spyder cannot start after install via pixi on MacOS (`python.app` versus `pythonapp`)

fangohr commented 2 months ago

Issue Report Checklist

[X] Searched the issues page for similar reports
- seems related to https://github.com/spyder-ide/spyder/issues/13013 which reports the same issue for conda in 2020
[X] Read the relevant sections of the Spyder Troubleshooting Guide and followed its advice
[X] Reproduced the issue after updating with conda update spyder (or pip, if not using Anaconda)
- pixi instead of conda, but yes, reproduced.
[X] Could not reproduce inside jupyter qtconsole (if console-related)
- not relevant
[X] Tried basic troubleshooting (if a bug/error)
- [X] Restarted Spyder
  - not applicable
- [X] Reset preferences with spyder --reset
  - problem arises before spyder attempts to start
- [X] Reinstalled the latest version of Anaconda
  - done although with most recent pixi. Also tried to install an older version of spyder (5.4.3) which shows the same problem.
- [X] Tried the other applicable steps from the Troubleshooting Guide
[X] Completed the Problem Description, Steps to Reproduce and Version sections below

Problem Description

When installing Spyder with pixi on MacOS, I run into this error:

❯ pixi run spyder
/Users/fangohr/spyder-pixi-issue/.pixi/envs/default/bin/pythonw: line 3: /Users/fangohr/spyder-pixi-issue/.pixi/envs/default/python.app/Contents/MacOS/python: No such file or directory

What steps reproduce the problem?

~ via 🐍 v3.12.2 
❯ cd spyder-pixi-issue 

~/spyder-pixi-issue 
❯ pixi init 
✔ Created /Users/fangohr/spyder-pixi-issue/pixi.toml

~/spyder-pixi-issue 
❯ pixi add python=3.12 spyder 
✔ Added python=3.12
✔ Added spyder >=5.5.5,<6

~/spyder-pixi-issue took 8s 
❯ pixi run spyder
/Users/fangohr/spyder-pixi-issue/.pixi/envs/default/bin/pythonw: line 3: /Users/fangohr/spyder-pixi-issue/.pixi/envs/default/python.app/Contents/MacOS/python: No such file or directory

What is the expected output? What do you see instead?

I expect spyder to start.

Possible cause of the problem / hack to fix

~/spyder-pixi-issue 
❯ pwd              
/Users/fangohr/spyder-pixi-issue

~/spyder-pixi-issue 
❯ pixi run spyder --paths     # this fails
/Users/fangohr/spyder-pixi-issue/.pixi/envs/default/bin/pythonw: line 3: /Users/fangohr/spyder-pixi-issue/.pixi/envs/default/python.app/Contents/MacOS/python: No such file or directory

~/spyder-pixi-issue 
❯ cat .pixi/envs/default/bin/pythonw 
#!/bin/bash
export PYTHONEXECUTABLE=/Users/fangohr/spyder-pixi-issue/.pixi/envs/default/bin/python
/Users/fangohr/spyder-pixi-issue/.pixi/envs/default/python.app/Contents/MacOS/python "$@"

~/spyder-pixi-issue 
❯ emacs -q -nw .pixi/envs/default/bin/pythonw  # edit file: python.app -> pythonapp

~/spyder-pixi-issue took 5s 
❯ cat .pixi/envs/default/bin/pythonw                                               
#!/bin/bash
export PYTHONEXECUTABLE=/Users/fangohr/spyder-pixi-issue/.pixi/envs/default/bin/python
/Users/fangohr/spyder-pixi-issue/.pixi/envs/default/pythonapp/Contents/MacOS/python "$@"

~/spyder-pixi-issue    
❯ pixi run spyder --paths    # now it works                                                        

config:
    /Users/fangohr/spyder-pixi-issue/.pixi/envs/default/etc/spyder
    /Users/fangohr/spyder-pixi-issue/.pixi/envs/default/etc/spyder
    /usr/local/etc/spyder
    /etc/spyder

~/spyder-pixi-issue took 9s

So in summary, editing the pythonw file to point to .../pythonapp/... instead of .../python.app/... fixes the issue.

I don't know if the problem is with pixi or the conda-forge package or something else.

I could not reproduce this on Linux (in a container): the pixi install of spyder worked fine there.

Versions

Spyder version: 5.5.5
Python version: 3.12.5 (I have tried Python 3.10 as well - same error.)

Qt version: Not sure what is needed here:

❯ pixi list | grep qt
pyqt                           5.15.9          py312h550cae4_5     3.8 MiB    conda  pyqt-5.15.9-py312h550cae4_5.conda
pyqt5-sip                      12.12.2         py312h9f69965_5     74.1 KiB   conda  pyqt5-sip-12.12.2-py312h9f69965_5.conda
pyqtwebengine                  5.15.9          py312h14105d7_5     124.8 KiB  conda  pyqtwebengine-5.15.9-py312h14105d7_5.conda
qt-main                        5.15.8          hcd44e0d_23         48.8 MiB   conda  qt-main-5.15.8-hcd44e0d_23.conda
qt-webengine                   5.15.8          h850e111_4          42.9 MiB   conda  qt-webengine-5.15.8-h850e111_4.conda
qtawesome                      1.3.1           pyh9208f05_0        1.5 MiB    conda  qtawesome-1.3.1-pyh9208f05_0.conda
qtconsole                      5.5.2           pyhd8ed1ab_0        7.2 KiB    conda  qtconsole-5.5.2-pyhd8ed1ab_0.conda
qtconsole-base                 5.5.2           pyha770c72_0        97.9 KiB   conda  qtconsole-base-5.5.2-pyha770c72_0.conda
qtpy                           2.4.1           pyhd8ed1ab_0        60.4 KiB   conda  qtpy-2.4.1-pyhd8ed1ab_0.conda
sphinxcontrib-qthelp           2.0.0           pyhd8ed1ab_0        26.2 KiB   conda  sphinxcontrib-qthelp-2.0.0-pyhd8ed1ab_0.conda

PyQt version: 5.15.9
Operating System name/version: MacOS Sonoma 14.6.1

Dependencies

❯ pixi list          
Package                        Version         Build               Size       Kind   Source
alabaster                      1.0.0           pyhd8ed1ab_0        18.1 KiB   conda  alabaster-1.0.0-pyhd8ed1ab_0.conda
applaunchservices              0.3.0           pyh534df25_3        10.9 KiB   conda  applaunchservices-0.3.0-pyh534df25_3.conda
appnope                        0.1.4           pyhd8ed1ab_0        10 KiB     conda  appnope-0.1.4-pyhd8ed1ab_0.conda
arrow                          1.3.0           pyhd8ed1ab_0        97.7 KiB   conda  arrow-1.3.0-pyhd8ed1ab_0.conda
astroid                        3.2.4           py312h81bd7bf_0     496.3 KiB  conda  astroid-3.2.4-py312h81bd7bf_0.conda
asttokens                      2.4.1           pyhd8ed1ab_0        28.2 KiB   conda  asttokens-2.4.1-pyhd8ed1ab_0.conda
atomicwrites                   1.4.1           pyhd8ed1ab_0        11.6 KiB   conda  atomicwrites-1.4.1-pyhd8ed1ab_0.tar.bz2
attrs                          24.2.0          pyh71513ae_0        54.7 KiB   conda  attrs-24.2.0-pyh71513ae_0.conda
autopep8                       2.0.4           pyhd8ed1ab_0        44.6 KiB   conda  autopep8-2.0.4-pyhd8ed1ab_0.conda
babel                          2.14.0          pyhd8ed1ab_0        7.3 MiB    conda  babel-2.14.0-pyhd8ed1ab_0.conda
backports                      1.0             pyhd8ed1ab_4        6.8 KiB    conda  backports-1.0-pyhd8ed1ab_4.conda
backports.tarfile              1.0.0           pyhd8ed1ab_1        31.2 KiB   conda  backports.tarfile-1.0.0-pyhd8ed1ab_1.conda
beautifulsoup4                 4.12.3          pyha770c72_0        115.4 KiB  conda  beautifulsoup4-4.12.3-pyha770c72_0.conda
binaryornot                    0.4.4           py_1                369.6 KiB  conda  binaryornot-0.4.4-py_1.tar.bz2
black                          24.8.0          py312h81bd7bf_0     382.4 KiB  conda  black-24.8.0-py312h81bd7bf_0.conda
bleach                         6.1.0           pyhd8ed1ab_0        128.1 KiB  conda  bleach-6.1.0-pyhd8ed1ab_0.conda
brotli-python                  1.1.0           py312h9f69965_1     335.4 KiB  conda  brotli-python-1.1.0-py312h9f69965_1.conda
bzip2                          1.0.8           h99b78c6_7          120 KiB    conda  bzip2-1.0.8-h99b78c6_7.conda
ca-certificates                2024.7.4        hf0a4a13_0          150.9 KiB  conda  ca-certificates-2024.7.4-hf0a4a13_0.conda
certifi                        2024.7.4        pyhd8ed1ab_0        155.6 KiB  conda  certifi-2024.7.4-pyhd8ed1ab_0.conda
cffi                           1.17.0          py312h80c9ed6_0     274.4 KiB  conda  cffi-1.17.0-py312h80c9ed6_0.conda
chardet                        5.2.0           py312h81bd7bf_1     257.4 KiB  conda  chardet-5.2.0-py312h81bd7bf_1.conda
charset-normalizer             3.3.2           pyhd8ed1ab_0        45.5 KiB   conda  charset-normalizer-3.3.2-pyhd8ed1ab_0.conda
click                          8.1.7           unix_pyh707e725_0   82.5 KiB   conda  click-8.1.7-unix_pyh707e725_0.conda
cloudpickle                    3.0.0           pyhd8ed1ab_0        24.2 KiB   conda  cloudpickle-3.0.0-pyhd8ed1ab_0.conda
colorama                       0.4.6           pyhd8ed1ab_0        24.6 KiB   conda  colorama-0.4.6-pyhd8ed1ab_0.tar.bz2
comm                           0.2.2           pyhd8ed1ab_0        11.8 KiB   conda  comm-0.2.2-pyhd8ed1ab_0.conda
cookiecutter                   2.6.0           pyhca7485f_0        98.5 KiB   conda  cookiecutter-2.6.0-pyhca7485f_0.conda
debugpy                        1.8.5           py312h5c2e7bc_0     2 MiB      conda  debugpy-1.8.5-py312h5c2e7bc_0.conda
decorator                      5.1.1           pyhd8ed1ab_0        11.8 KiB   conda  decorator-5.1.1-pyhd8ed1ab_0.tar.bz2
defusedxml                     0.7.1           pyhd8ed1ab_0        23.5 KiB   conda  defusedxml-0.7.1-pyhd8ed1ab_0.tar.bz2
diff-match-patch               20230430        pyhd8ed1ab_0        40.2 KiB   conda  diff-match-patch-20230430-pyhd8ed1ab_0.conda
dill                           0.3.8           pyhd8ed1ab_0        86.1 KiB   conda  dill-0.3.8-pyhd8ed1ab_0.conda
docstring-to-markdown          0.15            pyhd8ed1ab_0        33.3 KiB   conda  docstring-to-markdown-0.15-pyhd8ed1ab_0.conda
docutils                       0.21.2          pyhd8ed1ab_0        393.8 KiB  conda  docutils-0.21.2-pyhd8ed1ab_0.conda
entrypoints                    0.4             pyhd8ed1ab_0        9 KiB      conda  entrypoints-0.4-pyhd8ed1ab_0.tar.bz2
exceptiongroup                 1.2.2           pyhd8ed1ab_0        19.9 KiB   conda  exceptiongroup-1.2.2-pyhd8ed1ab_0.conda
executing                      2.0.1           pyhd8ed1ab_0        27 KiB     conda  executing-2.0.1-pyhd8ed1ab_0.conda
flake8                         7.0.0           pyhd8ed1ab_0        108.3 KiB  conda  flake8-7.0.0-pyhd8ed1ab_0.conda
giflib                         5.2.2           h93a5062_0          69.9 KiB   conda  giflib-5.2.2-h93a5062_0.conda
glib                           2.80.3          h59d46d9_2          569.8 KiB  conda  glib-2.80.3-h59d46d9_2.conda
glib-tools                     2.80.3          h8ba3eef_2          96.4 KiB   conda  glib-tools-2.80.3-h8ba3eef_2.conda
gst-plugins-base               1.24.6          h40577aa_0          1.9 MiB    conda  gst-plugins-base-1.24.6-h40577aa_0.conda
gstreamer                      1.24.6          h430e707_0          1.3 MiB    conda  gstreamer-1.24.6-h430e707_0.conda
h2                             4.1.0           pyhd8ed1ab_0        45.7 KiB   conda  h2-4.1.0-pyhd8ed1ab_0.tar.bz2
hpack                          4.0.0           pyh9f0ad1d_0        24.7 KiB   conda  hpack-4.0.0-pyh9f0ad1d_0.tar.bz2
hyperframe                     6.0.1           pyhd8ed1ab_0        14.3 KiB   conda  hyperframe-6.0.1-pyhd8ed1ab_0.tar.bz2
icu                            73.2            hc8870d7_0          11.4 MiB   conda  icu-73.2-hc8870d7_0.conda
idna                           3.8             pyhd8ed1ab_0        48.1 KiB   conda  idna-3.8-pyhd8ed1ab_0.conda
imagesize                      1.4.1           pyhd8ed1ab_0        9.9 KiB    conda  imagesize-1.4.1-pyhd8ed1ab_0.tar.bz2
importlib-metadata             8.4.0           pyha770c72_0        27.7 KiB   conda  importlib-metadata-8.4.0-pyha770c72_0.conda
importlib_metadata             8.4.0           hd8ed1ab_0          9.1 KiB    conda  importlib_metadata-8.4.0-hd8ed1ab_0.conda
importlib_resources            6.4.4           pyhd8ed1ab_0        31.5 KiB   conda  importlib_resources-6.4.4-pyhd8ed1ab_0.conda
inflection                     0.5.1           pyh9f0ad1d_0        9.1 KiB    conda  inflection-0.5.1-pyh9f0ad1d_0.tar.bz2
intervaltree                   3.1.0           pyhd8ed1ab_1        26.9 KiB   conda  intervaltree-3.1.0-pyhd8ed1ab_1.conda
ipykernel                      6.29.5          pyh57ce528_0        116.8 KiB  conda  ipykernel-6.29.5-pyh57ce528_0.conda
ipython                        8.26.0          pyh707e725_0        585.2 KiB  conda  ipython-8.26.0-pyh707e725_0.conda
isort                          5.13.2          pyhd8ed1ab_0        72.1 KiB   conda  isort-5.13.2-pyhd8ed1ab_0.conda
jaraco.classes                 3.4.0           pyhd8ed1ab_1        11.9 KiB   conda  jaraco.classes-3.4.0-pyhd8ed1ab_1.conda
jaraco.context                 5.3.0           pyhd8ed1ab_1        12.2 KiB   conda  jaraco.context-5.3.0-pyhd8ed1ab_1.conda
jaraco.functools               4.0.0           pyhd8ed1ab_0        14.8 KiB   conda  jaraco.functools-4.0.0-pyhd8ed1ab_0.conda
jedi                           0.19.1          pyhd8ed1ab_0        821.6 KiB  conda  jedi-0.19.1-pyhd8ed1ab_0.conda
jellyfish                      1.1.0           py312h552d48e_0     266.5 KiB  conda  jellyfish-1.1.0-py312h552d48e_0.conda
jinja2                         3.1.4           pyhd8ed1ab_0        109 KiB    conda  jinja2-3.1.4-pyhd8ed1ab_0.conda
jsonschema                     4.23.0          pyhd8ed1ab_0        72.6 KiB   conda  jsonschema-4.23.0-pyhd8ed1ab_0.conda
jsonschema-specifications      2023.12.1       pyhd8ed1ab_0        16 KiB     conda  jsonschema-specifications-2023.12.1-pyhd8ed1ab_0.conda
jupyter_client                 8.6.2           pyhd8ed1ab_0        103.8 KiB  conda  jupyter_client-8.6.2-pyhd8ed1ab_0.conda
jupyter_core                   5.7.2           py312h81bd7bf_0     91.6 KiB   conda  jupyter_core-5.7.2-py312h81bd7bf_0.conda
jupyterlab_pygments            0.3.0           pyhd8ed1ab_1        18.3 KiB   conda  jupyterlab_pygments-0.3.0-pyhd8ed1ab_1.conda
keyring                        25.3.0          pyh534df25_0        36.1 KiB   conda  keyring-25.3.0-pyh534df25_0.conda
krb5                           1.21.3          h237132a_0          1.1 MiB    conda  krb5-1.21.3-h237132a_0.conda
lerc                           4.0.0           h9a09cb3_0          210.7 KiB  conda  lerc-4.0.0-h9a09cb3_0.tar.bz2
libclang-cpp15                 15.0.7          default_he012953_5  10.9 MiB   conda  libclang-cpp15-15.0.7-default_he012953_5.conda
libclang13                     18.1.8          default_hfc66aa2_2  7.2 MiB    conda  libclang13-18.1.8-default_hfc66aa2_2.conda
libcxx                         18.1.8          h5a72898_4          1.2 MiB    conda  libcxx-18.1.8-h5a72898_4.conda
libdeflate                     1.21            h99b78c6_0          53.3 KiB   conda  libdeflate-1.21-h99b78c6_0.conda
libedit                        3.1.20191231    hc8eb9b7_2          94.3 KiB   conda  libedit-3.1.20191231-hc8eb9b7_2.tar.bz2
libexpat                       2.6.2           hebf3989_0          62.2 KiB   conda  libexpat-2.6.2-hebf3989_0.conda
libffi                         3.4.2           h3422bc3_5          38.1 KiB   conda  libffi-3.4.2-h3422bc3_5.tar.bz2
libglib                        2.80.3          h59d46d9_2          3.5 MiB    conda  libglib-2.80.3-h59d46d9_2.conda
libiconv                       1.17            h0d3ecfb_2          660.6 KiB  conda  libiconv-1.17-h0d3ecfb_2.conda
libintl                        0.22.5          h8414b35_3          79.3 KiB   conda  libintl-0.22.5-h8414b35_3.conda
libintl-devel                  0.22.5          h8414b35_3          37.7 KiB   conda  libintl-devel-0.22.5-h8414b35_3.conda
libjpeg-turbo                  3.0.0           hb547adb_1          534.7 KiB  conda  libjpeg-turbo-3.0.0-hb547adb_1.conda
libllvm15                      15.0.7          h2621b3d_4          21 MiB     conda  libllvm15-15.0.7-h2621b3d_4.conda
libllvm18                      18.1.8          h5090b49_2          24.6 MiB   conda  libllvm18-18.1.8-h5090b49_2.conda
libogg                         1.3.5           h99b78c6_0          200.6 KiB  conda  libogg-1.3.5-h99b78c6_0.conda
libopus                        1.3.1           h27ca646_1          246.9 KiB  conda  libopus-1.3.1-h27ca646_1.tar.bz2
libpng                         1.6.43          h091b4b1_0          258 KiB    conda  libpng-1.6.43-h091b4b1_0.conda
libpq                          16.4            h7afe498_0          2.3 MiB    conda  libpq-16.4-h7afe498_0.conda
libsodium                      1.0.18          h27ca646_1          317.3 KiB  conda  libsodium-1.0.18-h27ca646_1.tar.bz2
libspatialindex                2.0.0           h00cdb27_0          285.5 KiB  conda  libspatialindex-2.0.0-h00cdb27_0.conda
libsqlite                      3.46.0          hfb93653_0          810.7 KiB  conda  libsqlite-3.46.0-hfb93653_0.conda
libtiff                        4.6.0           hf8409c0_4          233.1 KiB  conda  libtiff-4.6.0-hf8409c0_4.conda
libvorbis                      1.3.7           h9f76cd9_0          248.9 KiB  conda  libvorbis-1.3.7-h9f76cd9_0.tar.bz2
libwebp                        1.4.0           h54798ee_0          85.6 KiB   conda  libwebp-1.4.0-h54798ee_0.conda
libwebp-base                   1.4.0           h93a5062_0          281 KiB    conda  libwebp-base-1.4.0-h93a5062_0.conda
libxml2                        2.12.7          h9a80f22_3          574.6 KiB  conda  libxml2-2.12.7-h9a80f22_3.conda
libzlib                        1.3.1           hfb2fe0b_1          45.8 KiB   conda  libzlib-1.3.1-hfb2fe0b_1.conda
markdown-it-py                 3.0.0           pyhd8ed1ab_0        62.8 KiB   conda  markdown-it-py-3.0.0-pyhd8ed1ab_0.conda
markupsafe                     2.1.5           py312he37b823_0     25.8 KiB   conda  markupsafe-2.1.5-py312he37b823_0.conda
matplotlib-inline              0.1.7           pyhd8ed1ab_0        14.3 KiB   conda  matplotlib-inline-0.1.7-pyhd8ed1ab_0.conda
mccabe                         0.7.0           pyhd8ed1ab_0        10.7 KiB   conda  mccabe-0.7.0-pyhd8ed1ab_0.tar.bz2
mdurl                          0.1.2           pyhd8ed1ab_0        14.3 KiB   conda  mdurl-0.1.2-pyhd8ed1ab_0.conda
mistune                        3.0.2           pyhd8ed1ab_0        64.5 KiB   conda  mistune-3.0.2-pyhd8ed1ab_0.conda
more-itertools                 10.4.0          pyhd8ed1ab_0        56 KiB     conda  more-itertools-10.4.0-pyhd8ed1ab_0.conda
mypy_extensions                1.0.0           pyha770c72_0        10.2 KiB   conda  mypy_extensions-1.0.0-pyha770c72_0.conda
mysql-common                   8.3.0           h1687695_5          789.3 KiB  conda  mysql-common-8.3.0-h1687695_5.conda
mysql-libs                     8.3.0           h0e80b4a_5          1.5 MiB    conda  mysql-libs-8.3.0-h0e80b4a_5.conda
nbclient                       0.10.0          pyhd8ed1ab_0        27.2 KiB   conda  nbclient-0.10.0-pyhd8ed1ab_0.conda
nbconvert                      7.16.4          hd8ed1ab_1          8.1 KiB    conda  nbconvert-7.16.4-hd8ed1ab_1.conda
nbconvert-core                 7.16.4          pyhd8ed1ab_1        185.2 KiB  conda  nbconvert-core-7.16.4-pyhd8ed1ab_1.conda
nbconvert-pandoc               7.16.4          hd8ed1ab_1          8.2 KiB    conda  nbconvert-pandoc-7.16.4-hd8ed1ab_1.conda
nbformat                       5.10.4          pyhd8ed1ab_0        98.9 KiB   conda  nbformat-5.10.4-pyhd8ed1ab_0.conda
ncurses                        6.5             h7bae524_1          783.5 KiB  conda  ncurses-6.5-h7bae524_1.conda
nest-asyncio                   1.6.0           pyhd8ed1ab_0        11.4 KiB   conda  nest-asyncio-1.6.0-pyhd8ed1ab_0.conda
nspr                           4.35            hb7217d7_0          215.6 KiB  conda  nspr-4.35-hb7217d7_0.conda
nss                            3.103           hc42bcbf_0          1.7 MiB    conda  nss-3.103-hc42bcbf_0.conda
numpydoc                       1.8.0           pyhd8ed1ab_0        56.6 KiB   conda  numpydoc-1.8.0-pyhd8ed1ab_0.conda
openssl                        3.3.1           h8359307_3          2.8 MiB    conda  openssl-3.3.1-h8359307_3.conda
packaging                      24.1            pyhd8ed1ab_0        49.1 KiB   conda  packaging-24.1-pyhd8ed1ab_0.conda
pandoc                         3.3             hce30654_0          21.8 MiB   conda  pandoc-3.3-hce30654_0.conda
pandocfilters                  1.5.0           pyhd8ed1ab_0        11.4 KiB   conda  pandocfilters-1.5.0-pyhd8ed1ab_0.tar.bz2
parso                          0.8.4           pyhd8ed1ab_0        73.4 KiB   conda  parso-0.8.4-pyhd8ed1ab_0.conda
pathspec                       0.12.1          pyhd8ed1ab_0        40.2 KiB   conda  pathspec-0.12.1-pyhd8ed1ab_0.conda
pcre2                          10.44           h297a79d_2          604.5 KiB  conda  pcre2-10.44-h297a79d_2.conda
pexpect                        4.9.0           pyhd8ed1ab_0        52.3 KiB   conda  pexpect-4.9.0-pyhd8ed1ab_0.conda
pickleshare                    0.7.5           py_1003             9.1 KiB    conda  pickleshare-0.7.5-py_1003.tar.bz2
pkgutil-resolve-name           1.3.10          pyhd8ed1ab_1        10.5 KiB   conda  pkgutil-resolve-name-1.3.10-pyhd8ed1ab_1.conda
platformdirs                   4.2.2           pyhd8ed1ab_0        20.1 KiB   conda  platformdirs-4.2.2-pyhd8ed1ab_0.conda
pluggy                         1.5.0           pyhd8ed1ab_0        23.3 KiB   conda  pluggy-1.5.0-pyhd8ed1ab_0.conda
ply                            3.11            pyhd8ed1ab_2        48 KiB     conda  ply-3.11-pyhd8ed1ab_2.conda
prompt-toolkit                 3.0.47          pyha770c72_0        264.4 KiB  conda  prompt-toolkit-3.0.47-pyha770c72_0.conda
psutil                         6.0.0           py312h7e5086c_0     489.9 KiB  conda  psutil-6.0.0-py312h7e5086c_0.conda
ptyprocess                     0.7.0           pyhd3deb0d_0        16.2 KiB   conda  ptyprocess-0.7.0-pyhd3deb0d_0.tar.bz2
pure_eval                      0.2.3           pyhd8ed1ab_0        16.2 KiB   conda  pure_eval-0.2.3-pyhd8ed1ab_0.conda
pycodestyle                    2.11.1          pyhd8ed1ab_0        33.5 KiB   conda  pycodestyle-2.11.1-pyhd8ed1ab_0.conda
pycparser                      2.22            pyhd8ed1ab_0        102.6 KiB  conda  pycparser-2.22-pyhd8ed1ab_0.conda
pydocstyle                     6.3.0           pyhd8ed1ab_0        38.9 KiB   conda  pydocstyle-6.3.0-pyhd8ed1ab_0.conda
pyflakes                       3.2.0           pyhd8ed1ab_0        57.3 KiB   conda  pyflakes-3.2.0-pyhd8ed1ab_0.conda
pygments                       2.18.0          pyhd8ed1ab_0        858.7 KiB  conda  pygments-2.18.0-pyhd8ed1ab_0.conda
pylint                         3.2.6           pyhd8ed1ab_0        343.3 KiB  conda  pylint-3.2.6-pyhd8ed1ab_0.conda
pylint-venv                    3.0.3           pyhd8ed1ab_0        10.9 KiB   conda  pylint-venv-3.0.3-pyhd8ed1ab_0.conda
pyls-spyder                    0.4.0           pyhd8ed1ab_0        9.6 KiB    conda  pyls-spyder-0.4.0-pyhd8ed1ab_0.tar.bz2
pyobjc-core                    10.3.1          py312hbb55c70_0     479.6 KiB  conda  pyobjc-core-10.3.1-py312hbb55c70_0.conda
pyobjc-framework-cocoa         10.3.1          py312hbb55c70_0     370.5 KiB  conda  pyobjc-framework-cocoa-10.3.1-py312hbb55c70_0.conda
pyobjc-framework-coreservices  10.3.1          py312h7e5086c_0     46.1 KiB   conda  pyobjc-framework-coreservices-10.3.1-py312h7e5086c_0.conda
pyobjc-framework-fsevents      10.3.1          py312h81bd7bf_0     16.9 KiB   conda  pyobjc-framework-fsevents-10.3.1-py312h81bd7bf_0.conda
pyqt                           5.15.9          py312h550cae4_5     3.8 MiB    conda  pyqt-5.15.9-py312h550cae4_5.conda
pyqt5-sip                      12.12.2         py312h9f69965_5     74.1 KiB   conda  pyqt5-sip-12.12.2-py312h9f69965_5.conda
pyqtwebengine                  5.15.9          py312h14105d7_5     124.8 KiB  conda  pyqtwebengine-5.15.9-py312h14105d7_5.conda
pysocks                        1.7.1           pyha2e5f31_6        18.5 KiB   conda  pysocks-1.7.1-pyha2e5f31_6.tar.bz2
python                         3.12.5          h30c5eda_0_cpython  12.3 MiB   conda  python-3.12.5-h30c5eda_0_cpython.conda
python-dateutil                2.9.0           pyhd8ed1ab_0        217.5 KiB  conda  python-dateutil-2.9.0-pyhd8ed1ab_0.conda
python-fastjsonschema          2.20.0          pyhd8ed1ab_0        220.9 KiB  conda  python-fastjsonschema-2.20.0-pyhd8ed1ab_0.conda
python-lsp-black               2.0.0           pyhd8ed1ab_0        12.3 KiB   conda  python-lsp-black-2.0.0-pyhd8ed1ab_0.conda
python-lsp-jsonrpc             1.1.2           pyhd8ed1ab_0        13.7 KiB   conda  python-lsp-jsonrpc-1.1.2-pyhd8ed1ab_0.conda
python-lsp-server              1.11.0          pyhd8ed1ab_0        7 KiB      conda  python-lsp-server-1.11.0-pyhd8ed1ab_0.conda
python-lsp-server-base         1.11.0          pyhd8ed1ab_0        59.4 KiB   conda  python-lsp-server-base-1.11.0-pyhd8ed1ab_0.conda
python-slugify                 8.0.4           pyhd8ed1ab_0        14.8 KiB   conda  python-slugify-8.0.4-pyhd8ed1ab_0.conda
python.app                     1.4             py312h7fd2b6f_3     18.2 KiB   conda  python.app-1.4-py312h7fd2b6f_3.conda
python_abi                     3.12            5_cp312             6.1 KiB    conda  python_abi-3.12-5_cp312.conda
pytoolconfig                   1.2.5           pyhd8ed1ab_0        20.8 KiB   conda  pytoolconfig-1.2.5-pyhd8ed1ab_0.conda
pytz                           2024.1          pyhd8ed1ab_0        184.1 KiB  conda  pytz-2024.1-pyhd8ed1ab_0.conda
pyyaml                         6.0.2           py312h7e5086c_0     183.3 KiB  conda  pyyaml-6.0.2-py312h7e5086c_0.conda
pyzmq                          26.2.0          py312hc6335d2_0     351.1 KiB  conda  pyzmq-26.2.0-py312hc6335d2_0.conda
qdarkstyle                     3.2.3           pyhd8ed1ab_0        614.4 KiB  conda  qdarkstyle-3.2.3-pyhd8ed1ab_0.conda
qstylizer                      0.2.3           pyhd8ed1ab_0        18.7 KiB   conda  qstylizer-0.2.3-pyhd8ed1ab_0.conda
qt-main                        5.15.8          hcd44e0d_23         48.8 MiB   conda  qt-main-5.15.8-hcd44e0d_23.conda
qt-webengine                   5.15.8          h850e111_4          42.9 MiB   conda  qt-webengine-5.15.8-h850e111_4.conda
qtawesome                      1.3.1           pyh9208f05_0        1.5 MiB    conda  qtawesome-1.3.1-pyh9208f05_0.conda
qtconsole                      5.5.2           pyhd8ed1ab_0        7.2 KiB    conda  qtconsole-5.5.2-pyhd8ed1ab_0.conda
qtconsole-base                 5.5.2           pyha770c72_0        97.9 KiB   conda  qtconsole-base-5.5.2-pyha770c72_0.conda
qtpy                           2.4.1           pyhd8ed1ab_0        60.4 KiB   conda  qtpy-2.4.1-pyhd8ed1ab_0.conda
readline                       8.2             h92ec313_1          244.5 KiB  conda  readline-8.2-h92ec313_1.conda
referencing                    0.35.1          pyhd8ed1ab_0        41.2 KiB   conda  referencing-0.35.1-pyhd8ed1ab_0.conda
requests                       2.32.3          pyhd8ed1ab_0        57.4 KiB   conda  requests-2.32.3-pyhd8ed1ab_0.conda
rich                           13.7.1          pyhd8ed1ab_0        180 KiB    conda  rich-13.7.1-pyhd8ed1ab_0.conda
rope                           1.13.0          pyhd8ed1ab_0        146.9 KiB  conda  rope-1.13.0-pyhd8ed1ab_0.conda
rpds-py                        0.20.0          py312h552d48e_0     286.7 KiB  conda  rpds-py-0.20.0-py312h552d48e_0.conda
rtree                          1.3.0           py312heed235c_1     69 KiB     conda  rtree-1.3.0-py312heed235c_1.conda
setuptools                     72.2.0          pyhd8ed1ab_0        1.4 MiB    conda  setuptools-72.2.0-pyhd8ed1ab_0.conda
sip                            6.8.3           py312h20a0b95_0     624.7 KiB  conda  sip-6.8.3-py312h20a0b95_0.conda
six                            1.16.0          pyh6c4a22f_0        13.9 KiB   conda  six-1.16.0-pyh6c4a22f_0.tar.bz2
snowballstemmer                2.2.0           pyhd8ed1ab_0        57.4 KiB   conda  snowballstemmer-2.2.0-pyhd8ed1ab_0.tar.bz2
sortedcontainers               2.4.0           pyhd8ed1ab_0        25.7 KiB   conda  sortedcontainers-2.4.0-pyhd8ed1ab_0.tar.bz2
soupsieve                      2.5             pyhd8ed1ab_1        35.9 KiB   conda  soupsieve-2.5-pyhd8ed1ab_1.conda
sphinx                         8.0.2           pyhd8ed1ab_0        1.3 MiB    conda  sphinx-8.0.2-pyhd8ed1ab_0.conda
sphinxcontrib-applehelp        2.0.0           pyhd8ed1ab_0        28.9 KiB   conda  sphinxcontrib-applehelp-2.0.0-pyhd8ed1ab_0.conda
sphinxcontrib-devhelp          2.0.0           pyhd8ed1ab_0        23.6 KiB   conda  sphinxcontrib-devhelp-2.0.0-pyhd8ed1ab_0.conda
sphinxcontrib-htmlhelp         2.1.0           pyhd8ed1ab_0        32 KiB     conda  sphinxcontrib-htmlhelp-2.1.0-pyhd8ed1ab_0.conda
sphinxcontrib-jsmath           1.0.1           pyhd8ed1ab_0        10.2 KiB   conda  sphinxcontrib-jsmath-1.0.1-pyhd8ed1ab_0.conda
sphinxcontrib-qthelp           2.0.0           pyhd8ed1ab_0        26.2 KiB   conda  sphinxcontrib-qthelp-2.0.0-pyhd8ed1ab_0.conda
sphinxcontrib-serializinghtml  1.1.10          pyhd8ed1ab_0        28.1 KiB   conda  sphinxcontrib-serializinghtml-1.1.10-pyhd8ed1ab_0.conda
spyder                         5.5.5           py312h81bd7bf_0     11.1 MiB   conda  spyder-5.5.5-py312h81bd7bf_0.conda
spyder-kernels                 2.5.2           unix_pyh707e725_0   79.2 KiB   conda  spyder-kernels-2.5.2-unix_pyh707e725_0.conda
stack_data                     0.6.2           pyhd8ed1ab_0        25.6 KiB   conda  stack_data-0.6.2-pyhd8ed1ab_0.conda
tabulate                       0.9.0           pyhd8ed1ab_1        35.1 KiB   conda  tabulate-0.9.0-pyhd8ed1ab_1.tar.bz2
text-unidecode                 1.3             pyhd8ed1ab_1        63.5 KiB   conda  text-unidecode-1.3-pyhd8ed1ab_1.conda
textdistance                   4.6.3           pyhd8ed1ab_0        29.7 KiB   conda  textdistance-4.6.3-pyhd8ed1ab_0.conda
three-merge                    0.1.1           pyh9f0ad1d_0        8.4 KiB    conda  three-merge-0.1.1-pyh9f0ad1d_0.tar.bz2
tinycss2                       1.3.0           pyhd8ed1ab_0        24.8 KiB   conda  tinycss2-1.3.0-pyhd8ed1ab_0.conda
tk                             8.6.13          h5083fa2_1          3 MiB      conda  tk-8.6.13-h5083fa2_1.conda
toml                           0.10.2          pyhd8ed1ab_0        18 KiB     conda  toml-0.10.2-pyhd8ed1ab_0.tar.bz2
tomli                          2.0.1           pyhd8ed1ab_0        15.6 KiB   conda  tomli-2.0.1-pyhd8ed1ab_0.tar.bz2
tomlkit                        0.13.2          pyha770c72_0        36.4 KiB   conda  tomlkit-0.13.2-pyha770c72_0.conda
tornado                        6.4.1           py312h7e5086c_0     822.1 KiB  conda  tornado-6.4.1-py312h7e5086c_0.conda
traitlets                      5.14.3          pyhd8ed1ab_0        107.6 KiB  conda  traitlets-5.14.3-pyhd8ed1ab_0.conda
types-python-dateutil          2.9.0.20240821  pyhd8ed1ab_0        21.1 KiB   conda  types-python-dateutil-2.9.0.20240821-pyhd8ed1ab_0.conda
typing-extensions              4.12.2          hd8ed1ab_0          9.9 KiB    conda  typing-extensions-4.12.2-hd8ed1ab_0.conda
typing_extensions              4.12.2          pyha770c72_0        39 KiB     conda  typing_extensions-4.12.2-pyha770c72_0.conda
tzdata                         2024a           h0c530f3_0          117 KiB    conda  tzdata-2024a-h0c530f3_0.conda
ujson                          5.10.0          py312h5c2e7bc_0     50.3 KiB   conda  ujson-5.10.0-py312h5c2e7bc_0.conda
urllib3                        2.2.2           pyhd8ed1ab_1        92.8 KiB   conda  urllib3-2.2.2-pyhd8ed1ab_1.conda
watchdog                       4.0.1           py312h7e5086c_0     142 KiB    conda  watchdog-4.0.1-py312h7e5086c_0.conda
wcwidth                        0.2.13          pyhd8ed1ab_0        31.9 KiB   conda  wcwidth-0.2.13-pyhd8ed1ab_0.conda
webencodings                   0.5.1           pyhd8ed1ab_2        15.2 KiB   conda  webencodings-0.5.1-pyhd8ed1ab_2.conda
whatthepatch                   1.0.6           pyhd8ed1ab_0        16.5 KiB   conda  whatthepatch-1.0.6-pyhd8ed1ab_0.conda
wurlitzer                      3.1.1           pyhd8ed1ab_0        13.9 KiB   conda  wurlitzer-3.1.1-pyhd8ed1ab_0.conda
xz                             5.2.6           h57fd34a_0          230.2 KiB  conda  xz-5.2.6-h57fd34a_0.tar.bz2
yaml                           0.2.5           h3422bc3_2          86 KiB     conda  yaml-0.2.5-h3422bc3_2.tar.bz2
yapf                           0.40.1          pyhd8ed1ab_0        172.2 KiB  conda  yapf-0.40.1-pyhd8ed1ab_0.conda
zeromq                         4.3.5           hcc0f68c_4          291.6 KiB  conda  zeromq-4.3.5-hcc0f68c_4.conda
zipp                           3.20.0          pyhd8ed1ab_0        20.4 KiB   conda  zipp-3.20.0-pyhd8ed1ab_0.conda
zstandard                      0.23.0          py312h721a963_0     324.7 KiB  conda  zstandard-0.23.0-py312h721a963_0.conda
zstd                           1.5.6           hb46c0d2_0          395.6 KiB  conda  zstd-1.5.6-hb46c0d2_0.conda

dalthviz commented 2 months ago

Hi @fangohr thank you for the feedback! I haven't used pixi myselft but checking around the pythonapp vs python.app difference you spotted, maybe this behavior is related with https://github.com/ContinuumIO/anaconda-issues/issues/12188 ? Seems like then a fix over python.app needs to be done somehow? 🤔

fangohr commented 1 month ago

Hi @dalthviz, thank you for picking this up. Yes, I think you are right that this is a python.app problem.

However, I installed from conda-forge (not anaconda default).

fangohr commented 1 month ago

I have a new data point: installing spyder with miniforge results in a working installation. Here are the key steps to reproduce:

# install miniforge from https://github.com/conda-forge/miniforge?tab=readme-ov-file#download
conda create --name spydertestenv python=3.12 spyder
conda activate spydertestenv 
spyder

This works.

Is there perhaps a difference in the installed packages?

This setup has installed (just listing spyder and python.app, output from conda list:

python.app                3               py312h80987f9_1 
spyder                    5.5.1           py312hca03da5_3  
spyder-kernels            2.5.0           py312hca03da5_0

whereas the install with pixi has installed (output from pixi list:

python.app                     1.4             py312h7fd2b6f_3     18.2 KiB   conda  python.app-1.4-py312h7fd2b6f_3.conda
spyder                         5.5.5           py312h81bd7bf_0     11.1 MiB   conda  spyder-5.5.5-py312h81bd7bf_0.conda
spyder-kernels                 2.5.2           unix_pyh707e725_0   79.2 KiB   conda  spyder-kernels-2.5.2-unix_pyh707e725_0.conda

Ticking of simple things first, I have forced pixi to use spyder/5.5.1, and that does not change the behaviour.

The difference in the python app version seems remarkable though: 1.4 in pixi and 3 in the miniforge based installation.

fangohr commented 1 month ago

Trying to force version 3 of python.app with pixi, results in this error:

MBAM2 pixi-env2 % pixi add python=3.12 python.app=3 spyder
  x failed to solve the conda requirements of 'default' 'osx-arm64'
  `-> Cannot solve the request because of: No candidates were found for python.app 3.*.

Perhaps other Python versions make it possible?

MBAM2 pixi-env2 % pixi add python python.app=3 spyder     
  x failed to solve the conda requirements of 'default' 'osx-arm64'
  `-> Cannot solve the request because of: No candidates were found for python.app 3.*.

No.

wolfv commented 1 month ago

Hm this is really weird because conda-forge only has 1.4 as far as I can see:

https://anaconda.org/conda-forge/python.app/files

wolfv commented 1 month ago

I double checked and the 3 version of python.app is only available from the Anaconda defaults channel. That makes an installation with conda-forge only impossible, if it is the real underlying problem.

dalthviz commented 1 month ago

Thank you @fangohr for the extra info! As @wolfv says then I would say this is an issue with the python.app package available from conda-forge (by the way thank you @wolfv for giving this a check!).

I think there is not much we can do from the Spyder side, sorry :/

spyder-ide / spyder