[MRG] update documentation & add notebooks to docs (#631)

This reorganizes the documentation and adds Jupyter notebooks + binder links. * remove out of date notebooks * remove outdated scripts * configure nbsphinx and add a test notebook * add nbsphinx to reqs * add 2019-upr-kmers notebooks and example files * add/update notebooks * add binder configuration * remove dockerfile * update notebooks, link into documentation * fix formatting issue that looks like a typo * update basic sourmash tutorial commands to work, mostly * fix sourmash_databases link * updated tutorials * fix spacing * significant documentation reorganization and (hopefully) simplification * add tutorial master index back in * add dashing and hulk refs * add bigsi * fix branch reference for notebook so that it works * update notebook with signature recalculation * fix order of bioconda channels * fix URLs
sourmash-bio · Mar 7, 2019 · 8797eb6 · 8797eb6
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diff --git a/Dockerfile b/Dockerfile
diff --git a/README.md b/README.md
@@ -13,10 +13,6 @@ Usage:
     sourmash compare *.sig -o distances
     sourmash plot distances
 
-We have demo notebooks on binder that you can interact with:
-
-[![Binder](http://mybinder.org/badge.svg)](http://mybinder.org/repo/dib-lab/sourmash)
-
 Sourmash 1.0 is [published on JOSS](https://doi.org/10.21105/joss.00027); please cite that paper if you use sourmash (`doi: 10.21105/joss.00027`):.
 
 ----

diff --git a/binder/README.md b/binder/README.md
@@ -0,0 +1,3 @@
+# binder directory
+
+Configuration files for [mybinder](https://mybinder.org).
diff --git a/binder/environment.yml b/binder/environment.yml
@@ -0,0 +1,12 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - sourmash
+  - screed
+  - matplotlib
+  - pandas
+  - pip:
+    - matplotlib_venn
+    - mmh3
diff --git a/demo/00-demo.ipynb b/demo/00-demo.ipynb
diff --git a/demo/README.md b/demo/README.md
diff --git a/demo/SRR2060939_1.fastq.gz.sig b/demo/SRR2060939_1.fastq.gz.sig
diff --git a/demo/SRR2060939_1.fastq.gz.trimnoV.fq.gz.sig b/demo/SRR2060939_1.fastq.gz.trimnoV.fq.gz.sig