Cannot install with pip in editable mode about aiidalab-docker-stack

[csadorf]

Thank you for reporting. We will have to evaluate whether we "officially support" editable installs, but it would certainly be desirable.

[mbercx]

Hmm, I think I've actually been doing this. In which environment was this? The root or the aiida (base)?

As a sidenote: it would be nice if the apps that ship by default are actually installed in editable mode. Makes it easier to start developing. 😁

[csadorf]

As a sidenote: it would be nice if the apps that ship by default are actually installed in editable mode. Makes it easier to start developing. 😁

Apps are just a set of notebooks so they are installed by being placed within the apps/ directory. This means they are essentially installed "editable" by default. This concerns the app dependencies which we generally don't want to install in editable mode.

[mbercx]

This means they are essentially installed "editable" by default.

You're right, my bad. The "editable" install I had to do was for the aiidalab-qe-workchain. :)

[ltalirz]

I confirm this issue

(base) aiida@1d12ef3a1eb7:~/pgsu$ pip install -e .
Defaulting to user installation because normal site-packages is not writeable
Obtaining file:///home/aiida/pgsu
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Requirement already satisfied: click in /opt/conda/lib/python3.7/site-packages (from pgsu==0.2.1) (7.1.2)
Requirement already satisfied: psycopg2-binary>=2.8.3 in /opt/conda/lib/python3.7/site-packages (from pgsu==0.2.1) (2.8.6)
Installing collected packages: pgsu
  Running setup.py develop for pgsu
    ERROR: Command errored out with exit status 1:
     command: /opt/conda/bin/python3.7 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/aiida/pgsu/setup.py'"'"'; __file__='"'"'/home/aiida/pgsu/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps --user --prefix=
         cwd: /home/aiida/pgsu/
    Complete output (28 lines):
    running develop
    WARNING: The user site-packages directory is disabled.
    error: can't create or remove files in install directory

    The following error occurred while trying to add or remove files in the
    installation directory:

        [Errno 13] Permission denied: '/opt/conda/lib/python3.7/site-packages/test-easy-install-3443.write-test'

    The installation directory you specified (via --install-dir, --prefix, or
    the distutils default setting) was:

        /opt/conda/lib/python3.7/site-packages/

    Perhaps your account does not have write access to this directory?  If the
    installation directory is a system-owned directory, you may need to sign in
    as the administrator or "root" account.  If you do not have administrative
    access to this machine, you may wish to choose a different installation
    directory, preferably one that is listed in your PYTHONPATH environment
    variable.

    For information on other options, you may wish to consult the
    documentation at:

      https://setuptools.readthedocs.io/en/latest/deprecated/easy_install.html

    Please make the appropriate changes for your system and try again.

    ----------------------------------------
ERROR: Command errored out with exit status 1: /opt/conda/bin/python3.7 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/aiida/pgsu/setup.py'"'"'; __file__='"'"'/home/aiida/pgsu/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps --user --prefix= Check the logs for full command output.

At first, it looks like pip realizes what it should do (Defaulting to user installation because normal site-packages is not writeable) but then it still ends up trying to write to the system directory.

It turns out that this pip issue is known since April 2020 and still not fixed.

For packages that don't use the pyproject.toml, you can work around it for the moment by using pip install --no-use-pep517 -e ..
For those that do, you'll need to do a manual fix, e.g. like here.

[danielhollas]

This issue is no longer present in the new docker stack, since pip can install into the system-wide environment under jovyan user.

CC @yakutovicha @unkcpz