Create more minimal examles of environment.yml files

[joelostblom]

The environment.yml files for both R and Py in the docs contain many more packages than what seems to be needed. Would it be possible to replace these with a more minimal configuration to increase clarity of what is required for otter to run? This would also make them slightly faster to build locally (about 10% in my experience with otter grade).

For Python

name: otter-env
channels:
    - conda-forge
    - defaults
dependencies:
    - python=3.11.*
    - otter-grader=5.2.2
    - pip

For R

name: otter-env
channels:
    - conda-forge
    - r
    - defaults
dependencies:
  - python=3.11.*
  - pip
  - otter-grader=5.2.2
  - rpy2
  - r-base>=4.1.1
  - r-essentials
  - r-devtools
  - r-gert
  - r-usethis
  - r-testthat
  - r-startup
  - r-rmarkdown
  - r-stringi
  - r-ottr

I understand that some packages are optional, and maybe this could be more clearly included in the env files? For example:

name: otter-env
channels:
    - conda-forge
    - defaults
dependencies:
    - python=3.9
    - otter-grader=5.*
    - pypdf # optional; for pdf export
    - libgomp # opttonal; for ...
    - libgit2 # opttonal; for ...
    - ... # optional; for ...

[nibheis]

The docker image build process is getting stuck : after investigations, we found out that our docker server is hosted somewhere where the "defaults" channel is not accessible. Downloads from the "defaults" channel receive HTTP 429... + retry in ~ 7 hours.

Side note: this happens when the organization is "in violation of Anaconda's terms of use". I don't know exactly what is going on for our hosting partner, but I'm SURE it falls into the exceptions since it is a public provider for the academic world here in Switzerland (switch.ch).

Anyway, I have not found a way to customize the environment.yml file generation ; we have to fix it manually, inside the .zip, file between the 'assign' and 'grade' steps.

Would you consider removing the problematic 'defaults' channel? or providing a way to get it removed on request?

[chrispyles]

@joelostblom for Python environments, otter includes some packages by default as a legacy from its roots as an autograder designed for data science courses. I agree that we could trim out all of the dependencies not specifically required by otter, but that's a breaking change (not sure how many users rely on those packages so that they don't need to use their own requirements.txt). The R dependencies are another matter -- all of the listed dependencies besides r-base, r-devtools, and r-ottr were added to fix issues with images builds as they cropped up. I'm not sure if it will be possible to remove them without breaking R image builds. That being said, I do agree that these environments are bloated, and it would be nice to slim them down; I'm just not sure how much it will be possible. I'm tagging this for v6 but it may get pushed to a later major version depending on whether I get a chance to look into it.

@nibheis thanks for pointing this out. It should be relatively easy to add a configuration that allows you to remove the defaults channel from the environment.yml files produced by otter; I've opened #778 as an FR for that.