlier cell failure | | 5 | FAIL | Execution halted due to earlier cell failure | | 6 | FAIL | Execution halted due to earlier cell failure | | 7 | FAIL | Execution halted due to earlier cell failure | | 8 | FAIL | Execution halted due to earlier cell failure |

example/notebooks/inference/inference.ipynb

Cell Status Error
0 FAIL [NbConvertApp] Converting notebook /home/forrest/Github/DNALLM/tmp3n9mrzx2.ipynb to notebook
Traceback (most recent call last):
File "/home/forrest/Github/DNALLM/.venv/bin/jupyter-nbconvert", line 6, in 
sys.exit(main())
         ~~~~^^

File "/home/forrest/Github/DNALLM/.venv/lib/python3.13/site-packages/jupyter_core/application.py", line 284, in launch_instance super().launch_instance(argv=argv, **kwargs) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/home/for | | 1 | FAIL | Execution halted due to earlier cell failure | | 3 | FAIL | Execution halted due to earlier cell failure | | 4 | FAIL | Execution halted due to earlier cell failure | | 5 | FAIL | Execution halted due to earlier cell failure | | 6 | FAIL | Execution halted due to earlier cell failure | | 7 | FAIL | Execution halted due to earlier cell failure |

example/notebooks/inference_for_tRNA/inference.ipynb

Cell Status Error
0 FAIL [NbConvertApp] Converting notebook /home/forrest/Github/DNALLM/tmp4atnxhvt.ipynb to notebook
Traceback (most recent call last):
File "/home/forrest/Github/DNALLM/.venv/bin/jupyter-nbconvert", line 6, in 
sys.exit(main())
         ~~~~^^

File "/home/forrest/Github/DNALLM/.venv/lib/python3.13/site-packages/jupyter_core/application.py", line 284, in launch_instance super().launch_instance(argv=argv, **kwargs) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/home/for | | 2 | FAIL | Execution halted due to earlier cell failure | | 3 | FAIL | Execution halted due to earlier cell failure | | 4 | FAIL | Execution halted due to earlier cell failure | | 7 | FAIL | Execution halted due to earlier cell failure | | 8 | FAIL | Execution halted due to earlier cell failure | | 9 | FAIL | Execution halted due to earlier cell failure |

example/notebooks/interpretation/interpretation.ipynb

Cell Status Error
0 FAIL [NbConvertApp] Converting notebook /home/forrest/Github/DNALLM/tmp0oz60w03.ipynb to notebook
Traceback (most recent call last):
File "/home/forrest/Github/DNALLM/.venv/bin/jupyter-nbconvert", line 6, in 
sys.exit(main())
         ~~~~^^

File "/home/forrest/Github/DNALLM/.venv/lib/python3.13/site-packages/jupyter_core/application.py", line 284, in launch_instance super().launch_instance(argv=argv, **kwargs) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/home/for | | 1 | FAIL | Execution halted due to earlier cell failure | | 2 | FAIL | Execution halted due to earlier cell failure | | 3 | FAIL | Execution halted due to earlier cell failure | | 4 | FAIL | Execution halted due to earlier cell failure | | 5 | FAIL | Execution halted due to earlier cell failure | | 6 | FAIL | Execution halted due to earlier cell failure | | 7 | FAIL | Execution halted due to earlier cell failure | | 8 | FAIL | Execution halted due to earlier cell failure | | 9 | FAIL | Execution halted due to earlier cell failure | | 11 | FAIL | Execution halted due to earlier cell failure | | 12 | FAIL | Execution halted due to earlier cell failure | | 13 | FAIL | Execution halted due to earlier cell failure | | 14 | FAIL | Execution halted due to earlier cell failure | | 15 | FAIL | Execution halted due to earlier cell failure | | 16 | FAIL | Execution halted due to earlier cell failure | | 17 | FAIL | Execution halted due to earlier cell failure |

example/notebooks/lora_finetune_inference/lora_finetune.ipynb

Cell Status Error
0 FAIL [NbConvertApp] Converting notebook /home/forrest/Github/DNALLM/tmprokzgtka.ipynb to notebook
Traceback (most recent call last):
File "/home/forrest/Github/DNALLM/.venv/bin/jupyter-nbconvert", line 6, in 
sys.exit(main())
         ~~~~^^

File "/home/forrest/Github/DNALLM/.venv/lib/python3.13/site-packages/jupyter_core/application.py", line 284, in launch_instance super().launch_instance(argv=argv, **kwargs) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/home/for | | 1 | FAIL | Execution halted due to earlier cell failure | | 2 | FAIL | Execution halted due to earlier cell failure | | 3 | FAIL | Execution halted due to earlier cell failure | | 4 | FAIL | Execution halted due to earlier cell failure | | 5 | FAIL | Execution halted due to earlier cell failure | | 6 | FAIL | Execution halted due to earlier cell failure |

example/notebooks/lora_finetune_inference/lora_inference.ipynb

Cell Status Error
0 FAIL [NbConvertApp] Converting notebook /home/forrest/Github/DNALLM/tmpjffjbfjs.ipynb to notebook
Traceback (most recent call last):
File "/home/forrest/Github/DNALLM/.venv/bin/jupyter-nbconvert", line 6, in 
sys.exit(main())
         ~~~~^^

File "/home/forrest/Github/DNALLM/.venv/lib/python3.13/site-packages/jupyter_core/application.py", line 284, in launch_instance super().launch_instance(argv=argv, **kwargs) ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ File "/home/for | | 1 | FAIL | Execution halted due to earlier cell failure | | 2 | FAIL | Execution halted due to earlier cell failure | | 3 | FAIL | Execution halted due to earlier cell failure | | 4 | FAIL | Execution halted due to earlier cell failure | | 5 | FAIL | Execution halted due to earlier cell failure | | 6 | FAIL | Execution halted due to earlier cell failure | | 7 | FAIL | Execution halted due to earlier cell failure |