pl-unstack-folders
is a ChRIS
ds plugin which copies deeply nested subfiles to the base level
of the specified output directory.
It is especially useful in ChRIS following "copy" (ts and unextpath) operations,
such as pl-dircopy
, because the ChRIS
backend renames paths to be inconveniently long.
pl-unstack-folders
is a ChRIS plugin, meaning it can
run from either within ChRIS or the command-line.
To get started with local command-line usage, use Apptainer
(a.k.a. Singularity) to run pl-unstack-folders
as a container:
singularity exec docker://fnndsc/pl-unstack-folders unstack [--args values...] input/ output/
To print its available options, run:
singularity exec docker://fnndsc/pl-unstack-folders unstack --help
unstack
requires two positional arguments: a directory containing
input data, and a directory where to create output data.
First, create the input directory and move input data into it.
mkdir incoming/ outgoing/
mv some.dat other.dat incoming/
singularity exec docker://fnndsc/pl-unstack-folders:latest unstack [--args] incoming/ outgoing/
Instructions for developers.
Build a local container image:
docker build -t localhost/fnndsc/pl-unstack-folders .
Mount the source code unstack.py
into a container to try out changes without rebuild.
docker run --rm -it --userns=host -u $(id -u):$(id -g) \
-v $PWD/unstack.py:/usr/local/lib/python3.10/site-packages/unstack.py:ro \
-v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
localhost/fnndsc/pl-unstack-folders unstack /incoming /outgoing
Run unit tests using pytest
.
It's recommended to rebuild the image to ensure that sources are up-to-date.
Use the option --build-arg extras_require=dev
to install extra dependencies for testing.
docker build -t localhost/fnndsc/pl-unstack-folders:dev --build-arg extras_require=dev .
docker run --rm -it localhost/fnndsc/pl-unstack-folders:dev pytest
Steps for release can be automated by Github Actions. This section is about how to do those steps manually.
Increase the version number in setup.py
and commit this file.
Build and push an image tagged by the version. For example, for version 1.2.3
:
docker build -t docker.io/fnndsc/pl-unstack-folders:1.2.3 .
docker push docker.io/fnndsc/pl-unstack-folders:1.2.3
Run chris_plugin_info
to produce a JSON description of this plugin, which can be uploaded to a ChRIS Store.
docker run --rm localhost/fnndsc/pl-unstack-folders:dev chris_plugin_info > chris_plugin_info.json