Why is blogdown putting a mamba command through normalizePath? - r

Question

Here's what I'm doing:
I have a blog that uses blogdown to render .Rmd files.
Some of the code snippets in the blog are in Python. I'm using reticulate for that.
I'm using a GitHub workflow to build and publish the blog as part of a larger website. This workflow sets up the environment and package dependencies in miniconda.
The last time this ran was six months ago. At that time, it worked. Now, it does not. I can't seem to replicate the behavior locally for more detailed debugging.
It seems to be trying to put a mamba command into normalizePath instead of a filesystem path (www-main is the name of the repository):
conda activate www-main
Rscript -e 'blogdown::build_site(local=FALSE, run_hugo=FALSE, build_rmd="content/blog/2020-08-28-api.Rmd")'
shell: /usr/bin/bash -l {0}
env:
CONDA_PKGS_DIR: /home/runner/conda_pkgs_dir
Rendering content/blog/2020-08-28-api.Rmd...
[...]
Quitting from lines 401-410 (2020-08-28-api.Rmd)
Error in normalizePath(conda, winslash = "/", mustWork = TRUE) :
path[1]="# cmd: /usr/share/miniconda/condabin/mamba update --name www-main --file /home/runner/work/www-main/www-main/conda": No such file or directory
Calls: local ... python_munge_path -> get_python_conda_info -> normalizePath
Execution halted
Error: Failed to render content/blog/2020-08-28-api.Rmd
Execution halted
Lines 401-410 of 2020-08-28-api.Rmd are a Python code block:
400 ```{python python-data, dev='svg'}
401 import covidcast
402 from datetime import date
403 import matplotlib.pyplot as plt
404
405 data = covidcast.signal("fb-survey", "smoothed_hh_cmnty_cli",
406 date(2020, 9, 8), date(2020, 9, 8),
407 geo_type="state")
408 covidcast.plot_choropleth(data, figsize=(7, 5))
409 plt.title("% who know someone who is sick, Sept 8, 2020")
410 ```
The useful bits of the output of conda info, in case it helps:
active environment : www-main
active env location : /usr/share/miniconda/envs/www-main
shell level : 1
user config file : /home/runner/.condarc
populated config files : /home/runner/.condarc
conda version : 4.12.0
conda-build version : not installed
python version : 3.9.12.final.0
virtual packages : __linux=5.15.0=0
__glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /usr/share/miniconda (writable)
conda av data dir : /usr/share/miniconda/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/runner/conda_pkgs_dir
envs directories : /usr/share/miniconda/envs
/home/runner/.conda/envs
platform : linux-64
user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.12 Linux/5.15.0-1020-azure ubuntu/20.04.5 glibc/2.31
UID:GID : 1001:121
netrc file : None
offline mode : False
I found this, but their workaround doesn't make sense for me since I'm not using papermill: https://github.com/rstudio/reticulate/issues/1184
I found this, but my paths don't have spaces: https://github.com/rstudio/reticulate/issues/1149
I found this, but their problem includes an entirely reasonable value for path[1], unlike mine: How can I tell R where the conda environment is via a docker image?
The build environment for this is a bit of a bear but I can probably put together a minimum working (/nonworking) example if needed, lmk

Answer 1

I tracked this down to at least two bits of weird/buggy behavior in reticulate and found a workaround: switch from vanilla miniconda to Mambaforge.
The TL;DR seems to be that whatever wacky ubuntu-latest setup-miniconda#v2 environment started putting into meta/history doesn't include a create line, which is what reticulate needs in order to figure out which conda goes with which python, because (1) it ignores the reticulate.conda_binary setting for some reason, and (2) it uses a more restrictive regex to parse the lines of the history file than the regex it uses to select them. Mambaforge does include the create line, so reticulate is happy.
- uses: conda-incubator/setup-miniconda#v2
with:
python-version: 3.9
activate-environment: www-main
miniforge-variant: Mambaforge
miniforge-version: latest
use-mamba: true
use-only-tar-bz2: true # (for caching support)
- name: Update environment
run: mamba env update -n www-main -f environment.yml