@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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47
|
+
|
|
48
|
+
def record_service_time(self, service_time):
|
|
49
|
+
self.service_times.append(service_time)
|
|
50
|
+
|
|
51
|
+
def report(self):
|
|
52
|
+
print("\n" + "=" * 50)
|
|
53
|
+
print("SIMULATION STATISTICS")
|
|
54
|
+
print("=" * 50)
|
|
55
|
+
|
|
56
|
+
if self.wait_times:
|
|
57
|
+
print(f"Total customers: {len(self.wait_times)}")
|
|
58
|
+
print(f"Average wait time: {sum(self.wait_times) / len(self.wait_times):.2f}")
|
|
59
|
+
print(f"Max wait time: {max(self.wait_times):.2f}")
|
|
60
|
+
print(f"Min wait time: {min(self.wait_times):.2f}")
|
|
61
|
+
|
|
62
|
+
if self.service_times:
|
|
63
|
+
print(f"Average service time: {sum(self.service_times) / len(self.service_times):.2f}")
|
|
64
|
+
|
|
65
|
+
if self.arrival_times and self.departure_times:
|
|
66
|
+
throughput = len(self.departure_times) / max(self.departure_times)
|
|
67
|
+
print(f"Throughput: {throughput:.2f} customers/time unit")
|
|
68
|
+
|
|
69
|
+
print("=" * 50)
|
|
70
|
+
|
|
71
|
+
|
|
72
|
+
def customer_process(env, name, resource, stats, config):
|
|
73
|
+
"""
|
|
74
|
+
Simulate a customer process.
|
|
75
|
+
|
|
76
|
+
Args:
|
|
77
|
+
env: SimPy environment
|
|
78
|
+
name: Customer identifier
|
|
79
|
+
resource: Shared resource (e.g., server, machine)
|
|
80
|
+
stats: Statistics collector
|
|
81
|
+
config: Simulation configuration
|
|
82
|
+
"""
|
|
83
|
+
# Record arrival
|
|
84
|
+
arrival_time = env.now
|
|
85
|
+
stats.record_arrival(arrival_time)
|
|
86
|
+
print(f"{name} arrived at {arrival_time:.2f}")
|
|
87
|
+
|
|
88
|
+
# Request resource
|
|
89
|
+
with resource.request() as request:
|
|
90
|
+
yield request
|
|
91
|
+
|
|
92
|
+
# Record service start and calculate wait time
|
|
93
|
+
service_start = env.now
|
|
94
|
+
wait_time = service_start - arrival_time
|
|
95
|
+
stats.record_service_start(service_start)
|
|
96
|
+
stats.record_wait_time(wait_time)
|
|
97
|
+
print(f"{name} started service at {service_start:.2f} (waited {wait_time:.2f})")
|
|
98
|
+
|
|
99
|
+
# Service time (normally distributed)
|
|
100
|
+
service_time = max(0.1, random.gauss(
|
|
101
|
+
config.service_time_mean,
|
|
102
|
+
config.service_time_std
|
|
103
|
+
))
|
|
104
|
+
stats.record_service_time(service_time)
|
|
105
|
+
|
|
106
|
+
yield env.timeout(service_time)
|
|
107
|
+
|
|
108
|
+
# Record departure
|
|
109
|
+
departure_time = env.now
|
|
110
|
+
stats.record_departure(departure_time)
|
|
111
|
+
print(f"{name} departed at {departure_time:.2f}")
|
|
112
|
+
|
|
113
|
+
|
|
114
|
+
def customer_generator(env, resource, stats, config):
|
|
115
|
+
"""
|
|
116
|
+
Generate customers arriving at random intervals.
|
|
117
|
+
|
|
118
|
+
Args:
|
|
119
|
+
env: SimPy environment
|
|
120
|
+
resource: Shared resource
|
|
121
|
+
stats: Statistics collector
|
|
122
|
+
config: Simulation configuration
|
|
123
|
+
"""
|
|
124
|
+
customer_count = 0
|
|
125
|
+
|
|
126
|
+
while True:
|
|
127
|
+
# Wait for next customer arrival (exponential distribution)
|
|
128
|
+
inter_arrival_time = random.expovariate(1.0 / config.arrival_rate)
|
|
129
|
+
yield env.timeout(inter_arrival_time)
|
|
130
|
+
|
|
131
|
+
# Create new customer process
|
|
132
|
+
customer_count += 1
|
|
133
|
+
customer_name = f"Customer {customer_count}"
|
|
134
|
+
env.process(customer_process(env, customer_name, resource, stats, config))
|
|
135
|
+
|
|
136
|
+
|
|
137
|
+
def run_simulation(config):
|
|
138
|
+
"""
|
|
139
|
+
Run the simulation with given configuration.
|
|
140
|
+
|
|
141
|
+
Args:
|
|
142
|
+
config: SimulationConfig object with simulation parameters
|
|
143
|
+
|
|
144
|
+
Returns:
|
|
145
|
+
SimulationStats object with collected statistics
|
|
146
|
+
"""
|
|
147
|
+
# Set random seed for reproducibility
|
|
148
|
+
random.seed(config.random_seed)
|
|
149
|
+
|
|
150
|
+
# Create environment
|
|
151
|
+
env = simpy.Environment()
|
|
152
|
+
|
|
153
|
+
# Create shared resource
|
|
154
|
+
resource = simpy.Resource(env, capacity=config.num_resources)
|
|
155
|
+
|
|
156
|
+
# Create statistics collector
|
|
157
|
+
stats = SimulationStats()
|
|
158
|
+
|
|
159
|
+
# Start customer generator
|
|
160
|
+
env.process(customer_generator(env, resource, stats, config))
|
|
161
|
+
|
|
162
|
+
# Run simulation
|
|
163
|
+
print(f"Starting simulation for {config.sim_time} time units...")
|
|
164
|
+
print(f"Resources: {config.num_resources}")
|
|
165
|
+
print(f"Average arrival rate: {config.arrival_rate:.2f}")
|
|
166
|
+
print(f"Average service time: {config.service_time_mean:.2f}")
|
|
167
|
+
print("-" * 50)
|
|
168
|
+
|
|
169
|
+
env.run(until=config.sim_time)
|
|
170
|
+
|
|
171
|
+
return stats
|
|
172
|
+
|
|
173
|
+
|
|
174
|
+
def main():
|
|
175
|
+
"""Main function to run the simulation."""
|
|
176
|
+
# Create configuration
|
|
177
|
+
config = SimulationConfig()
|
|
178
|
+
|
|
179
|
+
# Customize configuration if needed
|
|
180
|
+
config.num_resources = 2
|
|
181
|
+
config.sim_time = 50
|
|
182
|
+
config.arrival_rate = 2.0
|
|
183
|
+
config.service_time_mean = 3.0
|
|
184
|
+
|
|
185
|
+
# Run simulation
|
|
186
|
+
stats = run_simulation(config)
|
|
187
|
+
|
|
188
|
+
# Report statistics
|
|
189
|
+
stats.report()
|
|
190
|
+
|
|
191
|
+
|
|
192
|
+
if __name__ == "__main__":
|
|
193
|
+
main()
|
|
@@ -0,0 +1,345 @@
|
|
|
1
|
+
#!/usr/bin/env python3
|
|
2
|
+
"""
|
|
3
|
+
SimPy Resource Monitoring Utilities
|
|
4
|
+
|
|
5
|
+
This module provides reusable classes and functions for monitoring
|
|
6
|
+
SimPy resources during simulation. Includes utilities for tracking
|
|
7
|
+
queue lengths, utilization, wait times, and generating reports.
|
|
8
|
+
"""
|
|
9
|
+
|
|
10
|
+
import simpy
|
|
11
|
+
from collections import defaultdict
|
|
12
|
+
from typing import List, Tuple, Dict, Any
|
|
13
|
+
|
|
14
|
+
|
|
15
|
+
class ResourceMonitor:
|
|
16
|
+
"""
|
|
17
|
+
Monitor resource usage with detailed statistics tracking.
|
|
18
|
+
|
|
19
|
+
Tracks:
|
|
20
|
+
- Queue lengths over time
|
|
21
|
+
- Resource utilization
|
|
22
|
+
- Wait times for requests
|
|
23
|
+
- Request and release events
|
|
24
|
+
"""
|
|
25
|
+
|
|
26
|
+
def __init__(self, env: simpy.Environment, resource: simpy.Resource, name: str = "Resource"):
|
|
27
|
+
"""
|
|
28
|
+
Initialize the resource monitor.
|
|
29
|
+
|
|
30
|
+
Args:
|
|
31
|
+
env: SimPy environment
|
|
32
|
+
resource: Resource to monitor
|
|
33
|
+
name: Name for the resource (for reporting)
|
|
34
|
+
"""
|
|
35
|
+
self.env = env
|
|
36
|
+
self.resource = resource
|
|
37
|
+
self.name = name
|
|
38
|
+
|
|
39
|
+
# Data storage
|
|
40
|
+
self.queue_data: List[Tuple[float, int]] = [(0, 0)]
|
|
41
|
+
self.utilization_data: List[Tuple[float, float]] = [(0, 0.0)]
|
|
42
|
+
self.request_times: Dict[Any, float] = {}
|
|
43
|
+
self.wait_times: List[float] = []
|
|
44
|
+
self.events: List[Tuple[float, str, Dict]] = []
|
|
45
|
+
|
|
46
|
+
# Patch the resource
|
|
47
|
+
self._patch_resource()
|
|
48
|
+
|
|
49
|
+
def _patch_resource(self):
|
|
50
|
+
"""Patch resource methods to intercept requests and releases."""
|
|
51
|
+
original_request = self.resource.request
|
|
52
|
+
original_release = self.resource.release
|
|
53
|
+
|
|
54
|
+
def monitored_request(*args, **kwargs):
|
|
55
|
+
req = original_request(*args, **kwargs)
|
|
56
|
+
|
|
57
|
+
# Record request event
|
|
58
|
+
queue_length = len(self.resource.queue)
|
|
59
|
+
utilization = self.resource.count / self.resource.capacity
|
|
60
|
+
|
|
61
|
+
self.queue_data.append((self.env.now, queue_length))
|
|
62
|
+
self.utilization_data.append((self.env.now, utilization))
|
|
63
|
+
self.events.append((self.env.now, 'request', {
|
|
64
|
+
'queue_length': queue_length,
|
|
65
|
+
'utilization': utilization
|
|
66
|
+
}))
|
|
67
|
+
|
|
68
|
+
# Store request time for wait time calculation
|
|
69
|
+
self.request_times[req] = self.env.now
|
|
70
|
+
|
|
71
|
+
# Add callback to record when request is granted
|
|
72
|
+
def on_granted(event):
|
|
73
|
+
if req in self.request_times:
|
|
74
|
+
wait_time = self.env.now - self.request_times[req]
|
|
75
|
+
self.wait_times.append(wait_time)
|
|
76
|
+
del self.request_times[req]
|
|
77
|
+
|
|
78
|
+
req.callbacks.append(on_granted)
|
|
79
|
+
return req
|
|
80
|
+
|
|
81
|
+
def monitored_release(*args, **kwargs):
|
|
82
|
+
result = original_release(*args, **kwargs)
|
|
83
|
+
|
|
84
|
+
# Record release event
|
|
85
|
+
queue_length = len(self.resource.queue)
|
|
86
|
+
utilization = self.resource.count / self.resource.capacity
|
|
87
|
+
|
|
88
|
+
self.queue_data.append((self.env.now, queue_length))
|
|
89
|
+
self.utilization_data.append((self.env.now, utilization))
|
|
90
|
+
self.events.append((self.env.now, 'release', {
|
|
91
|
+
'queue_length': queue_length,
|
|
92
|
+
'utilization': utilization
|
|
93
|
+
}))
|
|
94
|
+
|
|
95
|
+
return result
|
|
96
|
+
|
|
97
|
+
self.resource.request = monitored_request
|
|
98
|
+
self.resource.release = monitored_release
|
|
99
|
+
|
|
100
|
+
def average_queue_length(self) -> float:
|
|
101
|
+
"""Calculate time-weighted average queue length."""
|
|
102
|
+
if len(self.queue_data) < 2:
|
|
103
|
+
return 0.0
|
|
104
|
+
|
|
105
|
+
total_time = 0.0
|
|
106
|
+
weighted_sum = 0.0
|
|
107
|
+
|
|
108
|
+
for i in range(len(self.queue_data) - 1):
|
|
109
|
+
time1, length1 = self.queue_data[i]
|
|
110
|
+
time2, length2 = self.queue_data[i + 1]
|
|
111
|
+
duration = time2 - time1
|
|
112
|
+
total_time += duration
|
|
113
|
+
weighted_sum += length1 * duration
|
|
114
|
+
|
|
115
|
+
return weighted_sum / total_time if total_time > 0 else 0.0
|
|
116
|
+
|
|
117
|
+
def average_utilization(self) -> float:
|
|
118
|
+
"""Calculate time-weighted average utilization."""
|
|
119
|
+
if len(self.utilization_data) < 2:
|
|
120
|
+
return 0.0
|
|
121
|
+
|
|
122
|
+
total_time = 0.0
|
|
123
|
+
weighted_sum = 0.0
|
|
124
|
+
|
|
125
|
+
for i in range(len(self.utilization_data) - 1):
|
|
126
|
+
time1, util1 = self.utilization_data[i]
|
|
127
|
+
time2, util2 = self.utilization_data[i + 1]
|
|
128
|
+
duration = time2 - time1
|
|
129
|
+
total_time += duration
|
|
130
|
+
weighted_sum += util1 * duration
|
|
131
|
+
|
|
132
|
+
return weighted_sum / total_time if total_time > 0 else 0.0
|
|
133
|
+
|
|
134
|
+
def average_wait_time(self) -> float:
|
|
135
|
+
"""Calculate average wait time for requests."""
|
|
136
|
+
return sum(self.wait_times) / len(self.wait_times) if self.wait_times else 0.0
|
|
137
|
+
|
|
138
|
+
def max_queue_length(self) -> int:
|
|
139
|
+
"""Get maximum queue length observed."""
|
|
140
|
+
return max(length for _, length in self.queue_data) if self.queue_data else 0
|
|
141
|
+
|
|
142
|
+
def report(self):
|
|
143
|
+
"""Print detailed statistics report."""
|
|
144
|
+
print(f"\n{'=' * 60}")
|
|
145
|
+
print(f"RESOURCE MONITOR REPORT: {self.name}")
|
|
146
|
+
print(f"{'=' * 60}")
|
|
147
|
+
print(f"Simulation time: 0.00 to {self.env.now:.2f}")
|
|
148
|
+
print(f"Capacity: {self.resource.capacity}")
|
|
149
|
+
print(f"\nUtilization:")
|
|
150
|
+
print(f" Average: {self.average_utilization():.2%}")
|
|
151
|
+
print(f" Final: {self.resource.count / self.resource.capacity:.2%}")
|
|
152
|
+
print(f"\nQueue Statistics:")
|
|
153
|
+
print(f" Average length: {self.average_queue_length():.2f}")
|
|
154
|
+
print(f" Max length: {self.max_queue_length()}")
|
|
155
|
+
print(f" Final length: {len(self.resource.queue)}")
|
|
156
|
+
print(f"\nWait Time Statistics:")
|
|
157
|
+
print(f" Total requests: {len(self.wait_times)}")
|
|
158
|
+
if self.wait_times:
|
|
159
|
+
print(f" Average wait: {self.average_wait_time():.2f}")
|
|
160
|
+
print(f" Max wait: {max(self.wait_times):.2f}")
|
|
161
|
+
print(f" Min wait: {min(self.wait_times):.2f}")
|
|
162
|
+
print(f"\nEvent Summary:")
|
|
163
|
+
print(f" Total events: {len(self.events)}")
|
|
164
|
+
request_count = sum(1 for _, event_type, _ in self.events if event_type == 'request')
|
|
165
|
+
release_count = sum(1 for _, event_type, _ in self.events if event_type == 'release')
|
|
166
|
+
print(f" Requests: {request_count}")
|
|
167
|
+
print(f" Releases: {release_count}")
|
|
168
|
+
print(f"{'=' * 60}")
|
|
169
|
+
|
|
170
|
+
def export_csv(self, filename: str):
|
|
171
|
+
"""
|
|
172
|
+
Export monitoring data to CSV file.
|
|
173
|
+
|
|
174
|
+
Args:
|
|
175
|
+
filename: Output CSV filename
|
|
176
|
+
"""
|
|
177
|
+
import csv
|
|
178
|
+
|
|
179
|
+
with open(filename, 'w', newline='') as f:
|
|
180
|
+
writer = csv.writer(f)
|
|
181
|
+
writer.writerow(['Time', 'Event', 'Queue Length', 'Utilization'])
|
|
182
|
+
|
|
183
|
+
for time, event_type, data in self.events:
|
|
184
|
+
writer.writerow([
|
|
185
|
+
time,
|
|
186
|
+
event_type,
|
|
187
|
+
data['queue_length'],
|
|
188
|
+
data['utilization']
|
|
189
|
+
])
|
|
190
|
+
|
|
191
|
+
print(f"Data exported to {filename}")
|
|
192
|
+
|
|
193
|
+
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|
194
|
+
class MultiResourceMonitor:
|
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195
|
+
"""Monitor multiple resources simultaneously."""
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196
|
+
|
|
197
|
+
def __init__(self, env: simpy.Environment):
|
|
198
|
+
"""
|
|
199
|
+
Initialize multi-resource monitor.
|
|
200
|
+
|
|
201
|
+
Args:
|
|
202
|
+
env: SimPy environment
|
|
203
|
+
"""
|
|
204
|
+
self.env = env
|
|
205
|
+
self.monitors: Dict[str, ResourceMonitor] = {}
|
|
206
|
+
|
|
207
|
+
def add_resource(self, resource: simpy.Resource, name: str):
|
|
208
|
+
"""
|
|
209
|
+
Add a resource to monitor.
|
|
210
|
+
|
|
211
|
+
Args:
|
|
212
|
+
resource: SimPy resource to monitor
|
|
213
|
+
name: Name for the resource
|
|
214
|
+
"""
|
|
215
|
+
monitor = ResourceMonitor(self.env, resource, name)
|
|
216
|
+
self.monitors[name] = monitor
|
|
217
|
+
return monitor
|
|
218
|
+
|
|
219
|
+
def report_all(self):
|
|
220
|
+
"""Generate reports for all monitored resources."""
|
|
221
|
+
for name, monitor in self.monitors.items():
|
|
222
|
+
monitor.report()
|
|
223
|
+
|
|
224
|
+
def summary(self):
|
|
225
|
+
"""Print summary statistics for all resources."""
|
|
226
|
+
print(f"\n{'=' * 60}")
|
|
227
|
+
print("MULTI-RESOURCE SUMMARY")
|
|
228
|
+
print(f"{'=' * 60}")
|
|
229
|
+
print(f"{'Resource':<20} {'Avg Util':<12} {'Avg Queue':<12} {'Avg Wait':<12}")
|
|
230
|
+
print(f"{'-' * 20} {'-' * 12} {'-' * 12} {'-' * 12}")
|
|
231
|
+
|
|
232
|
+
for name, monitor in self.monitors.items():
|
|
233
|
+
print(f"{name:<20} {monitor.average_utilization():<12.2%} "
|
|
234
|
+
f"{monitor.average_queue_length():<12.2f} "
|
|
235
|
+
f"{monitor.average_wait_time():<12.2f}")
|
|
236
|
+
|
|
237
|
+
print(f"{'=' * 60}")
|
|
238
|
+
|
|
239
|
+
|
|
240
|
+
class ContainerMonitor:
|
|
241
|
+
"""Monitor Container resources (for tracking level changes)."""
|
|
242
|
+
|
|
243
|
+
def __init__(self, env: simpy.Environment, container: simpy.Container, name: str = "Container"):
|
|
244
|
+
"""
|
|
245
|
+
Initialize container monitor.
|
|
246
|
+
|
|
247
|
+
Args:
|
|
248
|
+
env: SimPy environment
|
|
249
|
+
container: Container to monitor
|
|
250
|
+
name: Name for the container
|
|
251
|
+
"""
|
|
252
|
+
self.env = env
|
|
253
|
+
self.container = container
|
|
254
|
+
self.name = name
|
|
255
|
+
self.level_data: List[Tuple[float, float]] = [(0, container.level)]
|
|
256
|
+
|
|
257
|
+
self._patch_container()
|
|
258
|
+
|
|
259
|
+
def _patch_container(self):
|
|
260
|
+
"""Patch container methods to track level changes."""
|
|
261
|
+
original_put = self.container.put
|
|
262
|
+
original_get = self.container.get
|
|
263
|
+
|
|
264
|
+
def monitored_put(amount):
|
|
265
|
+
result = original_put(amount)
|
|
266
|
+
|
|
267
|
+
def on_put(event):
|
|
268
|
+
self.level_data.append((self.env.now, self.container.level))
|
|
269
|
+
|
|
270
|
+
result.callbacks.append(on_put)
|
|
271
|
+
return result
|
|
272
|
+
|
|
273
|
+
def monitored_get(amount):
|
|
274
|
+
result = original_get(amount)
|
|
275
|
+
|
|
276
|
+
def on_get(event):
|
|
277
|
+
self.level_data.append((self.env.now, self.container.level))
|
|
278
|
+
|
|
279
|
+
result.callbacks.append(on_get)
|
|
280
|
+
return result
|
|
281
|
+
|
|
282
|
+
self.container.put = monitored_put
|
|
283
|
+
self.container.get = monitored_get
|
|
284
|
+
|
|
285
|
+
def average_level(self) -> float:
|
|
286
|
+
"""Calculate time-weighted average level."""
|
|
287
|
+
if len(self.level_data) < 2:
|
|
288
|
+
return self.level_data[0][1] if self.level_data else 0.0
|
|
289
|
+
|
|
290
|
+
total_time = 0.0
|
|
291
|
+
weighted_sum = 0.0
|
|
292
|
+
|
|
293
|
+
for i in range(len(self.level_data) - 1):
|
|
294
|
+
time1, level1 = self.level_data[i]
|
|
295
|
+
time2, level2 = self.level_data[i + 1]
|
|
296
|
+
duration = time2 - time1
|
|
297
|
+
total_time += duration
|
|
298
|
+
weighted_sum += level1 * duration
|
|
299
|
+
|
|
300
|
+
return weighted_sum / total_time if total_time > 0 else 0.0
|
|
301
|
+
|
|
302
|
+
def report(self):
|
|
303
|
+
"""Print container statistics."""
|
|
304
|
+
print(f"\n{'=' * 60}")
|
|
305
|
+
print(f"CONTAINER MONITOR REPORT: {self.name}")
|
|
306
|
+
print(f"{'=' * 60}")
|
|
307
|
+
print(f"Capacity: {self.container.capacity}")
|
|
308
|
+
print(f"Current level: {self.container.level:.2f}")
|
|
309
|
+
print(f"Average level: {self.average_level():.2f}")
|
|
310
|
+
print(f"Utilization: {self.average_level() / self.container.capacity:.2%}")
|
|
311
|
+
|
|
312
|
+
if self.level_data:
|
|
313
|
+
levels = [level for _, level in self.level_data]
|
|
314
|
+
print(f"Max level: {max(levels):.2f}")
|
|
315
|
+
print(f"Min level: {min(levels):.2f}")
|
|
316
|
+
|
|
317
|
+
print(f"{'=' * 60}")
|
|
318
|
+
|
|
319
|
+
|
|
320
|
+
# Example usage
|
|
321
|
+
if __name__ == "__main__":
|
|
322
|
+
def example_process(env, name, resource, duration):
|
|
323
|
+
"""Example process using a resource."""
|
|
324
|
+
with resource.request() as req:
|
|
325
|
+
yield req
|
|
326
|
+
print(f"{name} started at {env.now}")
|
|
327
|
+
yield env.timeout(duration)
|
|
328
|
+
print(f"{name} finished at {env.now}")
|
|
329
|
+
|
|
330
|
+
# Create environment and resource
|
|
331
|
+
env = simpy.Environment()
|
|
332
|
+
resource = simpy.Resource(env, capacity=2)
|
|
333
|
+
|
|
334
|
+
# Create monitor
|
|
335
|
+
monitor = ResourceMonitor(env, resource, "Example Resource")
|
|
336
|
+
|
|
337
|
+
# Start processes
|
|
338
|
+
for i in range(5):
|
|
339
|
+
env.process(example_process(env, f"Process {i}", resource, 3 + i))
|
|
340
|
+
|
|
341
|
+
# Run simulation
|
|
342
|
+
env.run()
|
|
343
|
+
|
|
344
|
+
# Generate report
|
|
345
|
+
monitor.report()
|