Installing some plugins fails when conda-based environments are mixed with builtin pip installer

🐛 Bug

Hi all, I’m just testing napari 0.4.11rc0. This error is however a bit older. I have seen it in other versions of napari before. Typically I see it when using the napari-app. Today it happened in napari installed via pip in a conda environment.

When installing stardist-napari, it takes forever and eventually fails:

ERROR: Could not install packages due to an OSError: [WinError 5] Access is denied: 'C:\\Windows\\Temp\\pip-uninstall-5s9yygth\\core\\_multiarray_tests.cp38-win_amd64.pyd'

Full log:

WARNING: Ignoring invalid distribution -illow (c:\users\rober\miniconda3\envs\bio1\lib\site-packages)

WARNING: Ignoring invalid distribution -illow (c:\users\rober\miniconda3\envs\bio1\lib\site-packages)

Collecting stardist-napari

  Using cached stardist_napari-2021.6.28-py3-none-any.whl (28 kB)

Collecting tensorflow

  Downloading tensorflow-2.6.0-cp38-cp38-win_amd64.whl (423.2 MB)

Collecting stardist>=0.7.0

  Downloading stardist-0.7.3-cp38-cp38-win_amd64.whl (757 kB)

Requirement already satisfied: magicgui>=0.2.9 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from stardist-napari) (0.2.10)

Requirement already satisfied: napari>=0.4.8 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from stardist-napari) (0.4.11rc0)

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Requirement already satisfied: typing-extensions in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from magicgui>=0.2.9->stardist-napari) (3.7.4.3)

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Collecting csbdeep>=0.6.3

  Downloading csbdeep-0.6.3-py2.py3-none-any.whl (73 kB)

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Collecting tensorflow

  Downloading tensorflow-2.5.1-cp38-cp38-win_amd64.whl (422.6 MB)

  Using cached tensorflow-2.5.0-cp38-cp38-win_amd64.whl (422.6 MB)

  Downloading tensorflow-2.4.3-cp38-cp38-win_amd64.whl (370.9 MB)

Requirement already satisfied: tensorboard~=2.4 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from tensorflow->stardist-napari) (2.5.0)

Collecting six>=1.11.0

  Using cached six-1.15.0-py2.py3-none-any.whl (10 kB)

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Collecting numpy>=1.16.5

  Using cached numpy-1.19.5-cp38-cp38-win_amd64.whl (13.3 MB)

Requirement already satisfied: opt-einsum~=3.3.0 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from tensorflow->stardist-napari) (3.3.0)

Requirement already satisfied: wheel~=0.35 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from tensorflow->stardist-napari) (0.36.2)
Requirement already satisfied: termcolor~=1.1.0 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from tensorflow->stardist-napari) (1.1.0)

Requirement already satisfied: protobuf>=3.9.2 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from tensorflow->stardist-napari) (3.17.3)

Requirement already satisfied: tensorflow-estimator<2.5.0,>=2.4.0 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from tensorflow->stardist-napari) (2.4.0)

Requirement already satisfied: google-auth<2,>=1.6.3 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from tensorboard~=2.4->tensorflow->stardist-napari) (1.34.0)

Requirement already satisfied: google-auth-oauthlib<0.5,>=0.4.1 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from tensorboard~=2.4->tensorflow->stardist-napari) (0.4.5)

Requirement already satisfied: tensorboard-data-server<0.7.0,>=0.6.0 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from tensorboard~=2.4->tensorflow->stardist-napari) (0.6.1)
Requirement already satisfied: markdown>=2.6.8 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from tensorboard~=2.4->tensorflow->stardist-napari) (3.3.4)

Requirement already satisfied: tensorboard-plugin-wit>=1.6.0 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from tensorboard~=2.4->tensorflow->stardist-napari) (1.8.0)

Requirement already satisfied: werkzeug>=0.11.15 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from tensorboard~=2.4->tensorflow->stardist-napari) (2.0.1)

Requirement already satisfied: pyasn1-modules>=0.2.1 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from google-auth<2,>=1.6.3->tensorboard~=2.4->tensorflow->stardist-napari) (0.2.8)

Requirement already satisfied: cachetools<5.0,>=2.0.0 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from google-auth<2,>=1.6.3->tensorboard~=2.4->tensorflow->stardist-napari) (4.2.2)

Requirement already satisfied: rsa<5,>=3.1.4 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from google-auth<2,>=1.6.3->tensorboard~=2.4->tensorflow->stardist-napari) (4.7.2)

Requirement already satisfied: requests-oauthlib>=0.7.0 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from google-auth-oauthlib<0.5,>=0.4.1->tensorboard~=2.4->tensorflow->stardist-napari) (1.3.0)

Requirement already satisfied: pyasn1<0.5.0,>=0.4.6 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from pyasn1-modules>=0.2.1->google-auth<2,>=1.6.3->tensorboard~=2.4->tensorflow->stardist-napari) (0.4.8)

Requirement already satisfied: oauthlib>=3.0.0 in c:\users\rober\miniconda3\envs\bio1\lib\site-packages (from requests-oauthlib>=0.7.0->google-auth-oauthlib<0.5,>=0.4.1->tensorboard~=2.4->tensorflow->stardist-napari) (3.1.1)

WARNING: Ignoring invalid distribution -illow (c:\users\rober\miniconda3\envs\bio1\lib\site-packages)

Installing collected packages: six, numpy, csbdeep, tensorflow, stardist, stardist-napari

  Attempting uninstall: six
    WARNING: Ignoring invalid distribution -illow (c:\users\rober\miniconda3\envs\bio1\lib\site-packages)
    Found existing installation: six 1.16.0

    Uninstalling six-1.16.0:

      Successfully uninstalled six-1.16.0

  Attempting uninstall: numpy

    WARNING: Ignoring invalid distribution -illow (c:\users\rober\miniconda3\envs\bio1\lib\site-packages)

    Found existing installation: numpy 1.21.1

    Uninstalling numpy-1.21.1:

      Successfully uninstalled numpy-1.21.1

ERROR: Could not install packages due to an OSError: [WinError 5] Access is denied: 'C:\\Windows\\Temp\\pip-uninstall-5s9yygth\\core\\_multiarray_tests.cp38-win_amd64.pyd'
Consider using the `--user` option or check the permissions.


WARNING: Ignoring invalid distribution -illow (c:\users\rober\miniconda3\envs\bio1\lib\site-packages)
WARNING: Ignoring invalid distribution -illow (c:\users\rober\miniconda3\envs\bio1\lib\site-packages)

WARNING: Ignoring invalid distribution -illow (c:\users\rober\miniconda3\envs\bio1\lib\site-packages)

To Reproduce

Steps to reproduce the behavior:

1. Start Napari
2. Go to the plugins installer
3. Install stardist-napari (that also happens sometimes with other plugins)

Expected behavior

The installation works.

Environment

• Please copy and paste the information at napari info option in help menubar here: napari: 0.4.11rc0 Platform: Windows-10-10.0.19041-SP0 Python: 3.8.5 (default, Sep 3 2020, 21:29:08) [MSC v.1916 64 bit (AMD64)] Qt: 5.12.9 PyQt5: 5.12.3 NumPy: 1.21.1 SciPy: 1.7.1 Dask: 2021.05.1 VisPy: 0.7.0

OpenGL:

• GL version: 4.6.0 NVIDIA 466.77
• MAX_TEXTURE_SIZE: 32768

Screens:

• screen 1: resolution 1920x1200, scale 1.0

Plugins:

• Measurements (Plot profile): 0.1.3

• Measurements (skimage regionprops): 0.1.6

• Search (Plugin): 0.1.0

• Segmentation (OCLRFC): 0.4.4

• Segmentation (split/merge): 0.1.2

• Utilities (skimage regionprops): 0.1.6

• Visualization(B/C): 0.1.1

• aicsimageio-in-memory: 0.3.5

• cellpose-napari: 0.1.3

• clEsperanto: 0.10.0

• console: 0.0.3

• napari-yapic-prediction: 0.1.dev99

• ome-types: 0.2.7

• omero: 0.1.1

• scikit-image: 0.4.11rc0

• svg: 0.1.5

• Any other relevant information:

Additional context

[jaimergp]

I can install stardist after some “negotiations” 😃

The important part here is to realize that reproducing these issues do not require napari at all. It’s a Python packaging issue we can only circumvent by inspection, trial and error and experience. You can do:

$> conda create -n test napari
$> conda activate test
$> pip install stardist-napari

And see the errors without napari ever having run. In the end napari it just running pip install for you.

Most of these issues are solved by pre-providing packages expected by the plugin with conda so pip doesn’t have to mess with your conda environment. In the case of stardist, I needed this:

$> conda create -n napari-stardist napari
$> conda activate napari-stardist
$> conda install -c defaults tensorflow numpy llvmlite numba
$> pip install napari-stardist keras==2.6
# We need to fix keras version; its metadata is wrong and should match tensorflow version (2.6)
$> napari

How did I know whick conda packages I should install before the plugin? Pip doesn’t really have dry-runs… Well, I Ctrl+C mid tensorflow download 😬 But you can also run grayskull. Short tutorial:

$> conda install -c conda-forge grayskull
$> grayskull pypi stardist-napari
....
Host requirements:
  - pip
  - python >=3.7

Run requirements:
  - magicgui >=0.3.0
  - napari >=0.4.9
  - python >=3.7
! - stardist >=0.7.0
  - tensorflow

! = not available on conda-forge

We take the ! prefixed packages and run grayskull again:

$> grayskull pypi stardist
...
Build requirements:
  - {{ compiler('c') }}
Host requirements:
  - numpy
  - pip
  - python

Run requirements:
  - {{ pin_compatible('numpy') }}
!  - csbdeep >=0.6.3
  - numba
  - python
  - scikit-image

Rinse and repeat:

$> grayskull pypi csbdeep
...
Host requirements:
  - pip
  - python

Run requirements:
  - backports.tempfile # [py<34]
  - h5py <3 # [py<39]
  - imagecodecs-lite <=2020 # [py<36]
  - matplotlib-base
  - numpy
  - pathlib2 # [py<3]
  - python
  - scipy
  - six
  - tifffile
  - tqdm

No ! packages! Now we can compile the full list. Note that this is way more exhaustive than needed, but now we can compile that into something like this:

$> conda install \
        magicgui>=0.3.0 \
        matplotlib \
        napari>=0.4.9 \
        numba \
        numpy \
        scikit-image \
        scipy \
        six \
        tensorflow \
        tifffile \
        tqdm 

The ! packages must be installed with pip but now the dependencies will be in place and won’t be installed with pip. In practice it just means installing the plugin with pip.

$> pip install stardist-napari

Note that even with good tooling, we didn’t detect the keras requirement, which needs to be pinned to the same version as tensorflow. Why? Bad metadata, what else. We need to fix that after the installation and first attempt to run the plugin. As you can see, a big mess and we didn’t even run napari yet 😃

Hope this helps!

[tlambert03]

napari-autoalign

this one states directly on the readme that you might run into that issue. I believe that you have build tools installed, but there’s likely a PATH issue preventing pip from finding the appropriate compiler. That said, I would definitely say that this one is unfortunately up to plugin developers at the moment. That is, a plugin that requires the end-user to compile something (or depends on a package that does) is almost certainly going to fail for a lot of people. The “solution” here is for either for napari-autolign to not depend on probreg (which neither distributes wheels, nor does it appear on conda-forge), or for them to help probreg create a wheel.

they may also neither have the experience nor the time to figure out what’s the issue here (plugin developer speaking here)

I agree, this isn’t intro level stuff… but that’s definitely the state of the ecosystem for now. In other words, if conda forge and pypi haven’t figured out how to solve this problem universally for python developers, then it’s very unlikely that we (napari) are going to be able to swoop in and make it all smooth for beginner napari plugin developers. I’d say the best thing you can do to help at this point is encourage developers to consider their dependencies carefully.