MRG: fix installation documentation (#15)

* fix install and test stuff

* fix INSTALL

INSTALL.md

@@ -1,7 +1,42 @@
-# Installing mdbook
+# Installing software to build & test this book
+
+## Create conda environment with base software
+
+```
+mamba create -n mdbook -y rust snakemake-minimal pandas sourmash
+```
+
+and activate:
+```
+mamba activate mdbook
+```
+
+## Clone the repository
+
+```
+cd ~/
+git clone https://github.com/ngs-docs/2023-snakemake-book-draft
+cd 2023-snakemake-book-draft
+```
+
+## Install mdbook & plugins:
+
+We use [mdbook](https://github.com/rust-lang/mdBook) as well as
+[mdbook-admonish](https://github.com/tommilligan/mdbook-admonish) and
+[mdbook-cmdrun](https://crates.io/crates/mdbook-cmdrun).
+
+```
+cargo install mdbook mdbook-admonish mdbook-cmdrun
+```
+
+## Build book
 
-We use [mdbook-admonish](https://github.com/tommilligan/mdbook-admonish):
 ```
-cargo install mdbook-admonish
+make
 ```
 
+## Run snakemake tests
+
+```
+make test
+```

book.toml

@@ -17,7 +17,7 @@ on_failure = "bail"
 [output.html]
 additional-css = ["./extra/mdbook-admonish.css"]
 
-[output.linkcheck]
+#[output.linkcheck]
 
 [preprocessor.cmdrun]
 

code/examples/wildcards.basic_constrain/Snakefile

@@ -18,7 +18,7 @@ print(this_dir_files)
 print(prefix_only)
 print(prefix_and_dir_only)
 
-assert all_files == ['file1.subset', 'file1', 'subdir/file2', 'subdir/file2.subset', 'subdir/nested/file3']
-assert this_dir_files == ['file1.subset', 'file1']
-assert prefix_only == ['file1', 'subdir/file2', 'subdir/nested/file3']
+assert set(all_files) == { 'file1.subset', 'file1', 'subdir/file2', 'subdir/file2.subset', 'subdir/nested/file3' }
+assert set(this_dir_files) == { 'file1.subset', 'file1' }
+assert set(prefix_only) == { 'file1', 'subdir/file2', 'subdir/nested/file3' }
 assert prefix_and_dir_only == ['file1']