From df3c37603098f21bec64e2396e4fc9daa302e5f5 Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Sun, 27 Oct 2024 21:19:03 +0100
Subject: [PATCH 1/5] Update test_base.py

Added pytest case where both frames and start/stop/step are present to raise valueerror
---
 testsuite/MDAnalysisTests/analysis/test_base.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/testsuite/MDAnalysisTests/analysis/test_base.py b/testsuite/MDAnalysisTests/analysis/test_base.py
index 68b86fc943..de747e35fd 100644
--- a/testsuite/MDAnalysisTests/analysis/test_base.py
+++ b/testsuite/MDAnalysisTests/analysis/test_base.py
@@ -121,6 +121,14 @@ def test_incompatible_n_workers(u):
     with pytest.raises(ValueError):
         FrameAnalysis(u).run(backend=backend, n_workers=3)
 
+def test_frame_values_incompatability(u):
+    start, stop, step = 0, 4, 1
+    frames = [1, 2, 3, 4]
+
+    with pytest.raises(ValueError, match="start/stop/step cannot be combined with frames"):
+        FrameAnalysis(u.trajectory).run(frames=frames, start=start, stop=stop, step=step)
+
+
 @pytest.mark.parametrize('run_class,backend,n_workers', [
     (Parallelizable, 'not-existing-backend', 2),
     (Parallelizable, 'not-existing-backend', None),

From 664ac4e204ec437b57408bd70877a8879fe0bbfe Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Sun, 27 Oct 2024 21:23:16 +0100
Subject: [PATCH 2/5] Update CHANGELOG

Updated changelog to add coverage of raise error case where frames and start/stop/step are present
---
 package/CHANGELOG | 1 +
 1 file changed, 1 insertion(+)

diff --git a/package/CHANGELOG b/package/CHANGELOG
index 892e47d385..fc4782566f 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -82,6 +82,7 @@ Enhancements
    (Issue #4673) 
  * enables parallelization for analysis.dssp.dssp.DSSP (Issue #4674)
  * Enables parallelization for analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis (Issue #4664)
+ * Added pytest case to cover Raise errors cases frames and step/stop/step are present (Issue #4648)
  * Improve error message for `AtomGroup.unwrap()` when bonds are not present.(Issue #4436, PR #4642)
  * Add `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP)
  * Added a tqdm progress bar for `MDAnalysis.analysis.pca.PCA.transform()`

From 91eef3e4647ec0b0943068e1a64924162d83e4f0 Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Sun, 27 Oct 2024 21:43:27 +0100
Subject: [PATCH 3/5] Update test_base.py

---
 testsuite/MDAnalysisTests/analysis/test_base.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/testsuite/MDAnalysisTests/analysis/test_base.py b/testsuite/MDAnalysisTests/analysis/test_base.py
index de747e35fd..ead6e84c75 100644
--- a/testsuite/MDAnalysisTests/analysis/test_base.py
+++ b/testsuite/MDAnalysisTests/analysis/test_base.py
@@ -121,13 +121,19 @@ def test_incompatible_n_workers(u):
     with pytest.raises(ValueError):
         FrameAnalysis(u).run(backend=backend, n_workers=3)
 
+
 def test_frame_values_incompatability(u):
     start, stop, step = 0, 4, 1
     frames = [1, 2, 3, 4]
 
-    with pytest.raises(ValueError, match="start/stop/step cannot be combined with frames"):
-        FrameAnalysis(u.trajectory).run(frames=frames, start=start, stop=stop, step=step)
-
+    with pytest.raises(ValueError, 
+                       match="start/stop/step cannot be combined with frames"):
+        FrameAnalysis(u.trajectory).run(
+            frames=frames,
+            start=start,
+            stop=stop,
+            step=step
+        )
 
 @pytest.mark.parametrize('run_class,backend,n_workers', [
     (Parallelizable, 'not-existing-backend', 2),

From 24a65d671d0e054fb170e6a70a918d43e0f4b598 Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Sun, 27 Oct 2024 21:44:11 +0100
Subject: [PATCH 4/5] Update test_base.py

---
 testsuite/MDAnalysisTests/analysis/test_base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/testsuite/MDAnalysisTests/analysis/test_base.py b/testsuite/MDAnalysisTests/analysis/test_base.py
index ead6e84c75..c3d356a770 100644
--- a/testsuite/MDAnalysisTests/analysis/test_base.py
+++ b/testsuite/MDAnalysisTests/analysis/test_base.py
@@ -126,7 +126,7 @@ def test_frame_values_incompatability(u):
     start, stop, step = 0, 4, 1
     frames = [1, 2, 3, 4]
 
-    with pytest.raises(ValueError, 
+    with pytest.raises(ValueError,
                        match="start/stop/step cannot be combined with frames"):
         FrameAnalysis(u.trajectory).run(
             frames=frames,

From 29d4da927a9d30c0f0e4b714a4bf13e23e1dfc5c Mon Sep 17 00:00:00 2001
From: Valerij Talagayev <82884038+talagayev@users.noreply.github.com>
Date: Mon, 28 Oct 2024 10:06:30 +0100
Subject: [PATCH 5/5] Update CHANGELOG

removed Changelog change
---
 package/CHANGELOG | 1 -
 1 file changed, 1 deletion(-)

diff --git a/package/CHANGELOG b/package/CHANGELOG
index fc4782566f..892e47d385 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -82,7 +82,6 @@ Enhancements
    (Issue #4673) 
  * enables parallelization for analysis.dssp.dssp.DSSP (Issue #4674)
  * Enables parallelization for analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis (Issue #4664)
- * Added pytest case to cover Raise errors cases frames and step/stop/step are present (Issue #4648)
  * Improve error message for `AtomGroup.unwrap()` when bonds are not present.(Issue #4436, PR #4642)
  * Add `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP)
  * Added a tqdm progress bar for `MDAnalysis.analysis.pca.PCA.transform()`