diff --git a/.gitignore b/.gitignore index a1ae8d0..eeb74a2 100644 --- a/.gitignore +++ b/.gitignore @@ -53,7 +53,7 @@ coverage.xml docs/_build/ # Dexy generated files -dexy/output/ +notebooks/dexy/output/ dexy/.dexy dexy/.trash .dexy diff --git a/documents/LiterateProgramming.md b/documents/LiterateProgramming.md index 2524a18..3ad3e4b 100644 --- a/documents/LiterateProgramming.md +++ b/documents/LiterateProgramming.md @@ -2,19 +2,19 @@ ## Description -## Dexy - -## IPython +When writing up the results of research, how do we incorporate the results of scripts and calculations? -## ... +Manually typing results or copying & pasting of data is not reproducible. To +have a reproducible research document, we need to automate the process of +inserting results (code and data) into our documents (prose). +## IPython -TODO: bring back to environments/docker/README.md after dexy is fixed. - -To run dexy, +The IPython notebook is an integrated environment where you can write prose and +execute sections of code. - d['build-and-run.sh|idio']['run-dexy'] +## Dexy -In this case, we mount the local directory as a *volume* in the notebook so we -can process our local data with the computational environment. +Dexy is a project automation tool which runs code and inserts the results in a +document. (It does a lot of other things too.) diff --git a/environment/docker/Dockerfile b/environment/docker/Dockerfile index 6c9242b..01e0ad4 100644 --- a/environment/docker/Dockerfile +++ b/environment/docker/Dockerfile @@ -59,7 +59,7 @@ RUN easy_install SimpleITK RUN apt-get install -y mplayer ### "create-user" -RUN useradd -m repro +RUN useradd -m -p $(perl -e'print crypt("foobarbaz", "aa")') repro RUN adduser repro sudo ### "activate-user"