Bump upper version of NumPy

[nfahlgren]

Describe your changes
Removes upper limit restriction on NumPy by fixing issues with deprecated methods, more stringent types, etc.

Type of update
Is this a: Work in progress

Associated issues
#1343

For the reviewer
See this page for instructions on how to review the pull request.

• PR functionality reviewed in a Jupyter Notebook
• All tests pass
• Test coverage remains 100%
• Documentation tested
• New documentation pages added to plantcv/mkdocs.yml
• Changes to function input/output signatures added to updating.md
• Code reviewed
• PR approved

[codecov]

Codecov Report

Merging #1347 (a92ae7b) into main (7912b18) will not change coverage.
The diff coverage is 100.00%.

@@            Coverage Diff            @@
##              main     #1347   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files          155       155           
  Lines         6840      6841    +1     
=========================================
+ Hits          6840      6841    +1     

Flag	Coverage Δ
unittests	100.00% <100.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Changed	Coverage Δ
plantcv/plantcv/analyze/npq.py	100.00% <100.00%> (ø)
...ntcv/plantcv/visualize/chlorophyll_fluorescence.py	100.00% <100.00%> (ø)

[nfahlgren]

With NumPy 1.25.2 the tests for pcv.analyze.npq fail with the following errors:

test_data = <tests.conftest.TestData object at 0x292409f30>

    def test_npq_cropreporter(test_data):
        """Test for PlantCV."""
        # Clear results
        outputs.clear()
        da_dark = test_data.psii_cropreporter('ojip_dark')
        da_light = test_data.psii_cropreporter('ojip_light')
>       _ = analyze_npq(ps_da_light=da_light, ps_da_dark=da_dark, labeled_mask=test_data.create_ps_mask(),
                        auto_fm=False,
                        measurement_labels=["Fq/Fm"], label="prefix", min_bin="auto", max_bin="auto")

tests/plantcv/analyze/test_npq.py:14:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
plantcv/plantcv/analyze/npq.py:87: in npq
    npq_lbl = ps_da_light.sel(frame_label='Fmp').groupby('measurement', squeeze=False).map(_calc_npq, fm=fm)
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/groupby.py:1396: in map
    return self._combine(applied, shortcut=shortcut)
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/groupby.py:1415: in _combine
    applied_example, applied = peek_at(applied)
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/utils.py:188: in peek_at
    peek = next(gen)
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/groupby.py:1395: in <genexpr>
    applied = (maybe_wrap_array(arr, func(arr, *args, **kwargs)) for arr in grouped)
plantcv/plantcv/analyze/npq.py:133: in _calc_npq
    div = np.divide(fm, fmp, out=out_flt,
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/arithmetic.py:86: in __array_ufunc__
    return apply_ufunc(
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/computation.py:1197: in apply_ufunc
    return apply_dataarray_vfunc(
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/computation.py:304: in apply_dataarray_vfunc
    result_var = func(*data_vars)
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/computation.py:833: in apply_array_ufunc
    return func(*args)
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/arithmetic.py:86: in __array_ufunc__
    return apply_ufunc(
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/computation.py:1210: in apply_ufunc
    return apply_array_ufunc(func, *args, dask=dask)
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/computation.py:815: in apply_array_ufunc
    if any(is_chunked_array(arg) for arg in args):
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/computation.py:815: in <genexpr>
    if any(is_chunked_array(arg) for arg in args):
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/pycompat.py:99: in is_chunked_array
    return is_duck_dask_array(x) or (is_duck_array(x) and hasattr(x, "chunks"))
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/pycompat.py:95: in is_duck_dask_array
    return is_duck_array(x) and is_dask_collection(x)
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/pycompat.py:87: in is_dask_collection
    if module_available("dask"):
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/utils.py:1160: in module_available
    return importlib.util.find_spec(module) is not None
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

name = 'dask', package = None

    def find_spec(name, package=None):
        """Return the spec for the specified module.

        First, sys.modules is checked to see if the module was already imported. If
        so, then sys.modules[name].__spec__ is returned. If that happens to be
        set to None, then ValueError is raised. If the module is not in
        sys.modules, then sys.meta_path is searched for a suitable spec with the
        value of 'path' given to the finders. None is returned if no spec could
        be found.

        If the name is for submodule (contains a dot), the parent module is
        automatically imported.

        The name and package arguments work the same as importlib.import_module().
        In other words, relative module names (with leading dots) work.

        """
>       fullname = resolve_name(name, package) if name.startswith('.') else name
E       RecursionError: maximum recursion depth exceeded while calling a Python object

../../miniconda3/envs/plantcv-test/lib/python3.10/importlib/util.py:90: RecursionError
!!! Recursion error detected, but an error occurred locating the origin of recursion.
  The following exception happened when comparing locals in the stack frame:
    ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
  Displaying first and last 10 stack frames out of 2225.
_________________________________________________________________________________________________ test_npq_waltz __________________________________________________________________________________________________

test_data = <tests.conftest.TestData object at 0x292409f30>

    def test_npq_waltz(test_data):
        """Test for PlantCV."""
        # Clear results
        outputs.clear()
        da_dark = test_data.psii_walz('ojip_dark')
        da_light = test_data.psii_walz('ojip_light')
>       _ = analyze_npq(ps_da_light=da_light, ps_da_dark=da_dark, labeled_mask=test_data.create_ps_mask(), auto_fm=True,
                        measurement_labels=None, label="prefix", min_bin="auto", max_bin="auto")

tests/plantcv/analyze/test_npq.py:26:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
plantcv/plantcv/analyze/npq.py:87: in npq
    npq_lbl = ps_da_light.sel(frame_label='Fmp').groupby('measurement', squeeze=False).map(_calc_npq, fm=fm)
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/groupby.py:1396: in map
    return self._combine(applied, shortcut=shortcut)
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/groupby.py:1415: in _combine
    applied_example, applied = peek_at(applied)
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/utils.py:188: in peek_at
    peek = next(gen)
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/groupby.py:1395: in <genexpr>
    applied = (maybe_wrap_array(arr, func(arr, *args, **kwargs)) for arr in grouped)
plantcv/plantcv/analyze/npq.py:133: in _calc_npq
    div = np.divide(fm, fmp, out=out_flt,
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/arithmetic.py:86: in __array_ufunc__
    return apply_ufunc(
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/computation.py:1197: in apply_ufunc
    return apply_dataarray_vfunc(
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/computation.py:304: in apply_dataarray_vfunc
    result_var = func(*data_vars)
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/computation.py:833: in apply_array_ufunc
    return func(*args)
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/arithmetic.py:86: in __array_ufunc__
    return apply_ufunc(
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/computation.py:1210: in apply_ufunc
    return apply_array_ufunc(func, *args, dask=dask)
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/computation.py:815: in apply_array_ufunc
    if any(is_chunked_array(arg) for arg in args):
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/computation.py:815: in <genexpr>
    if any(is_chunked_array(arg) for arg in args):
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/pycompat.py:99: in is_chunked_array
    return is_duck_dask_array(x) or (is_duck_array(x) and hasattr(x, "chunks"))
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/pycompat.py:95: in is_duck_dask_array
    return is_duck_array(x) and is_dask_collection(x)
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/pycompat.py:87: in is_dask_collection
    if module_available("dask"):
../../miniconda3/envs/plantcv-test/lib/python3.10/site-packages/xarray/core/utils.py:1160: in module_available
    return importlib.util.find_spec(module) is not None
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

name = 'dask', package = None

    def find_spec(name, package=None):
        """Return the spec for the specified module.

        First, sys.modules is checked to see if the module was already imported. If
        so, then sys.modules[name].__spec__ is returned. If that happens to be
        set to None, then ValueError is raised. If the module is not in
        sys.modules, then sys.meta_path is searched for a suitable spec with the
        value of 'path' given to the finders. None is returned if no spec could
        be found.

        If the name is for submodule (contains a dot), the parent module is
        automatically imported.

        The name and package arguments work the same as importlib.import_module().
        In other words, relative module names (with leading dots) work.

        """
>       fullname = resolve_name(name, package) if name.startswith('.') else name
E       RecursionError: maximum recursion depth exceeded while calling a Python object

../../miniconda3/envs/plantcv-test/lib/python3.10/importlib/util.py:90: RecursionError
!!! Recursion error detected, but an error occurred locating the origin of recursion.
  The following exception happened when comparing locals in the stack frame:
    ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
  Displaying first and last 10 stack frames out of 2225.

[nfahlgren]

I have confirmed that with these updates, tests pass with NumPy versions 1.22 - 1.25

[HaleySchuhl]

Nothing changed and the start output changed back to the old values somehow? Re-run tests and now pass... shrug, So now planning to make different test assertion