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Hello community,
here is the log from the commit of package python-spyder-kernels for
openSUSE:Factory checked in at 2023-06-07 23:07:48
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-spyder-kernels (Old)
and /work/SRC/openSUSE:Factory/.python-spyder-kernels.new.15902 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-spyder-kernels"
Wed Jun 7 23:07:48 2023 rev:42 rq:1091239 version:2.4.3
Changes:
--------
---
/work/SRC/openSUSE:Factory/python-spyder-kernels/python-spyder-kernels.changes
2023-04-29 17:28:11.246553943 +0200
+++
/work/SRC/openSUSE:Factory/.python-spyder-kernels.new.15902/python-spyder-kernels.changes
2023-06-07 23:08:23.639681999 +0200
@@ -1,0 +2,6 @@
+Wed Jun 7 09:43:03 UTC 2023 - Ben Greiner <[email protected]>
+
+- Add spyder-kernels-pr453.patch gh#spyder-ide/spyder-kernels#453
+ * fixes test failure with pandas 2
+
+-------------------------------------------------------------------
New:
----
data.dcm
spyder-kernels-pr453.patch
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-spyder-kernels.spec ++++++
--- /var/tmp/diff_new_pack.H2uIt7/_old 2023-06-07 23:08:24.355686156 +0200
+++ /var/tmp/diff_new_pack.H2uIt7/_new 2023-06-07 23:08:24.359686179 +0200
@@ -26,7 +26,11 @@
Group: Development/Languages/Python
URL: https://github.com/spyder-ide/spyder-kernels
# PyPI tarballs do not include the tests:
https://github.com/spyder-ide/spyder-kernels/issues/66
-Source:
https://github.com/spyder-ide/spyder-kernels/archive/v%{version}.tar.gz#/spyder-kernels-%{version}-gh.tar.gz
+Source0:
https://github.com/spyder-ide/spyder-kernels/archive/v%{version}.tar.gz#/spyder-kernels-%{version}-gh.tar.gz
+# for Patch0
+Source1:
https://github.com/spyder-ide/spyder-kernels/raw/d14e5c982bfb75d6553a49667e3501648579e964/spyder_kernels/utils/tests/data.dcm
+# PATCH-FIX-UPSTREAM spyder-kernels-pr453.patch
gh#spyder-ide/spyder-kernels#453
+Patch0: spyder-kernels-pr453.patch
BuildRequires: %{python_module base >= 3.7}
BuildRequires: %{python_module setuptools}
BuildRequires: fdupes
@@ -37,6 +41,7 @@
BuildRequires: %{python_module Pillow}
BuildRequires: %{python_module cloudpickle}
BuildRequires: %{python_module flaky}
+BuildRequires: %{python_module h5py}
BuildRequires: %{python_module ipykernel >= 6.16.1 with %python-ipykernel < 7}
BuildRequires: %{python_module jupyter_client >= 7.4.9 with
%python-jupyter_client < 9}
BuildConflicts: %{python_module jupyter_client >= 8.8 with
%python-jupyter_client < 8.10.1}
@@ -44,6 +49,7 @@
BuildRequires: %{python_module matplotlib}
BuildRequires: %{python_module numpy}
BuildRequires: %{python_module pandas}
+BuildRequires: %{python_module pydicom}
BuildRequires: %{python_module pytest}
BuildRequires: %{python_module pyzmq >= 22.1}
BuildRequires: %{python_module scipy}
@@ -76,6 +82,7 @@
%prep
%autosetup -p1 -n spyder-kernels-%{version}
+cp %{SOURCE1} spyder_kernels/utils/tests/data.dcm
%build
%python_build
++++++ spyder-kernels-pr453.patch ++++++
>From ef612ee7df93bb462f05ebdfbce37a9c3b74bef1 Mon Sep 17 00:00:00 2001
From: Carlos Cordoba <[email protected]>
Date: Wed, 5 Apr 2023 11:50:21 -0500
Subject: [PATCH 1/3] Move code that loads and saves Hdf5 and Dicom files from
Spyder
That code was not working since the Spyder 5.0 release
---
spyder_kernels/utils/iofuncs.py | 130 ++++++++++++++++++++++++--------
1 file changed, 99 insertions(+), 31 deletions(-)
Index: spyder-kernels-2.4.3/spyder_kernels/utils/iofuncs.py
===================================================================
--- spyder-kernels-2.4.3.orig/spyder_kernels/utils/iofuncs.py
+++ spyder-kernels-2.4.3/spyder_kernels/utils/iofuncs.py
@@ -35,6 +35,8 @@ from spyder_kernels.utils.lazymodules im
FakeObject, numpy as np, pandas as pd, PIL, scipy as sp)
+# ---- For Matlab files
+# -----------------------------------------------------------------------------
class MatlabStruct(dict):
"""
Matlab style struct, enhanced.
@@ -44,7 +46,7 @@ class MatlabStruct(dict):
Examples
========
- >>> from spyder.utils.iofuncs import MatlabStruct
+ >>> from spyder_kernels.utils.iofuncs import MatlabStruct
>>> a = MatlabStruct()
>>> a.b = 'spam' # a["b"] == 'spam'
>>> a.c["d"] = 'eggs' # a.c.d == 'eggs'
@@ -169,6 +171,8 @@ def save_matlab(data, filename):
return str(error)
+# ---- For arrays
+# -----------------------------------------------------------------------------
def load_array(filename):
if np.load is FakeObject:
return None, ''
@@ -193,6 +197,8 @@ def __save_array(data, basename, index):
return fname
+# ---- For PIL images
+# -----------------------------------------------------------------------------
if sys.byteorder == 'little':
_ENDIAN = '<'
else:
@@ -237,6 +243,8 @@ def load_image(filename):
return None, str(error)
+# ---- For misc formats
+# -----------------------------------------------------------------------------
def load_pickle(filename):
"""Load a pickle file as a dictionary"""
try:
@@ -264,6 +272,8 @@ def load_json(filename):
return None, str(err)
+# ---- For Spydata files
+# -----------------------------------------------------------------------------
def save_dictionary(data, filename):
"""Save dictionary in a single file .spydata file"""
filename = osp.abspath(filename)
@@ -437,6 +447,89 @@ def load_dictionary(filename):
return data, error_message
+# ---- For HDF5 files
+# -----------------------------------------------------------------------------
+def load_hdf5(filename):
+ """
+ Load an hdf5 file.
+
+ Notes
+ -----
+ - This is a fairly dumb implementation which reads the whole HDF5 file into
+ Spyder's variable explorer. Since HDF5 files are designed for storing
+ very large data-sets, it may be much better to work directly with the
+ HDF5 objects, thus keeping the data on disk. Nonetheless, this gives
+ quick and dirty but convenient access to them.
+ - There is no support for creating files with compression, chunking etc,
+ although these can be read without problem.
+ - When reading an HDF5 file with sub-groups, groups in the file will
+ correspond to dictionaries with the same layout.
+ """
+ def get_group(group):
+ contents = {}
+ for name, obj in list(group.items()):
+ if isinstance(obj, h5py.Dataset):
+ contents[name] = np.array(obj)
+ elif isinstance(obj, h5py.Group):
+ # it is a group, so call self recursively
+ contents[name] = get_group(obj)
+ # other objects such as links are ignored
+ return contents
+
+ try:
+ import h5py
+
+ f = h5py.File(filename, 'r')
+ contents = get_group(f)
+ f.close()
+ return contents, None
+ except Exception as error:
+ return None, str(error)
+
+
+def save_hdf5(data, filename):
+ """
+ Save an hdf5 file.
+
+ Notes
+ -----
+ - All datatypes to be saved must be convertible to a numpy array, otherwise
+ an exception will be raised.
+ - Data attributes are currently ignored.
+ - When saving data after reading it with load_hdf5, dictionaries are not
+ turned into HDF5 groups.
+ """
+ try:
+ import h5py
+
+ f = h5py.File(filename, 'w')
+ for key, value in list(data.items()):
+ f[key] = np.array(value)
+ f.close()
+ except Exception as error:
+ return str(error)
+
+
+# ---- For DICOM files
+# -----------------------------------------------------------------------------
+def load_dicom(filename):
+ """Load a DICOM files."""
+ try:
+ from pydicom import dicomio
+
+ name = osp.splitext(osp.basename(filename))[0]
+ try:
+ data = dicomio.read_file(filename, force=True)
+ except TypeError:
+ data = dicomio.read_file(filename)
+ arr = data.pixel_array
+ return {name: arr}, None
+ except Exception as error:
+ return None, str(error)
+
+
+# ---- Class to group all IO functionality
+# -----------------------------------------------------------------------------
class IOFunctions(object):
def __init__(self):
self.load_extensions = None
@@ -447,7 +540,7 @@ class IOFunctions(object):
self.save_funcs = None
def setup(self):
- iofuncs = self.get_internal_funcs()+self.get_3rd_party_funcs()
+ iofuncs = self.get_internal_funcs()
load_extensions = {}
save_extensions = {}
load_funcs = {}
@@ -455,6 +548,7 @@ class IOFunctions(object):
load_filters = []
save_filters = []
load_ext = []
+
for ext, name, loadfunc, savefunc in iofuncs:
filter_str = to_text_string(name + " (*%s)" % ext)
if loadfunc is not None:
@@ -466,9 +560,11 @@ class IOFunctions(object):
save_extensions[filter_str] = ext
save_filters.append(filter_str)
save_funcs[ext] = savefunc
- load_filters.insert(0, to_text_string("Supported files"+" (*"+\
- " *".join(load_ext)+")"))
+ load_filters.insert(
+ 0, str("Supported files" + " (*" + " *".join(load_ext) + ")")
+ )
load_filters.append(to_text_string("All files (*.*)"))
+
self.load_filters = "\n".join(load_filters)
self.save_filters = "\n".join(save_filters)
self.load_funcs = load_funcs
@@ -478,35 +574,22 @@ class IOFunctions(object):
def get_internal_funcs(self):
return [
- ('.spydata', "Spyder data files",
- load_dictionary, save_dictionary),
- ('.npy', "NumPy arrays", load_array, None),
- ('.npz', "NumPy zip arrays", load_array, None),
- ('.mat', "Matlab files", load_matlab, save_matlab),
- ('.csv', "CSV text files", 'import_wizard', None),
- ('.txt', "Text files", 'import_wizard', None),
- ('.jpg', "JPEG images", load_image, None),
- ('.png', "PNG images", load_image, None),
- ('.gif', "GIF images", load_image, None),
- ('.tif', "TIFF images", load_image, None),
- ('.pkl', "Pickle files", load_pickle, None),
- ('.pickle', "Pickle files", load_pickle, None),
- ('.json', "JSON files", load_json, None),
- ]
-
- def get_3rd_party_funcs(self):
- other_funcs = []
- try:
- from spyder.otherplugins import get_spyderplugins_mods
- for mod in get_spyderplugins_mods(io=True):
- try:
- other_funcs.append((mod.FORMAT_EXT, mod.FORMAT_NAME,
- mod.FORMAT_LOAD, mod.FORMAT_SAVE))
- except AttributeError as error:
- print("%s: %s" % (mod, str(error)), file=sys.stderr)
- except ImportError:
- pass
- return other_funcs
+ ('.spydata', "Spyder data files", load_dictionary,
save_dictionary),
+ ('.npy', "NumPy arrays", load_array, None),
+ ('.npz', "NumPy zip arrays", load_array, None),
+ ('.mat', "Matlab files", load_matlab, save_matlab),
+ ('.csv', "CSV text files", 'import_wizard', None),
+ ('.txt', "Text files", 'import_wizard', None),
+ ('.jpg', "JPEG images", load_image, None),
+ ('.png', "PNG images", load_image, None),
+ ('.gif', "GIF images", load_image, None),
+ ('.tif', "TIFF images", load_image, None),
+ ('.pkl', "Pickle files", load_pickle, None),
+ ('.pickle', "Pickle files", load_pickle, None),
+ ('.json', "JSON files", load_json, None),
+ ('.h5', "HDF5 files", load_hdf5, save_hdf5),
+ ('.dcm', "DICOM images", load_dicom, None),
+ ]
def save(self, data, filename):
ext = osp.splitext(filename)[1].lower()
@@ -526,11 +609,8 @@ iofunctions = IOFunctions()
iofunctions.setup()
-def save_auto(data, filename):
- """Save data into filename, depending on file extension"""
- pass
-
-
+# ---- Test
+# -----------------------------------------------------------------------------
if __name__ == "__main__":
import datetime
testdict = {'d': 1, 'a': np.random.rand(10, 10), 'b': [1, 2]}
@@ -549,9 +629,9 @@ if __name__ == "__main__":
import time
t0 = time.time()
save_dictionary(example, "test.spydata")
- print(" Data saved in %.3f seconds" % (time.time()-t0)) # spyder:
test-skip
+ print(" Data saved in %.3f seconds" % (time.time()-t0))
t0 = time.time()
example2, ok = load_dictionary("test.spydata")
os.remove("test.spydata")
- print("Data loaded in %.3f seconds" % (time.time()-t0)) # spyder:
test-skip
+ print("Data loaded in %.3f seconds" % (time.time()-t0))
Index: spyder-kernels-2.4.3/.github/workflows/linux-pip-tests.yml
===================================================================
--- spyder-kernels-2.4.3.orig/.github/workflows/linux-pip-tests.yml
+++ spyder-kernels-2.4.3/.github/workflows/linux-pip-tests.yml
@@ -55,9 +55,9 @@ jobs:
- name: Run tests
shell: bash -l {0}
run: |
- xvfb-run --auto-servernum pytest spyder_kernels --color=yes
--cov=spyder_kernels -x -vv || \
- xvfb-run --auto-servernum pytest spyder_kernels --color=yes
--cov=spyder_kernels -x -vv || \
- xvfb-run --auto-servernum pytest spyder_kernels --color=yes
--cov=spyder_kernels -x -vv
+ xvfb-run --auto-servernum pytest spyder_kernels --color=yes
--cov=spyder_kernels -vv || \
+ xvfb-run --auto-servernum pytest spyder_kernels --color=yes
--cov=spyder_kernels -vv || \
+ xvfb-run --auto-servernum pytest spyder_kernels --color=yes
--cov=spyder_kernels -vv
- name: Upload coverage to Codecov
if: matrix.PYTHON_VERSION == '3.8'
shell: bash -l {0}
Index: spyder-kernels-2.4.3/.github/workflows/linux-tests.yml
===================================================================
--- spyder-kernels-2.4.3.orig/.github/workflows/linux-tests.yml
+++ spyder-kernels-2.4.3/.github/workflows/linux-tests.yml
@@ -62,9 +62,9 @@ jobs:
- name: Run tests
shell: bash -l {0}
run: |
- xvfb-run --auto-servernum pytest spyder_kernels --color=yes
--cov=spyder_kernels -x -vv || \
- xvfb-run --auto-servernum pytest spyder_kernels --color=yes
--cov=spyder_kernels -x -vv || \
- xvfb-run --auto-servernum pytest spyder_kernels --color=yes
--cov=spyder_kernels -x -vv
+ xvfb-run --auto-servernum pytest spyder_kernels --color=yes
--cov=spyder_kernels -vv || \
+ xvfb-run --auto-servernum pytest spyder_kernels --color=yes
--cov=spyder_kernels -vv || \
+ xvfb-run --auto-servernum pytest spyder_kernels --color=yes
--cov=spyder_kernels -vv
- name: Upload coverage to Codecov
if: matrix.PYTHON_VERSION == '3.8'
shell: bash -l {0}
Index: spyder-kernels-2.4.3/.github/workflows/macos-tests.yml
===================================================================
--- spyder-kernels-2.4.3.orig/.github/workflows/macos-tests.yml
+++ spyder-kernels-2.4.3/.github/workflows/macos-tests.yml
@@ -57,6 +57,6 @@ jobs:
- name: Run tests
shell: bash -l {0}
run: |
- pytest spyder_kernels --color=yes --cov=spyder_kernels -x -vv || \
- pytest spyder_kernels --color=yes --cov=spyder_kernels -x -vv || \
- pytest spyder_kernels --color=yes --cov=spyder_kernels -x -vv
+ pytest spyder_kernels --color=yes --cov=spyder_kernels -vv || \
+ pytest spyder_kernels --color=yes --cov=spyder_kernels -vv || \
+ pytest spyder_kernels --color=yes --cov=spyder_kernels -vv
Index: spyder-kernels-2.4.3/.github/workflows/windows-tests.yml
===================================================================
--- spyder-kernels-2.4.3.orig/.github/workflows/windows-tests.yml
+++ spyder-kernels-2.4.3/.github/workflows/windows-tests.yml
@@ -57,6 +57,6 @@ jobs:
- name: Run tests
shell: bash -l {0}
run: |
- pytest spyder_kernels --color=yes --cov=spyder_kernels -x -vv || \
- pytest spyder_kernels --color=yes --cov=spyder_kernels -x -vv || \
- pytest spyder_kernels --cov=spyder_kernels -x -vv
+ pytest spyder_kernels --color=yes --cov=spyder_kernels -vv || \
+ pytest spyder_kernels --color=yes --cov=spyder_kernels -vv || \
+ pytest spyder_kernels --cov=spyder_kernels -vv
Index: spyder-kernels-2.4.3/requirements/tests.txt
===================================================================
--- spyder-kernels-2.4.3.orig/requirements/tests.txt
+++ spyder-kernels-2.4.3/requirements/tests.txt
@@ -12,3 +12,5 @@ scipy
xarray
pillow
django
+h5py
+pydicom
Index: spyder-kernels-2.4.3/setup.py
===================================================================
--- spyder-kernels-2.4.3.orig/setup.py
+++ spyder-kernels-2.4.3/setup.py
@@ -65,6 +65,8 @@ TEST_REQUIREMENTS = [
'xarray',
'pillow',
'django',
+ 'h5py',
+ 'pydicom'
]
setup(
Index: spyder-kernels-2.4.3/spyder_kernels/utils/tests/test_iofuncs.py
===================================================================
--- spyder-kernels-2.4.3.orig/spyder_kernels/utils/tests/test_iofuncs.py
+++ spyder-kernels-2.4.3/spyder_kernels/utils/tests/test_iofuncs.py
@@ -16,6 +16,7 @@ import os
import copy
# Third party imports
+from PIL import ImageFile
import pytest
import numpy as np
@@ -25,8 +26,9 @@ from spyder_kernels.py3compat import is_
# Full path to this file's parent directory for loading data
-LOCATION = os.path.realpath(os.path.join(os.getcwd(),
- os.path.dirname(__file__)))
+LOCATION = os.path.realpath(
+ os.path.join(os.getcwd(), os.path.dirname(__file__))
+)
# =============================================================================
@@ -340,5 +342,25 @@ def test_spydata_export(input_namespace,
pass
+def test_save_load_hdf5_files():
+ """Simple test to check that we can save and load HDF5 files."""
+ data = {'a' : [1, 2, 3, 4], 'b' : 4.5}
+ iofuncs.save_hdf5(data, "test.h5")
+
+ expected = ({'a': np.array([1, 2, 3, 4]), 'b': np.array(4.5)}, None)
+ assert repr(iofuncs.load_hdf5("test.h5")) == repr(expected)
+
+
+def test_load_dicom_files():
+ """Check that we can load DICOM files."""
+ # This test pass locally but we need to set the variable below for it to
+ # pass on CIs.
+ # See https://stackoverflow.com/a/47958486/438386 for context.
+ ImageFile.LOAD_TRUNCATED_IMAGES = True
+
+ data = iofuncs.load_dicom(os.path.join(LOCATION, 'data.dcm'))
+ assert data[0]['data'].shape == (512, 512)
+
+
if __name__ == "__main__":
pytest.main()
Index: spyder-kernels-2.4.3/spyder_kernels/utils/tests/test_nsview.py
===================================================================
--- spyder-kernels-2.4.3.orig/spyder_kernels/utils/tests/test_nsview.py
+++ spyder-kernels-2.4.3/spyder_kernels/utils/tests/test_nsview.py
@@ -353,7 +353,7 @@ def test_get_type_string():
assert get_type_string(series) == 'Series'
index = pd.Index([1, 2, 3])
- assert get_type_string(index) == 'Int64Index'
+ assert get_type_string(index) in ['Int64Index', 'Index']
# PIL images
img = PIL.Image.new('RGB', (256,256))
