[Python] How can I maintain formatting while updating a yaml file using ruamel?

I have a multi-document YAML file. I am interested in modifying the third document only (this modification will be later made using other code and conditions). After some research, I selected ruamel since it was reported to preserve order and format.

My YAML looks like this (not including the whole thing since it is more than 3000 lines long):

---
"SOURCE": "mmmmm"
"VERSION": "5.4.2"
"DATE_WRITTEN": "Tue Oct 25 06:09:34 2022"
"CONFIG_CHECKSUM": "0XCD44F064"
"CONFIG_SIZE": "231212"
...
---
"moduleVersion": ["5.4.2 (AUG 2022)", "20:FIO w/2070-2A"]
"moduleModel": ["mmmmm", "mmmmm Linux Actuated Controller Unit"]
"maxPhases": 16
"maxVehicleDetectors": 72
"maxPedestrianDetectors": 8
"etcsAscPhsBanksMax": 4
"maxOverlaps": 16
"maxRings": 4
"etcsAscPriorityBanksMax": 4
"etcsAscMaxPriorityQueues": 6
"maxPatterns": 253
"etcsAscSFMapsMaskSize": 16
"etcsAscPFMapsMaskSize": 16
"etcsMaxSpcFuncMaps": 47
"etcsMaxPhsFuncMaps": 192
"maxTimebaseAscActions": 255
"maxTimebaseScheduleEntries": 255
"maxDayPlanEvents": 15
"maxDayPlans": 255
"maxDaylightSavingEntries": 2
"rs232Number": 3
"maxSequences": 16
"etcsAscMaxSerialPorts": 2
"maxChannels": 32
"ipAdEntAddr": [[192, 168, 1, 100], [192, 168, 0, 77]]
"etcsAscMaxSpatDestinations": 16
"etcsUnitBankMax": 4
"etcsMaxOutputLoadswitches": 32
"etcsPeerFunctionMax": 64
"etcsAscMaxPriorities": 12
"maxSplits": 253
"maxPreempts": 12
...
---
"phaseWalk": [0, 7, 0, 7, 0, 7, 0, 7, 0, 0, 0, 0, 0, 0, 0, 7]
"phasePedestrianClear": [0, 28, 0, 32, 0, 28, 0, 32, 0, 0, 0, 0, 0, 0, 0, 32]
"phaseMinimumGreen": [5, 7, 5, 7, 5, 7, 5, 7, 0, 0, 0, 0, 0, 0, 0, 7]
"phasePassage": [20, 10, 20, 25, 20, 10, 20, 25, 0, 0, 0, 0, 0, 0, 0, 0]
"phaseMaximum1": [5, 25, 5, 15, 5, 25, 5, 15, 0, 0, 0, 0, 0, 0, 0, 0]
"phaseMaximum2": [20, 0, 20, 55, 20, 0, 20, 65, 0, 0, 0, 0, 0, 0, 0, 0]
"phaseYellowChange": [44, 44, 40, 40, 44, 44, 40, 40, 0, 0, 0, 0, 0, 0, 0, 30]
"phaseRedClear": [20, 20, 26, 26, 20, 20, 26, 26, 0, 0, 0, 0, 0, 0, 0, 0]
"phaseAddedInitial": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
"phaseMaximumInitial": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
"phaseTimeBeforeReduction": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
"phaseCarsBeforeReduction": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
"phaseTimeToReduce": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
"phaseMinimumGap": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
"phaseDynamicMaxLimit": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
"phaseDynamicMaxStep": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
"phaseStartup": [2, 3, 2, 2, 2, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2]
"phaseOptions": [33, 165, 33, 1059, 33, 165, 33, 1059, 0, 0, 0, 0, 0, 0, 0, 1]
"phaseConcurrency": [[5, 6], [5, 6], [7, 8], [7, 8], [1, 2], [1, 2], [3, 4], [3, 4], [], [], [], [], [], [], [], []]
"etcsAscPhaseFlashWalk": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
"etcsAscPhaseExtPedClear": [0, 3, 0, 3, 0, 3, 0, 3, 0, 0, 0, 0, 0, 0, 0, 3]


This is the code I have:

#importing the yaml
directory = input("Please enter the directory path: ")
yml_file = glob.glob('*.yaml')
import ruamel.yaml

try:
# Create a new YAML object
yaml = ruamel.yaml.YAML()
# Open the YAML file in read-write mode
with open(yml_file[0], 'r+') as file:
# Load the YAML documents using the ruamel.yaml.safe_load() method
data = list(yaml.load_all(file))
# Get the third document
doc3 = data[2]
# Make changes to the third document
doc3["phaseWalk"][0] == 5
# Seek to the beginning of the file
file.seek(0)
# Overwrite the file with the updated documents
yaml.dump_all(data, file)
file.write("...\n")
# Close the file
file.truncate()

except FileNotFoundError:
print("The file 'file.yaml' was not found.")

except PermissionError:
print("You do not have permission to write to the file 'file.yaml'.")

except Exception as e:
print(f"An unexpected error occurred: {e}")


It yields the following YAML:

SOURCE: mmmmm
VERSION: 5.4.2
DATE_WRITTEN: Tue Oct 25 06:09:34 2022
CONFIG_CHECKSUM: 0XCD44F064
CONFIG_SIZE: '231212'
---
moduleVersion: [5.4.2 (AUG 2022), 20:FIO w/2070-2A]
moduleModel: [mmmmm, mmmmm Linux Actuated Controller Unit]
maxPhases: 16
maxVehicleDetectors: 72
maxPedestrianDetectors: 8
etcsAscPhsBanksMax: 4
maxOverlaps: 16
maxRings: 4
etcsAscPriorityBanksMax: 4
etcsAscMaxPriorityQueues: 6
maxPatterns: 253
etcsAscSFMapsMaskSize: 16
etcsAscPFMapsMaskSize: 16
etcsMaxSpcFuncMaps: 47
etcsMaxPhsFuncMaps: 192
maxTimebaseAscActions: 255
maxTimebaseScheduleEntries: 255
maxDayPlanEvents: 15
maxDayPlans: 255
maxDaylightSavingEntries: 2
rs232Number: 3
maxSequences: 16
etcsAscMaxSerialPorts: 2
maxChannels: 32
ipAdEntAddr: [[192, 168, 1, 100], [192, 168, 0, 77]]
etcsAscMaxSpatDestinations: 16
etcsUnitBankMax: 4
etcsMaxOutputLoadswitches: 32
etcsPeerFunctionMax: 64
etcsAscMaxPriorities: 12
maxSplits: 253
maxPreempts: 12
---
phaseWalk: [0, 7, 0, 7, 0, 7, 0, 7, 0, 0, 0, 0, 0, 0, 0, 7]
phasePedestrianClear: [0, 28, 0, 32, 0, 28, 0, 32, 0, 0, 0, 0, 0, 0, 0, 32]
phaseMinimumGreen: [5, 7, 5, 7, 5, 7, 5, 7, 0, 0, 0, 0, 0, 0, 0, 7]
phasePassage: [20, 10, 20, 25, 20, 10, 20, 25, 0, 0, 0, 0, 0, 0, 0, 0]
phaseMaximum1: [5, 25, 5, 15, 5, 25, 5, 15, 0, 0, 0, 0, 0, 0, 0, 0]
phaseMaximum2: [20, 0, 20, 55, 20, 0, 20, 65, 0, 0, 0, 0, 0, 0, 0, 0]
phaseYellowChange: [44, 44, 40, 40, 44, 44, 40, 40, 0, 0, 0, 0, 0, 0, 0, 30]
phaseRedClear: [20, 20, 26, 26, 20, 20, 26, 26, 0, 0, 0, 0, 0, 0, 0, 0]
phaseAddedInitial: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
phaseMaximumInitial: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
phaseTimeBeforeReduction: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
phaseCarsBeforeReduction: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
phaseTimeToReduce: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
phaseMinimumGap: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
phaseDynamicMaxLimit: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
phaseDynamicMaxStep: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
phaseStartup: [2, 3, 2, 2, 2, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2]
phaseOptions: [33, 165, 33, 1059, 33, 165, 33, 1059, 0, 0, 0, 0, 0, 0, 0, 1]
phaseConcurrency: [[5, 6], [5, 6], [7, 8], [7, 8], [1, 2], [1, 2], [3, 4], [3, 4],
[], [], [], [], [], [], [], []]
etcsAscPhaseFlashWalk: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
etcsAscPhaseExtPedClear: [0, 3, 0, 3, 0, 3, 0, 3, 0, 0, 0, 0, 0, 0, 0, 3]


The issues I have with this:

1. Where is the first 3 dashes for the first document?
2. Why have the data types been changed? Most of my data types were defined as strings. They're no longer that way.
3. The modification to the third document did not take effect? Am I doing anything wrong?

I am running ruamel v 0.17.21

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