@synsci/cli-darwin-x64-baseline 1.1.76 → 1.1.78
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/bin/skills/adaptyv/SKILL.md +114 -0
- package/bin/skills/adaptyv/reference/api_reference.md +308 -0
- package/bin/skills/adaptyv/reference/examples.md +913 -0
- package/bin/skills/adaptyv/reference/experiments.md +360 -0
- package/bin/skills/adaptyv/reference/protein_optimization.md +637 -0
- package/bin/skills/aeon/SKILL.md +374 -0
- package/bin/skills/aeon/references/anomaly_detection.md +154 -0
- package/bin/skills/aeon/references/classification.md +144 -0
- package/bin/skills/aeon/references/clustering.md +123 -0
- package/bin/skills/aeon/references/datasets_benchmarking.md +387 -0
- package/bin/skills/aeon/references/distances.md +256 -0
- package/bin/skills/aeon/references/forecasting.md +140 -0
- package/bin/skills/aeon/references/networks.md +289 -0
- package/bin/skills/aeon/references/regression.md +118 -0
- package/bin/skills/aeon/references/segmentation.md +163 -0
- package/bin/skills/aeon/references/similarity_search.md +187 -0
- package/bin/skills/aeon/references/transformations.md +246 -0
- package/bin/skills/alphafold-database/SKILL.md +513 -0
- package/bin/skills/alphafold-database/references/api_reference.md +423 -0
- package/bin/skills/anndata/SKILL.md +400 -0
- package/bin/skills/anndata/references/best_practices.md +525 -0
- package/bin/skills/anndata/references/concatenation.md +396 -0
- package/bin/skills/anndata/references/data_structure.md +314 -0
- package/bin/skills/anndata/references/io_operations.md +404 -0
- package/bin/skills/anndata/references/manipulation.md +516 -0
- package/bin/skills/arboreto/SKILL.md +243 -0
- package/bin/skills/arboreto/references/algorithms.md +138 -0
- package/bin/skills/arboreto/references/basic_inference.md +151 -0
- package/bin/skills/arboreto/references/distributed_computing.md +242 -0
- package/bin/skills/arboreto/scripts/basic_grn_inference.py +97 -0
- package/bin/skills/astropy/SKILL.md +331 -0
- package/bin/skills/astropy/references/coordinates.md +273 -0
- package/bin/skills/astropy/references/cosmology.md +307 -0
- package/bin/skills/astropy/references/fits.md +396 -0
- package/bin/skills/astropy/references/tables.md +489 -0
- package/bin/skills/astropy/references/time.md +404 -0
- package/bin/skills/astropy/references/units.md +178 -0
- package/bin/skills/astropy/references/wcs_and_other_modules.md +373 -0
- package/bin/skills/benchling-integration/SKILL.md +480 -0
- package/bin/skills/benchling-integration/references/api_endpoints.md +883 -0
- package/bin/skills/benchling-integration/references/authentication.md +379 -0
- package/bin/skills/benchling-integration/references/sdk_reference.md +774 -0
- package/bin/skills/biopython/SKILL.md +443 -0
- package/bin/skills/biopython/references/advanced.md +577 -0
- package/bin/skills/biopython/references/alignment.md +362 -0
- package/bin/skills/biopython/references/blast.md +455 -0
- package/bin/skills/biopython/references/databases.md +484 -0
- package/bin/skills/biopython/references/phylogenetics.md +566 -0
- package/bin/skills/biopython/references/sequence_io.md +285 -0
- package/bin/skills/biopython/references/structure.md +564 -0
- package/bin/skills/biorxiv-database/SKILL.md +483 -0
- package/bin/skills/biorxiv-database/references/api_reference.md +280 -0
- package/bin/skills/biorxiv-database/scripts/biorxiv_search.py +445 -0
- package/bin/skills/bioservices/SKILL.md +361 -0
- package/bin/skills/bioservices/references/identifier_mapping.md +685 -0
- package/bin/skills/bioservices/references/services_reference.md +636 -0
- package/bin/skills/bioservices/references/workflow_patterns.md +811 -0
- package/bin/skills/bioservices/scripts/batch_id_converter.py +347 -0
- package/bin/skills/bioservices/scripts/compound_cross_reference.py +378 -0
- package/bin/skills/bioservices/scripts/pathway_analysis.py +309 -0
- package/bin/skills/bioservices/scripts/protein_analysis_workflow.py +408 -0
- package/bin/skills/brenda-database/SKILL.md +719 -0
- package/bin/skills/brenda-database/references/api_reference.md +537 -0
- package/bin/skills/brenda-database/scripts/brenda_queries.py +844 -0
- package/bin/skills/brenda-database/scripts/brenda_visualization.py +772 -0
- package/bin/skills/brenda-database/scripts/enzyme_pathway_builder.py +1053 -0
- package/bin/skills/cellxgene-census/SKILL.md +511 -0
- package/bin/skills/cellxgene-census/references/census_schema.md +182 -0
- package/bin/skills/cellxgene-census/references/common_patterns.md +351 -0
- package/bin/skills/chembl-database/SKILL.md +389 -0
- package/bin/skills/chembl-database/references/api_reference.md +272 -0
- package/bin/skills/chembl-database/scripts/example_queries.py +278 -0
- package/bin/skills/cirq/SKILL.md +346 -0
- package/bin/skills/cirq/references/building.md +307 -0
- package/bin/skills/cirq/references/experiments.md +572 -0
- package/bin/skills/cirq/references/hardware.md +515 -0
- package/bin/skills/cirq/references/noise.md +515 -0
- package/bin/skills/cirq/references/simulation.md +350 -0
- package/bin/skills/cirq/references/transformation.md +416 -0
- package/bin/skills/clinicaltrials-database/SKILL.md +507 -0
- package/bin/skills/clinicaltrials-database/references/api_reference.md +358 -0
- package/bin/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +215 -0
- package/bin/skills/clinpgx-database/SKILL.md +638 -0
- package/bin/skills/clinpgx-database/references/api_reference.md +757 -0
- package/bin/skills/clinpgx-database/scripts/query_clinpgx.py +518 -0
- package/bin/skills/clinvar-database/SKILL.md +362 -0
- package/bin/skills/clinvar-database/references/api_reference.md +227 -0
- package/bin/skills/clinvar-database/references/clinical_significance.md +218 -0
- package/bin/skills/clinvar-database/references/data_formats.md +358 -0
- package/bin/skills/cobrapy/SKILL.md +463 -0
- package/bin/skills/cobrapy/references/api_quick_reference.md +655 -0
- package/bin/skills/cobrapy/references/workflows.md +593 -0
- package/bin/skills/cosmic-database/SKILL.md +336 -0
- package/bin/skills/cosmic-database/references/cosmic_data_reference.md +220 -0
- package/bin/skills/cosmic-database/scripts/download_cosmic.py +231 -0
- package/bin/skills/dask/SKILL.md +456 -0
- package/bin/skills/dask/references/arrays.md +497 -0
- package/bin/skills/dask/references/bags.md +468 -0
- package/bin/skills/dask/references/best-practices.md +277 -0
- package/bin/skills/dask/references/dataframes.md +368 -0
- package/bin/skills/dask/references/futures.md +541 -0
- package/bin/skills/dask/references/schedulers.md +504 -0
- package/bin/skills/datacommons-client/SKILL.md +255 -0
- package/bin/skills/datacommons-client/references/getting_started.md +417 -0
- package/bin/skills/datacommons-client/references/node.md +250 -0
- package/bin/skills/datacommons-client/references/observation.md +185 -0
- package/bin/skills/datacommons-client/references/resolve.md +246 -0
- package/bin/skills/datamol/SKILL.md +706 -0
- package/bin/skills/datamol/references/conformers_module.md +131 -0
- package/bin/skills/datamol/references/core_api.md +130 -0
- package/bin/skills/datamol/references/descriptors_viz.md +195 -0
- package/bin/skills/datamol/references/fragments_scaffolds.md +174 -0
- package/bin/skills/datamol/references/io_module.md +109 -0
- package/bin/skills/datamol/references/reactions_data.md +218 -0
- package/bin/skills/deepchem/SKILL.md +597 -0
- package/bin/skills/deepchem/references/api_reference.md +303 -0
- package/bin/skills/deepchem/references/workflows.md +491 -0
- package/bin/skills/deepchem/scripts/graph_neural_network.py +338 -0
- package/bin/skills/deepchem/scripts/predict_solubility.py +224 -0
- package/bin/skills/deepchem/scripts/transfer_learning.py +375 -0
- package/bin/skills/deeptools/SKILL.md +531 -0
- package/bin/skills/deeptools/assets/quick_reference.md +58 -0
- package/bin/skills/deeptools/references/effective_genome_sizes.md +116 -0
- package/bin/skills/deeptools/references/normalization_methods.md +410 -0
- package/bin/skills/deeptools/references/tools_reference.md +533 -0
- package/bin/skills/deeptools/references/workflows.md +474 -0
- package/bin/skills/deeptools/scripts/validate_files.py +195 -0
- package/bin/skills/deeptools/scripts/workflow_generator.py +454 -0
- package/bin/skills/denario/SKILL.md +215 -0
- package/bin/skills/denario/references/examples.md +494 -0
- package/bin/skills/denario/references/installation.md +213 -0
- package/bin/skills/denario/references/llm_configuration.md +265 -0
- package/bin/skills/denario/references/research_pipeline.md +471 -0
- package/bin/skills/diffdock/SKILL.md +483 -0
- package/bin/skills/diffdock/assets/batch_template.csv +4 -0
- package/bin/skills/diffdock/assets/custom_inference_config.yaml +90 -0
- package/bin/skills/diffdock/references/confidence_and_limitations.md +182 -0
- package/bin/skills/diffdock/references/parameters_reference.md +163 -0
- package/bin/skills/diffdock/references/workflows_examples.md +392 -0
- package/bin/skills/diffdock/scripts/analyze_results.py +334 -0
- package/bin/skills/diffdock/scripts/prepare_batch_csv.py +254 -0
- package/bin/skills/diffdock/scripts/setup_check.py +278 -0
- package/bin/skills/dnanexus-integration/SKILL.md +383 -0
- package/bin/skills/dnanexus-integration/references/app-development.md +247 -0
- package/bin/skills/dnanexus-integration/references/configuration.md +646 -0
- package/bin/skills/dnanexus-integration/references/data-operations.md +400 -0
- package/bin/skills/dnanexus-integration/references/job-execution.md +412 -0
- package/bin/skills/dnanexus-integration/references/python-sdk.md +523 -0
- package/bin/skills/document-skills/docx/LICENSE.txt +30 -0
- package/bin/skills/document-skills/docx/SKILL.md +233 -0
- package/bin/skills/document-skills/docx/docx-js.md +350 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
- package/bin/skills/document-skills/docx/ooxml.md +610 -0
- package/bin/skills/document-skills/docx/scripts/__init__.py +1 -0
- package/bin/skills/document-skills/docx/scripts/document.py +1276 -0
- package/bin/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/templates/people.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/utilities.py +374 -0
- package/bin/skills/document-skills/pdf/LICENSE.txt +30 -0
- package/bin/skills/document-skills/pdf/SKILL.md +330 -0
- package/bin/skills/document-skills/pdf/forms.md +205 -0
- package/bin/skills/document-skills/pdf/reference.md +612 -0
- package/bin/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
- package/bin/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
- package/bin/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
- package/bin/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
- package/bin/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
- package/bin/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
- package/bin/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
- package/bin/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
- package/bin/skills/document-skills/pptx/LICENSE.txt +30 -0
- package/bin/skills/document-skills/pptx/SKILL.md +520 -0
- package/bin/skills/document-skills/pptx/html2pptx.md +625 -0
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# self.observation_space = self.make_space((grid_size, grid_size, 3))
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+
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# Define action space
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# Option 1: Discrete actions
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self.action_space = self.make_discrete(4) # 0: up, 1: right, 2: down, 3: left
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+
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53
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# Option 2: Continuous actions
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# self.action_space = self.make_space((2,)) # [dx, dy]
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+
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# Option 3: Multi-discrete actions
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# self.action_space = self.make_multi_discrete([3, 3]) # Two 3-way choices
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# Initialize state
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self.agent_pos = None
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self.goal_pos = None
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self.step_count = 0
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self.reset()
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def reset(self):
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"""
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Reset environment to initial state.
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Returns:
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observation: Initial observation
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"""
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# Reset state
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self.agent_pos = np.array([0, 0], dtype=np.float32)
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self.goal_pos = np.array([self.grid_size - 1, self.grid_size - 1], dtype=np.float32)
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self.step_count = 0
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# Return initial observation
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return self._get_observation()
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+
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+
def step(self, action):
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"""
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Execute one environment step.
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Args:
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action: Action to take
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Returns:
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observation: New observation
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reward: Reward for this step
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done: Whether episode is complete
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info: Additional information
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+
"""
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self.step_count += 1
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+
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# Execute action
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self._apply_action(action)
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+
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# Compute reward
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reward = self._compute_reward()
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# Check if episode is done
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done = self._is_done()
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# Get new observation
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observation = self._get_observation()
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# Additional info
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info = {}
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if done:
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# Include episode statistics when episode ends
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info['episode'] = {
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'r': reward,
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'l': self.step_count
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}
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return observation, reward, done, info
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+
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+
def _apply_action(self, action):
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"""Apply action to update environment state."""
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+
# Discrete actions: 0=up, 1=right, 2=down, 3=left
|
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if action == 0: # Up
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+
self.agent_pos[1] = min(self.agent_pos[1] + 1, self.grid_size - 1)
|
|
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+
elif action == 1: # Right
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self.agent_pos[0] = min(self.agent_pos[0] + 1, self.grid_size - 1)
|
|
126
|
+
elif action == 2: # Down
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127
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+
self.agent_pos[1] = max(self.agent_pos[1] - 1, 0)
|
|
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|
+
elif action == 3: # Left
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+
self.agent_pos[0] = max(self.agent_pos[0] - 1, 0)
|
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+
|
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131
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+
def _compute_reward(self):
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"""Compute reward for current state."""
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|
+
# Distance to goal
|
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134
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+
distance = np.linalg.norm(self.agent_pos - self.goal_pos)
|
|
135
|
+
|
|
136
|
+
# Reward shaping: negative distance + bonus for reaching goal
|
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+
reward = -distance / self.grid_size
|
|
138
|
+
|
|
139
|
+
# Goal reached
|
|
140
|
+
if distance < 0.5:
|
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141
|
+
reward += 10.0
|
|
142
|
+
|
|
143
|
+
return reward
|
|
144
|
+
|
|
145
|
+
def _is_done(self):
|
|
146
|
+
"""Check if episode is complete."""
|
|
147
|
+
# Episode ends if goal reached or max steps exceeded
|
|
148
|
+
distance = np.linalg.norm(self.agent_pos - self.goal_pos)
|
|
149
|
+
goal_reached = distance < 0.5
|
|
150
|
+
timeout = self.step_count >= self.max_steps
|
|
151
|
+
|
|
152
|
+
return goal_reached or timeout
|
|
153
|
+
|
|
154
|
+
def _get_observation(self):
|
|
155
|
+
"""Generate observation from current state."""
|
|
156
|
+
# Return flat vector observation
|
|
157
|
+
observation = np.concatenate([
|
|
158
|
+
self.agent_pos,
|
|
159
|
+
self.goal_pos
|
|
160
|
+
]).astype(np.float32)
|
|
161
|
+
|
|
162
|
+
return observation
|
|
163
|
+
|
|
164
|
+
|
|
165
|
+
class MultiAgentEnvironment(PufferEnv):
|
|
166
|
+
"""
|
|
167
|
+
Multi-agent environment template.
|
|
168
|
+
|
|
169
|
+
Example: Cooperative navigation task where agents must reach individual goals.
|
|
170
|
+
"""
|
|
171
|
+
|
|
172
|
+
def __init__(self, buf=None, num_agents=4, grid_size=10, max_steps=1000):
|
|
173
|
+
super().__init__(buf)
|
|
174
|
+
|
|
175
|
+
self.num_agents = num_agents
|
|
176
|
+
self.grid_size = grid_size
|
|
177
|
+
self.max_steps = max_steps
|
|
178
|
+
|
|
179
|
+
# Per-agent observation space
|
|
180
|
+
self.single_observation_space = self.make_space({
|
|
181
|
+
'position': (2,),
|
|
182
|
+
'goal': (2,),
|
|
183
|
+
'others': (2 * (num_agents - 1),) # Positions of other agents
|
|
184
|
+
})
|
|
185
|
+
|
|
186
|
+
# Per-agent action space
|
|
187
|
+
self.single_action_space = self.make_discrete(5) # 4 directions + stay
|
|
188
|
+
|
|
189
|
+
# Initialize state
|
|
190
|
+
self.agent_positions = None
|
|
191
|
+
self.goal_positions = None
|
|
192
|
+
self.step_count = 0
|
|
193
|
+
|
|
194
|
+
self.reset()
|
|
195
|
+
|
|
196
|
+
def reset(self):
|
|
197
|
+
"""Reset all agents."""
|
|
198
|
+
# Random initial positions
|
|
199
|
+
self.agent_positions = np.random.rand(self.num_agents, 2) * self.grid_size
|
|
200
|
+
|
|
201
|
+
# Random goal positions
|
|
202
|
+
self.goal_positions = np.random.rand(self.num_agents, 2) * self.grid_size
|
|
203
|
+
|
|
204
|
+
self.step_count = 0
|
|
205
|
+
|
|
206
|
+
# Return observations for all agents
|
|
207
|
+
return {
|
|
208
|
+
f'agent_{i}': self._get_obs(i)
|
|
209
|
+
for i in range(self.num_agents)
|
|
210
|
+
}
|
|
211
|
+
|
|
212
|
+
def step(self, actions):
|
|
213
|
+
"""
|
|
214
|
+
Step all agents.
|
|
215
|
+
|
|
216
|
+
Args:
|
|
217
|
+
actions: Dict of {agent_id: action}
|
|
218
|
+
|
|
219
|
+
Returns:
|
|
220
|
+
observations: Dict of {agent_id: observation}
|
|
221
|
+
rewards: Dict of {agent_id: reward}
|
|
222
|
+
dones: Dict of {agent_id: done}
|
|
223
|
+
infos: Dict of {agent_id: info}
|
|
224
|
+
"""
|
|
225
|
+
self.step_count += 1
|
|
226
|
+
|
|
227
|
+
observations = {}
|
|
228
|
+
rewards = {}
|
|
229
|
+
dones = {}
|
|
230
|
+
infos = {}
|
|
231
|
+
|
|
232
|
+
# Update all agents
|
|
233
|
+
for agent_id, action in actions.items():
|
|
234
|
+
agent_idx = int(agent_id.split('_')[1])
|
|
235
|
+
|
|
236
|
+
# Apply action
|
|
237
|
+
self._apply_action(agent_idx, action)
|
|
238
|
+
|
|
239
|
+
# Generate outputs
|
|
240
|
+
observations[agent_id] = self._get_obs(agent_idx)
|
|
241
|
+
rewards[agent_id] = self._compute_reward(agent_idx)
|
|
242
|
+
dones[agent_id] = self._is_done(agent_idx)
|
|
243
|
+
infos[agent_id] = {}
|
|
244
|
+
|
|
245
|
+
# Global done condition
|
|
246
|
+
dones['__all__'] = all(dones.values()) or self.step_count >= self.max_steps
|
|
247
|
+
|
|
248
|
+
return observations, rewards, dones, infos
|
|
249
|
+
|
|
250
|
+
def _apply_action(self, agent_idx, action):
|
|
251
|
+
"""Apply action for specific agent."""
|
|
252
|
+
if action == 0: # Up
|
|
253
|
+
self.agent_positions[agent_idx, 1] += 1
|
|
254
|
+
elif action == 1: # Right
|
|
255
|
+
self.agent_positions[agent_idx, 0] += 1
|
|
256
|
+
elif action == 2: # Down
|
|
257
|
+
self.agent_positions[agent_idx, 1] -= 1
|
|
258
|
+
elif action == 3: # Left
|
|
259
|
+
self.agent_positions[agent_idx, 0] -= 1
|
|
260
|
+
# action == 4: Stay
|
|
261
|
+
|
|
262
|
+
# Clip to grid bounds
|
|
263
|
+
self.agent_positions[agent_idx] = np.clip(
|
|
264
|
+
self.agent_positions[agent_idx],
|
|
265
|
+
0,
|
|
266
|
+
self.grid_size - 1
|
|
267
|
+
)
|
|
268
|
+
|
|
269
|
+
def _compute_reward(self, agent_idx):
|
|
270
|
+
"""Compute reward for specific agent."""
|
|
271
|
+
distance = np.linalg.norm(
|
|
272
|
+
self.agent_positions[agent_idx] - self.goal_positions[agent_idx]
|
|
273
|
+
)
|
|
274
|
+
return -distance / self.grid_size
|
|
275
|
+
|
|
276
|
+
def _is_done(self, agent_idx):
|
|
277
|
+
"""Check if specific agent is done."""
|
|
278
|
+
distance = np.linalg.norm(
|
|
279
|
+
self.agent_positions[agent_idx] - self.goal_positions[agent_idx]
|
|
280
|
+
)
|
|
281
|
+
return distance < 0.5
|
|
282
|
+
|
|
283
|
+
def _get_obs(self, agent_idx):
|
|
284
|
+
"""Get observation for specific agent."""
|
|
285
|
+
# Get positions of other agents
|
|
286
|
+
other_positions = np.concatenate([
|
|
287
|
+
self.agent_positions[i]
|
|
288
|
+
for i in range(self.num_agents)
|
|
289
|
+
if i != agent_idx
|
|
290
|
+
])
|
|
291
|
+
|
|
292
|
+
return {
|
|
293
|
+
'position': self.agent_positions[agent_idx].astype(np.float32),
|
|
294
|
+
'goal': self.goal_positions[agent_idx].astype(np.float32),
|
|
295
|
+
'others': other_positions.astype(np.float32)
|
|
296
|
+
}
|
|
297
|
+
|
|
298
|
+
|
|
299
|
+
def test_environment():
|
|
300
|
+
"""Test environment to verify it works correctly."""
|
|
301
|
+
print("Testing single-agent environment...")
|
|
302
|
+
env = MyEnvironment()
|
|
303
|
+
|
|
304
|
+
obs = env.reset()
|
|
305
|
+
print(f"Initial observation shape: {obs.shape}")
|
|
306
|
+
|
|
307
|
+
for step in range(10):
|
|
308
|
+
action = env.action_space.sample()
|
|
309
|
+
obs, reward, done, info = env.step(action)
|
|
310
|
+
|
|
311
|
+
print(f"Step {step}: reward={reward:.3f}, done={done}")
|
|
312
|
+
|
|
313
|
+
if done:
|
|
314
|
+
obs = env.reset()
|
|
315
|
+
print("Episode finished, resetting...")
|
|
316
|
+
|
|
317
|
+
print("\nTesting multi-agent environment...")
|
|
318
|
+
multi_env = MultiAgentEnvironment(num_agents=4)
|
|
319
|
+
|
|
320
|
+
obs = multi_env.reset()
|
|
321
|
+
print(f"Number of agents: {len(obs)}")
|
|
322
|
+
|
|
323
|
+
for step in range(10):
|
|
324
|
+
actions = {
|
|
325
|
+
agent_id: multi_env.single_action_space.sample()
|
|
326
|
+
for agent_id in obs.keys()
|
|
327
|
+
}
|
|
328
|
+
obs, rewards, dones, infos = multi_env.step(actions)
|
|
329
|
+
|
|
330
|
+
print(f"Step {step}: mean_reward={np.mean(list(rewards.values())):.3f}")
|
|
331
|
+
|
|
332
|
+
if dones.get('__all__', False):
|
|
333
|
+
obs = multi_env.reset()
|
|
334
|
+
print("Episode finished, resetting...")
|
|
335
|
+
|
|
336
|
+
print("\n✓ Environment tests passed!")
|
|
337
|
+
|
|
338
|
+
|
|
339
|
+
if __name__ == '__main__':
|
|
340
|
+
test_environment()
|
|
@@ -0,0 +1,239 @@
|
|
|
1
|
+
#!/usr/bin/env python3
|
|
2
|
+
"""
|
|
3
|
+
PufferLib Training Template
|
|
4
|
+
|
|
5
|
+
This template provides a complete training script for reinforcement learning
|
|
6
|
+
with PufferLib. Customize the environment, policy, and training configuration
|
|
7
|
+
as needed for your use case.
|
|
8
|
+
"""
|
|
9
|
+
|
|
10
|
+
import argparse
|
|
11
|
+
import torch
|
|
12
|
+
import torch.nn as nn
|
|
13
|
+
import pufferlib
|
|
14
|
+
from pufferlib import PuffeRL
|
|
15
|
+
from pufferlib.pytorch import layer_init
|
|
16
|
+
|
|
17
|
+
|
|
18
|
+
class Policy(nn.Module):
|
|
19
|
+
"""Example policy network."""
|
|
20
|
+
|
|
21
|
+
def __init__(self, observation_space, action_space, hidden_size=256):
|
|
22
|
+
super().__init__()
|
|
23
|
+
|
|
24
|
+
self.observation_space = observation_space
|
|
25
|
+
self.action_space = action_space
|
|
26
|
+
|
|
27
|
+
# Encoder network
|
|
28
|
+
self.encoder = nn.Sequential(
|
|
29
|
+
layer_init(nn.Linear(observation_space.shape[0], hidden_size)),
|
|
30
|
+
nn.ReLU(),
|
|
31
|
+
layer_init(nn.Linear(hidden_size, hidden_size)),
|
|
32
|
+
nn.ReLU()
|
|
33
|
+
)
|
|
34
|
+
|
|
35
|
+
# Policy head (actor)
|
|
36
|
+
self.actor = layer_init(nn.Linear(hidden_size, action_space.n), std=0.01)
|
|
37
|
+
|
|
38
|
+
# Value head (critic)
|
|
39
|
+
self.critic = layer_init(nn.Linear(hidden_size, 1), std=1.0)
|
|
40
|
+
|
|
41
|
+
def forward(self, observations):
|
|
42
|
+
"""Forward pass through policy."""
|
|
43
|
+
features = self.encoder(observations)
|
|
44
|
+
logits = self.actor(features)
|
|
45
|
+
value = self.critic(features)
|
|
46
|
+
return logits, value
|
|
47
|
+
|
|
48
|
+
|
|
49
|
+
def make_env():
|
|
50
|
+
"""Create environment. Customize this for your task."""
|
|
51
|
+
# Option 1: Use Ocean environment
|
|
52
|
+
return pufferlib.make('procgen-coinrun', num_envs=256)
|
|
53
|
+
|
|
54
|
+
# Option 2: Use Gymnasium environment
|
|
55
|
+
# return pufferlib.make('gym-CartPole-v1', num_envs=256)
|
|
56
|
+
|
|
57
|
+
# Option 3: Use custom environment
|
|
58
|
+
# from my_envs import MyEnvironment
|
|
59
|
+
# return pufferlib.emulate(MyEnvironment, num_envs=256)
|
|
60
|
+
|
|
61
|
+
|
|
62
|
+
def create_policy(env):
|
|
63
|
+
"""Create policy network."""
|
|
64
|
+
return Policy(
|
|
65
|
+
observation_space=env.observation_space,
|
|
66
|
+
action_space=env.action_space,
|
|
67
|
+
hidden_size=256
|
|
68
|
+
)
|
|
69
|
+
|
|
70
|
+
|
|
71
|
+
def train(args):
|
|
72
|
+
"""Main training function."""
|
|
73
|
+
# Set random seeds
|
|
74
|
+
torch.manual_seed(args.seed)
|
|
75
|
+
|
|
76
|
+
# Create environment
|
|
77
|
+
print(f"Creating environment with {args.num_envs} parallel environments...")
|
|
78
|
+
env = pufferlib.make(
|
|
79
|
+
args.env_name,
|
|
80
|
+
num_envs=args.num_envs,
|
|
81
|
+
num_workers=args.num_workers
|
|
82
|
+
)
|
|
83
|
+
|
|
84
|
+
# Create policy
|
|
85
|
+
print("Initializing policy...")
|
|
86
|
+
policy = create_policy(env)
|
|
87
|
+
|
|
88
|
+
if args.device == 'cuda' and torch.cuda.is_available():
|
|
89
|
+
policy = policy.cuda()
|
|
90
|
+
print(f"Using GPU: {torch.cuda.get_device_name(0)}")
|
|
91
|
+
else:
|
|
92
|
+
print("Using CPU")
|
|
93
|
+
|
|
94
|
+
# Create logger
|
|
95
|
+
if args.logger == 'wandb':
|
|
96
|
+
from pufferlib import WandbLogger
|
|
97
|
+
logger = WandbLogger(
|
|
98
|
+
project=args.project,
|
|
99
|
+
name=args.exp_name,
|
|
100
|
+
config=vars(args)
|
|
101
|
+
)
|
|
102
|
+
elif args.logger == 'neptune':
|
|
103
|
+
from pufferlib import NeptuneLogger
|
|
104
|
+
logger = NeptuneLogger(
|
|
105
|
+
project=args.project,
|
|
106
|
+
name=args.exp_name,
|
|
107
|
+
api_token=args.neptune_token
|
|
108
|
+
)
|
|
109
|
+
else:
|
|
110
|
+
from pufferlib import NoLogger
|
|
111
|
+
logger = NoLogger()
|
|
112
|
+
|
|
113
|
+
# Create trainer
|
|
114
|
+
print("Creating trainer...")
|
|
115
|
+
trainer = PuffeRL(
|
|
116
|
+
env=env,
|
|
117
|
+
policy=policy,
|
|
118
|
+
device=args.device,
|
|
119
|
+
learning_rate=args.learning_rate,
|
|
120
|
+
batch_size=args.batch_size,
|
|
121
|
+
n_epochs=args.n_epochs,
|
|
122
|
+
gamma=args.gamma,
|
|
123
|
+
gae_lambda=args.gae_lambda,
|
|
124
|
+
clip_coef=args.clip_coef,
|
|
125
|
+
ent_coef=args.ent_coef,
|
|
126
|
+
vf_coef=args.vf_coef,
|
|
127
|
+
max_grad_norm=args.max_grad_norm,
|
|
128
|
+
logger=logger,
|
|
129
|
+
compile=args.compile
|
|
130
|
+
)
|
|
131
|
+
|
|
132
|
+
# Training loop
|
|
133
|
+
print(f"Starting training for {args.num_iterations} iterations...")
|
|
134
|
+
for iteration in range(1, args.num_iterations + 1):
|
|
135
|
+
# Collect rollouts
|
|
136
|
+
rollout_data = trainer.evaluate()
|
|
137
|
+
|
|
138
|
+
# Train on batch
|
|
139
|
+
train_metrics = trainer.train()
|
|
140
|
+
|
|
141
|
+
# Log results
|
|
142
|
+
trainer.mean_and_log()
|
|
143
|
+
|
|
144
|
+
# Save checkpoint
|
|
145
|
+
if iteration % args.save_freq == 0:
|
|
146
|
+
checkpoint_path = f"{args.checkpoint_dir}/checkpoint_{iteration}.pt"
|
|
147
|
+
trainer.save_checkpoint(checkpoint_path)
|
|
148
|
+
print(f"Saved checkpoint to {checkpoint_path}")
|
|
149
|
+
|
|
150
|
+
# Print progress
|
|
151
|
+
if iteration % args.log_freq == 0:
|
|
152
|
+
mean_reward = rollout_data.get('mean_reward', 0)
|
|
153
|
+
sps = rollout_data.get('sps', 0)
|
|
154
|
+
print(f"Iteration {iteration}/{args.num_iterations} | "
|
|
155
|
+
f"Mean Reward: {mean_reward:.2f} | "
|
|
156
|
+
f"SPS: {sps:,.0f}")
|
|
157
|
+
|
|
158
|
+
print("Training complete!")
|
|
159
|
+
|
|
160
|
+
# Save final model
|
|
161
|
+
final_path = f"{args.checkpoint_dir}/final_model.pt"
|
|
162
|
+
trainer.save_checkpoint(final_path)
|
|
163
|
+
print(f"Saved final model to {final_path}")
|
|
164
|
+
|
|
165
|
+
|
|
166
|
+
def main():
|
|
167
|
+
parser = argparse.ArgumentParser(description='PufferLib Training')
|
|
168
|
+
|
|
169
|
+
# Environment
|
|
170
|
+
parser.add_argument('--env-name', type=str, default='procgen-coinrun',
|
|
171
|
+
help='Environment name')
|
|
172
|
+
parser.add_argument('--num-envs', type=int, default=256,
|
|
173
|
+
help='Number of parallel environments')
|
|
174
|
+
parser.add_argument('--num-workers', type=int, default=8,
|
|
175
|
+
help='Number of vectorization workers')
|
|
176
|
+
|
|
177
|
+
# Training
|
|
178
|
+
parser.add_argument('--num-iterations', type=int, default=10000,
|
|
179
|
+
help='Number of training iterations')
|
|
180
|
+
parser.add_argument('--learning-rate', type=float, default=3e-4,
|
|
181
|
+
help='Learning rate')
|
|
182
|
+
parser.add_argument('--batch-size', type=int, default=32768,
|
|
183
|
+
help='Batch size for training')
|
|
184
|
+
parser.add_argument('--n-epochs', type=int, default=4,
|
|
185
|
+
help='Number of training epochs per batch')
|
|
186
|
+
parser.add_argument('--device', type=str, default='cuda',
|
|
187
|
+
choices=['cuda', 'cpu'], help='Device to use')
|
|
188
|
+
|
|
189
|
+
# PPO Parameters
|
|
190
|
+
parser.add_argument('--gamma', type=float, default=0.99,
|
|
191
|
+
help='Discount factor')
|
|
192
|
+
parser.add_argument('--gae-lambda', type=float, default=0.95,
|
|
193
|
+
help='GAE lambda')
|
|
194
|
+
parser.add_argument('--clip-coef', type=float, default=0.2,
|
|
195
|
+
help='PPO clipping coefficient')
|
|
196
|
+
parser.add_argument('--ent-coef', type=float, default=0.01,
|
|
197
|
+
help='Entropy coefficient')
|
|
198
|
+
parser.add_argument('--vf-coef', type=float, default=0.5,
|
|
199
|
+
help='Value function coefficient')
|
|
200
|
+
parser.add_argument('--max-grad-norm', type=float, default=0.5,
|
|
201
|
+
help='Maximum gradient norm')
|
|
202
|
+
|
|
203
|
+
# Logging
|
|
204
|
+
parser.add_argument('--logger', type=str, default='none',
|
|
205
|
+
choices=['wandb', 'neptune', 'none'],
|
|
206
|
+
help='Logger to use')
|
|
207
|
+
parser.add_argument('--project', type=str, default='pufferlib-training',
|
|
208
|
+
help='Project name for logging')
|
|
209
|
+
parser.add_argument('--exp-name', type=str, default='experiment',
|
|
210
|
+
help='Experiment name')
|
|
211
|
+
parser.add_argument('--neptune-token', type=str, default=None,
|
|
212
|
+
help='Neptune API token')
|
|
213
|
+
parser.add_argument('--log-freq', type=int, default=10,
|
|
214
|
+
help='Logging frequency (iterations)')
|
|
215
|
+
|
|
216
|
+
# Checkpointing
|
|
217
|
+
parser.add_argument('--checkpoint-dir', type=str, default='checkpoints',
|
|
218
|
+
help='Directory to save checkpoints')
|
|
219
|
+
parser.add_argument('--save-freq', type=int, default=100,
|
|
220
|
+
help='Checkpoint save frequency (iterations)')
|
|
221
|
+
|
|
222
|
+
# Misc
|
|
223
|
+
parser.add_argument('--seed', type=int, default=42,
|
|
224
|
+
help='Random seed')
|
|
225
|
+
parser.add_argument('--compile', action='store_true',
|
|
226
|
+
help='Use torch.compile for faster training')
|
|
227
|
+
|
|
228
|
+
args = parser.parse_args()
|
|
229
|
+
|
|
230
|
+
# Create checkpoint directory
|
|
231
|
+
import os
|
|
232
|
+
os.makedirs(args.checkpoint_dir, exist_ok=True)
|
|
233
|
+
|
|
234
|
+
# Run training
|
|
235
|
+
train(args)
|
|
236
|
+
|
|
237
|
+
|
|
238
|
+
if __name__ == '__main__':
|
|
239
|
+
main()
|