cotlab 0.8.1__tar.gz → 0.8.2__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.
Files changed (180) hide show
  1. {cotlab-0.8.1 → cotlab-0.8.2}/Containerfile +4 -1
  2. {cotlab-0.8.1 → cotlab-0.8.2}/PKG-INFO +1 -1
  3. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/__init__.py +1 -1
  4. {cotlab-0.8.1 → cotlab-0.8.2}/.env.example +0 -0
  5. {cotlab-0.8.1 → cotlab-0.8.2}/.github/dependabot.yml +0 -0
  6. {cotlab-0.8.1 → cotlab-0.8.2}/.github/workflows/container.yml +0 -0
  7. {cotlab-0.8.1 → cotlab-0.8.2}/.github/workflows/docs.yml +0 -0
  8. {cotlab-0.8.1 → cotlab-0.8.2}/.github/workflows/lint.yml +0 -0
  9. {cotlab-0.8.1 → cotlab-0.8.2}/.github/workflows/release.yml +0 -0
  10. {cotlab-0.8.1 → cotlab-0.8.2}/.github/workflows/tests.yml +0 -0
  11. {cotlab-0.8.1 → cotlab-0.8.2}/.gitignore +0 -0
  12. {cotlab-0.8.1 → cotlab-0.8.2}/.pre-commit-config.yaml +0 -0
  13. {cotlab-0.8.1 → cotlab-0.8.2}/Dockerfile.rocm +0 -0
  14. {cotlab-0.8.1 → cotlab-0.8.2}/LICENSE +0 -0
  15. {cotlab-0.8.1 → cotlab-0.8.2}/README.md +0 -0
  16. {cotlab-0.8.1 → cotlab-0.8.2}/conf/backend/transformers.yaml +0 -0
  17. {cotlab-0.8.1 → cotlab-0.8.2}/conf/backend/vllm.yaml +0 -0
  18. {cotlab-0.8.1 → cotlab-0.8.2}/conf/config.yaml +0 -0
  19. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/afrimedqa.yaml +0 -0
  20. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/cardiology.yaml +0 -0
  21. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/histopathology.yaml +0 -0
  22. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/m_arc.yaml +0 -0
  23. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/medbullets.yaml +0 -0
  24. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/medmcqa.yaml +0 -0
  25. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/medqa.yaml +0 -0
  26. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/medxpertqa.yaml +0 -0
  27. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/mmlu_medical.yaml +0 -0
  28. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/movie_ood.yaml +0 -0
  29. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/neurology.yaml +0 -0
  30. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/oncology.yaml +0 -0
  31. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/patching_pairs.yaml +0 -0
  32. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/pediatrics.yaml +0 -0
  33. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/plab.yaml +0 -0
  34. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/probing_diagnosis.yaml +0 -0
  35. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/pubhealthbench.yaml +0 -0
  36. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/pubmedqa.yaml +0 -0
  37. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/radiology.yaml +0 -0
  38. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/synthetic.yaml +0 -0
  39. {cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/tcga.yaml +0 -0
  40. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/activation_compare.yaml +0 -0
  41. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/activation_patching.yaml +0 -0
  42. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/attention_analysis.yaml +0 -0
  43. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/classification.yaml +0 -0
  44. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/composite_shift_detector.yaml +0 -0
  45. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/confabulation_analysis.yaml +0 -0
  46. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/cot_ablation.yaml +0 -0
  47. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/cot_faithfulness.yaml +0 -0
  48. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/cot_heads.yaml +0 -0
  49. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/entropy_neuron_overlap.yaml +0 -0
  50. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/full_layer_cot.yaml +0 -0
  51. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/full_layer_patching.yaml +0 -0
  52. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/h_neuron_analysis.yaml +0 -0
  53. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/logit_lens.yaml +0 -0
  54. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/multi_head_cot.yaml +0 -0
  55. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/multi_head_patching.yaml +0 -0
  56. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/probing_classifier.yaml +0 -0
  57. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/residual_norm_ood.yaml +0 -0
  58. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/sae_feature_analysis.yaml +0 -0
  59. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/sae_feature_neuron_overlap.yaml +0 -0
  60. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/steering_vectors.yaml +0 -0
  61. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/sycophancy_heads.yaml +0 -0
  62. {cotlab-0.8.1 → cotlab-0.8.2}/conf/experiment/token_group_contrast.yaml +0 -0
  63. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/adversarial.yaml +0 -0
  64. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/arrogance.yaml +0 -0
  65. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/cardiology.yaml +0 -0
  66. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/chain_of_thought.yaml +0 -0
  67. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/contrarian.yaml +0 -0
  68. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/contrarian_matched.yaml +0 -0
  69. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/cot_matched.yaml +0 -0
  70. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/direct_answer.yaml +0 -0
  71. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/direct_matched.yaml +0 -0
  72. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/expert_persona.yaml +0 -0
  73. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/few_shot.yaml +0 -0
  74. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/histopathology.yaml +0 -0
  75. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/mcq.yaml +0 -0
  76. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/neurology.yaml +0 -0
  77. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/no_instruction.yaml +0 -0
  78. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/oncology.yaml +0 -0
  79. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/plab.yaml +0 -0
  80. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/pubhealthbench.yaml +0 -0
  81. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/pubmedqa.yaml +0 -0
  82. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/radiology.yaml +0 -0
  83. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/simple.yaml +0 -0
  84. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/socratic.yaml +0 -0
  85. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/sycophantic.yaml +0 -0
  86. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/tcga.yaml +0 -0
  87. {cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/uncertainty.yaml +0 -0
  88. {cotlab-0.8.1 → cotlab-0.8.2}/data/datasets.yaml +0 -0
  89. {cotlab-0.8.1 → cotlab-0.8.2}/data/movie_ood.jsonl +0 -0
  90. {cotlab-0.8.1 → cotlab-0.8.2}/docker-compose.rocm.yml +0 -0
  91. {cotlab-0.8.1 → cotlab-0.8.2}/docs/api/core.md +0 -0
  92. {cotlab-0.8.1 → cotlab-0.8.2}/docs/api/experiments.md +0 -0
  93. {cotlab-0.8.1 → cotlab-0.8.2}/docs/api/prompts.md +0 -0
  94. {cotlab-0.8.1 → cotlab-0.8.2}/docs/getting-started/installation.md +0 -0
  95. {cotlab-0.8.1 → cotlab-0.8.2}/docs/getting-started/quickstart.md +0 -0
  96. {cotlab-0.8.1 → cotlab-0.8.2}/docs/guide/configuration.md +0 -0
  97. {cotlab-0.8.1 → cotlab-0.8.2}/docs/guide/experiments.md +0 -0
  98. {cotlab-0.8.1 → cotlab-0.8.2}/docs/guide/models.md +0 -0
  99. {cotlab-0.8.1 → cotlab-0.8.2}/docs/guide/prompts.md +0 -0
  100. {cotlab-0.8.1 → cotlab-0.8.2}/docs/index.md +0 -0
  101. {cotlab-0.8.1 → cotlab-0.8.2}/docs/rocm-setup.md +0 -0
  102. {cotlab-0.8.1 → cotlab-0.8.2}/mkdocs.yml +0 -0
  103. {cotlab-0.8.1 → cotlab-0.8.2}/notebooks/cotlab_tutorial.ipynb +0 -0
  104. {cotlab-0.8.1 → cotlab-0.8.2}/pyproject.toml +0 -0
  105. {cotlab-0.8.1 → cotlab-0.8.2}/scripts/analyze_json_compliance.py +0 -0
  106. {cotlab-0.8.1 → cotlab-0.8.2}/scripts/build_movie_ood_dataset.py +0 -0
  107. {cotlab-0.8.1 → cotlab-0.8.2}/scripts/compare_json_vs_freetext.py +0 -0
  108. {cotlab-0.8.1 → cotlab-0.8.2}/scripts/cotlab-rocm.sh +0 -0
  109. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/analyse_experiments.py +0 -0
  110. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/analysis/__init__.py +0 -0
  111. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/analysis/cot_parser.py +0 -0
  112. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/analysis/faithfulness_metrics.py +0 -0
  113. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/backends/__init__.py +0 -0
  114. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/backends/base.py +0 -0
  115. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/backends/transformers_backend.py +0 -0
  116. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/backends/vllm_backend.py +0 -0
  117. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/cli.py +0 -0
  118. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/core/__init__.py +0 -0
  119. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/core/base.py +0 -0
  120. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/core/config.py +0 -0
  121. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/core/registry.py +0 -0
  122. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/datasets/__init__.py +0 -0
  123. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/datasets/loaders.py +0 -0
  124. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiment/__init__.py +0 -0
  125. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/__init__.py +0 -0
  126. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/activation_compare.py +0 -0
  127. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/activation_patching.py +0 -0
  128. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/attention_analysis.py +0 -0
  129. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/classification.py +0 -0
  130. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/composite_shift_detector.py +0 -0
  131. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/confabulation_analysis.py +0 -0
  132. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/cot_ablation.py +0 -0
  133. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/cot_faithfulness.py +0 -0
  134. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/cot_heads.py +0 -0
  135. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/entropy_neuron_overlap.py +0 -0
  136. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/full_layer_cot.py +0 -0
  137. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/full_layer_patching.py +0 -0
  138. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/h_neuron_analysis.py +0 -0
  139. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/logit_lens.py +0 -0
  140. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/multi_head_cot.py +0 -0
  141. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/multi_head_patching.py +0 -0
  142. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/probing_classifier.py +0 -0
  143. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/residual_norm_ood.py +0 -0
  144. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/sae_feature_analysis.py +0 -0
  145. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/sae_feature_neuron_overlap.py +0 -0
  146. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/steering_vectors.py +0 -0
  147. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/experiments/sycophancy_heads.py +0 -0
  148. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/logging/__init__.py +0 -0
  149. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/logging/json_logger.py +0 -0
  150. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/main.py +0 -0
  151. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/patching/__init__.py +0 -0
  152. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/patching/cache.py +0 -0
  153. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/patching/hooks.py +0 -0
  154. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/patching/interventions.py +0 -0
  155. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/patching/patcher.py +0 -0
  156. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/patching/sae.py +0 -0
  157. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/prompts/__init__.py +0 -0
  158. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/prompts/cardiology.py +0 -0
  159. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/prompts/histopathology.py +0 -0
  160. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/prompts/length_matched_strategies.py +0 -0
  161. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/prompts/mcq.py +0 -0
  162. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/prompts/neurology.py +0 -0
  163. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/prompts/oncology.py +0 -0
  164. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/prompts/plab.py +0 -0
  165. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/prompts/pubhealthbench.py +0 -0
  166. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/prompts/pubmedqa.py +0 -0
  167. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/prompts/radiology.py +0 -0
  168. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/prompts/strategies.py +0 -0
  169. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/prompts/tcga.py +0 -0
  170. {cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/runner.py +0 -0
  171. {cotlab-0.8.1 → cotlab-0.8.2}/tests/conftest.py +0 -0
  172. {cotlab-0.8.1 → cotlab-0.8.2}/tests/test_analysis.py +0 -0
  173. {cotlab-0.8.1 → cotlab-0.8.2}/tests/test_backends.py +0 -0
  174. {cotlab-0.8.1 → cotlab-0.8.2}/tests/test_core.py +0 -0
  175. {cotlab-0.8.1 → cotlab-0.8.2}/tests/test_datasets.py +0 -0
  176. {cotlab-0.8.1 → cotlab-0.8.2}/tests/test_experiment_docs.py +0 -0
  177. {cotlab-0.8.1 → cotlab-0.8.2}/tests/test_experiments.py +0 -0
  178. {cotlab-0.8.1 → cotlab-0.8.2}/tests/test_patching.py +0 -0
  179. {cotlab-0.8.1 → cotlab-0.8.2}/tests/test_prompts.py +0 -0
  180. {cotlab-0.8.1 → cotlab-0.8.2}/uv.lock +0 -0
{cotlab-0.8.1 → cotlab-0.8.2}/Containerfile RENAMED
@@ -1,4 +1,4 @@
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- FROM nvidia/cuda:12.6.3-runtime-ubuntu24.04
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+ FROM nvidia/cuda:12.8.0-runtime-ubuntu24.04
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  ENV DEBIAN_FRONTEND=noninteractive \
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  PYTHONUNBUFFERED=1 \
@@ -12,6 +12,9 @@ RUN apt-get update && \
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  RUN uv venv /opt/venv
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+ # Install torch with CUDA 12 support explicitly to avoid version detection bugs
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+ RUN uv pip install torch==2.6.0 torchvision torchaudio --index-url https://download.pytorch.org/whl/cu126
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+
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  WORKDIR /app
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  COPY . .
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{cotlab-0.8.1 → cotlab-0.8.2}/PKG-INFO RENAMED
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  Metadata-Version: 2.4
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  Name: cotlab
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- Version: 0.8.1
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+ Version: 0.8.2
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  Summary: CoTLab - Chain of Thought Research Toolkit for LLMs
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  Project-URL: Repository, https://github.com/huseyincavusbi/CoTLab
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  Project-URL: Documentation, https://huseyincavusbi.github.io/CoTLab
{cotlab-0.8.1 → cotlab-0.8.2}/src/cotlab/__init__.py RENAMED
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  """CoTLab - Chain of Thought Research Toolkit."""
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- __version__ = "0.8.1"
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+ __version__ = "0.8.2"
{cotlab-0.8.1 → cotlab-0.8.2}/.env.example RENAMED
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{cotlab-0.8.1 → cotlab-0.8.2}/.github/dependabot.yml RENAMED
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{cotlab-0.8.1 → cotlab-0.8.2}/.gitignore RENAMED
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{cotlab-0.8.1 → cotlab-0.8.2}/.pre-commit-config.yaml RENAMED
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{cotlab-0.8.1 → cotlab-0.8.2}/Dockerfile.rocm RENAMED
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{cotlab-0.8.1 → cotlab-0.8.2}/LICENSE RENAMED
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{cotlab-0.8.1 → cotlab-0.8.2}/README.md RENAMED
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{cotlab-0.8.1 → cotlab-0.8.2}/conf/backend/vllm.yaml RENAMED
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{cotlab-0.8.1 → cotlab-0.8.2}/conf/config.yaml RENAMED
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{cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/m_arc.yaml RENAMED
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{cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/medmcqa.yaml RENAMED
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{cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/medqa.yaml RENAMED
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{cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/plab.yaml RENAMED
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{cotlab-0.8.1 → cotlab-0.8.2}/conf/dataset/tcga.yaml RENAMED
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{cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/few_shot.yaml RENAMED
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{cotlab-0.8.1 → cotlab-0.8.2}/conf/prompt/mcq.yaml RENAMED
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