Add step to enable conda envs

[bschilder]

Adding a step to setup conda/miniconda/mamba automatically within rworkflows could be quite helpful (came up here).

Possible parameters:

• Conda software: conda/miniconda/mamba
• Conda R interface: reticulate / basilisk/ echoconda
• Package list
• Predefined envs: via echoconda https://github.com/RajLabMSSM/echoconda/tree/main/inst/conda

[bschilder]

Potentially useful actions:

• https://github.com/marketplace/actions/setup-miniconda
• https://github.com/marketplace/actions/setup-conda
• https://github.com/actions/setup-python
• Feature request: how to use github actions with reticulate rstudio/reticulate#999

Tutorials:

• https://autobencoder.com/2020-08-24-conda-actions/
• https://ericmjl.github.io/blog/2021/12/30/better-conda-environments-on-github-actions/
• https://words.yuvi.in/post/conda-forge-github-actions/
• https://dev.to/epassaro/caching-anaconda-environments-in-github-actions-5hde
• https://community.rstudio.com/t/github-actions-workflow-option-for-a-project-using-reticulate-and-python-dependencies/100242
• https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

NOTE: I've previously tried using basilisk on GHA (unsuccessfully), but perhaps some of the above actions will help: Bioconductor/basilisk#16

[bschilder]

GHA offers runners with python (and miniconda?) pre-installed:
https://github.com/marketplace/actions/setup-miniconda#use-a-different-environment-name-or-path

This will be create a named env in $CONDA/envs/whatever, where $CONDA is the path to the infrequently-updated, but very fast to start, "bundled" Miniconda installation.

[bschilder]

rworkflows::use_workfow should offer options to read in different kinds of environment-specification files:

• conda env .yaml: Extract and use env name, channels, and deps
  Done.
• python requirements.txt: Extract deps
  Can export with new func conda_export.
  Conda should be able to use ".yml" or "requirements.txt", but i get an error each time I go to build with the latter:

+ /Users/bms20/anaconda3/bin/conda env create --quiet --name 'testenv2' -f '/var/folders/rd/rbc_wrdj4k3djf3brk6z0_dc0000gp/T//Rtmpd0gX2x/file3d7eae45b8b_requirements.txt'
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

ResolvePackageNotFound: 
  - tzdata==2023c=h71feb2d_0
  - bzip2==1.0.8=h3422bc3_4
  - urllib3==2.0.6=pypi_0
  - libzlib==1.2.13=h53f4e23_5
  - setuptools==68.2.2=pyhd8ed1ab_0
  - ncurses==6.4=h7ea286d_0
  - ca-certificates==2023.7.22=hf0a4a13_0
  - certifi==2023.7.22=pypi_0
  - idna==3.4=pypi_0
  - charset-normalizer==3.3.0=pypi_0
  - pip==23.2.1=pyhd8ed1ab_0
  - wheel==0.41.2=pyhd8ed1ab_0
  - libsqlite==3.43.2=h091b4b1_0
  - tk==8.6.13=hb31c410_0
  - requests==2.31.0=pypi_0
  - libexpat==2.5.0=hb7217d7_1
  - libffi==3.4.2=h3422bc3_5
  - openssl==3.1.3=h53f4e23_0
  - python==3.12.0=h47c9636_0_cpython
  - readline==8.2=h92ec313_1
  - xz==5.2.6=h57fd34a_0

Error: Error creating conda environment [exit code 1]

• poetry .toml: Extract and use env name and deps
  Probably possible, but gets a bit complicated. May return to this later.

Though these may be less necessary as the setup-miniconda action provides the environment-file: arg.

[bschilder]

rworkflows is now working well and passing GHA when creating/exporting conda envs via yaml files.

[bschilder]

Expose these new conda args to the use_workflows R function

[bschilder]

Conda installation isn't being recognized by rworkflows, and thus tests aren't being run:

Just set up a Codespace #103 and found these potentially useful env variables:

Reticulate registers conda as installed too (tho not sure if this is true for the setup-miniconda action too:

[bschilder]

Was able to get a bit further this time: one of the conda env variables was recognized, but reticulate::conda_create failed to find the conda executable:
https://github.com/neurogenomics/rworkflows/actions/runs/6711171547/job/18237958236#step:4:2738

[bschilder]

It appears that it's the CONDA env variable that's being detected:
https://github.com/neurogenomics/rworkflows/actions/runs/6711316713/job/18238415871#step:4:2563

Potentially related issues:

• GitHub Actions-installed miniconda on ubuntu defies assumptions, and a regex that should probably be fixed rstudio/reticulate#1293

Just asked the reticulate maintainers for a update on this ☝️ , but in the meantime a user suggested that miniforge_variant: "Mambaforge" is a useful workaround.

[bschilder]

but in the meantime a user suggested that miniforge_variant: "Mambaforge" is a useful workaround.
Setting miniforge_variant: "Mambaforge" didn't seem to work for me:

Nor did setting the additional parameter use-mamba: true at the same time (same error):
https://github.com/neurogenomics/rworkflows/actions/runs/6711618082/job/18239368376#step:4:2741