make fails in github action - something wrong with pipenv

[noelmcloughlin]

I cannot get the make GitHub action stage to succeed. It works locally but not in Github Actions CI.

I tried setting PATH in Makefile but had no success. Any ideas - error from Github is below:

https://github.com/noelmcloughlin/csolink-model/runs/4112495466?check_suite_focus=true

Run pip install pipx
  pip install pipx
  make
  shell: /usr/bin/bash -e {0}
  env:
    pythonLocation: /opt/hostedtoolcache/Python/3.8.12/x64
    LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.8.12/x64/lib
Collecting pipx
  Downloading pipx-0.16.4-py3-none-any.whl (53 kB)
Collecting argcomplete<2.0,>=1.9.4
  Downloading argcomplete-1.12.3-py2.py3-none-any.whl (38 kB)
Collecting userpath>=1.6.0
  Downloading userpath-1.7.0-py2.py3-none-any.whl (14 kB)
Requirement already satisfied: packaging>=20.0 in /opt/hostedtoolcache/Python/3.8.12/x64/lib/python3.8/site-packages (from pipx) (21.2)
Requirement already satisfied: pyparsing<3,>=2.0.2 in /opt/hostedtoolcache/Python/3.8.12/x64/lib/python3.8/site-packages (from packaging>=20.0->pipx) (2.4.7)
Requirement already satisfied: click in /opt/hostedtoolcache/Python/3.8.12/x64/lib/python3.8/site-packages (from userpath>=1.6.0->pipx) (8.0.3)
Installing collected packages: userpath, argcomplete, pipx
Successfully installed argcomplete-1.12.3 pipx-0.16.4 userpath-1.7.0
rm -rf target/docs
mkdir -p target/docs
export PIPENV_VENV_IN_PROJECT=true && export PIPENV_PIPFILE=make-venv/Pipfile && export PIPENV_IGNORE_VIRTUALENVS=1 && PATH=venv/bin:/opt/hostedtoolcache/Python/3.8.12/x64/bin:/opt/hostedtoolcache/Python/3.8.12/x64:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/runner/.local/bin:/opt/pipx_bin:/usr/share/rust/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin && pipenv run gen-markdown --log_level WARNING --mergeimports --notypesdir --warnonexist --dir target/docs model/schema/csolink-model.yaml
Creating a virtualenv for this project...
Pipfile: /home/runner/work/csolink-model/csolink-model/make-venv/Pipfile
Using /opt/hostedtoolcache/Python/3.8.12/x64/bin/python3 (3.8.12) to create virtualenv...
created virtual environment CPython3.8.12.final.0-64 in 514ms
  creator CPython3Posix(dest=/home/runner/work/csolink-model/csolink-model/make-venv/.venv, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/runner/.local/share/virtualenv)
    added seed packages: pip==21.3.1, setuptools==58.3.0, wheel==0.37.0
  activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator


Successfully created virtual environment!
Virtualenv location: /home/runner/work/csolink-model/csolink-model/make-venv/.venv
Error: the command gen-markdown could not be found within PATH or Pipfile's [scripts].
make: *** [Makefile:119: target/docs/index.md] Error 1
Error: Process completed with exit code 2.

[noelmcloughlin]

I cannot find the root cause inside GitHub Actions despite lots of troubleshooting.

• Various updates to ./github/workflow/main.yml did not help (refer to Pipenv no longer working under the root directory is not listed as a breaking change pypa/pipenv#4273);
• Using ubuntu-18.04 instead of ubuntu-latest did not help.
• The error suggests "pipenv run xxx" fails to execute "source venv/bin/activate" but adding && pipenv run env to Makefile confirmed PATH is updated by "pipenv run".
• Even setting a full path "$(RUN) /add/virtual_env/path/bin/gen-xxxxx" produces same error.

Maybe pypa/pipenv#3496 is related - pipenv code bug inside github ubuntu images.

[sierra-moxon]

This repo is archived. Equivalent functionality is now hosted at http://linkml/linkml-project-cookiecutter/. If we close an issue you still are waiting on, please feel free to reach out on the issue tracker and we will add it to the cookie-cutter. https://github.com/linkml/linkml/issues.