New upstream version 1.1.0+dfsg

16 files changed, 260 insertions, 25 deletions

diff --git a/src/silx/io/test/__init__.py b/src/silx/io/test/__init__.py
index 244d090..3c723bb 100644
--- a/src/silx/io/test/__init__.py
+++ b/src/silx/io/test/__init__.py
@@ -1,4 +1,3 @@
-# coding: utf-8
 # /*##########################################################################
 # Copyright (C) 2016-2017 European Synchrotron Radiation Facility
 #
diff --git a/src/silx/io/test/test_commonh5.py b/src/silx/io/test/test_commonh5.py
index 27f6e8c..d554d27 100644
--- a/src/silx/io/test/test_commonh5.py
+++ b/src/silx/io/test/test_commonh5.py
@@ -1,4 +1,3 @@
-# coding: utf-8
 # /*##########################################################################
 # Copyright (C) 2016-2017 European Synchrotron Radiation Facility
 #
diff --git a/src/silx/io/test/test_dictdump.py b/src/silx/io/test/test_dictdump.py
index 4cafa9b..e31d7a8 100644
--- a/src/silx/io/test/test_dictdump.py
+++ b/src/silx/io/test/test_dictdump.py
@@ -1,6 +1,5 @@
-# coding: utf-8
 # /*##########################################################################
-# Copyright (C) 2016-2021 European Synchrotron Radiation Facility
+# Copyright (C) 2016-2022 European Synchrotron Radiation Facility
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -27,15 +26,21 @@ __authors__ = ["P. Knobel"]
 __license__ = "MIT"
 __date__ = "17/01/2018"
 
-from collections import OrderedDict
-import numpy
+
+from collections import defaultdict, OrderedDict
+from copy import deepcopy
+from io import BytesIO
 import os
 import tempfile
 import unittest
-import h5py
-from copy import deepcopy
 
-from collections import defaultdict
+import h5py
+import numpy
+try:
+    import pint
+except ImportError:
+    pint = None
+import pytest
 
 from silx.utils.testutils import LoggingValidator
 
@@ -48,6 +53,13 @@ from ..utils import is_link
 from ..utils import h5py_read_dataset
 
 
+@pytest.fixture
+def tmp_h5py_file():
+    with BytesIO() as buffer:
+        with h5py.File(buffer, mode="w") as h5file:
+            yield h5file
+
+
 def tree():
     """Tree data structure as a recursive nested dictionary"""
     return defaultdict(tree)
@@ -512,6 +524,22 @@ class TestDictToH5(H5DictTestCase):
         assert_append("replace")
 
 
+@pytest.mark.skipif(pint is None, reason="Require pint")
+def test_dicttoh5_pint(tmp_h5py_file):
+    ureg = pint.UnitRegistry()
+    treedict = {
+        "array_mm": pint.Quantity([1, 2, 3], ureg.mm),
+        "value_kg": 3 * ureg.kg,
+    }
+
+    dicttoh5(treedict, tmp_h5py_file)
+
+    result = h5todict(tmp_h5py_file)
+    assert set(treedict.keys()) == set(result.keys())
+    for key, value in treedict.items():
+        assert numpy.array_equal(result[key], value.magnitude)
+
+
 class TestH5ToDict(H5DictTestCase):
     def setUp(self):
         self.tempdir = tempfile.mkdtemp()
@@ -800,6 +828,22 @@ class TestDictToNx(H5DictTestCase):
         assert_append("replace", add_nx_class=True)
 
 
+@pytest.mark.skipif(pint is None, reason="Require pint")
+def test_dicttonx_pint(tmp_h5py_file):
+    ureg = pint.UnitRegistry()
+    treedict = {
+        "array_mm": pint.Quantity([1, 2, 3], ureg.mm),
+        "value_kg": 3 * ureg.kg,
+    }
+
+    dictdump.dicttonx(treedict, tmp_h5py_file)
+
+    result = dictdump.nxtodict(tmp_h5py_file)
+    for key, value in treedict.items():
+        assert numpy.array_equal(result[key], value.magnitude)
+        assert result[f"{key}@units"] == f"{value.units:~C}"
+
+
 class TestNxToDict(H5DictTestCase):
     def setUp(self):
         self.tempdir = tempfile.mkdtemp()
diff --git a/src/silx/io/test/test_fabioh5.py b/src/silx/io/test/test_fabioh5.py
index c410024..fdeb1c3 100755
--- a/src/silx/io/test/test_fabioh5.py
+++ b/src/silx/io/test/test_fabioh5.py
@@ -1,4 +1,3 @@
-# coding: utf-8
 # /*##########################################################################
 # Copyright (C) 2016-2018 European Synchrotron Radiation Facility
 #
diff --git a/src/silx/io/test/test_fioh5.py b/src/silx/io/test/test_fioh5.py
index 8ffb4ad..18200c9 100644
--- a/src/silx/io/test/test_fioh5.py
+++ b/src/silx/io/test/test_fioh5.py
@@ -1,4 +1,3 @@
-# coding: utf-8
 # /*##########################################################################
 # Copyright (C) 2021 Timo Fuchs
 #
diff --git a/src/silx/io/test/test_h5py_utils.py b/src/silx/io/test/test_h5py_utils.py
index ea46eca..0d10a78 100644
--- a/src/silx/io/test/test_h5py_utils.py
+++ b/src/silx/io/test/test_h5py_utils.py
@@ -1,4 +1,3 @@
-# coding: utf-8
 # /*##########################################################################
 # Copyright (C) 2016-2017 European Synchrotron Radiation Facility
 #
@@ -449,3 +448,35 @@ class TestH5pyUtils(unittest.TestCase):
             f.write("0")
         with self.assertRaises(RetryTimeoutError):
             top_level_names_test(txtfilename, filename, **kw)
+
+    @subtests
+    def test_retry_generator(self):
+        filename = self._new_filename()
+        ncausefailure = 3
+        faildelay = 0.1
+        sufficient_timeout = ncausefailure * (faildelay + 10)
+        insufficient_timeout = ncausefailure * faildelay * 0.5
+
+        @h5py_utils.retry()
+        def iter_data(filename, name, start_index=0):
+            nonlocal failcounter
+            if start_index <= 0:
+                with h5py_utils.File(filename) as h5file:
+                    yield h5file[name][()]
+            if failcounter < ncausefailure:
+                time.sleep(faildelay)
+                failcounter += 1
+                raise RetryError
+            if start_index <= 1:
+                with h5py_utils.File(filename) as h5file:
+                    yield not h5file[name][()]
+
+        failcounter = 0
+        kw = {"retry_timeout": sufficient_timeout}
+        data = list(iter_data(filename, "/check", **kw))
+        self.assertEqual(data, [True, False])
+
+        failcounter = 0
+        kw = {"retry_timeout": insufficient_timeout}
+        with self.assertRaises(RetryTimeoutError):
+            list(iter_data(filename, "/check", **kw))
diff --git a/src/silx/io/test/test_nxdata.py b/src/silx/io/test/test_nxdata.py
index 9025d6d..52a2b8a 100644
--- a/src/silx/io/test/test_nxdata.py
+++ b/src/silx/io/test/test_nxdata.py
@@ -1,6 +1,5 @@
-# coding: utf-8
 # /*##########################################################################
-# Copyright (C) 2016-2021 European Synchrotron Radiation Facility
+# Copyright (C) 2016-2022 European Synchrotron Radiation Facility
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -30,10 +29,13 @@ __date__ = "24/03/2020"
 
 import tempfile
 import unittest
+
 import h5py
 import numpy
+import pytest
 
 from .. import nxdata
+from ..dictdump import dicttoh5
 
 
 text_dtype = h5py.special_dtype(vlen=str)
@@ -561,3 +563,144 @@ class TestSaveNXdata(unittest.TestCase):
         self.assertTrue(numpy.array_equal(nxd.axes[0],
                                           a0))
         h5f.close()
+
+
+class TestGetDefault:
+    """Test silx.io.nxdata.get_default function"""
+
+    @pytest.fixture
+    def hdf5_file(self, tmp_path):
+        with h5py.File(tmp_path / "test_file.h5", "w") as h5f:
+            yield h5f
+
+    def testDirectPath(self, hdf5_file):
+        dicttoh5(
+            {
+                ("", "default"): "/nxentry/nxprocess/nxdata",
+                "nxentry": {
+                    "nxprocess": {
+                        "nxdata": {
+                            ("", "NX_class"): "NXdata",
+                            ("", "signal"): "data",
+                            "data": (1, 2, 3),
+                        }
+                    }
+                }
+            },
+            hdf5_file)
+        default = nxdata.get_default(hdf5_file)
+        assert isinstance(default, nxdata.NXdata)
+        assert default.group.name == "/nxentry/nxprocess/nxdata"
+
+    def testAbsolutePath(self, hdf5_file):
+        dicttoh5(
+            {
+                ("", "default"): "/nxentry",
+                "nxentry": {
+                    ("", "default"): "/nxentry/nxprocess/nxdata",
+                    "nxprocess": {
+                        "nxdata": {
+                            ("", "NX_class"): "NXdata",
+                            ("", "signal"): "data",
+                            "data": (1, 2, 3),
+                        }
+                    }
+                }
+            },
+            hdf5_file)
+        default = nxdata.get_default(hdf5_file)
+        assert isinstance(default, nxdata.NXdata)
+        assert default.group.name == "/nxentry/nxprocess/nxdata"
+
+    def testRelativePath(self, hdf5_file):
+        dicttoh5(
+            {
+                ("", "default"): "nxentry",
+                "nxentry": {
+                    ("", "default"): "nxdata",
+                    "nxdata": {
+                        ("", "NX_class"): "NXdata",
+                        ("", "signal"): "data",
+                        "data": (1, 2, 3),
+                    }
+                }
+            },
+            hdf5_file)
+        default = nxdata.get_default(hdf5_file)
+        assert isinstance(default, nxdata.NXdata)
+        assert default.group.name == "/nxentry/nxdata"
+
+    def testRelativePathSubdir(self, hdf5_file):
+        dicttoh5(
+            {
+                ("", "default"): "nxentry",
+                "nxentry": {
+                    ("", "default"): "nxprocess/nxdata",
+                    "nxprocess": {
+                        "nxdata": {
+                            ("", "NX_class"): "NXdata",
+                            ("", "signal"): "data",
+                            "data": (1, 2, 3),
+                        }
+                    }
+                }
+            },
+            hdf5_file)
+        default = nxdata.get_default(hdf5_file)
+        assert isinstance(default, nxdata.NXdata)
+        assert default.group.name == "/nxentry/nxprocess/nxdata"
+
+    def testRecursiveAbsolutePath(self, hdf5_file):
+        dicttoh5(
+            {
+                ("", "default"): "/nxentry",
+                "nxentry": {
+                    ("", "default"): "/nxentry/nxprocess",
+                    "nxprocess": {
+                        ("", "default"): "/nxentry/nxprocess/nxdata",
+                        "nxdata": {
+                            ("", "NX_class"): "NXdata",
+                            ("", "signal"): "data",
+                            "data": (1, 2, 3),
+                        }
+                    }
+                }
+            },
+            hdf5_file)
+        default = nxdata.get_default(hdf5_file)
+        assert isinstance(default, nxdata.NXdata)
+        assert default.group.name == "/nxentry/nxprocess/nxdata"
+
+    def testRecursiveRelativePath(self, hdf5_file):
+        dicttoh5(
+            {
+                ("", "default"): "nxentry",
+                "nxentry": {
+                    ("", "default"): "nxprocess",
+                    "nxprocess": {
+                        ("", "default"): "nxdata",
+                        "nxdata": {
+                            ("", "NX_class"): "NXdata",
+                            ("", "signal"): "data",
+                            "data": (1, 2, 3),
+                        }
+                    }
+                }
+            },
+            hdf5_file)
+        default = nxdata.get_default(hdf5_file)
+        assert isinstance(default, nxdata.NXdata)
+        assert default.group.name == "/nxentry/nxprocess/nxdata"
+
+    def testLoop(self, hdf5_file):
+        """Infinite loop of @default"""
+        dicttoh5(
+            {
+                ("", "default"): "/nxentry",
+                "nxentry": {
+                    ("", "default"): "/nxentry",
+                }
+            },
+            hdf5_file)
+        default = nxdata.get_default(hdf5_file)
+        assert default is None
diff --git a/src/silx/io/test/test_octaveh5.py b/src/silx/io/test/test_octaveh5.py
index 1c3b3e0..19b8ad6 100644
--- a/src/silx/io/test/test_octaveh5.py
+++ b/src/silx/io/test/test_octaveh5.py
@@ -1,4 +1,3 @@
-# coding: utf-8
 # /*##########################################################################
 # Copyright (C) 2016 European Synchrotron Radiation Facility
 #
diff --git a/src/silx/io/test/test_rawh5.py b/src/silx/io/test/test_rawh5.py
index 236484d..947be0f 100644
--- a/src/silx/io/test/test_rawh5.py
+++ b/src/silx/io/test/test_rawh5.py
@@ -1,4 +1,3 @@
-# coding: utf-8
 # /*##########################################################################
 #
 # Copyright (c) 2016 European Synchrotron Radiation Facility
diff --git a/src/silx/io/test/test_specfile.py b/src/silx/io/test/test_specfile.py
index 44cb08c..748e31c 100644
--- a/src/silx/io/test/test_specfile.py
+++ b/src/silx/io/test/test_specfile.py
@@ -1,4 +1,3 @@
-# coding: utf-8
 # /*##########################################################################
 # Copyright (C) 2016-2021 European Synchrotron Radiation Facility
 #
diff --git a/src/silx/io/test/test_specfilewrapper.py b/src/silx/io/test/test_specfilewrapper.py
index a1ba5f4..7d2ce60 100644
--- a/src/silx/io/test/test_specfilewrapper.py
+++ b/src/silx/io/test/test_specfilewrapper.py
@@ -1,4 +1,3 @@
-# coding: utf-8
 # /*##########################################################################
 # Copyright (C) 2016 European Synchrotron Radiation Facility
 #
diff --git a/src/silx/io/test/test_spech5.py b/src/silx/io/test/test_spech5.py
index 1e67961..456a538 100644
--- a/src/silx/io/test/test_spech5.py
+++ b/src/silx/io/test/test_spech5.py
@@ -1,4 +1,3 @@
-# coding: utf-8
 # /*##########################################################################
 # Copyright (C) 2016-2021 European Synchrotron Radiation Facility
 #
diff --git a/src/silx/io/test/test_spectoh5.py b/src/silx/io/test/test_spectoh5.py
index 66bf8d6..5465ece 100644
--- a/src/silx/io/test/test_spectoh5.py
+++ b/src/silx/io/test/test_spectoh5.py
@@ -1,4 +1,3 @@
-# coding: utf-8
 # /*##########################################################################
 # Copyright (C) 2016-2019 European Synchrotron Radiation Facility
 #
diff --git a/src/silx/io/test/test_url.py b/src/silx/io/test/test_url.py
index 7346391..8cbfb34 100644
--- a/src/silx/io/test/test_url.py
+++ b/src/silx/io/test/test_url.py
@@ -1,4 +1,3 @@
-# coding: utf-8
 # /*##########################################################################
 # Copyright (C) 2016-2017 European Synchrotron Radiation Facility
 #
diff --git a/src/silx/io/test/test_utils.py b/src/silx/io/test/test_utils.py
index cc34100..b9fc3ab 100644
--- a/src/silx/io/test/test_utils.py
+++ b/src/silx/io/test/test_utils.py
@@ -1,6 +1,5 @@
-# coding: utf-8
 # /*##########################################################################
-# Copyright (C) 2016-2019 European Synchrotron Radiation Facility
+# Copyright (C) 2016-2022 European Synchrotron Radiation Facility
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -30,7 +29,6 @@ import re
 import shutil
 import tempfile
 import unittest
-import sys
 
 from .. import utils
 from ..._version import calc_hexversion
@@ -40,6 +38,7 @@ import h5py
 from ..utils import h5ls
 from silx.io import commonh5
 
+
 import fabio
 
 __authors__ = ["P. Knobel"]
@@ -921,3 +920,33 @@ def test_visitall_commonh5():
     soft_link = visited_items["/group/soft_link"]
     assert isinstance(soft_link, commonh5.SoftLink)
     assert soft_link.path == "/group/dataset"
+
+
+def test_match_hdf5(tmp_path):
+    """Test match function with HDF5 file"""
+    with h5py.File(tmp_path / "test_match.h5", "w") as h5f:
+        h5f.create_group("entry_0000/group")
+        h5f["entry_0000/data"] = 0
+        h5f.create_group("entry_0001/group")
+        h5f["entry_0001/data"] = 1
+        h5f.create_group("entry_0002")
+        h5f["entry_0003"] = 3
+
+        result = list(utils.match(h5f, "/entry_*/*"))
+
+        assert sorted(result) == ['entry_0000/data', 'entry_0000/group', 'entry_0001/data', 'entry_0001/group']
+
+
+def test_match_commonh5():
+    """Test match function with commonh5 objects"""
+    with commonh5.File("filename.file", mode="w") as fobj:
+        fobj.create_group("entry_0000/group")
+        fobj["entry_0000/data"] = 0
+        fobj.create_group("entry_0001/group")
+        fobj["entry_0001/data"] = 1
+        fobj.create_group("entry_0002")
+        fobj["entry_0003"] = 3
+
+        result = list(utils.match(fobj, "/entry_*/*"))
+
+        assert sorted(result) == ['entry_0000/data', 'entry_0000/group', 'entry_0001/data', 'entry_0001/group']
diff --git a/src/silx/io/test/test_write_to_h5.py b/src/silx/io/test/test_write_to_h5.py
index 06149c9..fe855e1 100644
--- a/src/silx/io/test/test_write_to_h5.py
+++ b/src/silx/io/test/test_write_to_h5.py
@@ -1,4 +1,3 @@
-# coding: utf-8
 # /*##########################################################################
 # Copyright (C) 2021 European Synchrotron Radiation Facility
 #