Add password.

.gitignore

@@ -53,7 +53,7 @@ coverage.xml
 docs/_build/
 
 # Dexy generated files
-dexy/output/
+notebooks/dexy/output/
 dexy/.dexy
 dexy/.trash
 .dexy

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.)
 

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"