environment.yml is missing

[alanocallaghan]

alan@pop-os:~/Documents/github/imaging/squidpy_notebooks/ (main) $ grep -r environment.yml
tutorials/tutorial_mibitof.ipynb:                "`environment.yml <https://github.com/scverse/squidpy_notebooks/blob/main/environment.yml>`_."
tutorials/tutorial_seqfish.ipynb:                "`environment.yml <https://github.com/scverse/squidpy_notebooks/blob/main/environment.yml>`_."
tutorials/tutorial_visium_hne.ipynb:                "`environment.yml <https://github.com/scverse/squidpy_notebooks/blob/main/environment.yml>`_."
tutorials/tutorial_visium_fluo.ipynb:                "`environment.yml <https://github.com/scverse/squidpy_notebooks/blob/main/environment.yml>`_."
tutorials/tutorial_slideseqv2.ipynb:                "`environment.yml <https://github.com/scverse/squidpy_notebooks/blob/main/environment.yml>`_."
tutorials/tutorial_imc.ipynb:                "`environment.yml <https://github.com/scverse/squidpy_notebooks/blob/main/environment.yml>`_."
tutorials/tutorial_fouri.ipynb:                "`environment.yml <https://github.com/scverse/squidpy_notebooks/blob/main/environment.yml>`_."
tutorials/tutorial_merfish.ipynb:                "`environment.yml <https://github.com/scverse/squidpy_notebooks/blob/main/environment.yml>`_."
alan@pop-os:~/Documents/github/imaging/squidpy_notebooks/ (main) $ find . -name "environment.yml"
alan@pop-os:~/Documents/github/imaging/squidpy_notebooks/ (main) $ 

[MikeWLloyd]

Not sure if the same file or not, but the link: https://github.com/scverse/squidpy_notebooks/blob/main/environment.yml resolves to 404. It is step 1 of certain tutorials, and the env should be present if you are recommending folks to install via that file.

[alanocallaghan]

I assumed this repo was dead given this never got addressed, but I see there are recent commits, issues, PRs etc. Truly bizarre to me, can't be hard to put together an environment yaml or just remove the link altogether

[MikeWLloyd]

Per https://squidpy.readthedocs.io/en/stable/notebooks/tutorials/tutorial_visium_hne.html

Import packages & data[](https://squidpy.readthedocs.io/en/stable/notebooks/tutorials/tutorial_visium_hne.html#import-packages-data)

To run the notebook locally, create a conda environment as conda env create -f environment.yml using this environment.yml <https://github.com/scverse/squidpy_notebooks/blob/main/environment.yml>_.

¯\_(ツ)_/¯

[alanocallaghan]

I gave up and went with an ecosystem that'll let me run the docs without needing to faff with dependencies first :)