When I ran the command pytest tests under the CellProfiler-plugins folder, it reported errors shown below. I had already run the pip install -e . and pip install -e .[imagejscript] for dependencies installation before I ran the test. What should I do to make these tests pass?
================================================= test session starts =================================================
platform win32 -- Python 3.8.19, pytest-8.3.2, pluggy-1.5.0
rootdir: C:\software\CellProfiler-plugins
collected 0 items / 1 error
======================================================= ERRORS ========================================================
___________________________________ ERROR collecting tests/test_runimagejscript.py ____________________________________
ImportError while importing test module 'C:\software\CellProfiler-plugins\tests\test_runimagejscript.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\importlib\__init__.py:127: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests\test_runimagejscript.py:17: in <module>
import cellprofiler.modules.runimagejscript
E ModuleNotFoundError: No module named 'cellprofiler.modules.runimagejscript'
================================================== warnings summary ===================================================
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\cellprofiler_core\utilities\image.py:11
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\cellprofiler_core\utilities\image.py:11: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
import pkg_resources
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\pkg_resources\__init__.py:3144
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\pkg_resources\__init__.py:3144: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('mpl_toolkits')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
declare_namespace(pkg)
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\util\dtype.py:27
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\util\dtype.py:27: DeprecationWarning: `np.bool8` is a deprecated alias for `np.bool_`. (Deprecated NumPy 1.24)
np.bool8: (False, True),
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\io\collection.py:15
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\io\collection.py:15
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\io\collection.py:15: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
if LooseVersion(pil_version) < LooseVersion('7.1.0'):
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\restoration\inpaint.py:6
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\restoration\inpaint.py:6: DeprecationWarning: Please use `laplace` from the `scipy.ndimage` namespace, the `scipy.ndimage.filters` namespace is deprecated.
from scipy.ndimage.filters import laplace
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\feature\_orb_descriptor_positions.py:8
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\feature\_orb_descriptor_positions.py:8: DeprecationWarning: loadtxt(): Parsing an integer via a float is deprecated. To avoid this warning, you can:
* make sure the original data is stored as integers.
* use the `converters=` keyword argument. If you only use
NumPy 1.23 or later, `converters=float` will normally work.
* Use `np.loadtxt(...).astype(np.int64)` parsing the file as
floating point and then convert it. (On all NumPy versions.)
(Deprecated NumPy 1.23)
POS = np.loadtxt(os.path.join(this_dir, "orb_descriptor_positions.txt"),
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\filters\_unsharp_mask.py:2
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\filters\_unsharp_mask.py:2: DeprecationWarning: Please use `gaussian_filter` from the `scipy.ndimage` namespace, the `scipy.ndimage.filters` namespace is deprecated.
from scipy.ndimage.filters import gaussian_filter
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\io\_plugins\imageio_plugin.py:10
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\io\_plugins\imageio_plugin.py:10
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\io\_plugins\imageio_plugin.py:10
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\io\_plugins\imageio_plugin.py:10: DeprecationWarning: Starting with ImageIO v3 the behavior of this function will switch to that of iio.v3.imread. To keep the current behavior (and make this warning disappear) use `import imageio.v2 as imageio` or call `imageio.v2.imread` directly.
return np.asarray(imageio_imread(*args, **kwargs))
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=============================================== short test summary info ===============================================
ERROR tests/test_runimagejscript.py
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
============================================ 11 warnings, 1 error in 0.55s ============================================
(test_plugin) C:\software\CellProfiler-plugins>pytest tests
================================================= test session starts =================================================
platform win32 -- Python 3.8.19, pytest-8.3.2, pluggy-1.5.0
rootdir: C:\software\CellProfiler-plugins
collected 0 items / 2 errors
======================================================= ERRORS ========================================================
________________________________ ERROR collecting tests/test_histogramequalization.py _________________________________
ImportError while importing test module 'C:\software\CellProfiler-plugins\tests\test_histogramequalization.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\importlib\__init__.py:127: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests\test_histogramequalization.py:6: in <module>
import histogramequalization
E ModuleNotFoundError: No module named 'histogramequalization'
___________________________________ ERROR collecting tests/test_runimagejscript.py ____________________________________
ImportError while importing test module 'C:\software\CellProfiler-plugins\tests\test_runimagejscript.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\importlib\__init__.py:127: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests\test_runimagejscript.py:17: in <module>
import cellprofiler.modules.runimagejscript
E ModuleNotFoundError: No module named 'cellprofiler.modules.runimagejscript'
================================================== warnings summary ===================================================
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\cellprofiler_core\utilities\image.py:11
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\cellprofiler_core\utilities\image.py:11: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
import pkg_resources
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\pkg_resources\__init__.py:3144
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\pkg_resources\__init__.py:3144: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('mpl_toolkits')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
declare_namespace(pkg)
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\util\dtype.py:27
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\util\dtype.py:27: DeprecationWarning: `np.bool8` is a deprecated alias for `np.bool_`. (Deprecated NumPy 1.24)
np.bool8: (False, True),
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\io\collection.py:15
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\io\collection.py:15
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\io\collection.py:15: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
if LooseVersion(pil_version) < LooseVersion('7.1.0'):
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\restoration\inpaint.py:6
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\restoration\inpaint.py:6: DeprecationWarning: Please use `laplace` from the `scipy.ndimage` namespace, the `scipy.ndimage.filters` namespace is deprecated.
from scipy.ndimage.filters import laplace
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\feature\_orb_descriptor_positions.py:8
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\feature\_orb_descriptor_positions.py:8: DeprecationWarning: loadtxt(): Parsing an integer via a float is deprecated. To avoid this warning, you can:
* make sure the original data is stored as integers.
* use the `converters=` keyword argument. If you only use
NumPy 1.23 or later, `converters=float` will normally work.
* Use `np.loadtxt(...).astype(np.int64)` parsing the file as
floating point and then convert it. (On all NumPy versions.)
(Deprecated NumPy 1.23)
POS = np.loadtxt(os.path.join(this_dir, "orb_descriptor_positions.txt"),
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\filters\_unsharp_mask.py:2
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\filters\_unsharp_mask.py:2: DeprecationWarning: Please use `gaussian_filter` from the `scipy.ndimage` namespace, the `scipy.ndimage.filters` namespace is deprecated.
from scipy.ndimage.filters import gaussian_filter
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\io\_plugins\imageio_plugin.py:10
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\io\_plugins\imageio_plugin.py:10
..\..\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\io\_plugins\imageio_plugin.py:10
C:\Users\alexliu\Anaconda3\envs\test_plugin\lib\site-packages\skimage\io\_plugins\imageio_plugin.py:10: DeprecationWarning: Starting with ImageIO v3 the behavior of this function will switch to that of iio.v3.imread. To keep the current behavior (and make this warning disappear) use `import imageio.v2 as imageio` or call `imageio.v2.imread` directly.
return np.asarray(imageio_imread(*args, **kwargs))
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=============================================== short test summary info ===============================================
ERROR tests/test_histogramequalization.py
ERROR tests/test_runimagejscript.py
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 2 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
=========================================== 11 warnings, 2 errors in 0.56s ============================================
When I ran the command
pytest testsunder the CellProfiler-plugins folder, it reported errors shown below. I had already run thepip install -e .andpip install -e .[imagejscript]for dependencies installation before I ran the test. What should I do to make these tests pass?