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

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

The CI failure in PR #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 #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 <noreply@anthropic.com>

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: