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

TL;DR; skip to text after horizontal line

Various parts of a YAML document are optional depending on the circumstances,
and likelwise the separation of documents in a multi-document file
has optional parts.

Historically ruamel.yaml started out with (only) dealing with preserving end-of-line comments that
were dropped by PyYAML, by combining PyYAMLs separate but largely overlapping sources for Python 2 and 3 (so
changes would only have to be made in one place) and then adding the code that preserved the comments. (The
source combination changes and those for YAML 1.2 support were first offered as PR requests to PyYAML, but were ignored, forcing me to fork)

Other things, like indenteation, were "normalised", i.e. made the same everywhere. Indentation
is still normalised, although you now have seperate indentation control for mappings and sequences.

Normalisation often does away with superfluous elements: such extra spaces between elements in a sequence.
Most of these normalisations, including removing comments, were in the original PyYAML code. Given
that parsing YAML is a multi-step process (scanning, tokenizing, compositing the structure, generating Python objects)
and if something is discarded during scanning, you might imagine the complexity of adding changes that the discarded
information. Additionally, although PyYAML works internally with instances of various classes adding
one extra parameter to a load or dump function, e.g. to optionally preserve quotes around scalars,
required changes in multiple files in multiple locations each. So that is why ruamel.yaml switched to using
a YAML() instance on which you can set attributes (and the the underlying code can query as necessary).

Apart from adding such code largely depending on the lazy-ness of ruamel.yaml‘s main developer, there is also
the question for some aspect of YAML round-tripping, whether to use PyYAML’s original normalisations,
make normalisations optional or always preserve. Apart from ease of implementation, the answer might depend on
personal preference, and decision either way were not always made consistent.

Things that were added later to ruamel.yaml are preservation of integer/float formats; of literal scalars (initially)
and quoted/folded scalars; space after colon for root level mappings. Some of these preservations are always
supplied, some depend on setting attributes on the YAML() instance.

---

Given that context, the short answer is that superfluous quotes around scalars are dropped unless you
set .preserve_quotes (otherwise they are normalised away), and that the end-of-document marker (...)
doesn’t get preserved when not necessary (i.e. when there are directives like %YAML 1.2 ), unless you set .explicit_end.
So you will have to tell your YAML() instance what you want explicitly.

(That you still have quotes around the value for CONFIG_SIZE is by the value otherwise being interpreted as
a number.)

I normally don’t overwrite an input file until I know the changes are correct (it is a pain when
they are partially what you want and you have to restore the input before the next test run)

The line doc3["phaseWalk"][0] == 5 evaluates to False and has no further side-effects, so
of course there is no modification of the first element of the value for key phaseWalk, and nothing gets updated.

If you run:

import sys
import ruamel.yaml
import pathlib

path = next(Path('.').glob('*.yaml'))  # first matching path
    
yaml = ruamel.yaml.YAML()
# yaml.indent(mapping=4, sequence=4, offset=2)  # this is the default, doesn't affect your code
yaml.preserve_quotes = True  # added in ruamel.yaml
yaml.explicit_start = True   # control also available in PyYAML
yaml.explicit_end = True     # control also available in PyYAML

data = list(yaml.load_all(path))
doc3 = data[2]
doc3['phaseWalk'][0] = 5    # single '=' for assignment
yaml.dump_all(data, sys.stdout)   # yaml.dump_all(data, path) -> overwrite original file

which gives:

---
"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": [5, 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]
...

Please realise that both your YAML output and your input load to the same internal data structure in
normal circumstances (the round-trip parser that ruamel.yaml implements is an exception). So
for practical purposes you should not care about dropped quotes unless you have to deal with a parser
that is non-compliant wrt the YAML specification.

If you don’t want such changes because of comparison difficulties, or you don’t want such extra changes in a repository,
you should consider to bite (byte?) the bullet, just what you would have to do if you run a code
formatter (such as oitnb) on your source code.