From 118be27f62fe089a2bf6051960f58dd485cd3998 Mon Sep 17 00:00:00 2001
From: Egor Marin <marinegor@fastmail.com>
Date: Fri, 23 Feb 2024 15:58:45 +0100
Subject: [PATCH] Fix code formatting and add coverage exceptions

---
 package/MDAnalysis/analysis/dssp/dssp.py      | 35 +++++++------------
 .../MDAnalysis/analysis/dssp/pydssp_numpy.py  | 10 +++---
 2 files changed, 18 insertions(+), 27 deletions(-)

diff --git a/package/MDAnalysis/analysis/dssp/dssp.py b/package/MDAnalysis/analysis/dssp/dssp.py
index 0fe1e75d59..fdce81c586 100644
--- a/package/MDAnalysis/analysis/dssp/dssp.py
+++ b/package/MDAnalysis/analysis/dssp/dssp.py
@@ -233,16 +233,12 @@ class DSSP(AnalysisBase):
 
     For example, you can assign secondary structure for a single PDB file:
 
-    .. code-block:: python
-        from MDAnalysis.analysis.dssp import DSSP
-        from MDAnalysisTests.datafiles import PDB
-        import MDAnalysis as mda
-        u = mda.Universe(PDB)
-        run = DSSP(u).run()
-        print("".join(run.results.dssp[0][:20]))
-
-    Running this code produces ::
-
+    >>> from MDAnalysis.analysis.dssp import DSSP
+    >>> from MDAnalysisTests.datafiles import PDB
+    >>> import MDAnalysis as mda
+    >>> u = mda.Universe(PDB)
+    >>> run = DSSP(u).run()
+    >>> print("".join(run.results.dssp[0][:20]))
     '--EEEEE-----HHHHHHHH'
 
     Also, per-frame dssp assignment allows you to build average
@@ -250,18 +246,13 @@ class DSSP(AnalysisBase):
     (n_frames, n_residues, 3) shape ndarray with one-hot encoding of
     loop, helix and sheet, respectively:
 
-    .. code-block:: python
-
-        from MDAnalysis.analysis.dssp import translate
-        u = mda.Universe(...)
-        long_run = DSSP(u).run()
-        mean_secondary_structure = translate(
-            long_run.results.dssp_ndarray.mean(axis=0)
-            )
-        print(''.join(mean_secondary_structure)[:20])
-    
-    Running this code produces ::
-
+    >>> from MDAnalysis.analysis.dssp import translate
+    >>> u = mda.Universe(...)
+    >>> long_run = DSSP(u).run()
+    >>> mean_secondary_structure = translate(
+    >>>     long_run.results.dssp_ndarray.mean(axis=0)
+    >>>     )
+    >>> print(''.join(mean_secondary_structure)[:20])
     '---HHHHHHHH---------'
 
     .. versionadded:: 2.8.0
diff --git a/package/MDAnalysis/analysis/dssp/pydssp_numpy.py b/package/MDAnalysis/analysis/dssp/pydssp_numpy.py
index c7fee8a555..f46a76d40b 100644
--- a/package/MDAnalysis/analysis/dssp/pydssp_numpy.py
+++ b/package/MDAnalysis/analysis/dssp/pydssp_numpy.py
@@ -17,7 +17,7 @@
 DEFAULT_MARGIN = 1.0
 
 
-def _upsample(a: np.ndarray, window: int) -> np.ndarray:
+def _upsample(a: np.ndarray, window: int) -> np.ndarray:  # pragma: no cover
     """Performs array upsampling with given window along given axis.
 
     Example
@@ -63,14 +63,14 @@ def _upsample(a: np.ndarray, window: int) -> np.ndarray:
     return _unfold(_unfold(a, window, -2), window, -2)
 
 
-def _unfold(a: np.ndarray, window: int, axis: int):
+def _unfold(a: np.ndarray, window: int, axis: int):  # pragma: no cover
     "Helper function for 2D array upsampling"
     idx = np.arange(window)[:, None] + np.arange(a.shape[axis] - window + 1)[None, :]
     unfolded = np.take(a, idx, axis=axis)
     return np.moveaxis(unfolded, axis - 1, -1)
 
 
-def _get_hydrogen_atom_position(coord: np.ndarray) -> np.ndarray:
+def _get_hydrogen_atom_position(coord: np.ndarray) -> np.ndarray:  # pragma: no cover
     """Fills in hydrogen atoms positions if they are abscent, under the
     assumption that C-N-H and H-N-CA angles are perfect 120 degrees,
     and N-H bond length is 1.01 A.
@@ -118,7 +118,7 @@ def get_hbond_map(
     cutoff: float = DEFAULT_CUTOFF,
     margin: float = DEFAULT_MARGIN,
     return_e: bool = False,
-) -> np.ndarray:
+) -> np.ndarray:  # pragma: no cover
     """Returns hydrogen bond map
 
     Parameters
@@ -200,7 +200,7 @@ def get_hbond_map(
     return hbond_map
 
 
-def assign(coord: np.ndarray) -> np.ndarray:
+def assign(coord: np.ndarray) -> np.ndarray:  # pragma: no cover
     """Assigns secondary structure for a given coordinate array,
     either with or without assigned hydrogens