Bo

Right now we are requiring that there is one and one step that generates the required target, something like ``` [convert: provides='{filename}.csv'] input: f'{filename}.xlsx' sh: expand=True xlsx2csv {_input} {_output} [plot]...

We have magic `%sessioninfo` to report sessioninfo for all involved kernels. SoS has a `report` feature, which can be used to report such information but there is no standard way...

depends: conda('package', channel='bioconda')

1

This can be useful but would be applicable to only conda environment. Of course `conda(['p1', 'p2'])` needs to be allowed.

An obvious advantage of singularity images is that it can be transferred to remote hosts. For example, if we build an `app.simg` locally, and run it with ``` run: container='app.simg'...

container automatically mount path of input file?

5

Currently we only mount `pwd` by default but it seems to make sense to mount directories for `_input`

We generate workflow reports with option `-p` using runtime information saved in `.sos/workflow_signatures.db`. There is currently no way to generate the reports after the completion of workflow. It would be...

Support docker with windows containers

1

This is forked from #996 It turns out that docker supports two types of images, windows and linux, and the docker run commands are image-specific. For example, for a linux...

When we preview `text/html` data, the generated HTML can mess with existing style/structure of HTML report It would be useful for preview them in iframe, and jupyter already has an...

github uses textmate to highlight syntax for a large number of languages. We might want to develop a textmate bundle to enable syntax highlighting for SoS if we plan to...

Method to wrap workflow into docker images.

2

Something like this: 1. User provide interpreter and possibly packages to use (e.g. `R` and related packages, through partial `Dockerfile` recipes. We can have a library for such things. 2....