bug: permission issues when overwriting domains_color_file

[currocam]

As explained in this issue, there are problems with Singularity because the code tries to overwrite the source file.

This is fine if the user has write permissions on that file (as I understand, in the Docker image and Singularity, if you use the --writable argument). However, I think there are better solutions than this (especially when integrating the program into a pipeline).

It is unclear how the code works: is it necessary to overwrite this file? Could you use temporary files? Although I do not have much knowledge, I would say that the program's current behavior (being able to edit a tsv file persistently) could be achieved by creating a "configuration" file in the user's home folder rather than overwriting the source code of the program. I have attached a PR with an initial proposal.

[currocam]

Instead of overwriting the source file, copy it into user's home directory

[jowodo]

I encountered the same issue as in #22, but in a centrally installed conda environment.
This is how I installed it:

VERSION=1.1.5
conda env create --name bigscape-$VERSION --file https://raw.githubusercontent.com/medema-group/BiG-SCAPE/v${VERSION}/bigscape_dependencies.yml
conda activate bigscape-$VERSION
mkdir -p ${CONDA_PREFIX}/share
pushd ${CONDA_PREFIX}/share
git clone --quiet --depth 1 --branch v$VERSION $URL
chmod +x BiG-SCAPE/bigscape.py
pushd ${CONDA_PREFIX}/bin/
ln -s ../share/BiG-SCAPE/bigscape.py bigscape.py
# resolve bug
# https://github.com/medema-group/BiG-SCAPE/issues/22
# https://stackoverflow.com/a/44853818/17440360
cp $CONDA_PREFIX/share/BiG-SCAPE/ArrowerSVG.py $CONDA_PREFIX/share/BiG-SCAPE/ArrowerSVG.py.bkp
grep -A8 -n " if len(new_color_domains)" $CONDA_PREFIX/share/BiG-SCAPE/ArrowerSVG.py | sed -e 's/[^0-9].*$//' -e 's/$/s|^|#|/' | sed -f- -i $CONDA_PREFIX/share/BiG-SCAPE/ArrowerSVG.py
popd; popd

I agree with @currocam that not editing the source code, but writing to a new file, would be advantages.

[adraismawur]

Hello! Thanks for the contribution and sorry it took us so long to address this. I have opened a new pull request which should resolve this issue by copying the colors file into the output directory instead. I'd prefer not to put anything in the users' home directory.

[jowodo]

Looking forward to the next release :)