Investigate CI failure in pyopenms-docs PR (OpenMS#489)

* Fix RST indentation bug in interactive_plots.rst for PR OpenMS#480

The CI failure in PR OpenMS#480 was caused by broken indentation in
interactive_plots.rst. The hd.dynspread(...) block was at column 0
instead of being indented with 4 spaces, placing it outside the
RST code-block directive.

When notebooks are generated from this RST file, the unindented code
becomes markdown text instead of Python code, causing notebook
execution to fail.

This commit applies the PR OpenMS#480 changes (PeptideIdentificationList,
get2DPeakDataLong 5th arg, refactored opts) with correct indentation.

* Remove broken setIntensityRange call in interactive_plots.rst

The DRange1 API changed in pyopenms 3.5.0 and no longer accepts
DPosition1 objects in its constructor. The setIntensityRange call
was causing a runtime error:

  Exception: can not handle type of (DPosition1, DPosition1)

Since intensity range filtering is optional for this visualization,
the simplest fix is to remove the call entirely. This also removes
the now-unused 'import sys' statement.

* Use ThresholdMower for intensity filtering in interactive_plots.rst

The DRange1(DPosition1, DPosition1) constructor is broken in pyopenms
3.5.0, causing setIntensityRange to fail with:

  Exception: can not handle type of (DPosition1, DPosition1)

This is a workaround that uses ThresholdMower to filter peaks with
intensity < 5000 after loading, achieving the same effect as the
original setIntensityRange call.

---------

Co-authored-by: Claude <[email protected]>

Author: timosachsenberg

docs/source/user_guide/interactive_plots.rst

@@ -19,7 +19,6 @@ interactively zoomed-in if you execute the code in a notebook
     import holoviews.operation.datashader as hd
     from holoviews.plotting.util import process_cmap
     from holoviews import opts, dim
-    import sys
 
     hv.extension("bokeh")
 
@@ -29,13 +28,20 @@ interactively zoomed-in if you execute the code in a notebook
     loadopts.setMSLevels([1])
     loadopts.setSkipXMLChecks(True)
     loadopts.setIntensity32Bit(True)
-    loadopts.setIntensityRange(oms.DRange1(oms.DPosition1(5000), oms.DPosition1(sys.maxsize)))
     loader.setOptions(loadopts)
     loader.load("../../../src/data/BSA1.mzML", exp)
+
+    # Filter out low-intensity peaks using ThresholdMower
+    threshold_filter = oms.ThresholdMower()
+    params = threshold_filter.getDefaults()
+    params.setValue(b"threshold", 5000.0)
+    threshold_filter.setParameters(params)
+    threshold_filter.filterPeakMap(exp)
+
     exp.updateRanges()
     expandcols = ["RT", "mz", "inty"]
     spectraarrs2d = exp.get2DPeakDataLong(
-        exp.getMinRT(), exp.getMaxRT(), exp.getMinMZ(), exp.getMaxMZ()
+        exp.getMinRT(), exp.getMaxRT(), exp.getMinMZ(), exp.getMaxMZ(), 1
     )
     spectradf = pd.DataFrame(dict(zip(expandcols, spectraarrs2d)))
     spectradf = spectradf.set_index(["RT", "mz"])
@@ -75,17 +81,14 @@ interactively zoomed-in if you execute the code in a notebook
             min_alpha=0,
         )
         .opts(active_tools=["box_zoom"], tools=["hover"], hooks=[new_bounds_hook])
-        .opts(  # weird.. I have no idea why one has to do this. But with one opts you will get an error
-            plot=dict(
-                width=800,
-                height=800,
-                xlabel="Retention time (s)",
-                ylabel="mass/charge (Da)",
-            )
-        )
     )
 
-    hd.dynspread(raster, threshold=0.7, how="add", shape="square")
+    hd.dynspread(raster, threshold=0.7, how="add", shape="square").opts(
+        width=800,
+        height=800,
+        xlabel="Retention time (s)",
+        ylabel="mass/charge (Da)",
+    )
 
 
 Result: