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Move various code snippets into their own files
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Lines changed: 645 additions & 441 deletions

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‎_extensions/quarto-ext/include-code-files/_extension.yml‎

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title: Include Code Files
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author: Bruno Beaufils
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version: 1.0.0
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quarto-required: ">=1.2"
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contributes:
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filters:
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- include-code-files.lua
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‎_extensions/quarto-ext/include-code-files/include-code-files.lua‎

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--- include-code-files.lua – filter to include code from source files
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---
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--- Copyright: © 2020 Bruno BEAUFILS
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--- License: MIT – see LICENSE file for details
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--- Dedent a line
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local function dedent(line, n)
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return line:sub(1, n):gsub(" ", "") .. line:sub(n + 1)
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end
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--- Find snippet start and end.
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--
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-- Use this to populate startline and endline.
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-- This should work like pandocs snippet functionality: https://github.com/owickstrom/pandoc-include-code/tree/master
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local function snippet(cb, fh)
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if not cb.attributes.snippet then
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return
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end
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-- Cannot capture enum: http://lua-users.org/wiki/PatternsTutorial
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local comment
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local comment_stop = ""
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if
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string.match(cb.attributes.include, ".py$")
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or string.match(cb.attributes.include, ".jl$")
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or string.match(cb.attributes.include, ".r$")
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then
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comment = "#"
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elseif string.match(cb.attributes.include, ".o?js$") or string.match(cb.attributes.include, ".css$") then
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comment = "//"
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elseif string.match(cb.attributes.include, ".lua$") then
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comment = "--"
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elseif string.match(cb.attributes.include, ".html$") then
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comment = "<!%-%-"
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comment_stop = " *%-%->"
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else
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-- If not known assume that it is something one or two long and not alphanumeric.
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comment = "%W%W?"
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end
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local p_start = string.format("^ *%s start snippet %s%s", comment, cb.attributes.snippet, comment_stop)
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local p_stop = string.format("^ *%s end snippet %s%s", comment, cb.attributes.snippet, comment_stop)
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local start, stop = nil, nil
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-- Cannot use pairs.
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local line_no = 1
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for line in fh:lines() do
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if start == nil then
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if string.match(line, p_start) then
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start = line_no + 1
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end
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elseif stop == nil then
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if string.match(line, p_stop) then
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stop = line_no - 1
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end
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else
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break
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end
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line_no = line_no + 1
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end
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-- Reset so nothing is broken later on.
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fh:seek("set")
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-- If start and stop not found, just continue
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if start == nil or stop == nil then
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return nil
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end
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cb.attributes.startLine = tostring(start)
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cb.attributes.endLine = tostring(stop)
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end
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--- Filter function for code blocks
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local function transclude(cb)
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if cb.attributes.include then
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local content = ""
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local fh = io.open(cb.attributes.include)
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if not fh then
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io.stderr:write("Cannot open file " .. cb.attributes.include .. " | Skipping includes\n")
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else
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local number = 1
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local start = 1
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-- change hyphenated attributes to PascalCase
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for i, pascal in pairs({ "startLine", "endLine" }) do
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local hyphen = pascal:gsub("%u", "-%0"):lower()
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if cb.attributes[hyphen] then
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cb.attributes[pascal] = cb.attributes[hyphen]
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cb.attributes[hyphen] = nil
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end
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end
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-- Overwrite startLine and stopLine with the snippet if any.
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snippet(cb, fh)
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if cb.attributes.startLine then
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cb.attributes.startFrom = cb.attributes.startLine
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start = tonumber(cb.attributes.startLine)
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end
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for line in fh:lines("L") do
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if cb.attributes.dedent then
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line = dedent(line, cb.attributes.dedent)
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end
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if number >= start then
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if not cb.attributes.endLine or number <= tonumber(cb.attributes.endLine) then
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content = content .. line
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end
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end
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number = number + 1
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end
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fh:close()
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end
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-- remove key-value pair for used keys
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cb.attributes.include = nil
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cb.attributes.startLine = nil
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cb.attributes.endLine = nil
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cb.attributes.dedent = nil
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-- return final code block
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return pandoc.CodeBlock(content, cb.attr)
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end
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end
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return {
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{ CodeBlock = transclude },
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}

‎animation_examples/entity_arrival.py‎

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from vidigi.logging import EventLogger
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from vidigi.utils import EventPosition, create_event_position_df
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from vidigi.animation import animate_activity_log
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import simpy
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import numpy as np
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class Patient:
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def __init__(self, p_id):
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self.id = p_id
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class SimpleActivityModel:
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def __init__(self, master_seed=42):
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self.env = simpy.Environment()
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self.patient_counter = 0
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self.logger = EventLogger(env=self.env)
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# Seed setup using numpy's SeedSequence
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self.master_seed = master_seed
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self.seed_seq = np.random.SeedSequence(master_seed)
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self.rng = np.random.default_rng(self.seed_seq)
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def generate_arrivals(self):
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while True:
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self.patient_counter += 1
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p = Patient(self.patient_counter)
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self.logger.log_arrival(entity_id=p.id)
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self.env.process(self.patient_journey(p))
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yield self.env.timeout(3)
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def patient_journey(self, patient):
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self.logger.log_queue(entity_id=patient.id, event="wait_here")
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yield self.env.timeout(70)
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self.logger.log_departure(entity_id=patient.id)
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def run(self):
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self.env.process(self.generate_arrivals())
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self.env.run(until=180)
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model = SimpleActivityModel()
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model.run()
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event_log = model.logger.to_dataframe()
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event_log.to_csv("test_log.csv")
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animate_activity_log(
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event_log = event_log,
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event_position_df = create_event_position_df([
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EventPosition(event="wait_here", x=250 , y=25 , label="Wait Here!"),
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EventPosition(event="depart", x=300, y=10, label="Exit")
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]),
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every_x_time_units=1,
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limit_duration=60,
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override_x_max=300,
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override_y_max=50,
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plotly_height=600,
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plotly_width=1200,
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display_stage_labels=False,
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# time_display_units="%M minutes",
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gap_between_entities=20,
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entity_icon_size=70,
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wrap_queues_at=10,
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simulation_time_unit="minutes",
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debug_write_intermediate_objects=True
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)

‎animation_examples/entity_arrival_varying_rates.py‎

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from vidigi.logging import EventLogger
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from vidigi.utils import EventPosition, create_event_position_df
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from vidigi.animation import animate_activity_log
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import simpy
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import numpy as np
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class Patient:
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def __init__(self, p_id):
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self.id = p_id
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class SimpleActivityModel:
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def __init__(self, master_seed=42):
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self.env = simpy.Environment()
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self.patient_counter = 0
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self.patient_inter = 2
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self.logger = EventLogger(env=self.env)
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# Seed setup using numpy's SeedSequence
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self.master_seed = master_seed
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self.seed_seq = np.random.SeedSequence(master_seed)
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self.rng = np.random.default_rng(self.seed_seq)
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def generate_arrivals(self):
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while True:
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self.patient_counter += 1
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p = Patient(self.patient_counter)
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self.logger.log_arrival(entity_id=p.id)
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self.env.process(self.patient_journey(p))
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sampled_inter = self.rng.exponential(scale=self.patient_inter)
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yield self.env.timeout(sampled_inter)
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def patient_journey(self, patient):
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self.logger.log_queue(entity_id=patient.id, event="wait_here")
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yield self.env.timeout(70)
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self.logger.log_departure(entity_id=patient.id)
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def run(self):
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self.env.process(self.generate_arrivals())
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self.env.run(until=180)
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model = SimpleActivityModel()
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model.run()
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event_log = model.logger.to_dataframe()
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event_log.to_csv("test_log.csv")
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animate_activity_log(
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event_log = event_log,
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event_position_df = create_event_position_df([
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EventPosition(event="wait_here", x=250 , y=25 , label="Wait Here!"),
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EventPosition(event="depart", x=300, y=10, label="Exit")
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]),
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every_x_time_units=1,
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limit_duration=60,
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override_x_max=300,
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override_y_max=50,
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plotly_height=600,
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plotly_width=1200,
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display_stage_labels=False,
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# time_display_units="%M minutes",
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gap_between_entities=20,
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entity_icon_size=70,
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wrap_queues_at=10,
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simulation_time_unit="minutes",
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debug_write_intermediate_objects=True
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)

‎animation_examples/entity_arrival_varying_rates_varying_time_in_system.py‎

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from vidigi.logging import EventLogger
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from vidigi.utils import EventPosition, create_event_position_df
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from vidigi.animation import animate_activity_log
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import simpy
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import numpy as np
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class Patient:
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def __init__(self, p_id):
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self.id = p_id
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class SimpleActivityModel:
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def __init__(self, master_seed=42):
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self.env = simpy.Environment()
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self.patient_counter = 0
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self.patient_inter = 4
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self.logger = EventLogger(env=self.env)
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# Seed setup using numpy's SeedSequence
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self.master_seed = master_seed
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self.seed_seq = np.random.SeedSequence(master_seed)
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self.rng = np.random.default_rng(self.seed_seq)
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def generate_arrivals(self):
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while True:
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self.patient_counter += 1
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p = Patient(self.patient_counter)
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self.logger.log_arrival(entity_id=p.id)
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self.env.process(self.patient_journey(p))
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sampled_inter = self.rng.exponential(scale=self.patient_inter)
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yield self.env.timeout(sampled_inter)
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def patient_journey(self, patient):
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self.logger.log_queue(entity_id=patient.id, event="wait_here")
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yield self.env.timeout(self.rng.uniform(low=1, high=20))
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self.logger.log_departure(entity_id=patient.id)
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def run(self):
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self.env.process(self.generate_arrivals())
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self.env.run(until=180)
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model = SimpleActivityModel()
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model.run()
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event_log = model.logger.to_dataframe()
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event_log.to_csv("test_log.csv")
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animate_activity_log(
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event_log = event_log,
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event_position_df = create_event_position_df([
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EventPosition(event="wait_here", x=250 , y=25 , label="Wait Here!"),
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EventPosition(event="depart", x=300, y=10, label="Exit")
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]),
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every_x_time_units=1,
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limit_duration=60,
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override_x_max=300,
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override_y_max=50,
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plotly_height=600,
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plotly_width=1200,
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display_stage_labels=False,
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# time_display_units="%M minutes",
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gap_between_entities=20,
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entity_icon_size=70,
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wrap_queues_at=10,
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simulation_time_unit="minutes",
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debug_write_intermediate_objects=True
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)

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