Clean-up, tests (#7)

* add binder badge to readme

* change name in readme

* try to make module

* try adding version to project

* add testing file

* make build function

Co-authored-by: Kevin Bonham <kevin@bonham.ch>

Author: kescobo

.gitignore

@@ -1 +1,3 @@
 .ipynb_checkpoints
+Manifest.toml
+.envrc

Manifest.toml

@@ -1,2 +1,7 @@
+title = "Testing"
+uuid = "33e7be4a-8e14-4baf-892c-424bb664d307"
+authors = ["Kevin Bonham (@kescobo)", "Kenta Sato (@bicycle1885)"]
+version = "0.1.0"
+
 [deps]
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"

Project.toml

@@ -1,7 +1,7 @@
-# Bio.jl Tutorial Notebooks
+# BioJulia Tutorial Notebooks
 
-* [Pairwise Alignment and Dotplot](https://nbviewer.jupyter.org/github/BioJulia/BioTutorials/blob/master/Pairwise%20Alignment%20and%20Dotplot/Pairwise%20Alignment%20and%20Dotplot.ipynb)
-* [RNA-Seq Coverage](https://nbviewer.jupyter.org/github/BioJulia/BioTutorials/blob/master/RNA-Seq%20Coverage/RNA-Seq%20Coverage.ipynb)
+* [Pairwise Alignment and Dotplot](Pairwise_Alignment/pairwise_alignment.jl) ([![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/BioJulia/BioTutorials/HEAD?labpath=Pairwise_Alignment%2Fpairwise_alignment.ipynb))
+* [RNA-Seq Coverage](RNASeq_Coverage/rnaseq_coverage.jl) (outdated)
 
 The programs under this repository are distributed in the public domain unless
 otherwise specified.

README.md

@@ -0,0 +1,17 @@
+module BioTutorials
+
+function build(dir)
+    isdir(dir) || throw(ArgumentError("Provide path to directory with tutorial file"))
+    files = filter(f-> splitext(f)[2] == ".jl", readdir(dir; join=true))
+    file = length(files) == 1 ? first(files) : throw(ArgumentError("Tutorial directory must have exactly one .jl file"))
+
+    c = Cmd([
+        "julia", "--project=@.", "-e",
+        """
+        using Literate; using Pkg; Pkg.activate("$dir"); Pkg.instantiate(); Literate.notebook("$file", "$dir")
+        """
+    ])
+    run(c)
+end
+
+end