Backend abstraction II: rename mds_conn to data_conn to reflect backend-agnostic DataConnection

[samc24]

Summary

• Renamed mds_conn → data_conn, process_mds_conn → process_data_conn, _get_mds_instance → _get_connection_instance to reflect the backend-agnostic DataConnection ABC
  introduced in Backend abstraction I: introduce DataConnection/ProcessConnection ABCs #523
• Renamed public API parameter mds_connection_initializer → connection_initializer in get_shots_data() (takes ProcessConnection, not MDS-specific)
• Updated user-facing docs (physics_method_reference.md, examples/defaults.py, docs/examples/)
• Fixed incomplete get_shots_data() docstring (missing params, stale "from CMOD" wording)

Details

24 files, ~370 line changes. Pure rename + formatting — no behavioral changes.

Test plan

• CI passes (rename is mechanical; no logic changes)
• Bit-identical validation (covered by Backend abstraction I: introduce DataConnection/ProcessConnection ABCs #523 validation, this PR stacks on it)

[gtrevisan]

LGTM! once again, let's merge in a few days, or at the end of the week at the latest.

[Copilot]

Pull request overview

This PR continues the backend-abstraction refactor by renaming MDSplus-specific identifiers (mds_conn, process_mds_conn, mds_connection_initializer, etc.) to backend-agnostic names (data_conn, process_data_conn, connection_initializer) to align with the DataConnection / ProcessConnection ABCs introduced in #523, and updates documentation/examples accordingly.

Changes:

• Renamed mds_conn → data_conn (and related helpers) across core retrieval, settings params, and physics/time/nickname codepaths.
• Renamed get_shots_data() public kwarg mds_connection_initializer → connection_initializer and refreshed the docstring parameter section.
• Added/updated documentation pages and examples to reference DataConnection and the new naming.

Reviewed changes

Copilot reviewed 26 out of 26 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
mkdocs.yml	Adds nav entry for the new DataConnection reference page.
examples/defaults.py	Updates example call to use connection_initializer.
docs/usage/physics_methods/physics_method_reference.md	Updates docs to reference params.data_conn instead of params.mds_conn.
docs/usage/data_connection_reference.md	New reference page for DataConnection/ProcessConnection base interfaces.
docs/examples/custom_time_setting.py	Updates example to use params.data_conn.
docs/examples/custom_physics_method.py	Updates example to use params.data_conn.
disruption_py/workflow.py	Renames initializer kwarg and internal helper/locals to connection-agnostic naming; updates get_shots_data() docstring.
disruption_py/settings/time_setting.py	Renames TimeSettingParams.mds_conn → data_conn and updates call sites.
disruption_py/settings/nickname_setting.py	Renames NicknameSettingParams.mds_conn → data_conn.
disruption_py/machine/mast/physics.py	Renames connection access to params.data_conn.
disruption_py/machine/mast/efit.py	Renames connection access to params.data_conn.
disruption_py/machine/hbtep/physics.py	Renames connection access to params.data_conn.
disruption_py/machine/generic/physics.py	Updates docstrings to say “data connection”.
disruption_py/machine/east/util.py	Renames arg name to data_conn and updates docstrings/calls accordingly.
disruption_py/machine/east/physics.py	Renames connection access to params.data_conn and updates docstrings.
disruption_py/machine/east/efit.py	Renames connection access to params.data_conn and updates docstrings.
disruption_py/machine/d3d/util.py	Updates docstrings and renames connection access to params.data_conn.
disruption_py/machine/d3d/physics.py	Renames connection access to params.data_conn and updates docstrings.
disruption_py/machine/d3d/efit.py	Renames connection access to params.data_conn and updates docstrings.
disruption_py/machine/cmod/thomson.py	Renames connection access to params.data_conn and updates docstrings.
disruption_py/machine/cmod/physics.py	Renames connection access to params.data_conn and updates docstrings.
disruption_py/machine/cmod/efit.py	Renames connection access to params.data_conn and updates docstrings.
disruption_py/core/retrieval_manager.py	Renames process_mds_conn → process_data_conn and propagates data_conn through setup/time init.
disruption_py/core/physics_method/runner.py	Updates reconnect path to use physics_method_params.data_conn.
disruption_py/core/physics_method/params.py	Renames dataclass field mds_conn → data_conn and updates cleanup.
disruption_py/core/physics_method/decorator.py	Updates decorator docstring to refer to data_conn.

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