How to make pip3 work inside Flatpak sandbox?

Andy · July 21, 2023, 2:02pm

Hi,

Anyone know how to make Python and pip3 work inside Flatpak?
I am experimenting with Spyder Flatpak package.

github.com/flathub/flathub

[WIP] Add org.spyder ide.spyder

flathub:new-pr ← kevinsmia1939:org.spyder_ide.spyder

opened 09:07AM - 21 Jul 23 UTC

kevinsmia1939

+3476 -0

### Please confirm your submission meets all the criteria - [x] I have read t…he [App Requirements][reqs] and [App Maintenance][maint] pages. - [x] My pull request follows the instructions at [App Submission][submission]. - [x] I am using only the minimal set of permissions. *(If not, please explain each non-standard permission.)* - [x] All assets referenced in the manifest are redistributable by any party. If not, the unredistributable parts are using an extra-data source type. - [x] I am an upstream contributor to the project. If not, I contacted upstream developers about submitting their software to Flathub. **Link:** https://github.com/spyder-ide/spyder/issues/6898 - [ ] I own the domain used in the application ID or the domain has a policy for delegating subdomains (e.g. GitHub, SourceForge). - [x] Any additional patches or files have been submitted to the upstream projects concerned. *(If not, explain why.)* [reqs]: https://docs.flathub.org/docs/for-app-authors/requirements [maint]: https://docs.flathub.org/docs/for-app-authors/maintanance [submission]: https://docs.flathub.org/docs/for-app-authors/submission From the link above, upstream are not interested to package and maintain Spyder as Flatpak. The branch was renamed to match appdata in the project, open new PR in continuation from https://github.com/flathub/flathub/pull/4339

I have issue with installing extra library in Spyder after installation. pip3 install new libs but could not import it afterward.

Here I create a simple manifest to test on.


app-id: org.test.test
runtime: org.freedesktop.Sdk
runtime-version: 22.08
sdk: org.freedesktop.Sdk
command: test
finish-args:
  - --share=ipc
  - --socket=wayland
  - --socket=fallback-x11
  - --device=dri
  - --share=network
  - --filesystem=home
modules:
  - name: test
    buildsystem: simple
    build-commands:
      - mkdir /app/bin && touch /app/bin/test

Install with
flatpak-builder build --force-clean --install --user org.test.test.yaml

Running and importing dill library failed.

kevin@localhost:~/Desktop/test_pip3> flatpak run --command=bash org.test.test
[📦 org.test.test test_pip3]$ pip3 install dill
Defaulting to user installation because normal site-packages is not writeable
Collecting dill
  Using cached dill-0.3.6-py3-none-any.whl (110 kB)
Installing collected packages: dill
Successfully installed dill-0.3.6
[📦 org.test.test test_pip3]$ python3
Python 3.10.11 (main, Nov 10 2011, 15:00:00) [GCC 12.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
Could not open PYTHONSTARTUP
FileNotFoundError: [Errno 2] No such file or directory: '/etc/pythonstart'
>>> import dill
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'dill'

pip3 also does not see dill that it just installed

[📦 org.test.test test_pip3]$ pip3 list
Package    Version
---------- -------
Cython     0.29.35
Mako       1.2.4
Markdown   3.4.3
MarkupSafe 2.1.2
meson      0.63.3
pip        23.1.2
Pygments   2.15.1
setuptools 67.8.0
six        1.16.0
wheel      0.38.4

Any one have any idea?

Andy · July 21, 2023, 3:12pm

After some digging it seems like there have something to do with sys.path.
An attempt to add path to sys.path with PYTHONPATH env does not work.

[📦 org.test.test test_pip3]$ export PYTHONPATH=/home/kevin/.local/lib/python3.10/site-packages:$PYTHONPATH
[📦 org.test.test test_pip3]$ python
Python 3.10.11 (main, Nov 10 2011, 15:00:00) [GCC 12.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
Could not open PYTHONSTARTUP
FileNotFoundError: [Errno 2] No such file or directory: '/etc/pythonstart'
>>> import sys
>>> print(sys.path)
['', '/usr/lib/python310.zip', '/usr/lib/python3.10', '/usr/lib/python3.10/lib-dynload', '/app/lib/python3.10/site-packages', '/usr/lib/python3.10/site-packages']
>>>

cxrvh · July 21, 2023, 5:19pm

This seems to be a bug in the runtime:

I don’t know Python therefore I can’t help much. But the package was found with pip list --path <site-package PATH>, maybe it helps in finding a workaround.

Andy · July 22, 2023, 12:48am

Thank for pointing it out. I have found the work around here [WIP] Add org.spyder ide.spyder by kevinsmia1939 · Pull Request #4344 · flathub/flathub · GitHub