Merge remote-tracking branch 'talagayev/fasteners_to_filelock' into s…

…sh_worker
yuxuanzhuang · Dec 6, 2024 · 1e3daa1 · 1e3daa1
2 parents ef401c2 + aa9f83f
commit 1e3daa1
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Showing 7 changed files with 15 additions and 17 deletions.
diff --git a/.github/actions/setup-deps/action.yaml b/.github/actions/setup-deps/action.yaml
@@ -21,8 +21,8 @@ inputs:
     default: 'codecov'
   cython:
     default: 'cython'
-  fasteners:
-    default: 'fasteners'
+  filelock:
+    default: 'filelock'
   griddataformats:
     default: 'griddataformats'
   hypothesis:
@@ -106,7 +106,7 @@ runs:
         CONDA_MIN_DEPS: |
           ${{ inputs.codecov }}
           ${{ inputs.cython }}
-          ${{ inputs.fasteners }}
+          ${{ inputs.filelock }}
           ${{ inputs.griddataformats }}
           ${{ inputs.hypothesis }}
           ${{ inputs.matplotlib }}

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -90,7 +90,7 @@ jobs:
       scikit-learn
       tqdm
       threadpoolctl
-      fasteners
+      filelock
     displayName: 'Install dependencies'
   # for wheel install testing, we pin to an
   # older NumPy, the oldest version we support and that

diff --git a/maintainer/conda/environment.yml b/maintainer/conda/environment.yml
@@ -7,7 +7,7 @@ dependencies:
   - codecov
   - cython
   - docutils
-  - fasteners
+  - filelock
   - griddataformats
   - gsd
   - h5py>=2.10

diff --git a/package/MDAnalysis/coordinates/XDR.py b/package/MDAnalysis/coordinates/XDR.py
@@ -38,7 +38,7 @@
 import numpy as np
 from os.path import getctime, getsize, isfile, split, join
 import warnings
-import fasteners
+from filelock import FileLock
 
 from . import base
 from ..lib.mdamath import triclinic_box
@@ -121,6 +121,8 @@ class XDRBaseReader(base.ReaderBase):
        Add a InterProcessLock when generating offsets
     .. versionchanged:: 2.4.0
        Use a direct read into ts attributes
+    .. versionchanged:: 2.9.0
+       Changed fasteners.InterProcessLock() to filelock.FileLock
     """
     @store_init_arguments
     def __init__(self, filename, convert_units=True, sub=None,
@@ -195,18 +197,18 @@ def _load_offsets(self):
 
         #  check if the location of the lock is writable.
         try:
-            with fasteners.InterProcessLock(lock_name) as filelock:
+            with FileLock(lock_name) as filelock:
                 pass
         except OSError as e:
             if isinstance(e, PermissionError) or e.errno == errno.EROFS:
                 warnings.warn(f"Cannot write lock/offset file in same location as "
                               f"{self.filename}. Using slow offset calculation.")
-                self._read_offsets(store=True)
+                self._read_offsets(store=False)
                 return
             else:
                 raise
 
-        with fasteners.InterProcessLock(lock_name) as filelock:
+        with FileLock(lock_name) as filelock:
             if not isfile(fname):
                 self._read_offsets(store=True)
                 return

diff --git a/package/pyproject.toml b/package/pyproject.toml
@@ -38,7 +38,7 @@ dependencies = [
     'tqdm>=4.43.0',
     'threadpoolctl',
     'packaging',
-    'fasteners',
+    'filelock',
     'mda-xdrlib',
     'waterdynamics',
     'pathsimanalysis',

diff --git a/package/requirements.txt b/package/requirements.txt
@@ -1,7 +1,7 @@
 biopython>=1.80
 codecov
 cython
-fasteners
+filelock
 griddataformats
 gsd
 hypothesis

diff --git a/testsuite/MDAnalysisTests/coordinates/test_xdr.py b/testsuite/MDAnalysisTests/coordinates/test_xdr.py
@@ -903,13 +903,10 @@ def test_persistent_offsets_readonly(self, tmpdir):
 
         filename = str(tmpdir.join(os.path.basename(self.filename)))
         # try to write a offsets file
-        with (pytest.warns(UserWarning, match="Couldn't save offsets") and
+        with (pytest.warns(UserWarning, match="Couldn't save offsets") or
               pytest.warns(UserWarning, match="Cannot write")):
             self._reader(filename)
         assert_equal(os.path.exists(XDR.offsets_filename(filename)), False)
-        # check the lock file is not created as well.
-        assert_equal(os.path.exists(XDR.offsets_filename(filename,
-                                                    ending='.lock')), False)
 
         # pre-teardown permission fix - leaving permission blocked dir
         # is problematic on py3.9 + Windows it seems. See issue
@@ -923,8 +920,7 @@ def test_persistent_offsets_readonly(self, tmpdir):
         shutil.rmtree(tmpdir)
 
     def test_offset_lock_created(self):
-        assert os.path.exists(XDR.offsets_filename(self.filename,
-                                                   ending='lock'))
+        assert os.path.exists(XDR.offsets_filename(self.filename))
 
 
 class TestXTCReader_offsets(_GromacsReader_offsets):