Repository: haesleinhuepf/devbio-napari (language: python)

Issue:
installation fails
Hi @haesleinhuepf , Hi team !

I'm trying to install devbio-napari using this `env_devbio.yml `: 

```
name: "devbio"
channels:
  - conda-forge
  - pytorch
dependencies:
  - napari=0.4.19
  - python=3.9
  - devbio-napari=0.10.1
  - pyqt
prefix: "/opt/conda/envs/devbio"

```

and this line `conda env update -n devbio -f /tmp/env_devbio.yml`
(I'm using conda but it uses the LibMambaSolver now, so it should be fine)

```
RUN conda env update -n devbio -f /tmp/env_devbio.yml     && conda clean --all -f -y     && conda env export -n "biop"      && rm /tmp/env_devbio.yml:
1.496 Channels:
1.496  - conda-forge
1.496  - pytorch
1.496  - defaults
1.496 Platform: linux-64
1.496 Collecting package metadata (repodata.json): ...working... done
28.93 Solving environment: ...working... failed
144.3 Channels:
144.3  - conda-forge
144.3  - pytorch
144.3  - defaults
144.3 Platform: linux-64
144.3 Collecting package metadata (repodata.json): ...working... done
146.5 Solving environment: ...working... failed
261.4
261.4 **LibMambaUnsatisfiableError**: Encountered problems while solving:
261.4   - package napari-0.4.19-pyh9208f05_0 requires npe2 >=0.7.2, but none of the providers can be installed
261.4
261.4
261.4 Could not solve for environment specs
261.4 The following packages are incompatible
261.4 ├─ devbio-napari 0.10.1**  is installable with the potential options
261.4 │  ├─ devbio-napari 0.10.1 would require
261.4 │  │  └─ npe2 <0.7.0 , which can be installed;
261.4 │  ├─ devbio-napari 0.10.1 would require
261.4 │  │  └─ __osx, which is missing on the system;
261.4 │  └─ devbio-napari 0.10.1 would require
261.4 │     └─ __win, which is missing on the system;
261.4 └─ napari 0.4.19**  is not installable because it requires
261.4    └─ npe2 >=0.7.2 , which conflicts with any installable versions previously reported.
```

from the error message I guess it would pass on Mac and Win and fails on linux because : 

```
261.4 │  ├─ devbio-napari 0.10.1 would require
261.4 │  │  └─ npe2 <0.7.0 , which can be installed;
```
and 
```
261.4 └─ napari 0.4.19**  is not installable because it requires
261.4    └─ npe2 >=0.7.2 , which conflicts with any installable versions previously reported.
```


I tried to : 
- add the "default" to the channels (doesn't work better)
- remove the version of napari, the build works but napari doesn't start as it's complaining about qt being installed but not working (see below)

![image](https://github.com/user-attachments/assets/3f19bbce-af9f-4fde-a84c-ea44c8b3b80c)


thank you in advance for your suggestions,

Best

Romain



Discussion / hints:
My last working build was with napari 0.4.18. I tried to build a new one speficying napari 0.4.18 and I got the same error as above.

Please find below the output of  `conda list` from the old working build and a newly non-working build 
[devbio_notworking.txt](https://github.com/user-attachments/files/17323877/devbio_notworking.txt)
[devio_working.txt](https://github.com/user-attachments/files/17323878/devio_working.txt)

Any suggestion is welcome ,

Cheeers

R

Hi @romainGuiet ,

what happens if you use this command from the installation instructions?

```
mamba create --name devbio-napari-env napari=0.4.19 python=3.9 devbio-napari pyqt -c conda-forge -c pytorch
```
Hi @haesleinhuepf ,

thank you for your suggestion !

I can confirm that using `mamba create --name devbio-napari-env napari=0.4.19 python=3.9 devbio-napari pyqt -c conda-forge -c pytorch -y` the build pass BUT from the created environment a `conda list` returns 
```
devbio-napari             0.8.1           linux_h41d4057_0    conda-forge
```

If I specify devbio-napari=0.10.1 , so the line become :
`mamba create --name devbio napari=0.4.19 python=3.9 devbio-napari=0.10.1 pyqt -c conda-forge -c pytorch -y`

it returns the same error as  `mamba env create -n devbio -f /tmp/env_devbio.yml` with _env_devbio.yml_
```yml
name: "devbio"
channels:
  - conda-forge
  - pytorch
dependencies:
  - napari=0.4.19
  - python=3.9
  - devbio-napari=0.10.1
  - pyqt
prefix: "/opt/conda/envs/devbio"
```


Best,

Romain

Ok, then one more try: Can you take the environment where there is devbio-napari 0.8 installed and install 0.10 using pip?

Thanks for your time!

Edit: When [comparing the conda package of devbio-napari between 0.8.1 and 0.10.1](https://github.com/conda-forge/devbio-napari-feedstock/compare/ee6da23f02e80bca0c841777e6426360a8f06ea5...main) I suspect there is a thing for linux missing, but my skills are very limited in this context. Maybe, @goanpeca or @jaimergp can help in making the conda receipe install on linux?

Via the pip install it manages to build! Please find the `conda list` returns below:

```
# packages in environment at /opt/conda/envs/devbio:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
aiofiles                  22.1.0             pyhd8ed1ab_0    conda-forge
aiosqlite                 0.20.0             pyhd8ed1ab_0    conda-forge
alabaster                 0.7.16             pyhd8ed1ab_0    conda-forge
alsa-lib                  1.2.12               h4ab18f5_0    conda-forge
annotated-types           0.7.0              pyhd8ed1ab_0    conda-forge
anyio                     3.7.1              pyhd8ed1ab_0    conda-forge
aom                       3.9.1                hac33072_0    conda-forge
apoc-backend              0.12.0             pyhd8ed1ab_0    conda-forge
app-model                 0.2.8              pyhd8ed1ab_0    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py39h8cd3c5a_5    conda-forge
arrow                     1.3.0              pyhd8ed1ab_0    conda-forge
asciitree                 0.3.3                      py_2    conda-forge
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
attr                      2.5.1                h166bdaf_1    conda-forge
attrs                     24.2.0             pyh71513ae_0    conda-forge
autopep8                  2.3.1              pyhd8ed1ab_0    conda-forge
babel                     2.14.0             pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.3             pyha770c72_0    conda-forge
bleach                    6.1.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.6               hef167b5_0    conda-forge
brotli                    1.1.0                hb9d3cd8_2    conda-forge
brotli-bin                1.1.0                hb9d3cd8_2    conda-forge
brotli-python             1.1.0            py39hf88036b_2    conda-forge
brunsli                   0.1                  h9c3ff4c_0    conda-forge
bzip2                     1.0.8                h4bc722e_7    conda-forge
c-ares                    1.34.1               heb4867d_0    conda-forge
c-blosc2                  2.15.1               hc57e6cf_0    conda-forge
ca-certificates           2024.8.30            hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachey                    0.2.1              pyh9f0ad1d_0    conda-forge
cairo                     1.18.0               hebfffa5_3    conda-forge
certifi                   2024.8.30          pyhd8ed1ab_0    conda-forge
cffi                      1.17.1           py39h15c3d72_0    conda-forge
charls                    2.4.2                h59595ed_0    conda-forge
charset-normalizer        3.4.0              pyhd8ed1ab_0    conda-forge
click                     8.1.7           unix_pyh707e725_0    conda-forge
click-default-group       1.2.4              pyhd8ed1ab_0    conda-forge
cloudpickle               3.0.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.2.2              pyhd8ed1ab_0    conda-forge
contourpy                 1.3.0            py39h74842e3_2    conda-forge
control                   0.9.4              pyhd8ed1ab_0    conda-forge
cpython                   3.9.20           py39hd8ed1ab_1    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
cython                    3.0.11           py39hde8bd2b_3    conda-forge
cytoolz                   1.0.0            py39h8cd3c5a_1    conda-forge
czifile                   2019.7.2           pyh9f0ad1d_0    conda-forge
dask-core                 2024.8.0           pyhd8ed1ab_0    conda-forge
dav1d                     1.2.1                hd590300_0    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
debugpy                   1.8.7            py39hf88036b_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
deprecated                1.2.14             pyh1a96a4e_0    conda-forge
devbio-napari             0.10.1                   pypi_0    pypi
docstring_parser          0.16               pyhd8ed1ab_0    conda-forge
docutils                  0.17.1                   pypi_0    pypi
eigen                     3.4.0                h00ab1b0_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.2.2              pyhd8ed1ab_0    conda-forge
executing                 2.1.0              pyhd8ed1ab_0    conda-forge
expat                     2.6.3                h5888daf_0    conda-forge
fasteners                 0.17.3             pyhd8ed1ab_0    conda-forge
ffmpeg                    7.1.0           gpl_he2fd91e_701    conda-forge
fftw                      3.3.10          nompi_hf1063bd_110    conda-forge
finesse                   3.0a28           py39hbb88e08_0    conda-forge
flexcache                 0.3                pyhd8ed1ab_0    conda-forge
flexparser                0.3.1              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 h77eed37_3    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.54.1           py39h8cd3c5a_0    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
freetype-py               2.5.1              pyhd8ed1ab_0    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
fsspec                    2024.9.0           pyhff2d567_0    conda-forge
funcsigs                  1.0.2                      py_3    conda-forge
gettext                   0.22.5               he02047a_3    conda-forge
gettext-tools             0.22.5               he02047a_3    conda-forge
giflib                    5.2.2                hd590300_0    conda-forge
glib                      2.82.1               h2ff4ddf_0    conda-forge
glib-tools                2.82.1               h4833e2c_0    conda-forge
gmp                       6.3.0                hac33072_2    conda-forge
gmpy2                     2.1.5            py39h7196dd7_2    conda-forge
graphite2                 1.3.13            h59595ed_1003    conda-forge
gst-plugins-base          1.24.7               h0a52356_0    conda-forge
gstreamer                 1.24.7               hf3bb09a_0    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
h5py                      3.11.0          nompi_py39h24b94d4_102    conda-forge
harfbuzz                  9.0.0                hda332d3_1    conda-forge
hdbscan                   0.8.38.post2     py39hf3d9206_0    conda-forge
hdf5                      1.14.3          nompi_hdf9ad27_105    conda-forge
heapdict                  1.0.1              pyhd8ed1ab_1    conda-forge
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
hsluv                     5.0.4              pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
icu                       75.1                 he02047a_0    conda-forge
idna                      3.10               pyhd8ed1ab_0    conda-forge
imagecodecs               2024.6.1         py39h1a335b5_5    conda-forge
imagecodecs-lite          2019.12.3        py39hd92a3bb_8    conda-forge
imageio                   2.35.1             pyh12aca89_0    conda-forge
imageio-ffmpeg            0.5.1              pyhd8ed1ab_0    conda-forge
imagesize                 1.4.1              pyhd8ed1ab_0    conda-forge
importlib-metadata        8.5.0              pyha770c72_0    conda-forge
importlib-resources       6.4.5              pyhd8ed1ab_0    conda-forge
importlib_metadata        8.5.0                hd8ed1ab_0    conda-forge
importlib_resources       6.4.5              pyhd8ed1ab_0    conda-forge
in-n-out                  0.2.1              pyhd8ed1ab_0    conda-forge
iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge
ipycanvas                 0.13.3             pyhd8ed1ab_0    conda-forge
ipyevents                 2.0.2              pyhd8ed1ab_0    conda-forge
ipykernel                 6.29.5             pyh3099207_0    conda-forge
ipympl                    0.9.4              pyhd8ed1ab_0    conda-forge
ipython                   8.18.1             pyh707e725_3    conda-forge
ipython_genutils          0.2.0              pyhd8ed1ab_1    conda-forge
ipywidgets                8.1.5              pyhd8ed1ab_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.4              pyhd8ed1ab_0    conda-forge
joblib                    1.4.2              pyhd8ed1ab_0    conda-forge
json5                     0.9.25             pyhd8ed1ab_0    conda-forge
jsonpointer               3.0.0            py39hf3d152e_1    conda-forge
jsonschema                4.23.0             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2024.10.1          pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.23.0               hd8ed1ab_0    conda-forge
jupyter                   1.1.1              pyhd8ed1ab_0    conda-forge
jupyter_client            7.4.9              pyhd8ed1ab_0    conda-forge
jupyter_console           6.6.3              pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.2              pyh31011fe_1    conda-forge
jupyter_events            0.10.0             pyhd8ed1ab_0    conda-forge
jupyter_server            1.24.0             pyhd8ed1ab_0    conda-forge
jupyter_server_fileid     0.9.2              pyhd8ed1ab_0    conda-forge
jupyter_server_ydoc       0.8.0              pyhd8ed1ab_0    conda-forge
jupyter_ydoc              0.2.4              pyhd8ed1ab_0    conda-forge
jupyterlab                3.6.8              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.27.3             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.13             pyhd8ed1ab_0    conda-forge
jupytext                  1.16.4             pyh80e38bb_0    conda-forge
jxrlib                    1.1                  hd590300_3    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.7            py39h74842e3_0    conda-forge
krb5                      1.21.3               h659f571_0    conda-forge
lame                      3.100             h166bdaf_1003    conda-forge
lazy-loader               0.4                pyhd8ed1ab_1    conda-forge
lazy_loader               0.4                pyhd8ed1ab_1    conda-forge
lcms2                     2.16                 hb7c19ff_0    conda-forge
ld_impl_linux-64          2.43                 h712a8e2_1    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libabseil                 20240722.0      cxx17_h5888daf_1    conda-forge
libaec                    1.1.3                h59595ed_0    conda-forge
libasprintf               0.22.5               he8f35ee_3    conda-forge
libasprintf-devel         0.22.5               he8f35ee_3    conda-forge
libass                    0.17.3               h1dc1e6a_0    conda-forge
libavif16                 1.1.1                h104a339_1    conda-forge
libblas                   3.9.0           24_linux64_openblas    conda-forge
libbrotlicommon           1.1.0                hb9d3cd8_2    conda-forge
libbrotlidec              1.1.0                hb9d3cd8_2    conda-forge
libbrotlienc              1.1.0                hb9d3cd8_2    conda-forge
libcap                    2.69                 h0f662aa_0    conda-forge
libcblas                  3.9.0           24_linux64_openblas    conda-forge
libclang-cpp15            15.0.7          default_h127d8a8_5    conda-forge
libclang13                19.1.1          default_h9c6a7e4_0    conda-forge
libcups                   2.3.3                h4637d8d_4    conda-forge
libcurl                   8.10.1               hbbe4b11_0    conda-forge
libdeflate                1.22                 hb9d3cd8_0    conda-forge
libdrm                    2.4.123              hb9d3cd8_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libegl                    1.7.0                ha4b6fd6_1    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libevent                  2.1.12               hf998b51_1    conda-forge
libexpat                  2.6.3                h5888daf_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libflac                   1.4.3                h59595ed_0    conda-forge
libgcc                    14.1.0               h77fa898_1    conda-forge
libgcc-ng                 14.1.0               h69a702a_1    conda-forge
libgcrypt                 1.11.0               h4ab18f5_1    conda-forge
libgettextpo              0.22.5               he02047a_3    conda-forge
libgettextpo-devel        0.22.5               he02047a_3    conda-forge
libgfortran               14.1.0               h69a702a_1    conda-forge
libgfortran-ng            14.1.0               h69a702a_1    conda-forge
libgfortran5              14.1.0               hc5f4f2c_1    conda-forge
libgl                     1.7.0                ha4b6fd6_1    conda-forge
libglib                   2.82.1               h2ff4ddf_0    conda-forge
libglvnd                  1.7.0                ha4b6fd6_1    conda-forge
libglx                    1.7.0                ha4b6fd6_1    conda-forge
libgomp                   14.1.0               h77fa898_1    conda-forge
libgpg-error              1.50                 h4f305b6_0    conda-forge
libhwloc                  2.11.1          default_hecaa2ac_1000    conda-forge
libhwy                    1.1.0                h00ab1b0_0    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libitk                    5.4.0                h5de25d7_3    conda-forge
libjpeg-turbo             3.0.0                hd590300_1    conda-forge
libjxl                    0.11.0               hdb8da77_1    conda-forge
liblapack                 3.9.0           24_linux64_openblas    conda-forge
libllvm14                 14.0.6               hcd5def8_4    conda-forge
libllvm15                 15.0.7               hb3ce162_4    conda-forge
libllvm19                 19.1.1               ha7bfdaf_0    conda-forge
libnghttp2                1.58.0               h47da74e_1    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libogg                    1.3.5                h4ab18f5_0    conda-forge
libopenblas               0.3.27          pthreads_hac2b453_1    conda-forge
libopenvino               2024.4.0             hac27bb2_1    conda-forge
libopenvino-auto-batch-plugin 2024.4.0             h4d9b6c2_1    conda-forge
libopenvino-auto-plugin   2024.4.0             h4d9b6c2_1    conda-forge
libopenvino-hetero-plugin 2024.4.0             h3f63f65_1    conda-forge
libopenvino-intel-cpu-plugin 2024.4.0             hac27bb2_1    conda-forge
libopenvino-intel-gpu-plugin 2024.4.0             hac27bb2_1    conda-forge
libopenvino-intel-npu-plugin 2024.4.0             hac27bb2_1    conda-forge
libopenvino-ir-frontend   2024.4.0             h3f63f65_1    conda-forge
libopenvino-onnx-frontend 2024.4.0             he882d9a_1    conda-forge
libopenvino-paddle-frontend 2024.4.0             he882d9a_1    conda-forge
libopenvino-pytorch-frontend 2024.4.0             h5888daf_1    conda-forge
libopenvino-tensorflow-frontend 2024.4.0             h9718a47_1    conda-forge
libopenvino-tensorflow-lite-frontend 2024.4.0             h5888daf_1    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpciaccess              0.18                 hd590300_0    conda-forge
libpng                    1.6.44               hadc24fc_0    conda-forge
libpq                     16.4                 h2d7952a_2    conda-forge
libprotobuf               5.27.5               h5b01275_2    conda-forge
libsndfile                1.2.2                hc60ed4a_1    conda-forge
libsodium                 1.0.20               h4ab18f5_0    conda-forge
libsqlite                 3.46.1               hadc24fc_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx                 14.1.0               hc0a3c3a_1    conda-forge
libstdcxx-ng              14.1.0               h4852527_1    conda-forge
libsystemd0               256.7                h2774228_0    conda-forge
libtiff                   4.7.0                he137b08_1    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libva                     2.22.0               h8a09558_1    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libvpx                    1.14.1               hac33072_0    conda-forge
libwebp-base              1.4.0                hd590300_0    conda-forge
libxcb                    1.17.0               h8a09558_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxkbcommon              1.7.0                h2c5496b_1    conda-forge
libxml2                   2.12.7               he7c6b58_4    conda-forge
libzlib                   1.3.1                hb9d3cd8_2    conda-forge
libzopfli                 1.0.3                h9c3ff4c_0    conda-forge
llvmlite                  0.43.0           py39hf8b6b1a_1    conda-forge
locket                    1.0.0              pyhd8ed1ab_0    conda-forge
loguru                    0.7.2            py39hf3d152e_2    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
magicgui                  0.8.3              pyhd8ed1ab_0    conda-forge
mako                      1.3.5              pyhd8ed1ab_0    conda-forge
markdown-it-py            3.0.0              pyhd8ed1ab_0    conda-forge
markupsafe                3.0.1            py39h9399b63_1    conda-forge
matplotlib-base           3.9.2            py39h16632d1_1    conda-forge
matplotlib-inline         0.1.7              pyhd8ed1ab_0    conda-forge
mdit-py-plugins           0.4.2              pyhd8ed1ab_0    conda-forge
mdurl                     0.1.2              pyhd8ed1ab_0    conda-forge
metis                     5.1.0             hd0bcaf9_1007    conda-forge
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
more-itertools            10.5.0             pyhd8ed1ab_0    conda-forge
mpc                       1.3.1                h24ddda3_1    conda-forge
mpfr                      4.2.1                h90cbb55_3    conda-forge
mpg123                    1.32.6               h59595ed_0    conda-forge
mpmath                    1.3.0              pyhd8ed1ab_0    conda-forge
msgpack-python            1.1.0            py39h74842e3_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mysql-common              9.0.1                h266115a_1    conda-forge
mysql-libs                9.0.1                he0572af_1    conda-forge
napari                    0.4.18                   pypi_0    pypi
napari-3d-ortho-viewer    0.1.5              pyhd8ed1ab_0    conda-forge
napari-accelerated-pixel-and-object-classification 0.14.1             pyh9208f05_0    conda-forge
napari-animation          0.0.7                    pypi_0    pypi
napari-assistant          0.4.8              pyha07c04f_0    conda-forge
napari-blob-detection     0.0.2              pyhd8ed1ab_0    conda-forge
napari-brightness-contrast 0.1.8              pyhd8ed1ab_0    conda-forge
napari-clusters-plotter   0.8.0                    pypi_0    pypi
napari-console            0.1.0              pyh73487a3_0    conda-forge
napari-crop               0.1.9              pyhd8ed1ab_0    conda-forge
napari-curtain            0.1.1              pyhd8ed1ab_0    conda-forge
napari-czifile2           0.2.7              pyhd8ed1ab_0    conda-forge
napari-folder-browser     0.1.3              pyhd8ed1ab_0    conda-forge
napari-layer-details-display 0.1.5              pyhd8ed1ab_0    conda-forge
napari-mouse-controls     0.1.3              pyhd8ed1ab_0    conda-forge
napari-plot-profile       0.2.2              pyhd8ed1ab_0    conda-forge
napari-plugin-engine      0.2.0              pyhd8ed1ab_2    conda-forge
napari-plugin-manager     0.1.3                    pypi_0    pypi
napari-plugin-search      0.1.3              pyhd8ed1ab_0    conda-forge
napari-pyclesperanto-assistant 0.22.1             pyhd8ed1ab_0    conda-forge
napari-pystackreg         0.1.4              pyhd8ed1ab_0    conda-forge
napari-roi                0.1.8              pyhd8ed1ab_0    conda-forge
napari-segment-blobs-and-things-with-membranes 0.3.11             pyha07c04f_0    conda-forge
napari-simpleitk-image-processing 0.4.8              pyhd0adb26_0    conda-forge
napari-skimage-regionprops 0.10.1             pyhd8ed1ab_0    conda-forge
napari-svg                0.2.0              pyhd8ed1ab_0    conda-forge
napari-tabu               0.1.5              pyhd8ed1ab_0    conda-forge
napari-time-slicer        0.5.0              pyhd8ed1ab_0    conda-forge
napari-tools-menu         0.1.19             pyhd8ed1ab_0    conda-forge
napari-workflow-inspector 0.2.2              pyhd8ed1ab_0    conda-forge
napari-workflow-optimizer 0.1.4              pyhd8ed1ab_0    conda-forge
napari-workflows          0.2.10             pyhd8ed1ab_0    conda-forge
nbclassic                 1.1.0              pyhd8ed1ab_0    conda-forge
nbclient                  0.10.0             pyhd8ed1ab_0    conda-forge
nbconvert-core            7.16.4             pyhd8ed1ab_1    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_0    conda-forge
ncurses                   6.5                  he02047a_1    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_0    conda-forge
networkx                  3.2.1              pyhd8ed1ab_0    conda-forge
notebook                  6.5.7              pyha770c72_0    conda-forge
notebook-shim             0.2.4              pyhd8ed1ab_0    conda-forge
npe2                      0.6.2                    pypi_0    pypi
nspr                      4.35                 h27087fc_0    conda-forge
nss                       3.105                hd34e28f_0    conda-forge
numba                     0.60.0           py39h0320e7d_0    conda-forge
numcodecs                 0.12.1           py39h84cc369_1    conda-forge
numpy                     1.23.5                   pypi_0    pypi
numpydoc                  1.5.0                    pypi_0    pypi
ocl-icd                   2.3.2                hd590300_1    conda-forge
ocl-icd-system            1.0.0                         1    conda-forge
openh264                  2.4.1                h59595ed_0    conda-forge
openjpeg                  2.5.2                h488ebb8_0    conda-forge
openssl                   3.3.2                hb9d3cd8_0    conda-forge
packaging                 24.1               pyhd8ed1ab_0    conda-forge
pandas                    2.2.3            py39h3b40f6f_1    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.4              pyhd8ed1ab_0    conda-forge
partd                     1.4.2              pyhd8ed1ab_0    conda-forge
pcre2                     10.44                hba22ea6_2    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.4.0           py39h648eaa6_1    conda-forge
pint                      0.24.3             pyhd8ed1ab_0    conda-forge
pip                       24.2               pyh8b19718_1    conda-forge
pixman                    0.43.2               h59595ed_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              4.3.6              pyhd8ed1ab_0    conda-forge
platymatch                0.0.3              pyhd8ed1ab_0    conda-forge
pluggy                    1.5.0              pyhd8ed1ab_0    conda-forge
ply                       3.11               pyhd8ed1ab_2    conda-forge
pooch                     1.8.2              pyhd8ed1ab_0    conda-forge
prometheus_client         0.21.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.48             pyha770c72_0    conda-forge
prompt_toolkit            3.0.48               hd8ed1ab_0    conda-forge
psutil                    6.0.0            py39h8cd3c5a_1    conda-forge
psygnal                   0.11.1             pyhd8ed1ab_0    conda-forge
pthread-stubs             0.4               hb9d3cd8_1002    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pugixml                   1.14                 h59595ed_0    conda-forge
pulseaudio-client         17.0                 hb77b528_0    conda-forge
pure_eval                 0.2.3              pyhd8ed1ab_0    conda-forge
pyclesperanto-prototype   0.24.4             pyhd8ed1ab_0    conda-forge
pycodestyle               2.12.1             pyhd8ed1ab_0    conda-forge
pyconify                  0.1.6              pyhd8ed1ab_0    conda-forge
pycparser                 2.22               pyhd8ed1ab_0    conda-forge
pydantic                  1.10.18                  pypi_0    pypi
pydantic-compat           0.1.2              pyhd8ed1ab_0    conda-forge
pydantic-core             2.23.4           py39he612d8f_0    conda-forge
pygments                  2.18.0             pyhd8ed1ab_0    conda-forge
pynndescent               0.5.13             pyhff2d567_0    conda-forge
pyopencl                  2024.2.7         py39h85c637f_0    conda-forge
pyopengl                  3.1.6              pyhd8ed1ab_1    conda-forge
pyparsing                 3.1.4              pyhd8ed1ab_0    conda-forge
pyperclip                 1.9.0              pyha804496_0    conda-forge
pyproject_hooks           1.2.0              pyh7850678_0    conda-forge
pyqt                      5.15.9           py39h52134e7_5    conda-forge
pyqt5-sip                 12.12.2          py39h3d6467e_5    conda-forge
pyqtgraph                 0.13.7             pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pyspellchecker            0.8.0              pyhd8ed1ab_0    conda-forge
pystackreg                0.2.8            py39h3b40f6f_2    conda-forge
pytest                    8.3.3              pyhd8ed1ab_0    conda-forge
python                    3.9.20          h13acc7a_1_cpython    conda-forge
python-build              1.2.2.post1        pyhff2d567_0    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.20.0             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-tzdata             2024.2             pyhd8ed1ab_0    conda-forge
python_abi                3.9                      5_cp39    conda-forge
pytomlpp                  1.0.13                   pypi_0    pypi
pytools                   2024.1.14          pyhd8ed1ab_0    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pywavelets                1.6.0            py39hd92a3bb_0    conda-forge
pyyaml                    6.0.2            py39h8cd3c5a_1    conda-forge
pyzmq                     26.2.0           py39h4e4fb57_2    conda-forge
qhull                     2020.2               h434a139_5    conda-forge
qt-main                   5.15.8              h3155989_26    conda-forge
qtconsole-base            5.6.0              pyha770c72_0    conda-forge
qtpy                      2.4.1              pyhd8ed1ab_0    conda-forge
quantiphy                 2.20               pyhd8ed1ab_1    conda-forge
rav1e                     0.6.6                he8a937b_2    conda-forge
readline                  8.2                  h8228510_1    conda-forge
redlionfish               0.9              py39hf3d152e_3    conda-forge
referencing               0.35.1             pyhd8ed1ab_0    conda-forge
reikna                    0.8.0              pyhd8ed1ab_0    conda-forge
requests                  2.32.3             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rich                      13.9.2             pyhd8ed1ab_0    conda-forge
rpds-py                   0.20.0           py39he612d8f_1    conda-forge
scikit-image              0.24.0           py39h5114956_2    conda-forge
scikit-learn              1.5.2            py39h4b7350c_1    conda-forge
scipy                     1.13.1           py39haf93ffa_0    conda-forge
seaborn                   0.13.2                   pypi_0    pypi
send2trash                1.8.3              pyh0d859eb_0    conda-forge
setuptools                75.1.0             pyhd8ed1ab_0    conda-forge
shellingham               1.5.4              pyhd8ed1ab_0    conda-forge
simpleitk                 2.4.0            py39hcd839a5_1    conda-forge
sip                       6.7.12           py39h3d6467e_0    conda-forge
siphash24                 1.6              py39hcd6043d_1    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sly                       0.4                pyhd8ed1ab_0    conda-forge
slycot                    0.5.4            py39hfe520f8_4    conda-forge
snappy                    1.2.1                ha2e4443_0    conda-forge
sniffio                   1.3.1              pyhd8ed1ab_0    conda-forge
snowballstemmer           2.2.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
sphinx                    4.5.0                    pypi_0    pypi
sphinxcontrib-applehelp   2.0.0              pyhd8ed1ab_0    conda-forge
sphinxcontrib-devhelp     2.0.0              pyhd8ed1ab_0    conda-forge
sphinxcontrib-htmlhelp    2.1.0              pyhd8ed1ab_0    conda-forge
sphinxcontrib-jsmath      1.0.1              pyhd8ed1ab_0    conda-forge
sphinxcontrib-qthelp      2.0.0              pyhd8ed1ab_0    conda-forge
sphinxcontrib-serializinghtml 1.1.10             pyhd8ed1ab_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
stackview                 0.11.2             pyhd8ed1ab_0    conda-forge
suitesparse               7.8.2                hb42a789_0    conda-forge
superqt                   0.6.7              pyh9208f05_0    conda-forge
svt-av1                   2.2.1                h5888daf_0    conda-forge
sympy                     1.13.3           pyh2585a3b_104    conda-forge
tabulate                  0.9.0              pyhd8ed1ab_1    conda-forge
tbb                       2021.13.0            h84d6215_0    conda-forge
terminado                 0.18.1             pyh0d859eb_0    conda-forge
the-segmentation-game     0.2.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             3.5.0              pyhc1e730c_0    conda-forge
tifffile                  2024.6.18          pyhd8ed1ab_0    conda-forge
tinycss2                  1.3.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.2              pyhd8ed1ab_0    conda-forge
tomli-w                   1.1.0              pyhd8ed1ab_0    conda-forge
toolz                     1.0.0              pyhd8ed1ab_0    conda-forge
tornado                   6.4.1            py39h8cd3c5a_1    conda-forge
tqdm                      4.66.5             pyhd8ed1ab_0    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_0    conda-forge
transforms3d              0.4.2              pyhd8ed1ab_0    conda-forge
typer                     0.12.5             pyhd8ed1ab_0    conda-forge
typer-slim                0.12.5             pyhd8ed1ab_0    conda-forge
typer-slim-standard       0.12.5               hd8ed1ab_0    conda-forge
types-python-dateutil     2.9.0.20241003     pyhff2d567_0    conda-forge
typing-extensions         4.12.2               hd8ed1ab_0    conda-forge
typing_extensions         4.12.2             pyha770c72_0    conda-forge
tzdata                    2024b                hc8b5060_0    conda-forge
umap-learn                0.5.6            py39hf3d152e_1    conda-forge
unicodedata2              15.1.0           py39hd1e30aa_0    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.2.3              pyhd8ed1ab_0    conda-forge
vispy                     0.12.2                   pypi_0    pypi
wayland                   1.23.1               h3e06ad9_0    conda-forge
wayland-protocols         1.37                 hd8ed1ab_0    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
webcolors                 24.8.0             pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.8.0              pyhd8ed1ab_0    conda-forge
wheel                     0.44.0             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.13             pyhd8ed1ab_0    conda-forge
wrapt                     1.16.0           py39h8cd3c5a_1    conda-forge
x264                      1!164.3095           h166bdaf_2    conda-forge
x265                      3.5                  h924138e_3    conda-forge
xcb-util                  0.4.1                hb711507_2    conda-forge
xcb-util-image            0.4.0                hb711507_2    conda-forge
xcb-util-keysyms          0.4.1                hb711507_0    conda-forge
xcb-util-renderutil       0.3.10               hb711507_0    conda-forge
xcb-util-wm               0.4.2                hb711507_0    conda-forge
xclip                     0.13                 h4ab18f5_3    conda-forge
xkeyboard-config          2.43                 hb9d3cd8_0    conda-forge
xorg-libice               1.1.1                hb9d3cd8_1    conda-forge
xorg-libsm                1.2.4                he73a12e_1    conda-forge
xorg-libx11               1.8.10               h4f16b4b_0    conda-forge
xorg-libxau               1.0.11               hb9d3cd8_1    conda-forge
xorg-libxdmcp             1.1.5                hb9d3cd8_0    conda-forge
xorg-libxext              1.3.6                hb9d3cd8_0    conda-forge
xorg-libxfixes            6.0.1                hb9d3cd8_0    conda-forge
xorg-libxmu               1.2.1                hb9d3cd8_1    conda-forge
xorg-libxrender           0.9.11               hb9d3cd8_1    conda-forge
xorg-libxt                1.3.0                hb9d3cd8_2    conda-forge
xorg-libxxf86vm           1.1.5                hb9d3cd8_3    conda-forge
xorg-xf86vidmodeproto     2.3.1             hb9d3cd8_1003    conda-forge
xorg-xorgproto            2024.1               hb9d3cd8_1    conda-forge
xsel                      1.2.1                hb9d3cd8_5    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
y-py                      0.5.9            py39h50f1755_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
ypy-websocket             0.8.2              pyhd8ed1ab_0    conda-forge
zarr                      2.18.2             pyhd8ed1ab_0    conda-forge
zeromq                    4.3.5                h3b0a872_6    conda-forge
zfp                       1.0.1                h5888daf_2    conda-forge
zipp                      3.20.2             pyhd8ed1ab_0    conda-forge
zlib                      1.3.1                hb9d3cd8_2    conda-forge
zlib-ng                   2.2.2                h5888daf_0    conda-forge
zstandard                 0.23.0           py39h08a7858_1    conda-forge
zstd                      1.5.6                ha6fb4c9_0    conda-forge
```

Now napari doesn't start I get an error : 
```
ARNING: QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-biop'
08:49:29 : WARNING : MainThread : QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-biop'
WARNING: QXcbIntegration: Cannot create platform OpenGL context, neither GLX nor EGL are enabled
08:49:29 : WARNING : MainThread : QXcbIntegration: Cannot create platform OpenGL context, neither GLX nor EGL are enabled
WARNING: QXcbIntegration: Cannot create platform offscreen surface, neither GLX nor EGL are enabled
08:49:29 : WARNING : MainThread : QXcbIntegration: Cannot create platform offscreen surface, neither GLX nor EGL are enabled
WARNING: QXcbIntegration: Cannot create platform OpenGL context, neither GLX nor EGL are enabled
08:49:32 : WARNING : MainThread : QXcbIntegration: Cannot create platform OpenGL context, neither GLX nor EGL are enabled
WARNING: QXcbIntegration: Cannot create platform OpenGL context, neither GLX nor EGL are enabled
08:49:32 : WARNING : MainThread : QXcbIntegration: Cannot create platform OpenGL context, neither GLX nor EGL are enabled
WARNING: composeAndFlush: QOpenGLContext creation failed
```
but tha'ts a different story, which is linked to napari itself 😅


Shall we leave this issue open until it builds "normally" (without pip install second step)

Cheers,

R
> Shall we leave this issue open until it builds "normally" (without pip install second step)

Yes, please. We need to fix the conda receipe obviously.
That kind of warning seems to originate from a headless deployment... is that a Docker container or similar? You might be lacking some of the virtual packages required.

Can you share the output of `conda info` in the target?
nvm this is a simple one:

- napari 0.4.19 requires `npe2>=0.7.2`
- devbio 0.10 requires `npe2<0.7.0`
- devbio 0.8 didn't have that npe2 pin

So if you don't specify any devbio version, then the solver will find a compatible one in the 0.8 series because the most recent ones prevent npe2 greater or equals than 0.7.0.

The questions are:

- Is the `npe2<0.7.0` necessary in the 0.10 series or was it a workaround for some problem that is no longer relevant? In that case, we can repodata patch to remove the pin.
- If it's necessary in the current source, is there a way the problem can be fixed so the pin can be lifted? That would involve a new PR plus a new release of the relevant projects.

Fix patch:
diff --git a/requirements.txt b/requirements.txt
index f0449f0..ee7acee 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
 napari-plugin-engine>=0.1.4
-npe2 to <0.7.0 # https://github.com/haesleinhuepf/devbio-napari/issues/41
+npe2
 numpy>=1.21.4
 napari-pyclesperanto-assistant
 napari-skimage-regionprops
@@ -35,5 +35,5 @@ pydantic!=1.10.0 # https://twitter.com/Czaki_PL/status/1564908046186434566?s=20&
 napari-pystackreg
 imageio!=2.22.1 # https://github.com/napari/napari/pull/5168
 redlionfish
-jupyter_server<2.0.0 # https://github.com/jupyter-server/jupyter_server/issues/1127
+jupyter_server
 seaborn
diff --git a/setup.cfg b/setup.cfg
index 87d6b63..3252853 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = devbio-napari
-version = 0.10.1
+version = 0.11.0
 author = Robert Haase
 author_email = robert.haase@tu-dresden.de
 license = BSD-3
@@ -14,8 +14,9 @@ classifiers =
     Framework :: napari
     Programming Language :: Python
     Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     Operating System :: OS Independent
     License :: OSI Approved :: BSD License
 project_urls =
@@ -26,12 +27,12 @@ project_urls =
 
 [options]
 packages = find:
-python_requires = >=3.8
+python_requires = >=3.9
 
 # add your package requirements here
 install_requires =
     napari-plugin-engine>=0.1.4
-    npe2<0.7.0 # https://github.com/haesleinhuepf/devbio-napari/issues/41
+    npe2
     numpy>=1.21.4
     napari-pyclesperanto-assistant
     napari-skimage-regionprops
@@ -64,7 +65,7 @@ install_requires =
     napari-pystackreg
     imageio!=2.22.1 # https://github.com/napari/napari/pull/5168
     redlionfish
-    jupyter_server<2.0.0 # https://github.com/jupyter-server/jupyter_server/issues/1127
+    jupyter_server
     seaborn
 
 
diff --git a/tox.ini b/tox.ini
index 8e8045c..e8d2b89 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,11 +1,12 @@
 # For more information about tox, see https://tox.readthedocs.io/en/latest/
 [tox]
-envlist = py{38,39}-{linux,macos,windows}
+envlist = py{39,310,311}-{linux,macos,windows}
 
 [gh-actions]
 python =
-    3.8: py38
     3.9: py39
+    3.10: py310
+    3.11: py311
 
 [gh-actions:env]
 PLATFORM =


Test patch:
diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index 892d0dc..7ebe2bc 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -23,7 +23,7 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, macos-latest]
-        python-version: [3.8, 3.9]
+        python-version: [3.9, '3.10', 3.11]
 
     steps:
       - uses: actions/checkout@v2