@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.
Files changed (830) hide show
  1. package/bin/skills/adaptyv/SKILL.md +114 -0
  2. package/bin/skills/adaptyv/reference/api_reference.md +308 -0
  3. package/bin/skills/adaptyv/reference/examples.md +913 -0
  4. package/bin/skills/adaptyv/reference/experiments.md +360 -0
  5. package/bin/skills/adaptyv/reference/protein_optimization.md +637 -0
  6. package/bin/skills/aeon/SKILL.md +374 -0
  7. package/bin/skills/aeon/references/anomaly_detection.md +154 -0
  8. package/bin/skills/aeon/references/classification.md +144 -0
  9. package/bin/skills/aeon/references/clustering.md +123 -0
  10. package/bin/skills/aeon/references/datasets_benchmarking.md +387 -0
  11. package/bin/skills/aeon/references/distances.md +256 -0
  12. package/bin/skills/aeon/references/forecasting.md +140 -0
  13. package/bin/skills/aeon/references/networks.md +289 -0
  14. package/bin/skills/aeon/references/regression.md +118 -0
  15. package/bin/skills/aeon/references/segmentation.md +163 -0
  16. package/bin/skills/aeon/references/similarity_search.md +187 -0
  17. package/bin/skills/aeon/references/transformations.md +246 -0
  18. package/bin/skills/alphafold-database/SKILL.md +513 -0
  19. package/bin/skills/alphafold-database/references/api_reference.md +423 -0
  20. package/bin/skills/anndata/SKILL.md +400 -0
  21. package/bin/skills/anndata/references/best_practices.md +525 -0
  22. package/bin/skills/anndata/references/concatenation.md +396 -0
  23. package/bin/skills/anndata/references/data_structure.md +314 -0
  24. package/bin/skills/anndata/references/io_operations.md +404 -0
  25. package/bin/skills/anndata/references/manipulation.md +516 -0
  26. package/bin/skills/arboreto/SKILL.md +243 -0
  27. package/bin/skills/arboreto/references/algorithms.md +138 -0
  28. package/bin/skills/arboreto/references/basic_inference.md +151 -0
  29. package/bin/skills/arboreto/references/distributed_computing.md +242 -0
  30. package/bin/skills/arboreto/scripts/basic_grn_inference.py +97 -0
  31. package/bin/skills/astropy/SKILL.md +331 -0
  32. package/bin/skills/astropy/references/coordinates.md +273 -0
  33. package/bin/skills/astropy/references/cosmology.md +307 -0
  34. package/bin/skills/astropy/references/fits.md +396 -0
  35. package/bin/skills/astropy/references/tables.md +489 -0
  36. package/bin/skills/astropy/references/time.md +404 -0
  37. package/bin/skills/astropy/references/units.md +178 -0
  38. package/bin/skills/astropy/references/wcs_and_other_modules.md +373 -0
  39. package/bin/skills/benchling-integration/SKILL.md +480 -0
  40. package/bin/skills/benchling-integration/references/api_endpoints.md +883 -0
  41. package/bin/skills/benchling-integration/references/authentication.md +379 -0
  42. package/bin/skills/benchling-integration/references/sdk_reference.md +774 -0
  43. package/bin/skills/biopython/SKILL.md +443 -0
  44. package/bin/skills/biopython/references/advanced.md +577 -0
  45. package/bin/skills/biopython/references/alignment.md +362 -0
  46. package/bin/skills/biopython/references/blast.md +455 -0
  47. package/bin/skills/biopython/references/databases.md +484 -0
  48. package/bin/skills/biopython/references/phylogenetics.md +566 -0
  49. package/bin/skills/biopython/references/sequence_io.md +285 -0
  50. package/bin/skills/biopython/references/structure.md +564 -0
  51. package/bin/skills/biorxiv-database/SKILL.md +483 -0
  52. package/bin/skills/biorxiv-database/references/api_reference.md +280 -0
  53. package/bin/skills/biorxiv-database/scripts/biorxiv_search.py +445 -0
  54. package/bin/skills/bioservices/SKILL.md +361 -0
  55. package/bin/skills/bioservices/references/identifier_mapping.md +685 -0
  56. package/bin/skills/bioservices/references/services_reference.md +636 -0
  57. package/bin/skills/bioservices/references/workflow_patterns.md +811 -0
  58. package/bin/skills/bioservices/scripts/batch_id_converter.py +347 -0
  59. package/bin/skills/bioservices/scripts/compound_cross_reference.py +378 -0
  60. package/bin/skills/bioservices/scripts/pathway_analysis.py +309 -0
  61. package/bin/skills/bioservices/scripts/protein_analysis_workflow.py +408 -0
  62. package/bin/skills/brenda-database/SKILL.md +719 -0
  63. package/bin/skills/brenda-database/references/api_reference.md +537 -0
  64. package/bin/skills/brenda-database/scripts/brenda_queries.py +844 -0
  65. package/bin/skills/brenda-database/scripts/brenda_visualization.py +772 -0
  66. package/bin/skills/brenda-database/scripts/enzyme_pathway_builder.py +1053 -0
  67. package/bin/skills/cellxgene-census/SKILL.md +511 -0
  68. package/bin/skills/cellxgene-census/references/census_schema.md +182 -0
  69. package/bin/skills/cellxgene-census/references/common_patterns.md +351 -0
  70. package/bin/skills/chembl-database/SKILL.md +389 -0
  71. package/bin/skills/chembl-database/references/api_reference.md +272 -0
  72. package/bin/skills/chembl-database/scripts/example_queries.py +278 -0
  73. package/bin/skills/cirq/SKILL.md +346 -0
  74. package/bin/skills/cirq/references/building.md +307 -0
  75. package/bin/skills/cirq/references/experiments.md +572 -0
  76. package/bin/skills/cirq/references/hardware.md +515 -0
  77. package/bin/skills/cirq/references/noise.md +515 -0
  78. package/bin/skills/cirq/references/simulation.md +350 -0
  79. package/bin/skills/cirq/references/transformation.md +416 -0
  80. package/bin/skills/clinicaltrials-database/SKILL.md +507 -0
  81. package/bin/skills/clinicaltrials-database/references/api_reference.md +358 -0
  82. package/bin/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +215 -0
  83. package/bin/skills/clinpgx-database/SKILL.md +638 -0
  84. package/bin/skills/clinpgx-database/references/api_reference.md +757 -0
  85. package/bin/skills/clinpgx-database/scripts/query_clinpgx.py +518 -0
  86. package/bin/skills/clinvar-database/SKILL.md +362 -0
  87. package/bin/skills/clinvar-database/references/api_reference.md +227 -0
  88. package/bin/skills/clinvar-database/references/clinical_significance.md +218 -0
  89. package/bin/skills/clinvar-database/references/data_formats.md +358 -0
  90. package/bin/skills/cobrapy/SKILL.md +463 -0
  91. package/bin/skills/cobrapy/references/api_quick_reference.md +655 -0
  92. package/bin/skills/cobrapy/references/workflows.md +593 -0
  93. package/bin/skills/cosmic-database/SKILL.md +336 -0
  94. package/bin/skills/cosmic-database/references/cosmic_data_reference.md +220 -0
  95. package/bin/skills/cosmic-database/scripts/download_cosmic.py +231 -0
  96. package/bin/skills/dask/SKILL.md +456 -0
  97. package/bin/skills/dask/references/arrays.md +497 -0
  98. package/bin/skills/dask/references/bags.md +468 -0
  99. package/bin/skills/dask/references/best-practices.md +277 -0
  100. package/bin/skills/dask/references/dataframes.md +368 -0
  101. package/bin/skills/dask/references/futures.md +541 -0
  102. package/bin/skills/dask/references/schedulers.md +504 -0
  103. package/bin/skills/datacommons-client/SKILL.md +255 -0
  104. package/bin/skills/datacommons-client/references/getting_started.md +417 -0
  105. package/bin/skills/datacommons-client/references/node.md +250 -0
  106. package/bin/skills/datacommons-client/references/observation.md +185 -0
  107. package/bin/skills/datacommons-client/references/resolve.md +246 -0
  108. package/bin/skills/datamol/SKILL.md +706 -0
  109. package/bin/skills/datamol/references/conformers_module.md +131 -0
  110. package/bin/skills/datamol/references/core_api.md +130 -0
  111. package/bin/skills/datamol/references/descriptors_viz.md +195 -0
  112. package/bin/skills/datamol/references/fragments_scaffolds.md +174 -0
  113. package/bin/skills/datamol/references/io_module.md +109 -0
  114. package/bin/skills/datamol/references/reactions_data.md +218 -0
  115. package/bin/skills/deepchem/SKILL.md +597 -0
  116. package/bin/skills/deepchem/references/api_reference.md +303 -0
  117. package/bin/skills/deepchem/references/workflows.md +491 -0
  118. package/bin/skills/deepchem/scripts/graph_neural_network.py +338 -0
  119. package/bin/skills/deepchem/scripts/predict_solubility.py +224 -0
  120. package/bin/skills/deepchem/scripts/transfer_learning.py +375 -0
  121. package/bin/skills/deeptools/SKILL.md +531 -0
  122. package/bin/skills/deeptools/assets/quick_reference.md +58 -0
  123. package/bin/skills/deeptools/references/effective_genome_sizes.md +116 -0
  124. package/bin/skills/deeptools/references/normalization_methods.md +410 -0
  125. package/bin/skills/deeptools/references/tools_reference.md +533 -0
  126. package/bin/skills/deeptools/references/workflows.md +474 -0
  127. package/bin/skills/deeptools/scripts/validate_files.py +195 -0
  128. package/bin/skills/deeptools/scripts/workflow_generator.py +454 -0
  129. package/bin/skills/denario/SKILL.md +215 -0
  130. package/bin/skills/denario/references/examples.md +494 -0
  131. package/bin/skills/denario/references/installation.md +213 -0
  132. package/bin/skills/denario/references/llm_configuration.md +265 -0
  133. package/bin/skills/denario/references/research_pipeline.md +471 -0
  134. package/bin/skills/diffdock/SKILL.md +483 -0
  135. package/bin/skills/diffdock/assets/batch_template.csv +4 -0
  136. package/bin/skills/diffdock/assets/custom_inference_config.yaml +90 -0
  137. package/bin/skills/diffdock/references/confidence_and_limitations.md +182 -0
  138. package/bin/skills/diffdock/references/parameters_reference.md +163 -0
  139. package/bin/skills/diffdock/references/workflows_examples.md +392 -0
  140. package/bin/skills/diffdock/scripts/analyze_results.py +334 -0
  141. package/bin/skills/diffdock/scripts/prepare_batch_csv.py +254 -0
  142. package/bin/skills/diffdock/scripts/setup_check.py +278 -0
  143. package/bin/skills/dnanexus-integration/SKILL.md +383 -0
  144. package/bin/skills/dnanexus-integration/references/app-development.md +247 -0
  145. package/bin/skills/dnanexus-integration/references/configuration.md +646 -0
  146. package/bin/skills/dnanexus-integration/references/data-operations.md +400 -0
  147. package/bin/skills/dnanexus-integration/references/job-execution.md +412 -0
  148. package/bin/skills/dnanexus-integration/references/python-sdk.md +523 -0
  149. package/bin/skills/document-skills/docx/LICENSE.txt +30 -0
  150. package/bin/skills/document-skills/docx/SKILL.md +233 -0
  151. package/bin/skills/document-skills/docx/docx-js.md +350 -0
  152. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  153. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  154. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  155. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  156. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  157. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  158. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
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  160. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  161. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  162. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
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  193. package/bin/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
  194. package/bin/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
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1
+ # PufferLib Environments Guide
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+
3
+ ## Overview
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+
5
+ PufferLib provides the PufferEnv API for creating high-performance custom environments, and the Ocean suite containing 20+ pre-built environments. Environments support both single-agent and multi-agent scenarios with native vectorization.
6
+
7
+ ## PufferEnv API
8
+
9
+ ### Core Characteristics
10
+
11
+ PufferEnv is designed for performance through in-place operations:
12
+ - Observations, actions, and rewards are initialized from a shared buffer object
13
+ - All operations happen in-place to avoid creating and copying arrays
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+ - Native support for both single-agent and multi-agent environments
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+ - Flat observation/action spaces for efficient vectorization
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+
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+ ### Creating a PufferEnv
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+
19
+ ```python
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+ import numpy as np
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+ import pufferlib
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+ from pufferlib import PufferEnv
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+
24
+ class MyEnvironment(PufferEnv):
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+ def __init__(self, buf=None):
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+ super().__init__(buf)
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+
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+ # Define observation and action spaces
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+ self.observation_space = self.make_space({
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+ 'image': (84, 84, 3),
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+ 'vector': (10,)
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+ })
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+
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+ self.action_space = self.make_discrete(4) # 4 discrete actions
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+
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+ # Initialize state
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+ self.reset()
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+
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+ def reset(self):
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+ """Reset environment to initial state."""
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+ # Reset internal state
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+ self.agent_pos = np.array([0, 0])
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+ self.step_count = 0
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+
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+ # Return initial observation
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+ obs = {
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+ 'image': np.zeros((84, 84, 3), dtype=np.uint8),
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+ 'vector': np.zeros(10, dtype=np.float32)
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+ }
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+
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+ return obs
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+
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+ def step(self, action):
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+ """Execute one environment step."""
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+ # Update state based on action
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+ self.step_count += 1
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+
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+ # Calculate reward
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+ reward = self._compute_reward()
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+
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+ # Check if episode is done
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+ done = self.step_count >= 1000
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+
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+ # Generate observation
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+ obs = self._get_observation()
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+
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+ # Additional info
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+ info = {'episode': {'r': reward, 'l': self.step_count}} if done else {}
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+
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+ return obs, reward, done, info
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+
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+ def _compute_reward(self):
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+ """Compute reward for current state."""
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+ return 1.0
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+
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+ def _get_observation(self):
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+ """Generate observation from current state."""
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+ return {
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+ 'image': np.random.randint(0, 256, (84, 84, 3), dtype=np.uint8),
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+ 'vector': np.random.randn(10).astype(np.float32)
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+ }
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+ ```
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+
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+ ### Observation Spaces
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+
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+ #### Discrete Spaces
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+
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+ ```python
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+ # Single discrete value
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+ self.observation_space = self.make_discrete(10) # Values 0-9
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+
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+ # Dict with discrete values
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+ self.observation_space = self.make_space({
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+ 'position': (1,), # Continuous
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+ 'type': self.make_discrete(5) # Discrete
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+ })
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+ ```
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+
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+ #### Continuous Spaces
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+
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+ ```python
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+ # Box space (continuous)
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+ self.observation_space = self.make_space({
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+ 'image': (84, 84, 3), # Image
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+ 'vector': (10,), # Vector
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+ 'scalar': (1,) # Single value
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+ })
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+ ```
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+
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+ #### Multi-Discrete Spaces
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+
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+ ```python
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+ # Multiple discrete values
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+ self.observation_space = self.make_multi_discrete([3, 5, 2]) # 3 values, 5 values, 2 values
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+ ```
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+
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+ ### Action Spaces
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+
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+ ```python
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+ # Discrete actions
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+ self.action_space = self.make_discrete(4) # 4 actions: 0, 1, 2, 3
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+
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+ # Continuous actions
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+ self.action_space = self.make_space((3,)) # 3D continuous action
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+
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+ # Multi-discrete actions
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+ self.action_space = self.make_multi_discrete([3, 3]) # Two 3-way discrete choices
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+ ```
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+
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+ ## Multi-Agent Environments
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+
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+ PufferLib has native multi-agent support, treating single-agent and multi-agent environments uniformly.
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+
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+ ### Multi-Agent PufferEnv
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+
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+ ```python
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+ class MultiAgentEnv(PufferEnv):
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+ def __init__(self, num_agents=4, buf=None):
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+ super().__init__(buf)
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+
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+ self.num_agents = num_agents
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+
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+ # Per-agent observation space
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+ self.single_observation_space = self.make_space({
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+ 'position': (2,),
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+ 'velocity': (2,),
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+ 'global': (10,)
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+ })
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+
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+ # Per-agent action space
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+ self.single_action_space = self.make_discrete(5)
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+
153
+ self.reset()
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+
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+ def reset(self):
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+ """Reset all agents."""
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+ self.agents = {f'agent_{i}': Agent(i) for i in range(self.num_agents)}
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+
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+ # Return observations for all agents
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+ return {
161
+ agent_id: self._get_obs(agent)
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+ for agent_id, agent in self.agents.items()
163
+ }
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+
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+ def step(self, actions):
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+ """Step all agents."""
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+ # actions is a dict: {agent_id: action}
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+ observations = {}
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+ rewards = {}
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+ dones = {}
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+ infos = {}
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+
173
+ for agent_id, action in actions.items():
174
+ agent = self.agents[agent_id]
175
+
176
+ # Update agent
177
+ agent.update(action)
178
+
179
+ # Generate results
180
+ observations[agent_id] = self._get_obs(agent)
181
+ rewards[agent_id] = self._compute_reward(agent)
182
+ dones[agent_id] = agent.is_done()
183
+ infos[agent_id] = {}
184
+
185
+ # Check for global done condition
186
+ dones['__all__'] = all(dones.values())
187
+
188
+ return observations, rewards, dones, infos
189
+ ```
190
+
191
+ ## Ocean Environment Suite
192
+
193
+ PufferLib provides the Ocean suite with 20+ pre-built environments:
194
+
195
+ ### Available Environments
196
+
197
+ #### Arcade Games
198
+ - **Atari**: Classic Atari 2600 games via Arcade Learning Environment
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+ - **Procgen**: Procedurally generated games for generalization testing
200
+
201
+ #### Grid-Based
202
+ - **Minigrid**: Partially observable gridworld environments
203
+ - **Crafter**: Open-ended survival crafting game
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+ - **NetHack**: Classic roguelike dungeon crawler
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+ - **MiniHack**: Simplified NetHack variants
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+
207
+ #### Multi-Agent
208
+ - **PettingZoo**: Multi-agent environment suite (including Butterfly)
209
+ - **MAgent**: Large-scale multi-agent scenarios
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+ - **Neural MMO**: Massively multi-agent survival game
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+
212
+ #### Specialized
213
+ - **Pokemon Red**: Classic Pokemon game environment
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+ - **GPUDrive**: High-performance driving simulator
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+ - **Griddly**: Grid-based game engine
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+ - **MicroRTS**: Real-time strategy game
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+
218
+ ### Using Ocean Environments
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+
220
+ ```python
221
+ import pufferlib
222
+
223
+ # Make environment
224
+ env = pufferlib.make('procgen-coinrun', num_envs=256)
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+
226
+ # With custom configuration
227
+ env = pufferlib.make(
228
+ 'atari-pong',
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+ num_envs=128,
230
+ frameskip=4,
231
+ framestack=4
232
+ )
233
+
234
+ # Multi-agent environment
235
+ env = pufferlib.make('pettingzoo-knights-archers-zombies', num_agents=4)
236
+ ```
237
+
238
+ ## Custom Environment Development
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+
240
+ ### Development Workflow
241
+
242
+ 1. **Prototype in Python**: Start with pure Python PufferEnv
243
+ 2. **Optimize Critical Paths**: Identify bottlenecks
244
+ 3. **Implement in C**: Rewrite performance-critical code in C
245
+ 4. **Create Bindings**: Use Python C API
246
+ 5. **Compile**: Build as extension module
247
+ 6. **Register**: Add to Ocean suite
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+
249
+ ### Performance Benchmarks
250
+
251
+ - **Pure Python**: 100k-500k steps/second
252
+ - **C Implementation**: 100M+ steps/second
253
+ - **Training with Python env**: ~400k total SPS
254
+ - **Training with C env**: ~4M total SPS
255
+
256
+ ### Python Optimization Tips
257
+
258
+ ```python
259
+ # Use NumPy operations instead of Python loops
260
+ # Bad
261
+ for i in range(len(array)):
262
+ array[i] = array[i] * 2
263
+
264
+ # Good
265
+ array *= 2
266
+
267
+ # Pre-allocate arrays instead of appending
268
+ # Bad
269
+ observations = []
270
+ for i in range(n):
271
+ observations.append(generate_obs())
272
+
273
+ # Good
274
+ observations = np.empty((n, obs_shape), dtype=np.float32)
275
+ for i in range(n):
276
+ observations[i] = generate_obs()
277
+
278
+ # Use in-place operations
279
+ # Bad
280
+ new_state = state + delta
281
+
282
+ # Good
283
+ state += delta
284
+ ```
285
+
286
+ ### C Extension Example
287
+
288
+ ```c
289
+ // my_env.c
290
+ #include <Python.h>
291
+ #include <numpy/arrayobject.h>
292
+
293
+ // Fast environment step implementation
294
+ static PyObject* fast_step(PyObject* self, PyObject* args) {
295
+ PyArrayObject* state;
296
+ int action;
297
+
298
+ if (!PyArg_ParseTuple(args, "O!i", &PyArray_Type, &state, &action)) {
299
+ return NULL;
300
+ }
301
+
302
+ // High-performance C implementation
303
+ // ...
304
+
305
+ return Py_BuildValue("Ofi", obs, reward, done);
306
+ }
307
+
308
+ static PyMethodDef methods[] = {
309
+ {"fast_step", fast_step, METH_VARARGS, "Fast environment step"},
310
+ {NULL, NULL, 0, NULL}
311
+ };
312
+
313
+ static struct PyModuleDef module = {
314
+ PyModuleDef_HEAD_INIT,
315
+ "my_env_c",
316
+ NULL,
317
+ -1,
318
+ methods
319
+ };
320
+
321
+ PyMODINIT_FUNC PyInit_my_env_c(void) {
322
+ import_array();
323
+ return PyModule_Create(&module);
324
+ }
325
+ ```
326
+
327
+ ## Third-Party Environment Integration
328
+
329
+ ### Gymnasium Environments
330
+
331
+ ```python
332
+ import gymnasium as gym
333
+ import pufferlib
334
+
335
+ # Wrap Gymnasium environment
336
+ gym_env = gym.make('CartPole-v1')
337
+ puffer_env = pufferlib.emulate(gym_env, num_envs=256)
338
+
339
+ # Or use make directly
340
+ env = pufferlib.make('gym-CartPole-v1', num_envs=256)
341
+ ```
342
+
343
+ ### PettingZoo Environments
344
+
345
+ ```python
346
+ from pettingzoo.butterfly import pistonball_v6
347
+ import pufferlib
348
+
349
+ # Wrap PettingZoo environment
350
+ pz_env = pistonball_v6.env()
351
+ puffer_env = pufferlib.emulate(pz_env, num_envs=128)
352
+
353
+ # Or use make directly
354
+ env = pufferlib.make('pettingzoo-pistonball', num_envs=128)
355
+ ```
356
+
357
+ ### Custom Wrappers
358
+
359
+ ```python
360
+ class CustomWrapper(pufferlib.PufferEnv):
361
+ """Wrapper to modify environment behavior."""
362
+
363
+ def __init__(self, base_env, buf=None):
364
+ super().__init__(buf)
365
+ self.base_env = base_env
366
+ self.observation_space = base_env.observation_space
367
+ self.action_space = base_env.action_space
368
+
369
+ def reset(self):
370
+ obs = self.base_env.reset()
371
+ # Modify observation
372
+ return self._process_obs(obs)
373
+
374
+ def step(self, action):
375
+ # Modify action
376
+ modified_action = self._process_action(action)
377
+
378
+ obs, reward, done, info = self.base_env.step(modified_action)
379
+
380
+ # Modify outputs
381
+ obs = self._process_obs(obs)
382
+ reward = self._process_reward(reward)
383
+
384
+ return obs, reward, done, info
385
+ ```
386
+
387
+ ## Environment Best Practices
388
+
389
+ ### State Management
390
+
391
+ ```python
392
+ # Store minimal state, compute on demand
393
+ class EfficientEnv(PufferEnv):
394
+ def __init__(self, buf=None):
395
+ super().__init__(buf)
396
+ self.agent_pos = np.zeros(2) # Minimal state
397
+
398
+ def _get_observation(self):
399
+ # Compute full observation on demand
400
+ observation = np.zeros((84, 84, 3), dtype=np.uint8)
401
+ self._render_scene(observation, self.agent_pos)
402
+ return observation
403
+ ```
404
+
405
+ ### Reward Scaling
406
+
407
+ ```python
408
+ # Normalize rewards to reasonable range
409
+ def step(self, action):
410
+ # ... environment logic ...
411
+
412
+ # Scale large rewards
413
+ raw_reward = compute_raw_reward()
414
+ reward = np.clip(raw_reward / 100.0, -10, 10)
415
+
416
+ return obs, reward, done, info
417
+ ```
418
+
419
+ ### Episode Termination
420
+
421
+ ```python
422
+ def step(self, action):
423
+ # ... environment logic ...
424
+
425
+ # Multiple termination conditions
426
+ timeout = self.step_count >= self.max_steps
427
+ success = self._check_success()
428
+ failure = self._check_failure()
429
+
430
+ done = timeout or success or failure
431
+
432
+ info = {
433
+ 'TimeLimit.truncated': timeout,
434
+ 'success': success
435
+ }
436
+
437
+ return obs, reward, done, info
438
+ ```
439
+
440
+ ### Memory Efficiency
441
+
442
+ ```python
443
+ # Reuse buffers instead of allocating new ones
444
+ class MemoryEfficientEnv(PufferEnv):
445
+ def __init__(self, buf=None):
446
+ super().__init__(buf)
447
+
448
+ # Pre-allocate observation buffer
449
+ self._obs_buffer = np.zeros((84, 84, 3), dtype=np.uint8)
450
+
451
+ def _get_observation(self):
452
+ # Reuse buffer, modify in place
453
+ self._render_scene(self._obs_buffer)
454
+ return self._obs_buffer # Return view, not copy
455
+ ```
456
+
457
+ ## Debugging Environments
458
+
459
+ ### Validation Checks
460
+
461
+ ```python
462
+ # Add assertions to catch bugs
463
+ def step(self, action):
464
+ assert self.action_space.contains(action), f"Invalid action: {action}"
465
+
466
+ obs, reward, done, info = self._step_impl(action)
467
+
468
+ assert self.observation_space.contains(obs), "Invalid observation"
469
+ assert np.isfinite(reward), "Non-finite reward"
470
+
471
+ return obs, reward, done, info
472
+ ```
473
+
474
+ ### Rendering
475
+
476
+ ```python
477
+ class DebuggableEnv(PufferEnv):
478
+ def __init__(self, buf=None, render_mode=None):
479
+ super().__init__(buf)
480
+ self.render_mode = render_mode
481
+
482
+ def render(self):
483
+ """Render environment for debugging."""
484
+ if self.render_mode == 'human':
485
+ # Display to screen
486
+ self._display_scene()
487
+ elif self.render_mode == 'rgb_array':
488
+ # Return image
489
+ return self._render_to_array()
490
+ ```
491
+
492
+ ### Logging
493
+
494
+ ```python
495
+ import logging
496
+
497
+ logger = logging.getLogger(__name__)
498
+
499
+ def step(self, action):
500
+ logger.debug(f"Step {self.step_count}: action={action}")
501
+
502
+ obs, reward, done, info = self._step_impl(action)
503
+
504
+ if done:
505
+ logger.info(f"Episode finished: reward={self.total_reward}")
506
+
507
+ return obs, reward, done, info
508
+ ```