@synsci/cli-darwin-x64-baseline 1.1.77 → 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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  809. package/bin/skills/uniprot-database/scripts/uniprot_client.py +341 -0
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@@ -0,0 +1,395 @@
1
+ # SimPy Real-Time Simulations
2
+
3
+ This guide covers real-time simulation capabilities in SimPy, where simulation time is synchronized with wall-clock time.
4
+
5
+ ## Overview
6
+
7
+ Real-time simulations synchronize simulation time with actual wall-clock time. This is useful for:
8
+
9
+ - **Hardware-in-the-loop (HIL)** testing
10
+ - **Human interaction** with simulations
11
+ - **Algorithm behavior analysis** under real-time constraints
12
+ - **System integration** testing
13
+ - **Demonstration** purposes
14
+
15
+ ## RealtimeEnvironment
16
+
17
+ Replace the standard `Environment` with `simpy.rt.RealtimeEnvironment` to enable real-time synchronization.
18
+
19
+ ### Basic Usage
20
+
21
+ ```python
22
+ import simpy.rt
23
+
24
+ def process(env):
25
+ while True:
26
+ print(f'Tick at {env.now}')
27
+ yield env.timeout(1)
28
+
29
+ # Real-time environment with 1:1 time mapping
30
+ env = simpy.rt.RealtimeEnvironment(factor=1.0)
31
+ env.process(process(env))
32
+ env.run(until=5)
33
+ ```
34
+
35
+ ### Constructor Parameters
36
+
37
+ ```python
38
+ simpy.rt.RealtimeEnvironment(
39
+ initial_time=0, # Starting simulation time
40
+ factor=1.0, # Real time per simulation time unit
41
+ strict=True # Raise errors on timing violations
42
+ )
43
+ ```
44
+
45
+ ## Time Scaling with Factor
46
+
47
+ The `factor` parameter controls how simulation time maps to real time.
48
+
49
+ ### Factor Examples
50
+
51
+ ```python
52
+ import simpy.rt
53
+ import time
54
+
55
+ def timed_process(env, label):
56
+ start = time.time()
57
+ print(f'{label}: Starting at {env.now}')
58
+ yield env.timeout(2)
59
+ elapsed = time.time() - start
60
+ print(f'{label}: Completed at {env.now} (real time: {elapsed:.2f}s)')
61
+
62
+ # Factor = 1.0: 1 simulation time unit = 1 second
63
+ print('Factor = 1.0 (2 sim units = 2 seconds)')
64
+ env = simpy.rt.RealtimeEnvironment(factor=1.0)
65
+ env.process(timed_process(env, 'Normal speed'))
66
+ env.run()
67
+
68
+ # Factor = 0.5: 1 simulation time unit = 0.5 seconds
69
+ print('\nFactor = 0.5 (2 sim units = 1 second)')
70
+ env = simpy.rt.RealtimeEnvironment(factor=0.5)
71
+ env.process(timed_process(env, 'Double speed'))
72
+ env.run()
73
+
74
+ # Factor = 2.0: 1 simulation time unit = 2 seconds
75
+ print('\nFactor = 2.0 (2 sim units = 4 seconds)')
76
+ env = simpy.rt.RealtimeEnvironment(factor=2.0)
77
+ env.process(timed_process(env, 'Half speed'))
78
+ env.run()
79
+ ```
80
+
81
+ **Factor interpretation:**
82
+ - `factor=1.0` → 1 simulation time unit takes 1 real second
83
+ - `factor=0.1` → 1 simulation time unit takes 0.1 real seconds (10x faster)
84
+ - `factor=60` → 1 simulation time unit takes 60 real seconds (1 minute)
85
+
86
+ ## Strict Mode
87
+
88
+ ### strict=True (Default)
89
+
90
+ Raises `RuntimeError` if computation exceeds allocated real-time budget.
91
+
92
+ ```python
93
+ import simpy.rt
94
+ import time
95
+
96
+ def heavy_computation(env):
97
+ print(f'Starting computation at {env.now}')
98
+ yield env.timeout(1)
99
+
100
+ # Simulate heavy computation (exceeds 1 second budget)
101
+ time.sleep(1.5)
102
+
103
+ print(f'Computation done at {env.now}')
104
+
105
+ env = simpy.rt.RealtimeEnvironment(factor=1.0, strict=True)
106
+ env.process(heavy_computation(env))
107
+
108
+ try:
109
+ env.run()
110
+ except RuntimeError as e:
111
+ print(f'Error: {e}')
112
+ ```
113
+
114
+ ### strict=False
115
+
116
+ Allows simulation to run slower than intended without crashing.
117
+
118
+ ```python
119
+ import simpy.rt
120
+ import time
121
+
122
+ def heavy_computation(env):
123
+ print(f'Starting at {env.now}')
124
+ yield env.timeout(1)
125
+
126
+ # Heavy computation
127
+ time.sleep(1.5)
128
+
129
+ print(f'Done at {env.now}')
130
+
131
+ env = simpy.rt.RealtimeEnvironment(factor=1.0, strict=False)
132
+ env.process(heavy_computation(env))
133
+ env.run()
134
+
135
+ print('Simulation completed (slower than real-time)')
136
+ ```
137
+
138
+ **Use strict=False when:**
139
+ - Development and debugging
140
+ - Computation time is unpredictable
141
+ - Acceptable to run slower than target rate
142
+ - Analyzing worst-case behavior
143
+
144
+ ## Hardware-in-the-Loop Example
145
+
146
+ ```python
147
+ import simpy.rt
148
+
149
+ class HardwareInterface:
150
+ """Simulated hardware interface."""
151
+
152
+ def __init__(self):
153
+ self.sensor_value = 0
154
+
155
+ def read_sensor(self):
156
+ """Simulate reading from hardware sensor."""
157
+ import random
158
+ self.sensor_value = random.uniform(20.0, 30.0)
159
+ return self.sensor_value
160
+
161
+ def write_actuator(self, value):
162
+ """Simulate writing to hardware actuator."""
163
+ print(f'Actuator set to {value:.2f}')
164
+
165
+ def control_loop(env, hardware, setpoint):
166
+ """Simple control loop running in real-time."""
167
+ while True:
168
+ # Read sensor
169
+ sensor_value = hardware.read_sensor()
170
+ print(f'[{env.now}] Sensor: {sensor_value:.2f}°C')
171
+
172
+ # Simple proportional control
173
+ error = setpoint - sensor_value
174
+ control_output = error * 0.1
175
+
176
+ # Write actuator
177
+ hardware.write_actuator(control_output)
178
+
179
+ # Control loop runs every 0.5 seconds
180
+ yield env.timeout(0.5)
181
+
182
+ # Real-time environment: 1 sim unit = 1 second
183
+ env = simpy.rt.RealtimeEnvironment(factor=1.0, strict=False)
184
+ hardware = HardwareInterface()
185
+ setpoint = 25.0
186
+
187
+ env.process(control_loop(env, hardware, setpoint))
188
+ env.run(until=5)
189
+ ```
190
+
191
+ ## Human Interaction Example
192
+
193
+ ```python
194
+ import simpy.rt
195
+
196
+ def interactive_process(env):
197
+ """Process that waits for simulated user input."""
198
+ print('Simulation started. Events will occur in real-time.')
199
+
200
+ yield env.timeout(2)
201
+ print(f'[{env.now}] Event 1: System startup')
202
+
203
+ yield env.timeout(3)
204
+ print(f'[{env.now}] Event 2: Initialization complete')
205
+
206
+ yield env.timeout(2)
207
+ print(f'[{env.now}] Event 3: Ready for operation')
208
+
209
+ # Real-time environment for human-paced demonstration
210
+ env = simpy.rt.RealtimeEnvironment(factor=1.0)
211
+ env.process(interactive_process(env))
212
+ env.run()
213
+ ```
214
+
215
+ ## Monitoring Real-Time Performance
216
+
217
+ ```python
218
+ import simpy.rt
219
+ import time
220
+
221
+ class RealTimeMonitor:
222
+ def __init__(self):
223
+ self.step_times = []
224
+ self.drift_values = []
225
+
226
+ def record_step(self, sim_time, real_time, expected_real_time):
227
+ self.step_times.append(sim_time)
228
+ drift = real_time - expected_real_time
229
+ self.drift_values.append(drift)
230
+
231
+ def report(self):
232
+ if self.drift_values:
233
+ avg_drift = sum(self.drift_values) / len(self.drift_values)
234
+ max_drift = max(abs(d) for d in self.drift_values)
235
+ print(f'\nReal-time performance:')
236
+ print(f'Average drift: {avg_drift*1000:.2f} ms')
237
+ print(f'Maximum drift: {max_drift*1000:.2f} ms')
238
+
239
+ def monitored_process(env, monitor, start_time, factor):
240
+ for i in range(5):
241
+ step_start = time.time()
242
+ yield env.timeout(1)
243
+
244
+ real_elapsed = time.time() - start_time
245
+ expected_elapsed = env.now * factor
246
+ monitor.record_step(env.now, real_elapsed, expected_elapsed)
247
+
248
+ print(f'Sim time: {env.now}, Real time: {real_elapsed:.2f}s, ' +
249
+ f'Expected: {expected_elapsed:.2f}s')
250
+
251
+ start = time.time()
252
+ factor = 1.0
253
+ env = simpy.rt.RealtimeEnvironment(factor=factor, strict=False)
254
+ monitor = RealTimeMonitor()
255
+
256
+ env.process(monitored_process(env, monitor, start, factor))
257
+ env.run()
258
+ monitor.report()
259
+ ```
260
+
261
+ ## Mixed Real-Time and Fast Simulation
262
+
263
+ ```python
264
+ import simpy.rt
265
+
266
+ def background_simulation(env):
267
+ """Fast background simulation."""
268
+ for i in range(100):
269
+ yield env.timeout(0.01)
270
+ print(f'Background simulation completed at {env.now}')
271
+
272
+ def real_time_display(env):
273
+ """Real-time display updates."""
274
+ for i in range(5):
275
+ print(f'Display update at {env.now}')
276
+ yield env.timeout(1)
277
+
278
+ # Note: This is conceptual - SimPy doesn't directly support mixed modes
279
+ # Consider running separate simulations or using strict=False
280
+ env = simpy.rt.RealtimeEnvironment(factor=1.0, strict=False)
281
+ env.process(background_simulation(env))
282
+ env.process(real_time_display(env))
283
+ env.run()
284
+ ```
285
+
286
+ ## Converting Standard to Real-Time
287
+
288
+ Converting a standard simulation to real-time is straightforward:
289
+
290
+ ```python
291
+ import simpy
292
+ import simpy.rt
293
+
294
+ def process(env):
295
+ print(f'Event at {env.now}')
296
+ yield env.timeout(1)
297
+ print(f'Event at {env.now}')
298
+ yield env.timeout(1)
299
+ print(f'Event at {env.now}')
300
+
301
+ # Standard simulation (runs instantly)
302
+ print('Standard simulation:')
303
+ env = simpy.Environment()
304
+ env.process(process(env))
305
+ env.run()
306
+
307
+ # Real-time simulation (2 real seconds)
308
+ print('\nReal-time simulation:')
309
+ env_rt = simpy.rt.RealtimeEnvironment(factor=1.0)
310
+ env_rt.process(process(env_rt))
311
+ env_rt.run()
312
+ ```
313
+
314
+ ## Best Practices
315
+
316
+ 1. **Factor selection**: Choose factor based on hardware/human constraints
317
+ - Human interaction: `factor=1.0` (1:1 time mapping)
318
+ - Fast hardware: `factor=0.01` (100x faster)
319
+ - Slow processes: `factor=60` (1 sim unit = 1 minute)
320
+
321
+ 2. **Strict mode usage**:
322
+ - Use `strict=True` for timing validation
323
+ - Use `strict=False` for development and variable workloads
324
+
325
+ 3. **Computation budget**: Ensure process logic executes faster than timeout duration
326
+
327
+ 4. **Error handling**: Wrap real-time runs in try-except for timing violations
328
+
329
+ 5. **Testing strategy**:
330
+ - Develop with standard Environment (fast iteration)
331
+ - Test with RealtimeEnvironment (validation)
332
+ - Deploy with appropriate factor and strict settings
333
+
334
+ 6. **Performance monitoring**: Track drift between simulation and real time
335
+
336
+ 7. **Graceful degradation**: Use `strict=False` when timing guarantees aren't critical
337
+
338
+ ## Common Patterns
339
+
340
+ ### Periodic Real-Time Tasks
341
+
342
+ ```python
343
+ import simpy.rt
344
+
345
+ def periodic_task(env, name, period, duration):
346
+ """Task that runs periodically in real-time."""
347
+ while True:
348
+ start = env.now
349
+ print(f'{name}: Starting at {start}')
350
+
351
+ # Simulate work
352
+ yield env.timeout(duration)
353
+
354
+ print(f'{name}: Completed at {env.now}')
355
+
356
+ # Wait for next period
357
+ elapsed = env.now - start
358
+ wait_time = period - elapsed
359
+ if wait_time > 0:
360
+ yield env.timeout(wait_time)
361
+
362
+ env = simpy.rt.RealtimeEnvironment(factor=1.0)
363
+ env.process(periodic_task(env, 'Task', period=2.0, duration=0.5))
364
+ env.run(until=6)
365
+ ```
366
+
367
+ ### Synchronized Multi-Device Control
368
+
369
+ ```python
370
+ import simpy.rt
371
+
372
+ def device_controller(env, device_id, update_rate):
373
+ """Control loop for individual device."""
374
+ while True:
375
+ print(f'Device {device_id}: Update at {env.now}')
376
+ yield env.timeout(update_rate)
377
+
378
+ # All devices synchronized to real-time
379
+ env = simpy.rt.RealtimeEnvironment(factor=1.0)
380
+
381
+ # Different update rates for different devices
382
+ env.process(device_controller(env, 'A', 1.0))
383
+ env.process(device_controller(env, 'B', 0.5))
384
+ env.process(device_controller(env, 'C', 2.0))
385
+
386
+ env.run(until=5)
387
+ ```
388
+
389
+ ## Limitations
390
+
391
+ 1. **Performance**: Real-time simulation adds overhead; not suitable for high-frequency events
392
+ 2. **Synchronization**: Single-threaded; all processes share same time base
393
+ 3. **Precision**: Limited by Python's time resolution and system scheduling
394
+ 4. **Strict mode**: May raise errors frequently with computationally intensive processes
395
+ 5. **Platform-dependent**: Timing accuracy varies across operating systems
@@ -0,0 +1,275 @@
1
+ # SimPy Shared Resources
2
+
3
+ This guide covers all resource types in SimPy for modeling congestion points and resource allocation.
4
+
5
+ ## Resource Types Overview
6
+
7
+ SimPy provides three main categories of shared resources:
8
+
9
+ 1. **Resources** - Limited capacity resources (e.g., gas pumps, servers)
10
+ 2. **Containers** - Homogeneous bulk materials (e.g., fuel tanks, silos)
11
+ 3. **Stores** - Python object storage (e.g., item queues, warehouses)
12
+
13
+ ## 1. Resources
14
+
15
+ Model resources that can be used by a limited number of processes at a time.
16
+
17
+ ### Resource (Basic)
18
+
19
+ The basic resource is a semaphore with specified capacity.
20
+
21
+ ```python
22
+ import simpy
23
+
24
+ env = simpy.Environment()
25
+ resource = simpy.Resource(env, capacity=2)
26
+
27
+ def process(env, resource, name):
28
+ with resource.request() as req:
29
+ yield req
30
+ print(f'{name} has the resource at {env.now}')
31
+ yield env.timeout(5)
32
+ print(f'{name} releases the resource at {env.now}')
33
+
34
+ env.process(process(env, resource, 'Process 1'))
35
+ env.process(process(env, resource, 'Process 2'))
36
+ env.process(process(env, resource, 'Process 3'))
37
+ env.run()
38
+ ```
39
+
40
+ **Key properties:**
41
+ - `capacity` - Maximum number of concurrent users (default: 1)
42
+ - `count` - Current number of users
43
+ - `queue` - List of queued requests
44
+
45
+ ### PriorityResource
46
+
47
+ Extends basic resource with priority levels (lower numbers = higher priority).
48
+
49
+ ```python
50
+ import simpy
51
+
52
+ env = simpy.Environment()
53
+ resource = simpy.PriorityResource(env, capacity=1)
54
+
55
+ def process(env, resource, name, priority):
56
+ with resource.request(priority=priority) as req:
57
+ yield req
58
+ print(f'{name} (priority {priority}) has the resource at {env.now}')
59
+ yield env.timeout(5)
60
+
61
+ env.process(process(env, resource, 'Low priority', priority=10))
62
+ env.process(process(env, resource, 'High priority', priority=1))
63
+ env.run()
64
+ ```
65
+
66
+ **Use cases:**
67
+ - Emergency services (ambulances before regular vehicles)
68
+ - VIP customer queues
69
+ - Job scheduling with priorities
70
+
71
+ ### PreemptiveResource
72
+
73
+ Allows high-priority requests to interrupt lower-priority users.
74
+
75
+ ```python
76
+ import simpy
77
+
78
+ env = simpy.Environment()
79
+ resource = simpy.PreemptiveResource(env, capacity=1)
80
+
81
+ def process(env, resource, name, priority):
82
+ with resource.request(priority=priority) as req:
83
+ try:
84
+ yield req
85
+ print(f'{name} acquired resource at {env.now}')
86
+ yield env.timeout(10)
87
+ print(f'{name} finished at {env.now}')
88
+ except simpy.Interrupt:
89
+ print(f'{name} was preempted at {env.now}')
90
+
91
+ env.process(process(env, resource, 'Low priority', priority=10))
92
+ env.process(process(env, resource, 'High priority', priority=1))
93
+ env.run()
94
+ ```
95
+
96
+ **Use cases:**
97
+ - Operating system CPU scheduling
98
+ - Emergency room triage
99
+ - Network packet prioritization
100
+
101
+ ## 2. Containers
102
+
103
+ Model production and consumption of homogeneous bulk materials (continuous or discrete).
104
+
105
+ ```python
106
+ import simpy
107
+
108
+ env = simpy.Environment()
109
+ container = simpy.Container(env, capacity=100, init=50)
110
+
111
+ def producer(env, container):
112
+ while True:
113
+ yield env.timeout(5)
114
+ yield container.put(20)
115
+ print(f'Produced 20. Level: {container.level}')
116
+
117
+ def consumer(env, container):
118
+ while True:
119
+ yield env.timeout(7)
120
+ yield container.get(15)
121
+ print(f'Consumed 15. Level: {container.level}')
122
+
123
+ env.process(producer(env, container))
124
+ env.process(consumer(env, container))
125
+ env.run(until=50)
126
+ ```
127
+
128
+ **Key properties:**
129
+ - `capacity` - Maximum amount (default: float('inf'))
130
+ - `level` - Current amount
131
+ - `init` - Initial amount (default: 0)
132
+
133
+ **Operations:**
134
+ - `put(amount)` - Add to container (blocks if full)
135
+ - `get(amount)` - Remove from container (blocks if insufficient)
136
+
137
+ **Use cases:**
138
+ - Gas station fuel tanks
139
+ - Buffer storage in manufacturing
140
+ - Water reservoirs
141
+ - Battery charge levels
142
+
143
+ ## 3. Stores
144
+
145
+ Model production and consumption of Python objects.
146
+
147
+ ### Store (Basic)
148
+
149
+ Generic FIFO object storage.
150
+
151
+ ```python
152
+ import simpy
153
+
154
+ env = simpy.Environment()
155
+ store = simpy.Store(env, capacity=2)
156
+
157
+ def producer(env, store):
158
+ for i in range(5):
159
+ yield env.timeout(2)
160
+ item = f'Item {i}'
161
+ yield store.put(item)
162
+ print(f'Produced {item} at {env.now}')
163
+
164
+ def consumer(env, store):
165
+ while True:
166
+ yield env.timeout(3)
167
+ item = yield store.get()
168
+ print(f'Consumed {item} at {env.now}')
169
+
170
+ env.process(producer(env, store))
171
+ env.process(consumer(env, store))
172
+ env.run()
173
+ ```
174
+
175
+ **Key properties:**
176
+ - `capacity` - Maximum number of items (default: float('inf'))
177
+ - `items` - List of stored items
178
+
179
+ **Operations:**
180
+ - `put(item)` - Add item to store (blocks if full)
181
+ - `get()` - Remove and return item (blocks if empty)
182
+
183
+ ### FilterStore
184
+
185
+ Allows retrieval of specific objects based on filter functions.
186
+
187
+ ```python
188
+ import simpy
189
+
190
+ env = simpy.Environment()
191
+ store = simpy.FilterStore(env, capacity=10)
192
+
193
+ def producer(env, store):
194
+ for color in ['red', 'blue', 'green', 'red', 'blue']:
195
+ yield env.timeout(1)
196
+ yield store.put({'color': color, 'time': env.now})
197
+ print(f'Produced {color} item at {env.now}')
198
+
199
+ def consumer(env, store, color):
200
+ while True:
201
+ yield env.timeout(2)
202
+ item = yield store.get(lambda x: x['color'] == color)
203
+ print(f'{color} consumer got item from {item["time"]} at {env.now}')
204
+
205
+ env.process(producer(env, store))
206
+ env.process(consumer(env, store, 'red'))
207
+ env.process(consumer(env, store, 'blue'))
208
+ env.run(until=15)
209
+ ```
210
+
211
+ **Use cases:**
212
+ - Warehouse item picking (specific SKUs)
213
+ - Job queues with skill matching
214
+ - Packet routing by destination
215
+
216
+ ### PriorityStore
217
+
218
+ Items retrieved in priority order (lowest first).
219
+
220
+ ```python
221
+ import simpy
222
+
223
+ class PriorityItem:
224
+ def __init__(self, priority, data):
225
+ self.priority = priority
226
+ self.data = data
227
+
228
+ def __lt__(self, other):
229
+ return self.priority < other.priority
230
+
231
+ env = simpy.Environment()
232
+ store = simpy.PriorityStore(env, capacity=10)
233
+
234
+ def producer(env, store):
235
+ items = [(10, 'Low'), (1, 'High'), (5, 'Medium')]
236
+ for priority, name in items:
237
+ yield env.timeout(1)
238
+ yield store.put(PriorityItem(priority, name))
239
+ print(f'Produced {name} priority item')
240
+
241
+ def consumer(env, store):
242
+ while True:
243
+ yield env.timeout(5)
244
+ item = yield store.get()
245
+ print(f'Retrieved {item.data} priority item')
246
+
247
+ env.process(producer(env, store))
248
+ env.process(consumer(env, store))
249
+ env.run()
250
+ ```
251
+
252
+ **Use cases:**
253
+ - Task scheduling
254
+ - Print job queues
255
+ - Message prioritization
256
+
257
+ ## Choosing the Right Resource Type
258
+
259
+ | Scenario | Resource Type |
260
+ |----------|---------------|
261
+ | Limited servers/machines | Resource |
262
+ | Priority-based queuing | PriorityResource |
263
+ | Preemptive scheduling | PreemptiveResource |
264
+ | Fuel, water, bulk materials | Container |
265
+ | Generic item queue (FIFO) | Store |
266
+ | Selective item retrieval | FilterStore |
267
+ | Priority-ordered items | PriorityStore |
268
+
269
+ ## Best Practices
270
+
271
+ 1. **Capacity planning**: Set realistic capacities based on system constraints
272
+ 2. **Request patterns**: Use context managers (`with resource.request()`) for automatic cleanup
273
+ 3. **Error handling**: Wrap preemptive resources in try-except for Interrupt handling
274
+ 4. **Monitoring**: Track queue lengths and utilization (see monitoring.md)
275
+ 5. **Performance**: FilterStore and PriorityStore have O(n) retrieval time; use wisely for large stores