Merge pull request #62 from astrofrog/bump-minimum-python-39

Bump minimum required Python version to 3.9

.github/workflows/main.yml

@@ -9,21 +9,20 @@ jobs:
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
     with:
       envs: |
-        - linux: py38-test-casa-oldestdeps
-        - linux: py38-test-casa
-        - linux: py39-test
-        - linux: py310-test
-        - linux: py311-test-devdeps
+        - linux: py39-test-oldestdeps
+        - linux: py310-test-casa
+        - linux: py311-test
+        - linux: py312-test-devdeps
 
-        - macos: py38-test-casa
         - macos: py39-test
-        - macos: py310-test
-        - macos: py311-test-devdeps
+        - macos: py310-test-casa
+        - macos: py311-test
+        - macos: py312-test-devdeps
 
-        - windows: py38-test
         - windows: py39-test
         - windows: py310-test
-        - windows: py311-test-devdeps
+        - windows: py311-test
+        - windows: py312-test-devdeps
 
         # NOTE: the tests below are disabled for now until tox-conda is compatible with tox 4
 

README.rst

@@ -8,4 +8,4 @@ the file format and have re-used some of the data class names. Therefore, since
 be considered translations of casacore into Python, we license casa-formats-io under the same LGPL license as casacore.
 
 
-casa-formats-io supports python versions >=3.8.
+casa-formats-io supports python versions >=3.9.

casa_formats_io/casa_dask.py

@@ -2,6 +2,7 @@
 
 from __future__ import print_function, absolute_import, division
 
+from math import prod
 import os
 from math import ceil
 import uuid
@@ -46,7 +47,7 @@ def __init__(self, filename, totalshape, chunkshape, chunkoversample=None,
         self.dtype = dtype
         self.ndim = len(self.shape)
         self._stacks = np.ceil(np.array(totalshape) / np.array(chunkshape)).astype(int)
-        self._chunksize = np.product(chunkshape)
+        self._chunksize = prod(chunkshape)
         self._itemsize = itemsize
         self._memmap = memmap
         self._offset = offset
@@ -97,7 +98,7 @@ def __getitem__(self, item):
         if self._itemsize == 1:
 
             if self._memmap:
-                n_native = np.product(self._chunkoversample)
+                n_native = prod(self._chunkoversample)
                 rounded_up_chunksize = ceil(self._chunksize / n_native / 8) * n_native
                 offset = offset // self._chunksize * rounded_up_chunksize
                 array_uint8 = np.fromfile(self._filename, dtype=np.uint8,
@@ -180,22 +181,22 @@ def image_to_dask(imagename, memmap=True, mask=False, target_chunksize=None):
 
     # chunkshape defines how the chunks (array subsets) are written to disk
     chunkshape = tuple(dm.default_tile_shape)
-    chunksize = np.product(chunkshape)
+    chunksize = prod(chunkshape)
 
     # the total shape defines the final output array shape
     totalshape = dm.cube_shapes[0]
 
     # we expect that the total size of the array will be determined by finding
     # the number of chunks along each dimension rounded up
-    totalsize = np.product(np.ceil(totalshape / chunkshape)) * chunksize
+    totalsize = prod(np.ceil(totalshape / chunkshape)) * chunksize
 
     # the file size helps us figure out what the dtype of the array is
     filesize = os.stat(img_fn).st_size
 
     # the ratio between these tells you how many chunks must be combined
     # to create a final stack
     stacks = np.ceil(totalshape / chunkshape).astype(int)
-    nchunks = int(np.product(stacks))
+    nchunks = int(prod(stacks))
 
     # check that the file size is as expected and determine the data dtype
     if mask:
@@ -247,7 +248,7 @@ def image_to_dask(imagename, memmap=True, mask=False, target_chunksize=None):
             factors = [f for f in range(stacks[dim] + 1) if stacks[dim] % f == 0]
             for factor in factors:
                 chunkoversample[dim] = factor
-                if np.product(chunkoversample) * chunksize > target_chunksize:
+                if prod(chunkoversample) * chunksize > target_chunksize:
                     chunkoversample = previous_chunkoversample
                     finished = True
                     break

casa_formats_io/casa_low_level_io/casa_functions.py

@@ -24,7 +24,7 @@ def getdminfo(filename, endian='>'):
 
     if isinstance(dm, StandardStMan):
 
-        dminfo['COLUMNS'] = np.array(sorted(col.name for col in colset.columns), '<U16')
+        dminfo['COLUMNS'] = np.array(sorted(col.name for col in colset.columns), 'U')
         dminfo['NAME'] = dm.name
         dminfo['SEQNR'] = 0
         dminfo['TYPE'] = 'StandardStMan'

casa_formats_io/casa_low_level_io/core.py

@@ -158,7 +158,7 @@ def read_iposition(f):
     'float': ('float', read_float32, np.float32),
     'double': ('double', read_float64, np.float64),
     'dcomplex': ('void', read_complex128, np.complex128),
-    'string': ('String', read_string, '<U16'),
+    'string': ('String', read_string, 'U'),
     'int': ('Int', read_int32, int),
     'uint': ('uInt', read_int32, int)
 }
@@ -172,7 +172,7 @@ def read_iposition(f):
 TO_DTYPE['int'] = 'i4'
 TO_DTYPE['uint'] = 'u4'
 TO_DTYPE['short'] = 'i2'
-TO_DTYPE['string'] = '<U16'
+TO_DTYPE['string'] = 'U'
 TO_DTYPE['bool'] = 'bool'
 TO_DTYPE['record'] = 'O'
 
@@ -192,10 +192,6 @@ def read_as_numpy_array(f, value_type, nelem, shape=None, length_modifier=0):
     if value_type == 'string':
         array = np.array([read_string(f, length_modifier=length_modifier)
                           for i in range(nelem)])
-        if nelem > 0:
-            # HACK: only needed for getdesc comparisons
-            if max([len(s) for s in array]) < 16:
-                array = array.astype('<U16')
     elif value_type == 'bool':
         length = int(np.ceil(nelem / 8)) * 8
         array = np.unpackbits(np.frombuffer(f.read(length), dtype='uint8'),

casa_formats_io/casa_low_level_io/table.py

@@ -231,17 +231,17 @@ def read(cls, f):
             elif rectype == 'table':
                 self.values[name] = 'Table: ' + os.path.abspath(os.path.join(f.original_filename, read_string(f)))
             elif rectype == 'arrayint':
-                self.values[name] = read_array(f, 'int')
+                self.values[name] = read_array(f, 'int').astype('<i4')
             elif rectype == 'arrayuint':
-                self.values[name] = read_array(f, 'uint')
+                self.values[name] = read_array(f, 'uint').astype('<u4')
             elif rectype == 'arrayfloat':
-                self.values[name] = read_array(f, 'float')
+                self.values[name] = read_array(f, 'float').astype('<f4')
             elif rectype == 'arraydouble':
-                self.values[name] = read_array(f, 'double')
+                self.values[name] = read_array(f, 'double').astype('<f8')
             elif rectype == 'arraycomplex':
-                self.values[name] = read_array(f, 'complex')
+                self.values[name] = read_array(f, 'complex').astype('<c8')
             elif rectype == 'arraydcomplex':
-                self.values[name] = read_array(f, 'dcomplex')
+                self.values[name] = read_array(f, 'dcomplex').astype('<c16')
             elif rectype == 'arraystr':
                 self.values[name] = read_array(f, 'string')
             elif rectype == 'record':

casa_formats_io/casa_low_level_io/tests/test_casa_low_level_io.py

@@ -50,7 +50,7 @@ def test_getdminfo(tmp_path, shape):
     # the Numpy arrays inside). Older versions of casatools represent some of
     # the vectors as int32 instead of native int but our implementation uses
     # native int so strip any mention of int32 from reference output
-    assert pformat(actual) == pformat(reference).replace(', dtype=int32', '')
+    assert pformat(actual) == pformat(reference).replace(', dtype=int32', '').replace('U3', 'U16')
 
 
 def test_getdminfo_large():
@@ -83,7 +83,6 @@ def filename(request):
     return request.getfixturevalue(request.param)
 
 
-@pytest.mark.openfiles_ignore
 @pytest.mark.skipif('not CASATOOLS_INSTALLED')
 def test_generic_table_read(tmp_path):
 
@@ -122,7 +121,7 @@ def test_generic_table_read(tmp_path):
         keywords['scalars']['s_' + name] = t[name][0]
         keywords['arrays']['a_' + name] = t[name]
 
-    tb.open(filename_casa)
+    tb.open(filename_casa, nomodify=False)
     tb.putkeywords(keywords)
     tb.flush()
     tb.close()
@@ -138,10 +137,7 @@ def test_generic_table_read(tmp_path):
 
     actual_getdminfo = getdminfo(filename_casa, endian='<')
 
-    # FIXME: For some reason IndexLength is zero in the CASA output
-    actual_getdminfo['*1']['SPEC']['IndexLength'] = 0
-
-    assert pformat(actual_getdminfo) == pformat(reference_getdminfo)
+    assert pformat(actual_getdminfo).replace('<U16', '<U8') == pformat(reference_getdminfo)
 
     tnew = Table.read(filename_casa)
 
@@ -155,7 +151,7 @@ def test_getdesc_floatarray():
 
     desc = getdesc(os.path.join(DATA, 'floatarray.image'))
     trc = desc['_keywords_']['masks']['mask0']['box']['trc']
-    assert trc.dtype == np.dtype('>f4')
+    assert trc.dtype == np.dtype('<f4')
     assert_equal(trc, [512, 512, 1, 100])
 
 
@@ -246,7 +242,6 @@ def test_ms_tables(tablename):
         tb.close()
 
 
-@pytest.mark.openfiles_ignore
 @pytest.mark.skipif('not CASATOOLS_INSTALLED')
 def test_vector_columns(tmp_path):
 

docs/index.rst

@@ -17,7 +17,7 @@ to provide:
 At this time (November 2020), only reading .image datasets is supported. Reading measurement sets
 (.ms) or writing data of any kind are not yet supported.
 
-casa-formats-io supports python versions >=3.8.
+casa-formats-io supports python versions >=3.9.
 
 Using casa-formats-io
 ---------------------

setup.cfg

@@ -16,7 +16,7 @@ install_requires =
     astropy>=4.0
     numpy>=1.21
     dask[array]>=2.0
-python_requires = >=3.8
+python_requires = >=3.9
 
 [options.extras_require]
 test =
@@ -28,7 +28,7 @@ docs =
 casa =
     # Note that it looks like there is a casatools bug in 6.4.3.8
     # https://github.com/radio-astro-tools/casa-formats-io/issues/39
-    casatools>=6.2.0.124,<6.4.3.8
+    casatools>=6.2.0.12
 
 [options.package_data]
 casa_formats_io.tests = data/*, data/*/*, data/*/*/*, data/*/*/*/*
@@ -37,9 +37,6 @@ casa_formats_io.casa_low_level_io.tests = data/*, data/*/*, data/*/*/*, data/*/*
 [tool:pytest]
 minversion = 3.0
 norecursedirs = build docs/_build
-doctest_plus = enabled
-filterwarnings =
-    error::ResourceWarning
 
 [coverage:run]
 omit =
@@ -79,4 +76,4 @@ glue.plugins =
     casa_ms_reader = casa_formats_io.glue_factory:setup
 
 [bdist_wheel]
-py_limited_api = cp38
+py_limited_api = cp39

tox.ini

@@ -1,6 +1,6 @@
 [tox]
 envlist =
-    py{38,39,310}-test{,-oldestdeps,-devdeps,-casa}{,-conda}
+    py{39,310,311,312}-test{,-oldestdeps,-devdeps,-casa}{,-conda}
     build_docs
     codestyle
 requires =