Merge pull request #181 from iterorganization/revert-reference

Revert "Load values from external IDSes" PR#170

Author: SBlokhuizen

docs/source/examples/imports.yaml

@@ -8,8 +8,6 @@ This document describes the different types of tendencies available in the Wavef
 
 Each tendency defines the behavior of the signal over a specific time interval. You can chain multiple tendencies together to create complex waveforms.
 
-If ``type`` is omitted it is inferred from the entry's keys: ``ref`` → :ref:`import <import-tendency>`, ``to`` → linear, ``time`` → :ref:`piecewise <piecewise-linear-tendency>`, ``value`` → constant; anything else defaults to ``linear`` (so a ``from``-only, ``rate``-only, or bare segment is still a linear ramp). Tendencies with no distinguishing key -- the periodic shapes, ``smooth``, and a value-less ``constant`` -- must name their ``type`` explicitly.
-
 Common Time Parameters
 ======================
 
@@ -190,48 +188,6 @@ Parameters
 .. warning::
     This tendency does **not** accept the common ``start``, ``duration``, or ``end`` parameters. These are derived directly from the required ``time`` list.
 
-.. _import-tendency:
-
-Import
-======
-
-Takes its values from an external entry in :ref:`globals.imports <global_properties>` instead of an analytic shape, resampled onto the export time base. By default it reads the waveform's own DD path.
-
-*Type:* ``import`` (inferred when ``ref`` is present)
-
-Parameters
-----------
-*   ``ref``: Entry in ``globals.imports`` to read from.
-*   ``path``: DD path to read. Defaults to the waveform's own path.
-*   ``time_offset``: Offset added to the export time when sampling. Defaults to ``0``.
-*   ``interp``: Resampling mode: ``closest`` (default), ``linear`` or ``previous``.
-
-.. code-block:: yaml
-
-    core_sources/source(1)/profiles_1d/electrons/energy:
-      - {ref: scenario, interp: linear}
-
-Wildcards expand against the source: a trailing ``*`` imports a whole subtree (``<ids>/*`` copies a whole IDS), and a ``(*)`` index wildcard iterates every element of an array of structure -- several may be combined, e.g. every ion of every source. An overlay may list several sources, applied in order:
-
-.. code-block:: yaml
-
-    core_sources/source(*)/profiles_1d/ion(*)/z_ion:
-      - {ref: scenario}
-
-    ec_launchers/*:        # whole-IDS overlay; sources stack
-      - {ref: machine}
-      - {ref: scenario}
-
-**Precedence.** Where imports or explicit waveforms write the same node, the most specific wins regardless of order: ``<ids>/*`` < subtree ``.../*`` < explicit leaf. Equal specificity falls back to listing order (last wins).
-
-Non-0D imports (a profile, a wildcard subtree) own the whole waveform. Only **0D (scalar)** imports combine with analytic segments, each filling its ``[start, end]`` window:
-
-.. code-block:: yaml
-
-    equilibrium/time_slice/global_quantities/ip:
-      - {type: constant, value: -1.0, duration: 1}   # analytic on [0, 1] s
-      - {ref: scenario, duration: 1}                 # imported on [1, 2] s
-
 Periodic Tendencies
 ===================
 

docs/source/tendencies.rst

@@ -50,29 +50,21 @@ These parameters can be changed under the "Edit Global Properties" tab in the GU
        globals:
          dd_version: 3.42.0
 
-*   **imports:** Named external data entries that waveforms read from (see
-    :ref:`Import <import-tendency>`), keyed by names you choose and refer to with
-    ``{ref: <name>}``. Each value is an IMAS URI, or ``{port: <name>}`` for an IDS
-    received on a MUSCLE3 port at run time (used by the actor).
+*   **machine_description:** Provides URIs for IMAS machine description entries.
+    The machine descriptions are relevant when you :ref:`export a waveform configuration to an IDS<export-ids>`.
+    When exporting, any existing data from the given machine description will be copied
+    to the new IDS, before the waveforms from the configuration are added.
+    To specify machine descriptions for a target IDS, use a dictionary where keys are 
+    the IDS names and values are their corresponding machine description URIs.
 
     .. code-block:: yaml
 
        globals:
          dd_version: 3.42.0
-         imports:
-           machine: imas:hdf5?path=machine_description1
-           scenario: imas:hdf5?path=scenario_run
-           live_eq: {port: equilibrium_in}
-
-    Overlay a machine-description IDS with an ``<ids>/*`` wildcard import, then override
-    individual nodes.
-
-    .. code-block:: yaml
-
-       ec_launchers:
-         ec_launchers/*:
-           - {ref: machine}                            # overlay base
-         ec_launchers/beam(1)/phase/angle: -1.65898    # then override leaves
+         machine_description:
+           ec_launchers: imas:hdf5?path=machine_description1
+           nbi: imas:hdf5?path=machine_description2
+           # Add other IDSs as needed
 
 Grouping Waveforms
 ------------------
@@ -114,8 +106,6 @@ a list of waveforms, or a single number (float or integer).
                # Implicit linear ramp back to 0 over 25 seconds
              - { duration: 25, to: 0 }
 
-        If ``type`` is omitted it is inferred from the entry's keys: ``ref`` → ``import``, ``to`` → ``linear``, ``time`` → ``piecewise``, ``value`` → ``constant``; anything else defaults to ``linear``. Tendencies with no distinguishing key (the periodic shapes, ``smooth``, a value-less ``constant``) must name their ``type``.
-
         Refer to the :ref:`Available Tendencies <available-tendencies>` documentation for details on the different tendency types and their parameters.
 
     2.  **Constant Value:** A simple number (integer or float) defines a constant waveform over time.
@@ -164,12 +154,4 @@ Slicing can be applied at multiple nested levels. For example, the following fil
 
    interferometer/channel(2:3)/wavelength(1:4)/phase_corrected/data: 15.0
 
-Complete Example
-----------------
-
-The following configuration exercises the full :ref:`imports <import-tendency>` mechanism: a machine-description overlay (``<ids>/*``), a scalar import with interpolation, a static value, trailing-subtree and index wildcards (``source(*)``, ``ion(*)``), a 0D composite, and a runtime port-import.
-
-.. literalinclude:: examples/imports.yaml
-   :language: yaml
-
 

docs/source/yaml_format.rst

@@ -14,7 +14,7 @@ model:
     waveform_actor:
       implementation: waveform_actor
       ports:
-        # An IDS-named input port exposes the received IDS as a port-import:
+        # An IDS-named input port selects overlay mode:
         f_init: equilibrium_in
         # Name of the output port is "<ids_name>_out":
         o_f:

tests/muscle3_integration/overlay.ymmsl.in

@@ -1,13 +1,8 @@
-# Waveform configuration for the overlay example: the equilibrium received on the
-# 'equilibrium_in' port is imported whole (overlay base), then a single plasma-current
-# ramp is written onto every time slice while its other data (the boundary) is kept.
+# Waveform configuration for the overlay example: a single plasma-current ramp that the
+# actor writes onto every time slice of the equilibrium it receives.
 globals:
   dd_version: 4.0.0
-  imports:
-    eq_in: {port: equilibrium_in}
 
 Plasma current:
-  equilibrium/*:
-    - {ref: eq_in}
   equilibrium/time_slice/global_quantities/ip:
     - {type: linear, to: -15e6, duration: 100}

tests/muscle3_integration/overlay_waveforms.yaml

@@ -256,7 +256,7 @@ def test_dump_comments():
     yaml_str = dedent("""
     globals:
       dd_version: 3.42.0
-      imports:
+      machine_description:
         ec_launchers: imas:hdf5?path=test_md
     ec_launchers:
       beams:
@@ -280,12 +280,12 @@ def test_dump_globals():
     config = WaveformConfiguration()
     config.load_yaml(yaml_str)
     config.globals.dd_version = "3.41.0"
-    config.globals.imports = {"ec_launchers": "imas:mdsplus?path=test"}
+    config.globals.machine_description = {"ec_launchers": "imas:mdsplus?path=test"}
     dumped_yaml = config.dump()
     expected_dump = dedent("""
     globals:
       dd_version: 3.41.0
-      imports:
+      machine_description:
         ec_launchers: imas:mdsplus?path=test
     ec_launchers:
       ec_launchers/beam(1)/phase/angle:
@@ -326,23 +326,23 @@ def test_load_yaml_globals():
     yaml_str = """
     globals:
       dd_version: 3.42.0
-      imports: 
+      machine_description: 
         ec_launchers: imas:hdf5?path=testdb
     ec_launchers:
       ec_launchers/beam(1)/phase/angle: 1e-3
     """
     config = WaveformConfiguration()
     config.load_yaml(yaml_str)
     assert config.globals.dd_version == "3.42.0"
-    assert config.globals.imports["ec_launchers"] == "imas:hdf5?path=testdb"
+    assert config.globals.machine_description["ec_launchers"] == "imas:hdf5?path=testdb"
 
     yaml_str = """
     ec_launchers:
       ec_launchers/beam(1)/phase/angle: 1e-3
     """
     config.load_yaml(yaml_str)
     assert config.globals.dd_version == LATEST_DD_VERSION
-    assert not config.globals.imports
+    assert not config.globals.machine_description
 
 
 def test_bounds(config):