Automatically renormalize line endings to \n (LF) (Fixes #5315)

.gitattributes

@@ -0,0 +1,6 @@
+# Ensure all line endings for text files are LF (UNIX, Python default) and not CRLF (Windows/DOS default)
+* text=auto eol=lf
+
+# Data files from testsuite/MDAnalysisTests/data/windows/* need to end with CRLF for Windows testing
+testsuite/MDAnalysisTests/data/windows/* text=auto eol=crlf
+

benchmarks/benchmarks/topology.py

@@ -1,47 +1,47 @@
-import MDAnalysis
-import numpy as np
-from MDAnalysis.guesser import DefaultGuesser
-
-try:
-    from MDAnalysis.exceptions import NoDataError
-    from MDAnalysisTests.datafiles import GRO
-except:
-    pass
-
-
-class TopologyGuessBench(object):
-    """Benchmarks for individual
-    topology functions
-    """
-
-    params = (10, 100, 1000, 10000)
-    param_names = ["num_atoms"]
-
-    def setup(self, num_atoms):
-        self.u = MDAnalysis.Universe(GRO)
-        self.ag = self.u.atoms[:num_atoms]
-        self.vdwradii = {"H": 1.0, "C": 1.0, "N": 1.0, "O": 1.0, "DUMMY": 1.0}
-
-    def time_guessbonds(self, num_atoms):
-        """Benchmark for guessing bonds"""
-        DefaultGuesser(None).guess_bonds(
-            self.ag, self.ag.positions, box=self.ag.dimensions, vdwradii=self.vdwradii
-        )
-
-
-class BondsBench(object):
-    """
-    Benchmarks for getting bonds
-    """
-
-    params = (1000, 10000, 100000, 1000000)
-    param_names = ["num_bonds"]
-
-    def setup(self, num_bonds):
-        self.u = MDAnalysis.Universe.empty(2 * num_bonds)
-        bonds = np.arange(2 * num_bonds).reshape(num_bonds, 2)
-        self.u.add_bonds(bonds)
-
-    def time_bonds(self, num_bonds):
-        """Benchmark for calculating bonds"""
-        self.u.bonds
+import MDAnalysis
+import numpy as np
+from MDAnalysis.guesser import DefaultGuesser
+
+try:
+    from MDAnalysis.exceptions import NoDataError
+    from MDAnalysisTests.datafiles import GRO
+except:
+    pass
+
+
+class TopologyGuessBench(object):
+    """Benchmarks for individual
+    topology functions
+    """
+
+    params = (10, 100, 1000, 10000)
+    param_names = ["num_atoms"]
+
+    def setup(self, num_atoms):
+        self.u = MDAnalysis.Universe(GRO)
+        self.ag = self.u.atoms[:num_atoms]
+        self.vdwradii = {"H": 1.0, "C": 1.0, "N": 1.0, "O": 1.0, "DUMMY": 1.0}
+
+    def time_guessbonds(self, num_atoms):
+        """Benchmark for guessing bonds"""
+        DefaultGuesser(None).guess_bonds(
+            self.ag, self.ag.positions, box=self.ag.dimensions, vdwradii=self.vdwradii
+        )
+
+
+class BondsBench(object):
+    """
+    Benchmarks for getting bonds
+    """
+
+    params = (1000, 10000, 100000, 1000000)
+    param_names = ["num_bonds"]
+
+    def setup(self, num_bonds):
+        self.u = MDAnalysis.Universe.empty(2 * num_bonds)
+        bonds = np.arange(2 * num_bonds).reshape(num_bonds, 2)
+        self.u.add_bonds(bonds)
+
+    def time_bonds(self, num_bonds):
+        """Benchmark for calculating bonds"""
+        self.u.bonds

mypy.ini

@@ -1,46 +1,46 @@
-[mypy]
-ignore_missing_imports = True
-exclude = doc/sphinx/source/
-
-
-[mypy-MDAnalysis.analysis.*]
-ignore_errors = True
-
-[mypy-MDAnalysis.auxiliary.*]
-ignore_errors = True
-
-[mypy-MDAnalysis.converters.*]
-ignore_errors = True
-
-[mypy-MDAnalysis.coordinates.*]
-ignore_errors = True
-
-[mypy-MDAnalysis.core.*]
-ignore_errors = True
-
-[mypy-MDAnalysis.selections.*]
-ignore_errors = True
-
-[mypy-MDAnalysis.tests.*]
-ignore_errors = True
-
-[mypy-MDAnalysis.topology.*]
-ignore_errors = True
-
-[mypy-MDAnalysis.transformations.*]
-ignore_errors = True
-
-[mypy-MDAnalysis.visualization.*]
-ignore_errors = True
-
-[mypy-MDAnalysis.due]
-ignore_errors = True
-
-[mypy-MDAnalysis.exceptions]
-ignore_errors = True
-
-[mypy-MDAnalysis.units]
-ignore_errors = True
-
-[mypy-MDAnalysis.version]
-ignore_errors = True
+[mypy]
+ignore_missing_imports = True
+exclude = doc/sphinx/source/
+
+
+[mypy-MDAnalysis.analysis.*]
+ignore_errors = True
+
+[mypy-MDAnalysis.auxiliary.*]
+ignore_errors = True
+
+[mypy-MDAnalysis.converters.*]
+ignore_errors = True
+
+[mypy-MDAnalysis.coordinates.*]
+ignore_errors = True
+
+[mypy-MDAnalysis.core.*]
+ignore_errors = True
+
+[mypy-MDAnalysis.selections.*]
+ignore_errors = True
+
+[mypy-MDAnalysis.tests.*]
+ignore_errors = True
+
+[mypy-MDAnalysis.topology.*]
+ignore_errors = True
+
+[mypy-MDAnalysis.transformations.*]
+ignore_errors = True
+
+[mypy-MDAnalysis.visualization.*]
+ignore_errors = True
+
+[mypy-MDAnalysis.due]
+ignore_errors = True
+
+[mypy-MDAnalysis.exceptions]
+ignore_errors = True
+
+[mypy-MDAnalysis.units]
+ignore_errors = True
+
+[mypy-MDAnalysis.version]
+ignore_errors = True

mypy_requirements.txt

@@ -1,2 +1,2 @@
-mypy==0.960
+mypy==0.960
 typing_extensions

package/CHANGELOG

@@ -68,6 +68,8 @@ Fixes
    to version 5.1.0 (Issue #5145, PR #5146)
  * Fixes incorrect assignment of secondary structure to proline residues in
    DSSP by porting upstream PyDSSP 0.9.1 fix (Issue #4913)
+ * Added `.gitattributes` to enforce LF (\n) as line endings and renormalized
+   existing files to conform (Issue #5315, PR #5446)
 
 Enhancements
  * Added ASV benchmark for PDB trajectory reading (PR #5394)