rc-foundry 0.1.5__tar.gz → 0.1.6__tar.gz

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Files changed (415) hide show
  1. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/PKG-INFO +1 -1
  2. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rfd3/src/rfd3/cli.py +10 -4
  3. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/pyproject.toml +4 -0
  4. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/src/foundry/version.py +2 -2
  5. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/.git +0 -0
  6. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/.github/workflows/lint_trunk.yaml +0 -0
  7. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/.gitignore +0 -0
  8. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/.gitmodules +0 -0
  9. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/.pre-commit-config.yaml +0 -0
  10. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/.project-root +0 -0
  11. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/LICENSE.md +0 -0
  12. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/Makefile +0 -0
  13. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/README.md +0 -0
  14. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/docs/releases/rf3/examples/3en2_from_file.cif +0 -0
  15. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/docs/releases/rf3/examples/3en2_from_json_with_msa.json +0 -0
  16. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/docs/releases/rf3/examples/5hkn_from_file.cif +0 -0
  17. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/docs/releases/rf3/examples/7o1r_from_json.json +0 -0
  18. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/docs/releases/rf3/examples/7xli_template_antigen_and_framework.json +0 -0
  19. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/docs/releases/rf3/examples/9dfn.cif +0 -0
  20. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/docs/releases/rf3/examples/9dfn_template_ligand_and_protein.json +0 -0
  21. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/docs/releases/rf3/examples/ligands/HEM.sdf +0 -0
  22. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/docs/releases/rf3/examples/ligands/NAG.cif +0 -0
  23. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/docs/releases/rf3/examples/msas/3en2_A.a3m.gz +0 -0
  24. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/docs/releases/rf3/examples/msas/7o1r_A.a3m.gz +0 -0
  25. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/docs/releases/rf3/examples/msas/8cdz_A.a3m.gz +0 -0
  26. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/docs/releases/rf3/examples/multiple_examples_from_json.json +0 -0
  27. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/docs/releases/rf3/examples/templates/7xli_chain_A.cif +0 -0
  28. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/docs/releases/rf3/examples/templates/7xli_chain_B.cif +0 -0
  29. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/docs/releases/rfd3/examples/README.md +0 -0
  30. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/examples/all.ipynb +0 -0
  31. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/examples/enzymes.ipynb +0 -0
  32. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/README.md +0 -0
  33. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/__init__.py +0 -0
  34. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/collate/feature_collator.py +0 -0
  35. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/inference.py +0 -0
  36. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/inference_engines/mpnn.py +0 -0
  37. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/loss/nll_loss.py +0 -0
  38. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/metrics/nll.py +0 -0
  39. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/metrics/sequence_recovery.py +0 -0
  40. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/model/layers/graph_embeddings.py +0 -0
  41. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/model/layers/message_passing.py +0 -0
  42. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/model/layers/position_wise_feed_forward.py +0 -0
  43. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/model/layers/positional_encoding.py +0 -0
  44. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/model/mpnn.py +0 -0
  45. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/pipelines/mpnn.py +0 -0
  46. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/samplers/samplers.py +0 -0
  47. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/train.py +0 -0
  48. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/trainers/mpnn.py +0 -0
  49. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/transforms/feature_aggregation/mpnn.py +0 -0
  50. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/transforms/feature_aggregation/polymer_ligand_interface.py +0 -0
  51. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/transforms/feature_aggregation/token_encodings.py +0 -0
  52. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/transforms/feature_aggregation/user_settings.py +0 -0
  53. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/transforms/polymer_ligand_interface.py +0 -0
  54. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/utils/inference.py +0 -0
  55. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/utils/probability.py +0 -0
  56. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/utils/weights.py +0 -0
  57. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/tests/conftest.py +0 -0
  58. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/tests/test_feature_collator.py +0 -0
  59. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/tests/test_inference_engine.py +0 -0
  60. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/tests/test_inference_utils.py +0 -0
  61. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/tests/test_integration.py +0 -0
  62. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/tests/test_loss.py +0 -0
  63. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/tests/test_metrics.py +0 -0
  64. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/tests/test_model.py +0 -0
  65. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/tests/test_pipeline.py +0 -0
  66. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/tests/test_polymer_ligand_interface.py +0 -0
  67. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/tests/test_samplers.py +0 -0
  68. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/mpnn/tests/test_utils.py +0 -0
  69. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/README.md +0 -0
  70. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/callbacks/default.yaml +0 -0
  71. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/callbacks/dump_validation_structures.yaml +0 -0
  72. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/callbacks/metrics_logging.yaml +0 -0
  73. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/callbacks/train_logging.yaml +0 -0
  74. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/dataloader/default.yaml +0 -0
  75. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/datasets/base.yaml +0 -0
  76. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/datasets/pdb_and_distillation.yaml +0 -0
  77. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/datasets/pdb_only.yaml +0 -0
  78. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/disorder_distillation.yaml +0 -0
  79. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/domain_distillation.yaml +0 -0
  80. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/monomer_distillation.yaml +0 -0
  81. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/na_complex_distillation.yaml +0 -0
  82. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/pdb/af3_weighted_sampling.yaml +0 -0
  83. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/pdb/base.yaml +0 -0
  84. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/pdb/plinder.yaml +0 -0
  85. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/pdb/train_interface.yaml +0 -0
  86. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/pdb/train_pn_unit.yaml +0 -0
  87. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/rna_monomer_distillation.yaml +0 -0
  88. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/datasets/val/af3_ab_set.yaml +0 -0
  89. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/datasets/val/af3_validation.yaml +0 -0
  90. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/datasets/val/base.yaml +0 -0
  91. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/datasets/val/runs_and_poses.yaml +0 -0
  92. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/debug/default.yaml +0 -0
  93. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/debug/train_specific_examples.yaml +0 -0
  94. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/experiment/pretrained/rf3.yaml +0 -0
  95. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/experiment/pretrained/rf3_with_confidence.yaml +0 -0
  96. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/experiment/quick-rf3-with-confidence.yaml +0 -0
  97. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/experiment/quick-rf3.yaml +0 -0
  98. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/hydra/default.yaml +0 -0
  99. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/hydra/no_logging.yaml +0 -0
  100. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/inference.yaml +0 -0
  101. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/inference_engine/base.yaml +0 -0
  102. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/inference_engine/rf3.yaml +0 -0
  103. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/logger/csv.yaml +0 -0
  104. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/logger/default.yaml +0 -0
  105. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/logger/wandb.yaml +0 -0
  106. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/model/components/ema.yaml +0 -0
  107. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/model/components/rf3_net.yaml +0 -0
  108. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/model/components/rf3_net_with_confidence_head.yaml +0 -0
  109. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/model/optimizers/adam.yaml +0 -0
  110. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/model/rf3.yaml +0 -0
  111. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/model/rf3_with_confidence.yaml +0 -0
  112. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/model/schedulers/af3.yaml +0 -0
  113. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/paths/data/default.yaml +0 -0
  114. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/paths/default.yaml +0 -0
  115. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/train.yaml +0 -0
  116. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/trainer/cpu.yaml +0 -0
  117. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/trainer/ddp.yaml +0 -0
  118. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/trainer/loss/losses/confidence_loss.yaml +0 -0
  119. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/trainer/loss/losses/diffusion_loss.yaml +0 -0
  120. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/trainer/loss/losses/distogram_loss.yaml +0 -0
  121. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/trainer/loss/structure_prediction.yaml +0 -0
  122. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/trainer/loss/structure_prediction_with_confidence.yaml +0 -0
  123. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/trainer/metrics/structure_prediction.yaml +0 -0
  124. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/trainer/rf3.yaml +0 -0
  125. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/trainer/rf3_with_confidence.yaml +0 -0
  126. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/configs/validate.yaml +0 -0
  127. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/__init__.py +0 -0
  128. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/_version.py +0 -0
  129. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/alignment.py +0 -0
  130. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/callbacks/dump_validation_structures.py +0 -0
  131. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/callbacks/metrics_logging.py +0 -0
  132. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/chemical.py +0 -0
  133. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/cli.py +0 -0
  134. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/data/cyclic_transform.py +0 -0
  135. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/data/extra_xforms.py +0 -0
  136. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/data/ground_truth_template.py +0 -0
  137. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/data/paired_msa.py +0 -0
  138. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/data/pipeline_utils.py +0 -0
  139. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/data/pipelines.py +0 -0
  140. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/diffusion_samplers/inference_sampler.py +0 -0
  141. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/inference.py +0 -0
  142. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/inference_engines/__init__.py +0 -0
  143. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/inference_engines/rf3.py +0 -0
  144. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/kinematics.py +0 -0
  145. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/loss/af3_confidence_loss.py +0 -0
  146. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/loss/af3_losses.py +0 -0
  147. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/loss/loss.py +0 -0
  148. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/metrics/chiral.py +0 -0
  149. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/metrics/clashing_chains.py +0 -0
  150. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/metrics/distogram.py +0 -0
  151. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/metrics/lddt.py +0 -0
  152. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/metrics/metadata.py +0 -0
  153. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/metrics/metric_utils.py +0 -0
  154. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/metrics/predicted_error.py +0 -0
  155. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/metrics/rasa.py +0 -0
  156. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/metrics/selected_distances.py +0 -0
  157. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/RF3.py +0 -0
  158. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/RF3_blocks.py +0 -0
  159. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/RF3_structure.py +0 -0
  160. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/layers/af3_auxiliary_heads.py +0 -0
  161. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/layers/af3_diffusion_transformer.py +0 -0
  162. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/layers/attention.py +0 -0
  163. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/layers/layer_utils.py +0 -0
  164. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/layers/mlff.py +0 -0
  165. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/layers/outer_product.py +0 -0
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  332. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rfd3/src/rfd3/testing/debug.py +0 -0
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  334. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rfd3/src/rfd3/testing/testing_utils.py +0 -0
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  336. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rfd3/src/rfd3/trainer/dump_validation_structures.py +0 -0
  337. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rfd3/src/rfd3/trainer/fabric_trainer.py +0 -0
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  342. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rfd3/src/rfd3/transforms/conditioning_utils.py +0 -0
  343. {rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rfd3/src/rfd3/transforms/design_transforms.py +0 -0
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{rc_foundry-0.1.5 → rc_foundry-0.1.6}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: rc-foundry
3
- Version: 0.1.5
3
+ Version: 0.1.6
4
4
  Summary: Shared utilities and training infrastructure for biomolecular structure prediction models.
5
5
  Author-email: Institute for Protein Design <contact@ipd.uw.edu>
6
6
  License: BSD 3-Clause License
{rc_foundry-0.1.5 → rc_foundry-0.1.6}/models/rfd3/src/rfd3/cli.py RENAMED
@@ -12,10 +12,16 @@ app = typer.Typer()
12
12
  def design(ctx: typer.Context):
13
13
  """Run design using hydra config overrides and input files."""
14
14
  # Find the RFD3 configs directory relative to this file
15
- # This file is at: models/rfd3/src/rfd3/cli.py
16
- # Configs are at: models/rfd3/configs/
17
- rfd3_package_dir = Path(__file__).parent.parent.parent # Go up to models/rfd3/
18
- config_path = str(rfd3_package_dir / "configs")
15
+ # Development: models/rfd3/src/rfd3/cli.py -> models/rfd3/configs/
16
+ # Installed: site-packages/rfd3/cli.py -> site-packages/rfd3/configs/
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+
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+ # Try development location first
19
+ dev_config_path = Path(__file__).parent.parent.parent / "configs"
20
+ if dev_config_path.exists():
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+ config_path = str(dev_config_path)
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+ else:
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+ # Fall back to installed package location
24
+ config_path = str(Path(__file__).parent / "configs")
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  # Get all arguments
21
27
  args = ctx.params.get("args", []) + ctx.args
{rc_foundry-0.1.5 → rc_foundry-0.1.6}/pyproject.toml RENAMED
@@ -115,6 +115,10 @@ packages = [
115
115
  "models/mpnn/src/mpnn",
116
116
  ]
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+ [tool.hatch.build.targets.wheel.force-include]
119
+ "models/rfd3/configs" = "rfd3/configs"
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+ "models/rf3/configs" = "rf3/configs"
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+
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122
  # Formatting & linting settings -------------------------------------------------------
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123
  [tool.ruff]
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  line-length = 88
{rc_foundry-0.1.5 → rc_foundry-0.1.6}/src/foundry/version.py RENAMED
@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
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  commit_id: COMMIT_ID
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  __commit_id__: COMMIT_ID
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30
 
31
- __version__ = version = '0.1.5'
32
- __version_tuple__ = version_tuple = (0, 1, 5)
31
+ __version__ = version = '0.1.6'
32
+ __version_tuple__ = version_tuple = (0, 1, 6)
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  __commit_id__ = commit_id = None
{rc_foundry-0.1.5 → rc_foundry-0.1.6}/.git RENAMED
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{rc_foundry-0.1.5 → rc_foundry-0.1.6}/.gitignore RENAMED
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{rc_foundry-0.1.5 → rc_foundry-0.1.6}/.gitmodules RENAMED
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{rc_foundry-0.1.5 → rc_foundry-0.1.6}/.project-root RENAMED
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{rc_foundry-0.1.5 → rc_foundry-0.1.6}/LICENSE.md RENAMED
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{rc_foundry-0.1.5 → rc_foundry-0.1.6}/Makefile RENAMED
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{rc_foundry-0.1.5 → rc_foundry-0.1.6}/README.md RENAMED
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