Spyder has a problem with numpy - numpy isnt up to date

[aco200-blib]

Description

What steps will reproduce the problem?

When I try to run code with simple numpy functions, the code does not want to run and has an error with numpy

Traceback

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.1.1 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last):  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\plugins\application\container.py", line 492, in _compute_dependencies
    dependencies.declare_dependencies()
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\dependencies.py", line 458, in declare_dependencies
    add(dep['modname'], dep['package_name'],
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\dependencies.py", line 389, in add
    DEPENDENCIES += [Dependency(modname, package_name, features,
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\dependencies.py", line 331, in __init__
    self.installed_version = programs.get_module_version(modname)
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\utils\programs.py", line 839, in get_module_version
    mod = __import__(module_name)
  File "C:\Users\stasi\anaconda3\Lib\site-packages\matplotlib\__init__.py", line 161, in <module>
    from . import _api, _version, cbook, _docstring, rcsetup
  File "C:\Users\stasi\anaconda3\Lib\site-packages\matplotlib\rcsetup.py", line 27, in <module>
    from matplotlib.colors import Colormap, is_color_like
  File "C:\Users\stasi\anaconda3\Lib\site-packages\matplotlib\colors.py", line 57, in <module>
    from matplotlib import _api, _cm, cbook, scale
  File "C:\Users\stasi\anaconda3\Lib\site-packages\matplotlib\scale.py", line 22, in <module>
    from matplotlib.ticker import (
  File "C:\Users\stasi\anaconda3\Lib\site-packages\matplotlib\ticker.py", line 143, in <module>
    from matplotlib import transforms as mtransforms
  File "C:\Users\stasi\anaconda3\Lib\site-packages\matplotlib\transforms.py", line 49, in <module>
    from matplotlib._path import (
Traceback (most recent call last):
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\numpy\core\_multiarray_umath.py", line 44, in __getattr__
    raise ImportError(msg)
ImportError: 
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.1.1 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.



A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.1.1 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last):  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\plugins\application\container.py", line 492, in _compute_dependencies
    dependencies.declare_dependencies()
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\dependencies.py", line 458, in declare_dependencies
    add(dep['modname'], dep['package_name'],
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\dependencies.py", line 389, in add
    DEPENDENCIES += [Dependency(modname, package_name, features,
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\dependencies.py", line 331, in __init__
    self.installed_version = programs.get_module_version(modname)
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\utils\programs.py", line 839, in get_module_version
    mod = __import__(module_name)
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\__init__.py", line 39, in <module>
    from pandas.compat import (
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\compat\__init__.py", line 27, in <module>
    from pandas.compat.pyarrow import (
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\compat\pyarrow.py", line 8, in <module>
    import pyarrow as pa
  File "C:\Users\stasi\anaconda3\Lib\site-packages\pyarrow\__init__.py", line 65, in <module>
    import pyarrow.lib as _lib
Traceback (most recent call last):
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\numpy\core\_multiarray_umath.py", line 44, in __getattr__
    raise ImportError(msg)
ImportError: 
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.1.1 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.



A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.1.1 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last):  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\plugins\application\container.py", line 492, in _compute_dependencies
    dependencies.declare_dependencies()
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\dependencies.py", line 458, in declare_dependencies
    add(dep['modname'], dep['package_name'],
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\dependencies.py", line 389, in add
    DEPENDENCIES += [Dependency(modname, package_name, features,
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\dependencies.py", line 331, in __init__
    self.installed_version = programs.get_module_version(modname)
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\utils\programs.py", line 839, in get_module_version
    mod = __import__(module_name)
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\__init__.py", line 62, in <module>
    from pandas.core.api import (
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\core\api.py", line 9, in <module>
    from pandas.core.dtypes.dtypes import (
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\core\dtypes\dtypes.py", line 24, in <module>
    from pandas._libs import (
  File "C:\Users\stasi\anaconda3\Lib\site-packages\pyarrow\__init__.py", line 65, in <module>
    import pyarrow.lib as _lib
Traceback (most recent call last):
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\numpy\core\_multiarray_umath.py", line 44, in __getattr__
    raise ImportError(msg)
ImportError: 
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.1.1 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.



A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.1.1 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last):  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\plugins\application\container.py", line 492, in _compute_dependencies
    dependencies.declare_dependencies()
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\dependencies.py", line 458, in declare_dependencies
    add(dep['modname'], dep['package_name'],
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\dependencies.py", line 389, in add
    DEPENDENCIES += [Dependency(modname, package_name, features,
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\dependencies.py", line 331, in __init__
    self.installed_version = programs.get_module_version(modname)
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\utils\programs.py", line 839, in get_module_version
    mod = __import__(module_name)
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\__init__.py", line 62, in <module>
    from pandas.core.api import (
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\core\api.py", line 28, in <module>
    from pandas.core.arrays import Categorical
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\core\arrays\__init__.py", line 1, in <module>
    from pandas.core.arrays.arrow import ArrowExtensionArray
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\core\arrays\arrow\__init__.py", line 5, in <module>
    from pandas.core.arrays.arrow.array import ArrowExtensionArray
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\core\arrays\arrow\array.py", line 50, in <module>
    from pandas.core import (
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\core\ops\__init__.py", line 8, in <module>
    from pandas.core.ops.array_ops import (
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\core\ops\array_ops.py", line 56, in <module>
    from pandas.core.computation import expressions
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\core\computation\expressions.py", line 21, in <module>
    from pandas.core.computation.check import NUMEXPR_INSTALLED
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\core\computation\check.py", line 5, in <module>
    ne = import_optional_dependency("numexpr", errors="warn")
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\compat\_optional.py", line 135, in import_optional_dependency
    module = importlib.import_module(name)
  File "C:\Users\stasi\anaconda3\Lib\importlib\__init__.py", line 90, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "C:\Users\stasi\anaconda3\Lib\site-packages\numexpr\__init__.py", line 24, in <module>
    from numexpr.interpreter import MAX_THREADS, use_vml, __BLOCK_SIZE1__
AttributeError: _ARRAY_API not found

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.1.1 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last):  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\plugins\application\container.py", line 492, in _compute_dependencies
    dependencies.declare_dependencies()
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\dependencies.py", line 458, in declare_dependencies
    add(dep['modname'], dep['package_name'],
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\dependencies.py", line 389, in add
    DEPENDENCIES += [Dependency(modname, package_name, features,
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\dependencies.py", line 331, in __init__
    self.installed_version = programs.get_module_version(modname)
  File "C:\Users\stasi\anaconda3\Lib\site-packages\spyder\utils\programs.py", line 839, in get_module_version
    mod = __import__(module_name)
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\__init__.py", line 62, in <module>
    from pandas.core.api import (
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\core\api.py", line 28, in <module>
    from pandas.core.arrays import Categorical
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\core\arrays\__init__.py", line 1, in <module>
    from pandas.core.arrays.arrow import ArrowExtensionArray
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\core\arrays\arrow\__init__.py", line 5, in <module>
    from pandas.core.arrays.arrow.array import ArrowExtensionArray
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\core\arrays\arrow\array.py", line 64, in <module>
    from pandas.core.arrays.masked import BaseMaskedArray
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\core\arrays\masked.py", line 60, in <module>
    from pandas.core import (
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\core\nanops.py", line 52, in <module>
    bn = import_optional_dependency("bottleneck", errors="warn")
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\pandas\compat\_optional.py", line 135, in import_optional_dependency
    module = importlib.import_module(name)
  File "C:\Users\stasi\anaconda3\Lib\importlib\__init__.py", line 90, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "C:\Users\stasi\anaconda3\Lib\site-packages\bottleneck\__init__.py", line 7, in <module>
    from .move import (move_argmax, move_argmin, move_max, move_mean, move_median,
Traceback (most recent call last):
  File "C:\Users\stasi\AppData\Roaming\Python\Python312\site-packages\numpy\core\_multiarray_umath.py", line 44, in __getattr__
    raise ImportError(msg)
ImportError: 
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.1.1 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Versions

• Spyder version: 5.5.1 (conda)
• Python version: 3.12.4 64-bit
• Qt version: 5.15.2
• PyQt5 version: 5.15.10
• Operating System: Windows-11-10.0.22631-SP0

Dependencies

# Mandatory:
atomicwrites >=1.2.0             :  1.4.0 (OK)
chardet >=2.0.0                  :  4.0.0 (OK)
cloudpickle >=0.5.0              :  2.2.1 (OK)
cookiecutter >=1.6.0             :  2.6.0 (OK)
diff_match_patch >=20181111      :  20200713 (OK)
intervaltree >=3.0.2             :  3.1.0 (OK)
IPython >=8.13.0,<9.0.0,!=8.17.1 :  8.25.0 (OK)
jedi >=0.17.2,<0.20.0            :  0.18.1 (OK)
jellyfish >=0.7                  :  1.0.1 (OK)
jsonschema >=3.2.0               :  4.19.2 (OK)
keyring >=17.0.0                 :  24.3.1 (OK)
nbconvert >=4.0                  :  7.10.0 (OK)
numpydoc >=0.6.0                 :  1.7.0 (OK)
paramiko >=2.4.0                 :  2.8.1 (OK)
parso >=0.7.0,<0.9.0             :  0.8.3 (OK)
pexpect >=4.4.0                  :  4.8.0 (OK)
pickleshare >=0.4                :  0.7.5 (OK)
psutil >=5.3                     :  5.9.0 (OK)
pygments >=2.0                   :  2.15.1 (OK)
pylint >=2.5.0,<3.1              :  2.16.2 (OK)
pylint_venv >=3.0.2              :  3.0.3 (OK)
pyls_spyder >=0.4.0              :  0.4.0 (OK)
pylsp >=1.10.0,<1.11.0           :  1.10.0 (OK)
pylsp_black >=2.0.0,<3.0.0       :  2.0.0 (OK)
qdarkstyle >=3.2.0,<3.3.0        :  3.2.3 (OK)
qstylizer >=0.2.2                :  0.2.2 (OK)
qtawesome >=1.2.1                :  1.2.2 (OK)
qtconsole >=5.5.1,<5.6.0         :  5.5.1 (OK)
qtpy >=2.1.0                     :  2.4.1 (OK)
rtree >=0.9.7                    :  1.0.1 (OK)
setuptools >=49.6.0              :  69.5.1 (OK)
sphinx >=0.6.6                   :  7.3.7 (OK)
spyder_kernels >=2.5.0,<2.6.0    :  2.5.0 (OK)
textdistance >=4.2.0             :  4.2.1 (OK)
three_merge >=0.1.1              :  0.1.1 (OK)
watchdog >=0.10.3                :  4.0.1 (OK)
zmq >=22.1.0                     :  25.1.2 (OK)

# Optional:
cython >=0.21                    :  None (NOK)
matplotlib >=3.0.0               :  None (NOK)
numpy >=1.7                      :  2.1.1 (OK)
pandas >=1.1.1                   :  2.2.2 (OK)
scipy >=0.17.0                   :  1.14.1 (OK)
sympy >=0.7.3                    :  1.12 (OK)

[PhilipYip1988]

This is likely an issue with the Anaconda installation. You have numpy 2.1.1 in your base Anaconda Python environment but Anaconda have not updated numpy in their base Python environment to that version yet. It should be at version 1.26.4 according to the 2024.06-1 Anaconda Release Notes. Therefore it is likely that you have been installing community conda-forge channel packages into the base Anaconda Python environment which normally results in an unstable base environment...

The commercial channel anaconda is a limited set of packages, repackaged by Anaconda for use in their Anaconda base Python environment. The Anaconda base Python environment should generally be used "as is" with limited updates to the conda package manager and anaconda-navigator until the standalone installer is updated by Anaconda. Installation of community channel conda-forge packages into the base Python environment, generally results in instabilities.

You should uninstall Anaconda and reinstall Anaconda if you want to use base "as is". Alternatively if you want to use the latest version of Spyder, install Spyder using the standalone installer.

If you need to use a custom set of packages you can create a custom conda-forge Python environment with spyder-kernels. To create a custom conda-forge environment you will need to install Miniconda or Anaconda. Miniconda is a minimal version of Anaconda and can be used if you do not plan to use the base Python environment for other purposes. The following Python environment for example can be used for seaborn:

conda create -n spyder-env -c conda-forge spyder-kernels cython seaborn pyarrow sympy openpyxl xlrd xlsxwriter lxml sqlalchemy tabulate pyqt