For dials/dials#1998 bring in UUID4 (#477)

UUID generation involves spawning a subprocess on import which appears to
cause problems in large-rank MPI jobs - however we only really need random
128 bit UUID4's which can be generated easily.

This also fixes the otherwise currently broken CI tests due to the pytest v7 release.

Co-authored-by: Markus Gerstel <markus.gerstel@diamond.ac.uk>

.azure-pipelines/ci-conda-env.txt

@@ -30,7 +30,7 @@ conda-forge::pytest-forked
 conda-forge::pytest-mock
 conda-forge::pytest-timeout
 conda-forge::pytest-xdist
-conda-forge::pytest
+conda-forge::pytest<7
 conda-forge::requests
 conda-forge::scipy
 conda-forge::scons

newsfragments/477.bugfix

@@ -0,0 +1 @@
+Add method ersatz_uuid4 which gives an implementation of a random 128 bit UUID4

newsfragments/477.misc

@@ -0,0 +1 @@
+Avoid currently broken pytest v7 in CI tests

src/dxtbx/format/FormatHDF5EigerNearlyNexus.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import sys
-import uuid
 
 import h5py
 import numpy as np
@@ -23,6 +22,7 @@
     NXmxReader,
     generate_scan_model,
 )
+from dxtbx.util import ersatz_uuid4
 
 
 def find_entries(nx_file):
@@ -319,7 +319,7 @@ def understand(image_file):
 
     def _start(self):
         # Read the file structure
-        temp_file = "tmp_master_%s.nxs" % uuid.uuid1().hex
+        temp_file = "tmp_master_%s.nxs" % ersatz_uuid4()
         fixer = EigerNXmxFixer(self._image_file, temp_file)
         reader = NXmxReader(handle=fixer.handle)
 

src/dxtbx/util/__init__.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import math
+import os
 import sys
 from urllib.parse import urlparse
 
@@ -80,3 +81,10 @@ def get_url_scheme(url) -> str:
     """Extract the URL scheme from the string url, respecting Windows file paths"""
 
     return urlparse(str(url)).scheme if "://" in str(url) else ""
+
+
+def ersatz_uuid4() -> str:
+    """Generate an ersatz UUID4 i.e. random 128 bit UUID."""
+
+    h = "%032x" % int.from_bytes(os.urandom(16), byteorder="little")
+    return "%s-%s-%s-%s-%s" % (h[:8], h[8:12], h[12:16], h[16:20], h[20:])

tests/test_util.py

@@ -1,3 +1,4 @@
+from dxtbx.util import ersatz_uuid4
 from dxtbx.util import format_float_with_standard_uncertainty as ffwsu
 
 
@@ -14,3 +15,20 @@ def test_format_float_with_standard_uncertainty():
     assert ffwsu(90, 0) == "90"
     assert ffwsu(90.0, 0) == "90.0"
     assert ffwsu(90 + 1e-14, 0) == "90.0"
+
+
+def test_ersatz_uuid4():
+    """Test ersatz UUID4 behaviour:
+    - (pseudo)randomness and uniqueness
+    - shape e.g. 00000000-0000-0000-0000-000000000000
+    - content e.g. hex digits"""
+
+    uuids = [ersatz_uuid4() for j in range(1000)]
+
+    assert len(uuids) == len(set(uuids))
+
+    for uuid in uuids:
+        bits = uuid.split("-")
+        assert tuple(len(b) for b in bits) == (8, 4, 4, 4, 12)
+        for b in bits:
+            assert set(b) <= set("0123456789abcdef")