Merge pull request #979 from PyTables/tables-3.8.0

Tables 3.8.0

.github/workflows/ci.yml

@@ -30,8 +30,6 @@ jobs:
     - name: Install dependencies
       run: |
         conda install setuptools pip wheel build packaging numpy cython bzip2 hdf5 lzo 'typing_extensions<4.2'
-        # We can use either the c-blosc2 package in conda/conda-forge or the official wheel (blosc2 in PyPI).
-        # conda install c-blosc2
         pip install -r requirements.txt
         # conda install sphinx sphinx_rtd_theme numpydoc ipython
     - name: Source distribution

.github/workflows/wheels.yml

@@ -64,8 +64,9 @@ jobs:
         include:
           - os: macos-latest
             arch: x86_64
-          - os: macos-latest
-            arch: arm64
+          # Still having issues here: https://github.com/PyTables/PyTables/pull/979
+          # - os: macos-latest
+          #   arch: arm64
 
     steps:
       - uses: actions/checkout@v3
@@ -183,11 +184,14 @@ jobs:
         os: [ 'ubuntu-latest', 'windows-latest', 'macos-latest' ]
         python-version: ['3.8', '3.9', '3.10', '3.11']
         arch: ['x64']
-#        include:
-#           This cannot be tested because NumPy does not distribute wheels for arm64
-#           - arch: arm64
-#             cibw_python: "cp*"
-#             os: macos-latest
+        include:
+          - arch: aarch64
+            cibw_python: "cp*"
+            os: ubuntu-latest
+          # Still having issues with wheels for Mac arm64
+          # - arch: arm64
+          #   cibw_python: "cp*"
+          #   os: macos-latest
 
     steps:
       - uses: actions/download-artifact@v3
@@ -202,7 +206,7 @@ jobs:
 
       - name: Install tables on ${{ matrix.python-version }}
         run: |
-          python -m pip install cython>=0.29.21 numpy>=1.19.0 numexpr>=2.6.2 packaging py-cpuinfo>=9.0.0 blosc2
+          python -m pip install cython>=0.29.21 numpy>=1.19.0 numexpr>=2.6.2 packaging py-cpuinfo>=9.0.0 blosc2~=2.0.0
           python -m pip install --no-index --find-links wheelhouse/artifact/ tables
 
       - name: Run tests on ${{ matrix.python-version }}

doc/source/usersguide/installation.rst

@@ -57,8 +57,9 @@ First, make sure that you have
 * c-blosc_ >= 1.11.1 (sources are bundled with PyTables sources but the user can
   use an external version of sources using the :envvar:`BLOSC_DIR` environment
   variable or the `--blosc` flag of the :file:`setup.py`)
-* blosc2_ >= 0.6.6 This is the Python wheel containing *both* the C-Blosc2 libs
-  and headers (>= 2.3.0), as well as the Python wrapper for Blosc2 (not used).
+* python-blosc2_ ~= 2.0.0 This is the Python wheel containing *both* the C-Blosc2 libs
+  and headers (>= 2.6.0), as well as the Python wrapper for Blosc2 (not currently
+  used, but it might be in the future).
 
 installed (for testing purposes, we are using HDF5_ 1.10.7, NumPy_ 1.23.2
 and Numexpr_ 2.8.1 currently). If you don't, fetch and install them before
@@ -70,7 +71,7 @@ proceeding.
 .. _Numexpr: http://code.google.com/p/numexpr
 .. _Cython: http://www.cython.org
 .. _c-blosc: https://github.com/Blosc/c-blosc
-.. _blosc2_: https://github.com/Blosc/python-blosc2
+.. _python-blosc2_: https://github.com/Blosc/python-blosc2
 
 Compile and install these packages (but see :ref:`prerequisitesBinInst` for
 instructions on how to install pre-compiled binaries if you are not willing

pyproject.toml

@@ -6,6 +6,6 @@ requires = [
     "packaging",
     "py-cpuinfo",
     "Cython >=0.29.21",
-    "blosc2 >=0.6.6"
+    "blosc2 ~=2.0.0"
 ]
 build-backend = "setuptools.build_meta"

requirements.txt

@@ -6,6 +6,6 @@ numpy>=1.19.0
 numexpr>=2.6.2
 # blosc2 wheel is actually only needed when compiling on conda envs.
 # Otherwise, lib comes bundled in PyTables wheels (but it doesn't hurt either).
-blosc2>=0.6.6
+blosc2~=2.0.0
 packaging
 py-cpuinfo

setup.py

@@ -113,9 +113,7 @@ def get_blosc2_directories():
     try:
         import blosc2
     except ModuleNotFoundError:
-        raise EnvironmentError(
-            "Cannot find neither the c-blosc2 package nor the "
-            "python-blosc2 wheel")
+        raise EnvironmentError("Cannot import the blosc2 requirement")
     version = blosc2.__version__
     basepath = Path(os.path.dirname(blosc2.__file__))
     recinfo = basepath.parent / f'blosc2-{version}.dist-info' / 'RECORD'

tables/__init__.py

@@ -31,7 +31,7 @@
 # Necessary imports to get versions stored on the cython extension
 from .utilsextension import get_hdf5_version as _get_hdf5_version
 
-__version__ = "3.7.1.dev0"
+__version__ = "3.8.0"
 """The PyTables version number."""
 
 hdf5_version = _get_hdf5_version()

tables/tests/test_numpy.py

@@ -548,24 +548,24 @@ def test04_setIndexNumPy(self):
         # Modify row 1
         # From PyTables 2.0 on, assignments to records can be done
         # only as tuples (see http://projects.scipy.org/scipy/numpy/ticket/315)
-        # table[coords[0]] = ["aasa","x"]+[232]*12
+        # table[coords[0]] = ["aasa","x"]+[123]*12
 
         n = len(Record.columns) - 2
 
-        table[coords[0]] = tuple(["aasa", "x"]+[232]*n)     # XXX
+        table[coords[0]] = tuple(["aasa", "x"]+[123]*n)     # XXX
         # record = list(table[coords[0]])
         record = table.read(coords[0], coords[0] + 1)
         if common.verbose:
             print("Original row:\n"
-                  "['aasa', 'x', True, -24, 232, 232, 232, 232, 232L, "
-                  "232, 232.0, 232.0, (232 + 0j), (232+0j), 232.0, "
-                  "(232+0j)]\n")
+                  "['aasa', 'x', True, 123, 123, 123, 123, 123, 123L, "
+                  "123, 123.0, 123.0, (123 + 0j), (123+0j), 123.0, "
+                  "(123+0j)]\n")
             print("Read row:\n", record)
         self.assertEqual(record['var1'], b'aasa')
         self.assertEqual(record['var2'], b'x')
         self.assertEqual(record['var3'], True)
-        self.assertEqual(record['var4'], -24)
-        self.assertEqual(record['var7'], 232)
+        self.assertEqual(record['var4'], 123)
+        self.assertEqual(record['var7'], 123)
 
 
 # The declaration of the nested table:

tables/tests/test_timetype.py

@@ -348,7 +348,7 @@ def test00_CompareTable(self):
 
         row = tbl.row
         for i in range(nrows):
-            row['i8col'] = i
+            row['i8col'] = np.array(i).astype('i1')
             row['t32col'] = i
             j = i * 2
             row['t64col'] = (j + 0.012, j+1+0.012)

tables/tests/test_types.py

@@ -51,7 +51,7 @@ def test00_range(self):
         i = self.maxshort
         rec['var1'] = '%04d' % (i)
         rec['var2'] = i
-        rec['var3'] = i
+        rec['var3'] = np.array(i).astype('i2')
         rec['var4'] = float(i)
         rec['var5'] = float(i)
         rec['var6'] = float(i)
@@ -83,7 +83,7 @@ def test01_type(self):
         i = self.maxshort
         rec['var1'] = '%04d' % (i)
         rec['var2'] = i
-        rec['var3'] = i % self.maxshort
+        rec['var3'] = np.array(i % self.maxshort).astype('i2')
         rec['var5'] = float(i)
 
         with self.assertRaises(TypeError):