The quarto conda pkg requires a few environment variables that are defined upon activation of a conda env (under etc/conda/activate.d/quarto.sh). But we don't explicitly activate any environments in PCGR, since we rely on just using the full path to Rscript to execute the R-related code, so those env vars need to be defined before the R part. So that's what I'm doing with the export_quarto_evars-related code.
I'm also exporting the bin path for pcgrr and using it as a CONDA_PREFIX before executing. This seems to work on my Mac tests and I'm fairly positive the Linux/Docker installation will also pass.
Edit: added support for cpsr.py as well
The CNAqc installation is problematic on my Mac, giving the following annoying error:
library(CNAqc)
Error in library.dynam(lib, package, package.lib) :
shared object 'sp.dylib' not found
Upon disabling it and running without any CNA files, PCGR works fine.
I'm also cleaning up the installation docs a bit. Conda is on par with mamba as of the last year or so, so we don't need mamba.
I'm bringing in the bslib, shiny and crosstalk dependencies which were used in the qmd files but not defined in DESCRIPTION (bslib and crosstalk were dependencies of other dependencies so were getting imported, but shiny wasn't).
Creating the output_dir using utils.safe_makedir in main.py.
Fixing some typos and cleaning up trailing whitespace in main.py.
Adding .dockerignore file which only copies the conda directory into the image
This one was a bit of a doozy.
The quarto conda pkg requires a few environment variables that are defined upon activation of a conda env (under
etc/conda/activate.d/quarto.sh). But we don't explicitly activate any environments in PCGR, since we rely on just using the full path to Rscript to execute the R-related code, so those env vars need to be defined before the R part. So that's what I'm doing with theexport_quarto_evars-related code. I'm also exporting the bin path for pcgrr and using it as aCONDA_PREFIXbefore executing. This seems to work on my Mac tests and I'm fairly positive the Linux/Docker installation will also pass.cpsr.pyas wellThe CNAqc installation is problematic on my Mac, giving the following annoying error:
Upon disabling it and running without any CNA files, PCGR works fine.
I'm also cleaning up the installation docs a bit. Conda is on par with mamba as of the last year or so, so we don't need mamba.
I'm bringing in the
bslib,shinyandcrosstalkdependencies which were used in the qmd files but not defined in DESCRIPTION (bslibandcrosstalkwere dependencies of other dependencies so were getting imported, butshinywasn't).Creating the
output_dirusingutils.safe_makedirinmain.py.Fixing some typos and cleaning up trailing whitespace in
main.py.Adding
.dockerignorefile which only copies thecondadirectory into the image