use pytest temporary dir factory to write some of the test hdf5 files and move all fixed hdf5 sample data files to tests/data

tests/conftest.py

@@ -106,3 +106,8 @@ def s3fs_s3(s3_base):
     s3.invalidate_cache()
 
     yield s3
+
+
+@pytest.fixture(scope="module")
+def modular_tmp_path(tmp_path_factory):
+    return tmp_path_factory.mktemp("temp")

tests/make_attr_datatypes_file_2.py

@@ -1,60 +1,70 @@
 #! /usr/bin/env python
 
 """ Create a HDF5 file with all the supported attribute types (2)"""
+import sys
+
 import h5py
 import numpy as np
 
+from pathlib import Path
 
-with h5py.File('attr_datatypes_2.hdf5', 'w') as ds:
-    dt = h5py.string_dtype("utf-8")
-    unicode = "unicodé"
-    ds.attrs["unicode"] = unicode
-    ds.attrs["unicode_0dim"] = np.array(unicode, dtype=dt)
-    ds.attrs["unicode_1dim"] = np.array([unicode], dtype=dt)
-    ds.attrs["unicode_arrary"] = np.array([unicode, "foobár"], dtype=dt)
-    ds.attrs["unicode_list"] = [unicode]
-
-    dt = h5py.string_dtype("ascii")
-    # if dtype is ascii it's irrelevant if the data is provided as bytes or string
-    ascii = "ascii"
-    ds.attrs["ascii"] = ascii
-    ds.attrs["ascii_0dim"] = np.array(ascii, dtype=dt)
-    ds.attrs["ascii_1dim"] = np.array([ascii], dtype=dt)
-    ds.attrs["ascii_array"] = np.array([ascii, "foobar"], dtype=dt)
-    ds.attrs["ascii_list"] = [ascii]
-
-    ascii = b"ascii"
-    ds.attrs["bytes"] = ascii
-    ds.attrs["bytes_0dim"] = np.array(ascii, dtype=dt)
-    ds.attrs["bytes_1dim"] = np.array([ascii], dtype=dt)
-    ds.attrs["bytes_array"] = np.array([ascii, b"foobar"], dtype=dt)
-    ds.attrs["bytes_list"] = [ascii]
-
-    dt = h5py.string_dtype("utf-8", 10)
-    # unicode needs to be encoded properly for fixed size string type
-    ds.attrs["unicode_fixed"] = np.array(unicode.encode("utf-8"), dtype=dt)
-    ds.attrs["unicode_fixed_0dim"] = np.array(unicode.encode("utf-8"), dtype=dt)
-    ds.attrs["unicode_fixed_1dim"] = np.array([unicode.encode("utf-8")], dtype=dt)
-    ds.attrs["unicode_fixed_arrary"] = np.array(
-        [unicode.encode("utf-8"), "foobár".encode()], dtype=dt
-    )
-
-    dt = h5py.string_dtype("ascii", 10)
-    ascii = "ascii"
-    ds.attrs["ascii_fixed"] = np.array(ascii, dtype=dt)
-    ds.attrs["ascii_fixed_0dim"] = np.array(ascii, dtype=dt)
-    ds.attrs["ascii_fixed_1dim"] = np.array([ascii], dtype=dt)
-    ds.attrs["ascii_fixed_array"] = np.array([ascii, "foobar"], dtype=dt)
-
-    ascii = b"ascii"
-    ds.attrs["bytes_fixed"] = np.array(ascii, dtype=dt)
-    ds.attrs["bytes_fixed_0dim"] = np.array(ascii, dtype=dt)
-    ds.attrs["bytes_fixed_1dim"] = np.array([ascii], dtype=dt)
-    ds.attrs["bytes_fixed_array"] = np.array([ascii, b"foobar"], dtype=dt)
-
-    ds.attrs["int"] = 1
-    ds.attrs["intlist"] = [1]
-    ds.attrs["int_array"] = np.arange(10)
-    ds.attrs["empty_list"] = []
-    ds.attrs["empty_array"] = np.array([])
+
+def create_file(fpath):
+    with h5py.File(fpath, 'w') as ds:
+        dt = h5py.string_dtype("utf-8")
+        unicode = "unicodé"
+        ds.attrs["unicode"] = unicode
+        ds.attrs["unicode_0dim"] = np.array(unicode, dtype=dt)
+        ds.attrs["unicode_1dim"] = np.array([unicode], dtype=dt)
+        ds.attrs["unicode_arrary"] = np.array([unicode, "foobár"], dtype=dt)
+        ds.attrs["unicode_list"] = [unicode]
+
+        dt = h5py.string_dtype("ascii")
+        # if dtype is ascii it's irrelevant if the data is provided as bytes or string
+        ascii = "ascii"
+        ds.attrs["ascii"] = ascii
+        ds.attrs["ascii_0dim"] = np.array(ascii, dtype=dt)
+        ds.attrs["ascii_1dim"] = np.array([ascii], dtype=dt)
+        ds.attrs["ascii_array"] = np.array([ascii, "foobar"], dtype=dt)
+        ds.attrs["ascii_list"] = [ascii]
+
+        ascii = b"ascii"
+        ds.attrs["bytes"] = ascii
+        ds.attrs["bytes_0dim"] = np.array(ascii, dtype=dt)
+        ds.attrs["bytes_1dim"] = np.array([ascii], dtype=dt)
+        ds.attrs["bytes_array"] = np.array([ascii, b"foobar"], dtype=dt)
+        ds.attrs["bytes_list"] = [ascii]
+
+        dt = h5py.string_dtype("utf-8", 10)
+        # unicode needs to be encoded properly for fixed size string type
+        ds.attrs["unicode_fixed"] = np.array(unicode.encode("utf-8"), dtype=dt)
+        ds.attrs["unicode_fixed_0dim"] = np.array(unicode.encode("utf-8"), dtype=dt)
+        ds.attrs["unicode_fixed_1dim"] = np.array([unicode.encode("utf-8")], dtype=dt)
+        ds.attrs["unicode_fixed_arrary"] = np.array(
+            [unicode.encode("utf-8"), "foobár".encode()], dtype=dt
+        )
 
+        dt = h5py.string_dtype("ascii", 10)
+        ascii = "ascii"
+        ds.attrs["ascii_fixed"] = np.array(ascii, dtype=dt)
+        ds.attrs["ascii_fixed_0dim"] = np.array(ascii, dtype=dt)
+        ds.attrs["ascii_fixed_1dim"] = np.array([ascii], dtype=dt)
+        ds.attrs["ascii_fixed_array"] = np.array([ascii, "foobar"], dtype=dt)
+
+        ascii = b"ascii"
+        ds.attrs["bytes_fixed"] = np.array(ascii, dtype=dt)
+        ds.attrs["bytes_fixed_0dim"] = np.array(ascii, dtype=dt)
+        ds.attrs["bytes_fixed_1dim"] = np.array([ascii], dtype=dt)
+        ds.attrs["bytes_fixed_array"] = np.array([ascii, b"foobar"], dtype=dt)
+
+        ds.attrs["int"] = 1
+        ds.attrs["intlist"] = [1]
+        ds.attrs["int_array"] = np.arange(10)
+        ds.attrs["empty_list"] = []
+        ds.attrs["empty_array"] = np.array([])
+
+
+if __name__ == "__main__":
+    default_path = Path(__file__).parent / "attr_datatypes_2.hdf5"
+    filepath = Path(sys.argv[1]) if len(sys.argv) > 1 else default_path
+    create_file(filepath)

tests/test_attr_datatypes.py

@@ -10,9 +10,10 @@
 import pyfive
 
 DIRNAME = os.path.dirname(__file__)
-ATTR_DATATYPES_HDF5_FILE = os.path.join(DIRNAME, 'attr_datatypes.hdf5')
+ATTR_DATATYPES_HDF5_FILE = os.path.join(DIRNAME, "data", 'attr_datatypes.hdf5')
 MAKE_ATTR_DATATYPES_SCRIPT = os.path.join(DIRNAME, 'make_attr_datatypes_file.py')
 ATTR_DATATYPES_HDF5_FILE_2 = os.path.join(DIRNAME, 'attr_datatypes_2.hdf5')
+MAKE_ATTR_DATATYPES_SCRIPT_2 = os.path.join(DIRNAME, 'make_attr_datatypes_file_2.py')
 
 
 @pytest.fixture(scope="module")
@@ -23,6 +24,14 @@ def attr_datatypes_hdf5(tmp_path_factory):
     return str(path)
 
 
+@pytest.fixture(scope="module")
+def attr_datatypes_hdf5_2(tmp_path_factory):
+    tmp_dir = tmp_path_factory.mktemp("attr_datatypes")
+    path = tmp_dir / "attr_datatypes_2.hdf5"
+    subprocess.run([sys.executable, MAKE_ATTR_DATATYPES_SCRIPT_2, str(path)], check=True)
+    return str(path)
+
+
 def test_numeric_scalar_attr_datatypes():
 
     with pyfive.File(ATTR_DATATYPES_HDF5_FILE) as hfile:
@@ -156,12 +165,12 @@ def test_empty_string_datatypes(attr_datatypes_hdf5):
         assert enum_attr.dtype == np.dtype('|S1')
 
 
-def test_attributes_2():
+def test_attributes_2(attr_datatypes_hdf5_2):
 
     ascii = "ascii"
     unicode = "unicodé"
 
-    with pyfive.File(ATTR_DATATYPES_HDF5_FILE_2) as ds:
+    with pyfive.File(attr_datatypes_hdf5_2) as ds:
         foobar = "foobár"
         assert isinstance(ds.attrs["unicode"], str)
         assert ds.attrs["unicode"] == unicode

tests/test_chunked.py

@@ -7,7 +7,7 @@
 import pyfive
 
 DIRNAME = os.path.dirname(__file__)
-DATASET_CHUNKED_HDF5_FILE = os.path.join(DIRNAME, 'chunked.hdf5')
+DATASET_CHUNKED_HDF5_FILE = os.path.join(DIRNAME, "data", 'chunked.hdf5')
 
 
 def test_chunked_dataset():

tests/test_compact.py

@@ -21,8 +21,8 @@ def data():
 
 
 @pytest.fixture(scope='module')
-def name(data):
-    name = os.path.join(os.path.dirname(__file__), 'compact.hdf5')
+def name(data, modular_tmp_path):
+    name = modular_tmp_path / 'compact.hdf5'
 
     f = h5py.File(name, 'w', libver='earliest')
     dtype = h5py.h5t.NATIVE_INT32

tests/test_compressed.py

@@ -7,7 +7,7 @@
 import pyfive
 
 DIRNAME = os.path.dirname(__file__)
-DATASET_COMPRESSED_HDF5_FILE = os.path.join(DIRNAME, 'compressed.hdf5')
+DATASET_COMPRESSED_HDF5_FILE = os.path.join(DIRNAME, "data", 'compressed.hdf5')
 
 
 def test_compressed_dataset():

tests/test_compressed_v1.py

@@ -6,7 +6,7 @@
 import pyfive
 
 DIRNAME = os.path.dirname(__file__)
-DATASET_COMPRESSED_HDF5_FILE = os.path.join(DIRNAME, 'compressed_v1.hdf5')
+DATASET_COMPRESSED_HDF5_FILE = os.path.join(DIRNAME, 'data', 'compressed_v1.hdf5')
 
 
 def test_compressed_v1_dataset():

tests/test_dataset_datatypes.py

@@ -10,7 +10,7 @@
 import pyfive
 
 DIRNAME = os.path.dirname(__file__)
-DATASET_DATATYPES_HDF5_FILE = os.path.join(DIRNAME, 'dataset_datatypes.hdf5')
+DATASET_DATATYPES_HDF5_FILE = os.path.join(DIRNAME, 'data', 'dataset_datatypes.hdf5')
 MAKE_DATASET_DATATYPES_SCRIPT = os.path.join(DIRNAME, 'make_dataset_datatypes_file.py')
 
 

tests/test_dim_scales.py

@@ -7,7 +7,7 @@
 import pyfive
 
 DIRNAME = os.path.dirname(__file__)
-DIM_SCALES_HDF5_FILE = os.path.join(DIRNAME, './dim_scales.hdf5')
+DIM_SCALES_HDF5_FILE = os.path.join(DIRNAME, 'data', 'dim_scales.hdf5')
 
 
 def test_dim_labels():

tests/test_earliest.py

@@ -8,7 +8,7 @@
 import pyfive
 
 DIRNAME = os.path.dirname(__file__)
-EARLIEST_HDF5_FILE = os.path.join(DIRNAME, 'earliest.hdf5')
+EARLIEST_HDF5_FILE = os.path.join(DIRNAME, 'data', 'earliest.hdf5')
 
 # Polygot string type for representing unicode
 try:

tests/test_enum_var.py

@@ -10,8 +10,8 @@
 import pyfive
 
 DIRNAME = os.path.dirname(__file__)
-ENUMVAR_NC_FILE = os.path.join(DIRNAME, 'enum_variable.nc')
-ENUMVAR_H5_FILE = os.path.join(DIRNAME, 'enum_variable.hdf5')
+ENUMVAR_NC_FILE = os.path.join(DIRNAME, "data", 'enum_variable.nc')
+ENUMVAR_H5_FILE = os.path.join(DIRNAME, "data", 'enum_variable.hdf5')
 MAKE_ENUM_VARIABLE_SCRIPT = os.path.join(DIRNAME, 'make_enum_file.py')
 
 

tests/test_file_like.py

@@ -10,7 +10,7 @@
 import pyfive
 
 DIRNAME = os.path.dirname(__file__)
-LATEST_HDF5_FILE = os.path.join(DIRNAME, 'latest.hdf5')
+LATEST_HDF5_FILE = os.path.join(DIRNAME, 'data', 'latest.hdf5')
 
 # Polygot string type for representing unicode
 try:

tests/test_fillvalue.py

@@ -9,9 +9,9 @@
 
 DIRNAME = os.path.dirname(__file__)
 DATASET_FILLVALUE_EARLIEST_HDF5_FILE = os.path.join(
-    DIRNAME, 'fillvalue_earliest.hdf5')
+    DIRNAME, 'data', 'fillvalue_earliest.hdf5')
 DATASET_FILLVALUE_LATEST_HDF5_FILE = os.path.join(
-    DIRNAME, 'fillvalue_latest.hdf5')
+    DIRNAME, 'data', 'fillvalue_latest.hdf5')
 
 
 def test_dataset_fillvalue_earliest():

tests/test_filter_pipeline_v2.py

@@ -7,7 +7,7 @@
 import pyfive
 
 DIRNAME = os.path.dirname(__file__)
-FILTER_PIPELINE_V2_FILE = os.path.join(DIRNAME, 'filter_pipeline_v2.hdf5')
+FILTER_PIPELINE_V2_FILE = os.path.join(DIRNAME, 'data', 'filter_pipeline_v2.hdf5')
 
 
 def test_filter_pipeline_descr_v2():

tests/test_fletcher32.py

@@ -9,7 +9,7 @@
 from pyfive.btree import BTreeV1RawDataChunks
 
 DIRNAME = os.path.dirname(__file__)
-DATASET_FLETCHER_HDF5_FILE = os.path.join(DIRNAME, 'fletcher32.hdf5')
+DATASET_FLETCHER_HDF5_FILE = os.path.join(DIRNAME, 'data', 'fletcher32.hdf5')
 
 
 def test_fletcher32_datasets():

tests/test_groups.py

@@ -4,7 +4,7 @@
 import pyfive
 
 DIRNAME = os.path.dirname(__file__)
-GROUPS_HDF5_FILE = os.path.join(DIRNAME, 'groups.hdf5')
+GROUPS_HDF5_FILE = os.path.join(DIRNAME, 'data', 'groups.hdf5')
 
 
 def test_groups():

tests/test_h5d.py

@@ -1,11 +1,14 @@
+import os
+
 import h5py
 import pyfive
 from pathlib import Path
 import pytest
 from operator import mul
 
+
 mypath = Path(__file__).parent
-filename = 'compressed.hdf5'
+filename = os.path.join(mypath, "data", 'compressed.hdf5')
 variable_name = 'dataset3'
 breaking_address=(2,0)
 

tests/test_h5netcdf.py

@@ -1,6 +1,8 @@
 # tests the variables found in the file h5netcdf_test.hdf5,
 # which is produced by the write_h5netcdf test routine in the h5netcdf package
 #
+import os
+
 import pyfive
 import h5py
 import warnings
@@ -9,8 +11,9 @@
 DIRNAME = Path(__file__).parent
 
 def test_file_contents():
-    p5file = pyfive.File(DIRNAME/'h5netcdf_test.hdf5') 
-    h5file = h5py.File(DIRNAME/'h5netcdf_test.hdf5')
+    fpath = os.path.join(DIRNAME, 'data', 'h5netcdf_test.hdf5')
+    p5file = pyfive.File(fpath) 
+    h5file = h5py.File(fpath)
 
     expected_variables = [
         "foo",

tests/test_high_level.py

@@ -9,7 +9,7 @@
 import pyfive
 
 DIRNAME = os.path.dirname(__file__)
-EARLIEST_HDF5_FILE = os.path.join(DIRNAME, 'earliest.hdf5')
+EARLIEST_HDF5_FILE = os.path.join(DIRNAME, 'data', 'earliest.hdf5')
 
 # Polyglot string type for representing unicode
 try:

tests/test_latest.py

@@ -7,7 +7,7 @@
 import pyfive
 
 DIRNAME = os.path.dirname(__file__)
-LATEST_HDF5_FILE = os.path.join(DIRNAME, 'latest.hdf5')
+LATEST_HDF5_FILE = os.path.join(DIRNAME, 'data', 'latest.hdf5')
 
 # Polygot string type for representing unicode
 try:

tests/test_netcd4_classic.py

@@ -8,7 +8,7 @@
 import pyfive
 
 DIRNAME = os.path.dirname(__file__)
-NETCDF4_CLASSIC_FILE = os.path.join(DIRNAME, 'netcdf4_classic.nc')
+NETCDF4_CLASSIC_FILE = os.path.join(DIRNAME, "data", 'netcdf4_classic.nc')
 
 
 def test_read_netcdf4_classic():

tests/test_new_style_groups.py

@@ -3,7 +3,7 @@
 import pyfive
 
 DIRNAME = os.path.dirname(__file__)
-NEW_STYLE_GROUPS_HDF5_FILE = os.path.join(DIRNAME, "new_style_groups.hdf5")
+NEW_STYLE_GROUPS_HDF5_FILE = os.path.join(DIRNAME, "data", "new_style_groups.hdf5")
 
 
 def test_groups():

tests/test_opaque.py

@@ -80,12 +80,10 @@ def test_opaque_dataset2_fixed(really_opaque):
         assert pyfive.check_enum_dtype(dset.dtype) is None
 
 
-
-
 @pytest.fixture(scope='module')
-def really_opaque():
+def really_opaque(modular_tmp_path):
     """ Create an HDF5 file with a fixed size opaque dataset. """
-    name = os.path.join(os.path.dirname(__file__), "opaque_fixed.hdf5")
+    name = modular_tmp_path / "opaque_fixed.hdf5"
 
     with h5py.File(name, "w") as f:
         # Define a fixed-size opaque dtype as NumPy void
@@ -127,9 +125,9 @@ def data():
 
 
 @pytest.fixture(scope='module')
-def name(data):
+def name(data, modular_tmp_path):
     """Create an HDF5 file with datetime64 data stored as opaque."""
-    name = os.path.join(os.path.dirname(__file__), "opaque_datetime.hdf5")
+    name = modular_tmp_path / "opaque_datetime.hdf5"
 
     (ordinary_data, string_data, opdata) = data