clean up, reqs

almlab · Aug 11, 2016 · b49f575 · b49f575
1 parent 6ce7217
commit b49f575
Show file tree

Hide file tree

Showing 3 changed files with 10 additions and 5 deletions.
diff --git a/README.md b/README.md
@@ -32,11 +32,6 @@ sequences with small numbers of counts, the p-value from the chi-square test
 had to be computed empirically, which was expensive. In this software, I use
 a likelihood ratio test, which I think performs very well.
 
-More details about the math of DBC are in the `doc` folder, which is currently a markdown
-file intended to be turned into a pdf with
-
-    pandoc --to latex --output math.pdf math.md
-
 ## Getting started
 
 ### Prerequisites
@@ -62,6 +57,11 @@ Feed the sequences and the table of sequence counts by samples into this program
 
 Chimera-check the OTUs, possibly with the script in `tools/`.
 
+## Documentation
+
+The `sphinx`-generated documentation is in `doc/`. It contains a rough API and
+some explanation of the math used in this implementation.
+
 ## Running the tests
 
 The testing framework is [py.test](http://docs.pytest.org/en/latest/). The tests (in `test/`) can be run with `make test` in the top directory.

diff --git a/doc/.gitignore b/doc/.gitignore
@@ -0,0 +1 @@
+build/
diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,4 @@
+numpy
+pandas
+scipy
+Bio
-Original file line number
+Diff line change
@@ -0,0 +1,4 @@
+    numpy
+    pandas
+    scipy
+    Bio