From f2936087b0dd259d4ecee13cdea9c7891256a472 Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Wed, 13 Dec 2023 11:25:54 -0800
Subject: [PATCH] Close files when we're done with them

---
 modules/cnmultifit/test/test_chimera_models.py | 3 ++-
 modules/cnmultifit/test/test_do_all_fitting.py | 3 ++-
 modules/cnmultifit/test/test_param.py          | 3 ++-
 modules/cnmultifit/test/test_rmsd.py           | 9 ++++++---
 modules/cnmultifit/test/test_surface.py        | 3 ++-
 5 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/modules/cnmultifit/test/test_chimera_models.py b/modules/cnmultifit/test/test_chimera_models.py
index 84d7f2d9fc..58eee5c001 100644
--- a/modules/cnmultifit/test/test_chimera_models.py
+++ b/modules/cnmultifit/test/test_chimera_models.py
@@ -22,7 +22,8 @@ def test_chimera_models_usage(self):
 
     def test_chimera_models_run(self):
         """Test chimera_models module run"""
-        open('test.pdb', 'w').write("""
+        with open('test.pdb', 'w') as fh:
+            fh.write("""
 ATOM      1  N   ALA A   2     -27.425   4.153 -19.130  1.00  0.00           N
 ATOM      2  CA  ALA A   2     -18.390   4.442 -18.049  1.00  0.00           C
 """)
diff --git a/modules/cnmultifit/test/test_do_all_fitting.py b/modules/cnmultifit/test/test_do_all_fitting.py
index c1a94d6e0c..2f105939ac 100644
--- a/modules/cnmultifit/test/test_do_all_fitting.py
+++ b/modules/cnmultifit/test/test_do_all_fitting.py
@@ -28,7 +28,8 @@ def test_do_all_fitting(self):
         fin.close()
         fout.close()
         IMP.cnmultifit.do_all_fitting('trimer.param')
-        self.assertEqual(len(open('multifit.output').readlines()), 4)
+        with open('multifit.output') as fh:
+            self.assertEqual(len(fh.readlines()), 4)
 
         m = IMP.Model()
         ref = IMP.atom.read_pdb(self.get_input_file_name('trimer-ref.pdb'), m)
diff --git a/modules/cnmultifit/test/test_param.py b/modules/cnmultifit/test/test_param.py
index b5d1250ba0..5b32a6b27f 100644
--- a/modules/cnmultifit/test/test_param.py
+++ b/modules/cnmultifit/test/test_param.py
@@ -28,7 +28,8 @@ def test_param_run(self):
                                 '--numsols', '42', '--',
                                 '7', 'testmonomer.pdb', 'test.mrc', '8.0',
                                 '4.0', '5.0', '-10.0', '-20.0', '-30.0'])
-        contents = open('test.params').read()
+        with open('test.params') as fh:
+            contents = fh.read()
         self.assertIn('output = test.output', contents)
         self.assertIn('intermediate = test.int', contents)
         self.assertIn('model = test.model', contents)
diff --git a/modules/cnmultifit/test/test_rmsd.py b/modules/cnmultifit/test/test_rmsd.py
index ae3c4e6973..6ab18f652e 100644
--- a/modules/cnmultifit/test/test_rmsd.py
+++ b/modules/cnmultifit/test/test_rmsd.py
@@ -37,8 +37,10 @@ def test_rmsd_run(self):
                                 'multifit.param', self.get_input_file_name(
                                     'multifit.output'),
                                 self.get_input_file_name('mini-ref-complex.pdb')])
-        self.assertEqual(len(open('rmsd.output').readlines()), 10)
-        self.assertEqual(len(open('test.vec').read().split(' ')), 10)
+        with open('rmsd.output') as fh:
+            self.assertEqual(len(fh.readlines()), 10)
+        with open('test.vec') as fh:
+            self.assertEqual(len(fh.read().split(' ')), 10)
         os.unlink('rmsd.output')
         os.unlink('test.vec')
 
@@ -47,7 +49,8 @@ def test_rmsd_run(self):
                                 'multifit.param', self.get_input_file_name(
                                     'multifit.output'),
                                 self.get_input_file_name('mini-ref-complex.pdb')])
-        self.assertEqual(len(open('rmsd.output').readlines()), 2)
+        with open('rmsd.output') as fh:
+            self.assertEqual(len(fh.readlines()), 2)
         os.unlink('rmsd.output')
         os.unlink('multifit.param')
 
diff --git a/modules/cnmultifit/test/test_surface.py b/modules/cnmultifit/test/test_surface.py
index 5742a7576b..aa76ddf3ae 100644
--- a/modules/cnmultifit/test/test_surface.py
+++ b/modules/cnmultifit/test/test_surface.py
@@ -26,7 +26,8 @@ def assert_surface_ok(leaves, outfile, density, rp):
             self.assertEqual(outfile, 'test.pdb.ms')
             self.assertEqual(density, 5.0)
             self.assertEqual(rp, 3.0)
-        open('test.pdb', 'w').write("""
+        with open('test.pdb', 'w') as fh:
+            fh.write("""
 ATOM      1  N   ALA A   2     -27.425   4.153 -19.130  1.00  0.00           N
 ATOM      2  CA  ALA A   2     -18.390   4.442 -18.049  1.00  0.00           C
 """)