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CharlelieLrtcoreyjadamsAlexey-Kamenevjeis4wpipzharrington
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Refactored diffusion sampler (#1363)
* Add missing init files * Update build system and specify some deps. * Reorganize tests. * Update init files * Clean up neighbor tools. * Update testing * Fix compat tests * Move core model tests to tests/core/ * Add import lint config * Relocate layers * Move graphcast utils into model directory * Relocating util functionalities. * Further clean up and organize tests. * utils tests are passing now * Cleaning up distributed tests * Patching tests working again in nn * Fix sdf test * Fix zenith angle tests * Some organization of tests. Checkpoints is moved into utils. * Remove launch.utils and launch.config. Checkpointing is moved to phsyicsnemo.utils, launch.config is just gone. It was empty. * Most nn tests are passing * Further cleanup. Getting there! * Remove constants file * Add import linting to pre-commit. * Refactor (#1208) * Move filesystems and version_check to core * Fix version check tests * Reorganize distributed, domain_parallel, and begin nn / utils cleanup. * Move modules and meta to core. Move registry to core. No tests fixed yet. * Add missing init files * Update build system and specify some deps. * Reorganize tests. * Update init files * Clean up neighbor tools. * Update testing * Fix compat tests * Move core model tests to tests/core/ * Add import lint config * Relocate layers * Move graphcast utils into model directory * Relocating util functionalities. * Add FIGConvNet to crash example (#1207) * Add FIGConvNet to crash example. * Add FIGConvNet to crash example * Update model config * propose fix some typos (#1209) Signed-off-by: John E <jeis4wpi@outlook.com> Co-authored-by: Corey adams <6619961+coreyjadams@users.noreply.github.com> * Further clean up and organize tests. * utils tests are passing now * Cleaning up distributed tests * Patching tests working again in nn * Fix sdf test * Fix zenith angle tests * Some organization of tests. Checkpoints is moved into utils. * Remove launch.utils and launch.config. Checkpointing is moved to phsyicsnemo.utils, launch.config is just gone. It was empty. * Most nn tests are passing * Further cleanup. Getting there! * Remove constants file * Add import linting to pre-commit. --------- Signed-off-by: John E <jeis4wpi@outlook.com> Co-authored-by: Alexey Kamenev <alex.kamenev@gmail.com> Co-authored-by: John Eismeier <42679190+jeis4wpi@users.noreply.github.com> * Unmigrate the insolation utils (#1211) * unmigrate the insolation utils * Revert test and compat map * Update importlinter * Move gnn layers and start to fix several model tests. * AFNO is now passing. * Rnn models passing. * Fix improt * Healpix tests are working * Domino and unet working * Refactor (#1216) * Move filesystems and version_check to core * Fix version check tests * Reorganize distributed, domain_parallel, and begin nn / utils cleanup. * Move modules and meta to core. Move registry to core. No tests fixed yet. * Add missing init files * Update build system and specify some deps. * Reorganize tests. * Update init files * Clean up neighbor tools. * Update testing * Fix compat tests * Move core model tests to tests/core/ * Add import lint config * Relocate layers * Move graphcast utils into model directory * Relocating util functionalities. * Further clean up and organize tests. * utils tests are passing now * Cleaning up distributed tests * Patching tests working again in nn * Fix sdf test * Fix zenith angle tests * Some organization of tests. Checkpoints is moved into utils. * Remove launch.utils and launch.config. Checkpointing is moved to phsyicsnemo.utils, launch.config is just gone. It was empty. * Most nn tests are passing * Further cleanup. Getting there! * Remove constants file * Add import linting to pre-commit. * Move gnn layers and start to fix several model tests. * AFNO is now passing. * Rnn models passing. * Fix improt * Healpix tests are working * Domino and unet working * Update activations path in dlwp tests (#1217) * Update activations path in dlwp tests * Update example paths * Updating to address some test issues * MGN tests passing again * Most graphcast tests passing again * Move nd conv layers. * update fengwu and pangu * Update sfno and pix2pix test * update tests for figconvnet, swinrnn, superresnet * updating more models to pass * Update distributed tests, now passing. * Domain parallel tests now passing. * Fix active learning imports so tests pass in refactor * Fix some metric imports * Remove deploy package * Remove unused test file * unmigrate these files ... again? * Update import linter. * Refactor (#1224) * Move filesystems and version_check to core * Fix version check tests * Reorganize distributed, domain_parallel, and begin nn / utils cleanup. * Move modules and meta to core. Move registry to core. No tests fixed yet. * Add missing init files * Update build system and specify some deps. * Reorganize tests. * Update init files * Clean up neighbor tools. * Update testing * Fix compat tests * Move core model tests to tests/core/ * Add import lint config * Relocate layers * Move graphcast utils into model directory * Relocating util functionalities. * Further clean up and organize tests. * utils tests are passing now * Cleaning up distributed tests * Patching tests working again in nn * Fix sdf test * Fix zenith angle tests * Some organization of tests. Checkpoints is moved into utils. * Remove launch.utils and launch.config. Checkpointing is moved to phsyicsnemo.utils, launch.config is just gone. It was empty. * Most nn tests are passing * Further cleanup. Getting there! * Remove constants file * Add import linting to pre-commit. * Update crash readme (#1212) * update license headers- second try * update readme * Bump multi-storage-client to v0.33.0 with rust client (#1156) * Move gnn layers and start to fix several model tests. * AFNO is now passing. * Rnn models passing. * Fix improt * Healpix tests are working * Domino and unet working * Add jaxtyping to requirements.txt for crash sample (#1218) * update license headers- second try * Update requirements.txt * Updating to address some test issues * MGN tests passing again * Most graphcast tests passing again * Move nd conv layers. * update fengwu and pangu * Update sfno and pix2pix test * update tests for figconvnet, swinrnn, superresnet * updating more models to pass * Update distributed tests, now passing. * Domain parallel tests now passing. * Fix active learning imports so tests pass in refactor * Fix some metric imports * Remove deploy package * Remove unused test file * unmigrate these files ... again? * Update import linter. --------- Co-authored-by: Mohammad Amin Nabian <m.a.nabiyan@gmail.com> Co-authored-by: Yongming Ding <yongmingd@nvidia.com> * Cleaning up diffusion models. Not quite done yet. * Restore deleted files * Updating more tests. * Further updates to tests. Datapipes almost working. * Refactor (#1231) * Move filesystems and version_check to core * Fix version check tests * Reorganize distributed, domain_parallel, and begin nn / utils cleanup. * Move modules and meta to core. Move registry to core. No tests fixed yet. * Add missing init files * Update build system and specify some deps. * Reorganize tests. * Update init files * Clean up neighbor tools. * Update testing * Fix compat tests * Move core model tests to tests/core/ * Add import lint config * Relocate layers * Move graphcast utils into model directory * Relocating util functionalities. * Further clean up and organize tests. * utils tests are passing now * Cleaning up distributed tests * Patching tests working again in nn * Fix sdf test * Fix zenith angle tests * Some organization of tests. Checkpoints is moved into utils. * Remove launch.utils and launch.config. Checkpointing is moved to phsyicsnemo.utils, launch.config is just gone. It was empty. * Most nn tests are passing * Further cleanup. Getting there! * Remove constants file * Add import linting to pre-commit. * Update crash readme (#1212) * update license headers- second try * update readme * Bump multi-storage-client to v0.33.0 with rust client (#1156) * Move gnn layers and start to fix several model tests. * AFNO is now passing. * Rnn models passing. * Fix improt * Healpix tests are working * Domino and unet working * Add jaxtyping to requirements.txt for crash sample (#1218) * update license headers- second try * Update requirements.txt * Updating to address some test issues * Replace 'License' link with 'Dev blog' link (#1215) Co-authored-by: Corey adams <6619961+coreyjadams@users.noreply.github.com> * MGN tests passing again * Most graphcast tests passing again * Move nd conv layers. * update fengwu and pangu * Update sfno and pix2pix test * update tests for figconvnet, swinrnn, superresnet * updating more models to pass * Update distributed tests, now passing. * Validation fu added to examples/structural_mechanics/crash/train.py (#1204) * validation added: works for multi-node job. * rename and rearrange validation function * validate_every_n_epochs, save_ckpt_every_n_epochs added in config * corrected bug (args of model) in inference * args in validation code updated * val path added and args name changed * validation split added -> write_vtp=False * fixed inference bug * bug fix: write_vtp * Domain parallel tests now passing. * Fix active learning imports so tests pass in refactor * Fix some metric imports * Remove deploy package * Remove unused test file * unmigrate these files ... again? * Update import linter. * Add saikrishnanc-nv to github actors (#1225) * Integrate Curator instructions to the Crash example (#1213) * Integrate Curator instructions * Update docs * Formatting changes * Adding code of conduct (#1214) * Adding code of conduct Adopting the code of conduct from the https://www.contributor-covenant.org/ * Update CODE_OF_CONDUCT.MD Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * Create .markdownlintignore * Revise README for PhysicsNeMo resources and guidance Updated the 'Getting Started' section and added new resources for learning AI Physics. * Update README.md --------- Co-authored-by: Mohammad Amin Nabian <m.a.nabiyan@gmail.com> Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> Co-authored-by: Corey adams <6619961+coreyjadams@users.noreply.github.com> * Cleaning up diffusion models. Not quite done yet. * Restore deleted files * Updating more tests. * Further updates to tests. Datapipes almost working. --------- Co-authored-by: Mohammad Amin Nabian <m.a.nabiyan@gmail.com> Co-authored-by: Yongming Ding <yongmingd@nvidia.com> Co-authored-by: ram-cherukuri <104155145+ram-cherukuri@users.noreply.github.com> Co-authored-by: Deepak Akhare <dakhare@nvidia.com> Co-authored-by: Sai Krishnan Chandrasekar <157182662+saikrishnanc-nv@users.noreply.github.com> Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * update import paths * Starting to clean up dependency tree. * Refactor (#1233) * Move filesystems and version_check to core * Fix version check tests * Reorganize distributed, domain_parallel, and begin nn / utils cleanup. * Move modules and meta to core. Move registry to core. No tests fixed yet. * Add missing init files * Update build system and specify some deps. * Reorganize tests. * Update init files * Clean up neighbor tools. * Update testing * Fix compat tests * Move core model tests to tests/core/ * Add import lint config * Relocate layers * Move graphcast utils into model directory * Relocating util functionalities. * Further clean up and organize tests. * utils tests are passing now * Cleaning up distributed tests * Patching tests working again in nn * Fix sdf test * Fix zenith angle tests * Some organization of tests. Checkpoints is moved into utils. * Remove launch.utils and launch.config. Checkpointing is moved to phsyicsnemo.utils, launch.config is just gone. It was empty. * Most nn tests are passing * Further cleanup. Getting there! * Remove constants file * Add import linting to pre-commit. * Update crash readme (#1212) * update license headers- second try * update readme * Bump multi-storage-client to v0.33.0 with rust client (#1156) * Move gnn layers and start to fix several model tests. * AFNO is now passing. * Rnn models passing. * Fix improt * Healpix tests are working * Domino and unet working * Add jaxtyping to requirements.txt for crash sample (#1218) * update license headers- second try * Update requirements.txt * Updating to address some test issues * Replace 'License' link with 'Dev blog' link (#1215) Co-authored-by: Corey adams <6619961+coreyjadams@users.noreply.github.com> * MGN tests passing again * Most graphcast tests passing again * Move nd conv layers. * update fengwu and pangu * Update sfno and pix2pix test * update tests for figconvnet, swinrnn, superresnet * updating more models to pass * Update distributed tests, now passing. * Validation fu added to examples/structural_mechanics/crash/train.py (#1204) * validation added: works for multi-node job. * rename and rearrange validation function * validate_every_n_epochs, save_ckpt_every_n_epochs added in config * corrected bug (args of model) in inference * args in validation code updated * val path added and args name changed * validation split added -> write_vtp=False * fixed inference bug * bug fix: write_vtp * Domain parallel tests now passing. * Fix active learning imports so tests pass in refactor * Fix some metric imports * Remove deploy package * Remove unused test file * unmigrate these files ... again? * Update import linter. * Add saikrishnanc-nv to github actors (#1225) * Integrate Curator instructions to the Crash example (#1213) * Integrate Curator instructions * Update docs * Formatting changes * Adding code of conduct (#1214) * Adding code of conduct Adopting the code of conduct from the https://www.contributor-covenant.org/ * Update CODE_OF_CONDUCT.MD Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * Create .markdownlintignore * Revise README for PhysicsNeMo resources and guidance Updated the 'Getting Started' section and added new resources for learning AI Physics. * Update README.md --------- Co-authored-by: Mohammad Amin Nabian <m.a.nabiyan@gmail.com> Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> Co-authored-by: Corey adams <6619961+coreyjadams@users.noreply.github.com> * Cleaning up diffusion models. Not quite done yet. * Restore deleted files * Updating more tests. * Fixed minor bug in shape validation in SongUNet (#1230) Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Add Zarr reader for Crash (#1228) * Add Zarr reader for Crash * Update README * Update validation logic of point data in Zarr reader Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * Update examples/structural_mechanics/crash/zarr_reader.py Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * Add a test for 2D feature arrays * Update examples/structural_mechanics/crash/zarr_reader.py Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> --------- Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * Further updates to tests. Datapipes almost working. * update import paths * Starting to clean up dependency tree. --------- Signed-off-by: Charlelie Laurent <claurent@nvidia.com> Co-authored-by: Mohammad Amin Nabian <m.a.nabiyan@gmail.com> Co-authored-by: Yongming Ding <yongmingd@nvidia.com> Co-authored-by: ram-cherukuri <104155145+ram-cherukuri@users.noreply.github.com> Co-authored-by: Deepak Akhare <dakhare@nvidia.com> Co-authored-by: Sai Krishnan Chandrasekar <157182662+saikrishnanc-nv@users.noreply.github.com> Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> Co-authored-by: Charlelie Laurent <84199758+CharlelieLrt@users.noreply.github.com> * Added coding standards for model implementations as a custom context for greptile (#1219) * Added initial set of coding standards for model implementations Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Fixed typos + review comments + added details Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Added more rules for models Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Added model rules to PR checklist Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Added cusror rules for models Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Linked the wiki page to the PR template Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Fixed typo in PR checklist Signed-off-by: Charlelie Laurent <claurent@nvidia.com> --------- Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Fixing and adjusting a broad suite of tests. * Update test/domain_parallel/conftest.py Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * Minor fix * Refactor (#1234) * Move filesystems and version_check to core * Fix version check tests * Reorganize distributed, domain_parallel, and begin nn / utils cleanup. * Move modules and meta to core. Move registry to core. No tests fixed yet. * Add missing init files * Update build system and specify some deps. * Reorganize tests. * Update init files * Clean up neighbor tools. * Update testing * Fix compat tests * Move core model tests to tests/core/ * Add import lint config * Relocate layers * Move graphcast utils into model directory * Relocating util functionalities. * Further clean up and organize tests. * utils tests are passing now * Cleaning up distributed tests * Patching tests working again in nn * Fix sdf test * Fix zenith angle tests * Some organization of tests. Checkpoints is moved into utils. * Remove launch.utils and launch.config. Checkpointing is moved to phsyicsnemo.utils, launch.config is just gone. It was empty. * Most nn tests are passing * Further cleanup. Getting there! * Remove constants file * Add import linting to pre-commit. * Update crash readme (#1212) * update license headers- second try * update readme * Bump multi-storage-client to v0.33.0 with rust client (#1156) * Move gnn layers and start to fix several model tests. * AFNO is now passing. * Rnn models passing. * Fix improt * Healpix tests are working * Domino and unet working * Add jaxtyping to requirements.txt for crash sample (#1218) * update license headers- second try * Update requirements.txt * Updating to address some test issues * Replace 'License' link with 'Dev blog' link (#1215) Co-authored-by: Corey adams <6619961+coreyjadams@users.noreply.github.com> * MGN tests passing again * Most graphcast tests passing again * Move nd conv layers. * update fengwu and pangu * Update sfno and pix2pix test * update tests for figconvnet, swinrnn, superresnet * updating more models to pass * Update distributed tests, now passing. * Validation fu added to examples/structural_mechanics/crash/train.py (#1204) * validation added: works for multi-node job. * rename and rearrange validation function * validate_every_n_epochs, save_ckpt_every_n_epochs added in config * corrected bug (args of model) in inference * args in validation code updated * val path added and args name changed * validation split added -> write_vtp=False * fixed inference bug * bug fix: write_vtp * Domain parallel tests now passing. * Fix active learning imports so tests pass in refactor * Fix some metric imports * Remove deploy package * Remove unused test file * unmigrate these files ... again? * Update import linter. * Add saikrishnanc-nv to github actors (#1225) * Integrate Curator instructions to the Crash example (#1213) * Integrate Curator instructions * Update docs * Formatting changes * Adding code of conduct (#1214) * Adding code of conduct Adopting the code of conduct from the https://www.contributor-covenant.org/ * Update CODE_OF_CONDUCT.MD Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * Create .markdownlintignore * Revise README for PhysicsNeMo resources and guidance Updated the 'Getting Started' section and added new resources for learning AI Physics. * Update README.md --------- Co-authored-by: Mohammad Amin Nabian <m.a.nabiyan@gmail.com> Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> Co-authored-by: Corey adams <6619961+coreyjadams@users.noreply.github.com> * Cleaning up diffusion models. Not quite done yet. * Restore deleted files * Updating more tests. * Fixed minor bug in shape validation in SongUNet (#1230) Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Add Zarr reader for Crash (#1228) * Add Zarr reader for Crash * Update README * Update validation logic of point data in Zarr reader Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * Update examples/structural_mechanics/crash/zarr_reader.py Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * Add a test for 2D feature arrays * Update examples/structural_mechanics/crash/zarr_reader.py Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> --------- Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * Further updates to tests. Datapipes almost working. * update import paths * Starting to clean up dependency tree. * Add AR RT and OT schemes to Crash FIGConvNet (#1232) * Add AR and OT schemes for FIGConvNet * Add tests * Soothe the linter * Fix the tests * Fixing and adjusting a broad suite of tests. * Update test/domain_parallel/conftest.py Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * Minor fix --------- Signed-off-by: Charlelie Laurent <claurent@nvidia.com> Co-authored-by: Mohammad Amin Nabian <m.a.nabiyan@gmail.com> Co-authored-by: Yongming Ding <yongmingd@nvidia.com> Co-authored-by: ram-cherukuri <104155145+ram-cherukuri@users.noreply.github.com> Co-authored-by: Deepak Akhare <dakhare@nvidia.com> Co-authored-by: Sai Krishnan Chandrasekar <157182662+saikrishnanc-nv@users.noreply.github.com> Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> Co-authored-by: Charlelie Laurent <84199758+CharlelieLrt@users.noreply.github.com> Co-authored-by: Alexey Kamenev <alex.kamenev@gmail.com> * Not seeing any errors in testing ... * Breakdown of rules into smaller rules (#1236) * Breakdown of rules into smaller rules Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Fix mismatches in rule IDs referenced in rule text Signed-off-by: Charlelie Laurent <claurent@nvidia.com> --------- Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Refactor (#1240) * Move filesystems and version_check to core * Fix version check tests * Reorganize distributed, domain_parallel, and begin nn / utils cleanup. * Move modules and meta to core. Move registry to core. No tests fixed yet. * Add missing init files * Update build system and specify some deps. * Reorganize tests. * Update init files * Clean up neighbor tools. * Update testing * Fix compat tests * Move core model tests to tests/core/ * Add import lint config * Relocate layers * Move graphcast utils into model directory * Relocating util functionalities. * Further clean up and organize tests. * utils tests are passing now * Cleaning up distributed tests * Patching tests working again in nn * Fix sdf test * Fix zenith angle tests * Some organization of tests. Checkpoints is moved into utils. * Remove launch.utils and launch.config. Checkpointing is moved to phsyicsnemo.utils, launch.config is just gone. It was empty. * Most nn tests are passing * Further cleanup. Getting there! * Remove constants file * Add import linting to pre-commit. * Move gnn layers and start to fix several model tests. * AFNO is now passing. * Rnn models passing. * Fix improt * Healpix tests are working * Domino and unet working * Updating to address some test issues * MGN tests passing again * Most graphcast tests passing again * Move nd conv layers. * update fengwu and pangu * Update sfno and pix2pix test * update tests for figconvnet, swinrnn, superresnet * updating more models to pass * Update distributed tests, now passing. * Domain parallel tests now passing. * Fix active learning imports so tests pass in refactor * Fix some metric imports * Remove deploy package * Remove unused test file * unmigrate these files ... again? * Update import linter. * Cleaning up diffusion models. Not quite done yet. * Restore deleted files * Updating more tests. * Further updates to tests. Datapipes almost working. * update import paths * Starting to clean up dependency tree. * Fixing and adjusting a broad suite of tests. * Update test/domain_parallel/conftest.py Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * Minor fix * Not seeing any errors in testing ... * Formatting active learning module docstrings (#1238) * docs: fixing Protocol class reference formatting Signed-off-by: Kelvin Lee <kinlongkelvi@nvidia.com> * docs: removing mermaid diagram from protocols Signed-off-by: Kelvin Lee <kinlongkelvi@nvidia.com> * docs: adding active learning index * docs: revising docstrings for sphinx formatting * docs: fix placeholder URL for active learning main docs --------- Signed-off-by: Kelvin Lee <kinlongkelvi@nvidia.com> --------- Signed-off-by: Kelvin Lee <kinlongkelvi@nvidia.com> Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> Co-authored-by: Kelvin Lee <kin.long.kelvin.lee@gmail.com> * Refactor (#1247) * Move filesystems and version_check to core * Fix version check tests * Reorganize distributed, domain_parallel, and begin nn / utils cleanup. * Move modules and meta to core. Move registry to core. No tests fixed yet. * Add missing init files * Update build system and specify some deps. * Reorganize tests. * Update init files * Clean up neighbor tools. * Update testing * Fix compat tests * Move core model tests to tests/core/ * Add import lint config * Relocate layers * Move graphcast utils into model directory * Relocating util functionalities. * Further clean up and organize tests. * utils tests are passing now * Cleaning up distributed tests * Patching tests working again in nn * Fix sdf test * Fix zenith angle tests * Some organization of tests. Checkpoints is moved into utils. * Remove launch.utils and launch.config. Checkpointing is moved to phsyicsnemo.utils, launch.config is just gone. It was empty. * Most nn tests are passing * Further cleanup. Getting there! * Remove constants file * Add import linting to pre-commit. * Move gnn layers and start to fix several model tests. * AFNO is now passing. * Rnn models passing. * Fix improt * Healpix tests are working * Domino and unet working * Updating to address some test issues * MGN tests passing again * Most graphcast tests passing again * Move nd conv layers. * update fengwu and pangu * Update sfno and pix2pix test * update tests for figconvnet, swinrnn, superresnet * updating more models to pass * Update distributed tests, now passing. * Domain parallel tests now passing. * Fix active learning imports so tests pass in refactor * Fix some metric imports * Remove deploy package * Remove unused test file * unmigrate these files ... again? * Update import linter. * Cleaning up diffusion models. Not quite done yet. * Restore deleted files * Updating more tests. * Further updates to tests. Datapipes almost working. * update import paths * Starting to clean up dependency tree. * Fixing and adjusting a broad suite of tests. * Update test/domain_parallel/conftest.py Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * Minor fix * Not seeing any errors in testing ... * A new X-MeshGraphNet example for reservoir simulation. (#1186) * X-MGN for reservoir simulation Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * installation bug fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * well object docstring fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * more well object docstring fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve path_utils Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fix while space in config Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fix version inconsistency in requirement.txt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * add versions for some libs in requirement.txt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve exception handling in mldlow_utils Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve mldlow_utils Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve datetiem in mlflow_utils Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve exception handling in inference Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve inference Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve ecl_reader Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * formatting Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve preprocessor Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve preprocessor loop Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * grad accum bug fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * total loss bug fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * added some safe guard for connection indexing Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * bug fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * bug fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update ecl_reader Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup utils Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup * cleanup * update configs * Update README.md style guide rule changes * Update README.md * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve docstring fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update license yr Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup well Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup preproc fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup preproc fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cimprove infrence fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve datetime Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve readme fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve readme Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve train.py fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve readme fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve requirement Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * ilcense header Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve ecl reader logging Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * license header Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve graph builder (parallel) + added results to readme Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * delete some unsed files Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * address PR comments Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve inference grdecl header Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve readme Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve readme Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * support time series Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update config Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * minor update Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve graph builder Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update ecl_reader logging Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * replace pickle with json Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * add license headers Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * remove unused png files Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * remove unsed import Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * remove emojis Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * replace print with logger Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update docstring Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update readme Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * minor updates Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update readme Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update header Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> --------- Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> Co-authored-by: megnvidia <mmiranda@nvidia.com> * Add knn to autodoc table. (#1244) --------- Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> Co-authored-by: tonishi-nv <tonishi@nvidia.com> Co-authored-by: megnvidia <mmiranda@nvidia.com> * Enable import linting on internal imports. * Remove ensure_available function, it's confusing * Add logging imports to utils, and fix imports in examples. * Update imports in minimal examples * Update structural mechanics examples * Update import paths: reservoir_sim * Update import paths: additive manufacturing * Update import paths: topodiff * Update import paths: weather part 1 * Update import paths: weather part 2 * Update import paths: molecular dynamics * Update import paths: geophysics * Update import paths: cfd + external_aero 1 * Update import paths: cfd + external_aero 2 * Remove more DGL examples * Remove more DGL examples * cfd examples 3 * Last batch of example import fixes! * Enforce and protect external deps in utils. * Remove DGL. :party: * Don't force models yet * Refactor (#1249) * Move filesystems and version_check to core * Fix version check tests * Reorganize distributed, domain_parallel, and begin nn / utils cleanup. * Move modules and meta to core. Move registry to core. No tests fixed yet. * Add missing init files * Update build system and specify some deps. * Reorganize tests. * Update init files * Clean up neighbor tools. * Update testing * Fix compat tests * Move core model tests to tests/core/ * Add import lint config * Relocate layers * Move graphcast utils into model directory * Relocating util functionalities. * Further clean up and organize tests. * utils tests are passing now * Cleaning up distributed tests * Patching tests working again in nn * Fix sdf test * Fix zenith angle tests * Some organization of tests. Checkpoints is moved into utils. * Remove launch.utils and launch.config. Checkpointing is moved to phsyicsnemo.utils, launch.config is just gone. It was empty. * Most nn tests are passing * Further cleanup. Getting there! * Remove constants file * Add import linting to pre-commit. * Move gnn layers and start to fix several model tests. * AFNO is now passing. * Rnn models passing. * Fix improt * Healpix tests are working * Domino and unet working * Updating to address some test issues * MGN tests passing again * Most graphcast tests passing again * Move nd conv layers. * update fengwu and pangu * Update sfno and pix2pix test * update tests for figconvnet, swinrnn, superresnet * updating more models to pass * Update distributed tests, now passing. * Domain parallel tests now passing. * Fix active learning imports so tests pass in refactor * Fix some metric imports * Remove deploy package * Remove unused test file * unmigrate these files ... again? * Update import linter. * Cleaning up diffusion models. Not quite done yet. * Restore deleted files * Updating more tests. * Further updates to tests. Datapipes almost working. * update import paths * Starting to clean up dependency tree. * Fixing and adjusting a broad suite of tests. * Update test/domain_parallel/conftest.py Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * Minor fix * Not seeing any errors in testing ... * A new X-MeshGraphNet example for reservoir simulation. (#1186) * X-MGN for reservoir simulation Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * installation bug fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * well object docstring fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * more well object docstring fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve path_utils Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fix while space in config Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fix version inconsistency in requirement.txt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * add versions for some libs in requirement.txt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve exception handling in mldlow_utils Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve mldlow_utils Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve datetiem in mlflow_utils Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve exception handling in inference Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve inference Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve ecl_reader Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * formatting Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve preprocessor Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve preprocessor loop Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * grad accum bug fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * total loss bug fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * added some safe guard for connection indexing Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * bug fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * bug fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update ecl_reader Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup utils Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup * cleanup * update configs * Update README.md style guide rule changes * Update README.md * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve docstring fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update license yr Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup well Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup preproc fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup preproc fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cimprove infrence fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve datetime Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve readme fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve readme Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve train.py fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve readme fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve requirement Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * ilcense header Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve ecl reader logging Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * license header Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve graph builder (parallel) + added results to readme Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * delete some unsed files Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * address PR comments Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve inference grdecl header Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve readme Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve readme Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * support time series Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update config Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * minor update Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve graph builder Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update ecl_reader logging Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * replace pickle with json Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * add license headers Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * remove unused png files Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * remove unsed import Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * remove emojis Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * replace print with logger Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update docstring Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update readme Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * minor updates Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update readme Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update header Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> --------- Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> Co-authored-by: megnvidia <mmiranda@nvidia.com> * Add knn to autodoc table. (#1244) * Enable import linting on internal imports. * Remove ensure_available function, it's confusing * Add logging imports to utils, and fix imports in examples. * Update imports in minimal examples * Update structural mechanics examples * Update import paths: reservoir_sim * Update import paths: additive manufacturing * Update import paths: topodiff * Update import paths: weather part 1 * Update import paths: weather part 2 * Update import paths: molecular dynamics * Update import paths: geophysics * Update import paths: cfd + external_aero 1 * Update import paths: cfd + external_aero 2 * Remove more DGL examples * Remove more DGL examples * cfd examples 3 * Last batch of example import fixes! * Enforce and protect external deps in utils. * Remove DGL. :party: * Don't force models yet --------- Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> Co-authored-by: tonishi-nv <tonishi@nvidia.com> Co-authored-by: megnvidia <mmiranda@nvidia.com> * Automated model registry (#1252) * Deleted RegistreableModule Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Removed 'PhysicsNeMo' suffix in Module.from_torch method Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Implemented automatic registration for Module subclasses Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Fixed unused name Signed-off-by: Charlelie Laurent <claurent@nvidia.com> --------- Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Metadata name deprecation (#1257) * Initiated deprecation of field 'name' in ModelMetaData Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Removed all occurences of 'name' field in ModelMetaData Signed-off-by: Charlelie Laurent <claurent@nvidia.com> --------- Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Refactor (#1258) * Move filesystems and version_check to core * Fix version check tests * Reorganize distributed, domain_parallel, and begin nn / utils cleanup. * Move modules and meta to core. Move registry to core. No tests fixed yet. * Add missing init files * Update build system and specify some deps. * Reorganize tests. * Update init files * Clean up neighbor tools. * Update testing * Fix compat tests * Move core model tests to tests/core/ * Add import lint config * Relocate layers * Move graphcast utils into model directory * Relocating util functionalities. * Further clean up and organize tests. * utils tests are passing now * Cleaning up distributed tests * Patching tests working again in nn * Fix sdf test * Fix zenith angle tests * Some organization of tests. Checkpoints is moved into utils. * Remove launch.utils and launch.config. Checkpointing is moved to phsyicsnemo.utils, launch.config is just gone. It was empty. * Most nn tests are passing * Further cleanup. Getting there! * Remove constants file * Add import linting to pre-commit. * Move gnn layers and start to fix several model tests. * AFNO is now passing. * Rnn models passing. * Fix improt * Healpix tests are working * Domino and unet working * Updating to address some test issues * MGN tests passing again * Most graphcast tests passing again * Move nd conv layers. * update fengwu and pangu * Update sfno and pix2pix test * update tests for figconvnet, swinrnn, superresnet * updating more models to pass * Update distributed tests, now passing. * Domain parallel tests now passing. * Fix active learning imports so tests pass in refactor * Fix some metric imports * Remove deploy package * Remove unused test file * unmigrate these files ... again? * Update import linter. * Cleaning up diffusion models. Not quite done yet. * Restore deleted files * Updating more tests. * Further updates to tests. Datapipes almost working. * update import paths * Starting to clean up dependency tree. * Fixing and adjusting a broad suite of tests. * Update test/domain_parallel/conftest.py Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * Minor fix * Not seeing any errors in testing ... * A new X-MeshGraphNet example for reservoir simulation. (#1186) * X-MGN for reservoir simulation Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * installation bug fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * well object docstring fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * more well object docstring fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve path_utils Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fix while space in config Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fix version inconsistency in requirement.txt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * add versions for some libs in requirement.txt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve exception handling in mldlow_utils Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve mldlow_utils Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve datetiem in mlflow_utils Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve exception handling in inference Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve inference Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve ecl_reader Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * formatting Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve preprocessor Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve preprocessor loop Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * grad accum bug fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * total loss bug fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * added some safe guard for connection indexing Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * bug fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * bug fix Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update ecl_reader Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup utils Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup * cleanup * update configs * Update README.md style guide rule changes * Update README.md * fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve docstring fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update license yr Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup well Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup preproc fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup preproc fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cimprove infrence fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve datetime Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve readme fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve readme Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve train.py fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve readme fmt Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve requirement Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * ilcense header Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve ecl reader logging Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * cleanup Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * license header Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve graph builder (parallel) + added results to readme Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * delete some unsed files Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * address PR comments Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve inference grdecl header Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve readme Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve readme Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * support time series Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update config Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * minor update Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * improve graph builder Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update ecl_reader logging Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * replace pickle with json Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * add license headers Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * remove unused png files Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * remove unsed import Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * remove emojis Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * replace print with logger Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update docstring Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update readme Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * minor updates Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update readme Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> * update header Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> --------- Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> Co-authored-by: megnvidia <mmiranda@nvidia.com> * Add knn to autodoc table. (#1244) * Enable import linting on internal imports. * Remove ensure_available function, it's confusing * Add logging imports to utils, and fix imports in examples. * Update imports in minimal examples * Update structural mechanics examples * Update import paths: reservoir_sim * Update import paths: additive manufacturing * Update import paths: topodiff * Update import paths: weather part 1 * Update import paths: weather part 2 * Update import paths: molecular dynamics * Update import paths: geophysics * Update import paths: cfd + external_aero 1 * Update import paths: cfd + external_aero 2 * Remove more DGL examples * Remove more DGL examples * cfd examples 3 * Last batch of example import fixes! * Enforce and protect external deps in utils. * Remove DGL. :party: * Don't force models yet * Update version (#1193) * Fix depenedncies to enable hello world (#1195) * Remove zero-len arrays from test dataset (#1198) * Merge updates to Gray Scott example (#1239) * Remove pyevtk * update dependency * update dimensions * ci issues * Interpolation model example (#1149) * Temporal interpolation training recipe * Add README * Docs changes based on comments * Update docstrings and README * Add temporal interpolation animation * Add animation link * Add shape check in loss * Updates of configs + trainer * Update config comments * Update README.md style guide edits * Added wandb logging Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Reformated sections in docstring for GeometricL2Loss Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Update README and configs * README changes + type hint fixes * Update README.md * Draft of validation script * Update validation and README * Fixed command in README.md for temporal_interpolation example Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Removed unused import in datapipe/climate_interp.py Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Updated license headers in temporal_interpolation example Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Renamed methods to avoid implicit shadowing in Trainer class Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Cosmetic changes in train.py and removed unused import in validate.py Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Added clamp in validate.py to make sure step does not go out of bounds Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Added the temporal_interpolation example to the docs + updated CHANGELOG.md Signed-off-by: Charlelie Laurent <claurent@nvidia.com> * Addressing remaining comments * Merged two data source classes in climate_interp.py Signed-off-by: Charlelie Laurent <claurent@nvidia.com> --------- Signed-off-by: Charlelie Laurent <claurent@nvidia.com> Co-authored-by: Charlelie Laurent <claurent@nvidia.com> Co-authored-by: megnvidia <mmiranda@nvidia.com> Co-authored-by: Charlelie Laurent <84199758+CharlelieLrt@users.noreply.github.com> * update versions --------- Signed-off-by: Tsubasa Onishi <tonishi@nvidia.com> Signed-off-by: Charlelie Laurent <claurent@nvidia.com> Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> Co-authored-by: tonishi-nv <tonishi@nvidia.com> Co-authored-by: megnvidia <mmiranda@nvidia.com> Co-authored-by: Kaustubh Tangsali <71059996+ktangsali@users.noreply.github.com> Co-authored-by: Jussi Leinonen <jleinonen@nvidia.com> Co-authored-by: Charlelie Laurent <claurent@nvidia.com> Co-authored-by: Charlelie Laurent <84199758+CharlelieLrt@users.noreply.github.com> Co-authored-by: Kaustubh Tangsali <ktangsali@nvidia.com> * Remove IPDB * Few more dep fixes. * Refactor (#1261) * Move filesystems and version_check to core * Fix version check tests * Reorganize distributed, domain_parallel, and begin nn / utils cleanup. * Move modules and meta to core. Move registry to core. No tests fixed yet. * Add missing init files * Update build system and specify some deps. * Reorganize tests. * Update init files * Clean up neighbor tools. * Update testing * Fix compat tests * Move core model tests to tests/core/ * Add import lint config * Relocate layers * Move graphcast utils into model directory * Relocating util functionalities. * Further clean up and organize tests. * utils tests are passing now * Cleaning up distributed tests * Patching tests working again in nn * Fix sdf test * Fix zenith angle tests * Some organization of tests. Checkpoints is moved into utils. * Remove launch.utils and launch.config. Checkpointing is moved to phsyicsnemo.utils, launch.config is just gone. It was empty. * Most nn tests are passing * Further cleanup. Getting there! * Remove constants file * Add import linting to pre-commit. * Move gnn layers and start to fix several model tests. * AFNO is now passing. * Rnn models passing. * Fix improt * Healpix tests are working * Domino and unet working * Updating to address some test issues * MGN tests passing again * Most graphcast tests passing again * Move nd conv layers. * update fengwu and pangu * Update sfno and pix2pix test * update tests for figconvnet, swinrnn, superresnet * updating more models to pass * Update distributed tests, now passing. * Domain parallel tests now passing. * Fix active learning imports so tests pass in refactor * Fix some metric imports * Remove deploy package * Remove unused test file * unmigrate these files ... again? * Update import linter. * Cleaning up diffusion models. Not quite done yet. * Restore deleted files * Updating more tests. * Further updates to tests. Datapipes almost working. * update import paths * Starting to clean up dependency tree. * Fixing and adjusting a broad suite of tests. * Update test/domain_parallel/conftest.py Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * Minor fix * Not seeing any errors in testing ... * Enable import linting on internal imports. * Remove ensure_available function, it's confusing * Add logging imports to utils, and fix imports in examples. * Update imports in minimal examples * Update structural mechanics examples * Update import paths: reservoir_sim * Update import paths: additive manufacturing * Update import paths: topodiff * Update import paths: weather part 1 * Update import paths: weather part 2 * Update import paths: molecular dynamics * Update import paths: geophysics * Update import paths: cfd + external_aero 1 * Update import paths: cfd + external_aero 2 * Remove more DGL examples * Remove more DGL examples * cfd examples 3 * Last batch of example import fixes! * Enforce and protect external deps in utils. * Remove DGL. :party: * Don't force models yet * Remove IPDB * Few more dep fixes. * Enhance checkpoint configuration for DLWP Healpix and GraphCast (#1253) * feat(weather): Improve configuration for DLWP Healpix and GraphCast examples - Added configurable checkpoint directory to DLWP Healpix config and training script. - Implemented Trainer logic to use specific checkpoint directory. - Updated utils.py to respect exact checkpoint path. - Made Weights & Biases entity and project configurable in GraphCast example. * fix(dlwp_healpix): remove deprecated configs - Removed the deprecated `verbose` parameter from the `CosineAnnealingLR` configuration in DLWP HEALPix, which was causing a TypeError. - Removed unused configs from examples/weather/dlwp_healpix/ * Transolver volume (#1242) * Implement transolver ++ physics attention * Enable ++ in Transolver. * Fix temperature correction terms. * Starting work adapting the domino datapipe techniques to transolver. * Working towards transolver volume training by mergeing with domino dataset. Surface dataloading is prototyped, not finished yet. * Updating * Remove printout * Enable transolver for volumetric data * Update transolver training script to support either surface or volume data. Applied some cleanup to make the datapipe similar to domino, which is a step towards unification. * Updating datapipe * Tweak transolver volume configs * Add transolverX model * Enable nearly-uniform sampling of very very large arrays * limit benchmarking to train epoch, enable profiler in config * Update volume config slightly * Update training scripts to properly enable data preloading * Working towards adding a muon optimzier in transolver * Add peter's implementation of muon with a combined optimizer. switch to a flat LR. * Add updated inference script that can also calculate drag and lift * Add better docstrings for typhon * Move typhon to experimental * Move forwards docstring * Adding typhon model and configs. * Update readme. * Update * Remove extra model. Update recipes. * Update cae_dataset.py Implement abstract methods in base classes. * Update Physics_Attention.py Ensure plus parameter is passed to base class. * Update test_mesh_datapipe.py Update import path for mesh datapipe. * Fix ruff issues --------- Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> Co-authored-by: Dileep Ranganathan <8152399+dran-dev@users.noreply.github.com> * Add external import coding standards. * Update external import standards. * Ensure vtk functions are protected. * Protect pyvista import * Closing more import gaps * Remove DGL from meshgraphkan * All models now comply with external import linting. * Remove DGL datapipes * cae datapipes in compliance * Update pyproject.toml * Add version numbers to deps * Refactor (#1261) * Move filesystems and version_check to core * Fix version check tests * Reorganize distributed, domain_parallel, and begin nn / utils cleanup. * Move modules and meta to core. Move registry to core. No tests fixed yet. * Add missing init files * Update build system and specify some deps. * Reorganize tests. * Update init files * Clean up neighbor tools. * Update testing * Fix compat tests * Move core model tests to tests/core/ * Add import lint config * Relocate layers * Move graphcast utils into model directory * Relocating util functionalities. * Further clean up and organize tests. * utils tests are passing now * Cleaning up distributed tests * Patching tests working again in nn * Fix sdf test * Fix zenith angle tests * Some organization of tests. Checkpoints is moved into utils. * Remove launch.utils and launch.config. Checkpointing is moved to phsyicsnemo.utils, launch.config is just gone. It was empty. * Most nn tests are passing * Further cleanup. Getting there! * Remove constants file * Add import linting to pre-commit. * Move gnn layers and start to fix several model tests. * AFNO is now passing. * Rnn models passing. * Fix improt * Healpix tests are working * Domino and unet working * Updating to address some test issues * MGN tests passing again * Most graphcast tests passing again * Move nd conv layers. * update fengwu and pangu * Update sfno and pix2pix test * update tests for figconvnet, swinrnn, superresnet * updating more models to pass * Update distributed tests, now passing. * Domain parallel tests now passing. * Fix active learning imports so tests pass in refactor * Fix some metric imports * Remove deploy package * Remove unused test file * unmigrate these files ... again? * Update import linter. * Cleaning up diffusion models. Not quite done yet. * Restore deleted files * Updating more tests. * Further updates to tests. Datapipes almost working. * update import paths * Starting to clean up dependency tree. * Fixing and adjusting a broad suite of tests. * Update test/domain_parallel/conftest.py Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com> * Minor fix * Not seeing any errors in testing ... * Enable import linting on internal imports. * Remove ensure_available function, it's confusing * Add logging imports to utils, and fix imports in examples. * Update imports in minimal examples * Update structural mechanics examples * Update import paths: reservoir_sim * Update import paths: additive manufacturing * Update import paths: topodiff * Update import paths: weather part 1 * Update import paths: weather part 2 * Update import paths: molecular dynamics * Update import paths: geophysics * Update import paths: cfd + external_aero 1 * Update import paths: cfd + external_aero 2 * Remove more DGL examples * Remove more DGL examples * cfd examples 3 * Last batch of example import fixes! * Enforce and protect externa…
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Makefile

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@@ -48,9 +48,10 @@ pytest-internal:
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pytest && \
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cd ../../
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# NOTE: temporarily omitting diffusion coverage until we have a better way to test it.
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coverage:
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coverage combine && \
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coverage report --show-missing --omit=*test* --omit=*internal* --omit=*experimental* --fail-under=60 && \
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coverage report --show-missing --omit=*test* --omit=*internal* --omit=*experimental* --omit=*diffusion* --fail-under=60 && \
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coverage html
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all-ci: get-data setup-ci black interrogate lint license install pytest doctest coverage

physicsnemo/diffusion/__init__.py

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# See the License for the specific language governing permissions and
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# limitations under the License.
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from .base import DiffusionModel # noqa: F401
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from .base import Denoiser, DiffusionModel, Predictor # noqa: F401

physicsnemo/diffusion/base.py

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@@ -58,11 +58,11 @@ class DiffusionModel(Protocol):
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>>> import torch.nn.functional as F
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>>> from physicsnemo.diffusion import DiffusionModel
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>>>
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>>> class Denoiser:
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>>> class Model:
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... def __call__(self, x, t, condition=None, **kwargs):
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... return F.relu(x)
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...
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>>> isinstance(Denoiser(), DiffusionModel)
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>>> isinstance(Model(), DiffusionModel)
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True
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"""
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Model output with the same shape as ``x``.
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"""
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...
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@runtime_checkable
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class Predictor(Protocol):
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r"""
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Protocol defining a predictor interface for diffusion models.
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A predictor is any callable that takes a noisy state ``x``
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and diffusion time ``t``, and returns a prediction about the clean data or
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the noise. Common types of predictors include x0-predictor (predicts the
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clean data :math:`\mathbf{x}_0`), score-predictor, noise-predictor
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(predicts the noise :math:`\boldsymbol{\epsilon}`), velocity-predictor etc.
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This protocol is **generic** and does not assume any specific type of
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prediction. A predictor can be a trained neural network, a guidance
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function (e.g., classifier-free guidance, DPS-style guidance), or any
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combination thereof. The exact meaning of the output depends on the
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predictor type and how it is used. Any callable that implements this
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interface can be used as a predictor in sampling utilities.
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This protocol is typically used during inference. For training, which
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often requires additional inputs like conditioning, use the more general
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:class:`DiffusionModel` protocol instead. A :class:`Predictor` can be
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obtained from a :class:`DiffusionModel` by partially applying the
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``condition`` and any other keyword arguments using
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``functools.partial``.
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**Relationship to Denoiser:**
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A :class:`Denoiser` is the update function used during sampling (e.g.,
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the right-hand side of an ODE/SDE). It is obtained from a
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:class:`Predictor` via the
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:meth:`~physicsnemo.diffusion.noise_schedulers.NoiseScheduler.get_denoiser`
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factory. A typical case is ODE/SDE-based sampling, where one solves:
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.. math::
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\frac{d\mathbf{x}}{dt} = D(\mathbf{x}, t;\, P(\mathbf{x}, t))
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where :math:`P` is the **predictor** and :math:`D` is the **denoiser**
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that wraps it. This equation captures the essence of how these two
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concepts are related in the framework.
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See Also
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--------
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:class:`Denoiser` : The interface for sampling update functions.
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:meth:`~physicsnemo.diffusion.noise_schedulers.NoiseScheduler.get_denoiser` :
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Factory to convert a predictor into a denoiser.
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Examples
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--------
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**Example 1:** Convert a trained conditional model into a predictor using
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``functools.partial``:
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>>> import torch
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>>> from functools import partial
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>>> from tensordict import TensorDict
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>>> from physicsnemo.diffusion import Predictor
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>>>
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>>> class MyModel:
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... def __call__(self, x, t, condition=None):
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... # x0-predictor: returns estimate of clean data
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... # (here assumes conditional normal distribution N(x|y))
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... t_bc = t.view(-1, *([1] * (x.ndim - 1)))
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... return x / (1 + t_bc**2) + condition["y"]
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...
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>>> model = MyModel()
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>>> cond = TensorDict({"y": torch.randn(2, 4)}, batch_size=[2])
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>>> x0_predictor = partial(model, condition=cond)
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>>> isinstance(x0_predictor, Predictor)
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True
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**Example 2:** Convert the x0-predictor above into a score-predictor
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(using a simple EDM-like schedule where :math:`\sigma(t) = t` and
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:math:`\alpha(t) = 1`):
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>>> def x0_to_score(x0, x_t, t):
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... sigma_sq = t.view(-1, 1) ** 2
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... return (x0 - x_t) / sigma_sq
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>>>
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>>> def score_predictor(x, t):
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... x0_pred = x0_predictor(x, t)
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... return x0_to_score(x0_pred, x, t)
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>>>
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>>> isinstance(score_predictor, Predictor)
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True
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"""
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def __call__(
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self,
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x: Float[torch.Tensor, " B *dims"],
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t: Float[torch.Tensor, " B"],
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) -> Float[torch.Tensor, " B *dims"]:
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r"""
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Forward pass of the predictor.
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Parameters
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----------
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x : torch.Tensor
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Noisy latent state of shape :math:`(B, *)` where :math:`B` is the
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batch size and :math:`*` denotes any number of additional
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dimensions (e.g., channels and spatial dimensions).
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t : torch.Tensor
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Batched diffusion time tensor of shape :math:`(B,)`.
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Returns
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-------
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torch.Tensor
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Prediction output with the same shape as ``x``. The exact meaning
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depends on the predictor type (x0, score, noise, velocity, etc.).
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"""
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...
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@runtime_checkable
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class Denoiser(Protocol):
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r"""
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Protocol defining a denoiser interface for diffusion model sampling.
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A denoiser is the **update function** used during sampling. It takes a
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noisy state ``x`` and diffusion time ``t``, and returns the update term
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consumed by a :class:`~physicsnemo.diffusion.samplers.solvers.Solver`.
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For continuous-time methods this is typically the right-hand side of the
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ODE/SDE, but the interface is generic and can support other sampling
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methods as well.
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This is the interface used by
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:class:`~physicsnemo.diffusion.samplers.solvers.Solver` classes and the
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:func:`~physicsnemo.diffusion.samplers.sample` function. Any callable
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that implements this interface can be used as a denoiser.
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**Important distinction from Predictor:**
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- A :class:`Predictor` is any callable that outputs a raw prediction
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(e.g., clean data :math:`\mathbf{x}_0`, score, guidance signal, etc.).
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- A :class:`Denoiser` is the update function derived from one or more
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predictors, used directly by the solver during sampling.
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**Typical workflow:**
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1. Start with one or more :class:`Predictor` instances (e.g. trained model)
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2. Optionally combine predictors (e.g., conditional + guidance scores)
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3. Convert to a :class:`Denoiser` using
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:meth:`~physicsnemo.diffusion.noise_schedulers.NoiseScheduler.get_denoiser`
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4. Pass the denoiser to
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:func:`~physicsnemo.diffusion.samplers.sample` together with a
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:class:`~physicsnemo.diffusion.samplers.solvers.Solver`
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See Also
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--------
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:class:`Predictor` : The interface for raw predictions.
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:meth:`~physicsnemo.diffusion.noise_schedulers.NoiseScheduler.get_denoiser` :
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Factory to convert a predictor into a denoiser.
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:func:`~physicsnemo.diffusion.samplers.sample` : The sampling function
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that uses this denoiser interface.
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Examples
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--------
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Manually creating a denoiser from an x0-predictor using a simple EDM-like
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schedule (:math:`\sigma(t)=t`, :math:`\alpha(t)=1`):
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>>> import torch
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>>> from physicsnemo.diffusion import Denoiser
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>>>
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>>> # Start from a predictor (x0-predictor)
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>>> def x0_predictor(x, t):
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... t_bc = t.view(-1, *([1] * (x.ndim - 1)))
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... return x / (1 + t_bc**2)
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>>>
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>>> # Build a denoiser (ODE RHS) from scratch:
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>>> # score = (x0 - x) / sigma^2, ODE RHS = -0.5 * g^2 * score
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>>> # For EDM: sigma = t, g^2 = 2*t, so RHS = (x0 - x) / t
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>>> def my_denoiser(x, t):
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... x0 = x0_predictor(x, t)
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... t_bc = t.view(-1, *([1] * (x.ndim - 1)))
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... return (x0 - x) / t_bc
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...
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>>> isinstance(my_denoiser, Denoiser)
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True
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"""
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def __call__(
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self,
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x: Float[torch.Tensor, " B *dims"],
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t: Float[torch.Tensor, " B"],
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) -> Float[torch.Tensor, " B *dims"]:
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r"""
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Compute the denoising update at the given state and time.
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Parameters
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----------
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x : torch.Tensor
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Noisy latent state of shape :math:`(B, *)` where :math:`B` is the
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batch size and :math:`*` denotes any number of additional
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dimensions (e.g., channels and spatial dimensions).
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t : torch.Tensor
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Batched diffusion time tensor of shape :math:`(B,)`.
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All batch elements in the latent state ``x`` typically share the
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same diffusion time values, but ``t`` is still required to be a
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batched tensor.
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Returns
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-------
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torch.Tensor
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Denoising update term with the same shape as ``x``.
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"""
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...

physicsnemo/diffusion/noise_schedulers/__init__.py

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# See the License for the specific language governing permissions and
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# limitations under the License.
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import warnings
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from physicsnemo.core.warnings import FutureFeatureWarning
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warnings.warn(
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"The 'physicsnemo.diffusion.noise_schedulers' module is a placeholder for "
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"future functionality that will be implemented in an upcoming release.",
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FutureFeatureWarning,
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stacklevel=2,
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from .noise_schedulers import ( # noqa: F401
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EDMNoiseScheduler,
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IDDPMNoiseScheduler,
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LinearGaussianNoiseScheduler,
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NoiseScheduler,
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StudentTEDMNoiseScheduler,
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VENoiseScheduler,
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VPNoiseScheduler,
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)

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