add tags to readme

* convert 2018-snakemake-cli to python package (setup.py)

converts the simple example in 2018-snakemake-cli,
which used a shell script sitting in a directory to
run the Snakemake workflow, into a full-fledged
python package that uses a setup.py file.

this is a way of bridging the complexity of taco
with the simplicity of 2018-snakemake-cli.

documentation/readme has not yet been updated.

tests have not yet been udpated.

* update how/where we look for Snakefile

* add Snakefile to manifest

* move config and params to test/

* include Snakefile with Manifest.in to make it run automagically

* update readme instructions

* manifest should include files, not graft them (graft is for directories)

* update gh-pages url in setup.py

* fix tests and fix the way we are looking for param and config files (use os.getcwd())

* clean up after test

* banana -> bananas. update gitignore.

* add .travis.yml

* change newline to trigger travis

* add shields

* python version >= 3.5

* remove unused import

* travis.yml: python 3.7 -> 3.7-dev

* remove 3.7-dev from travis

* change newline to trigger travis

.travis.yml

@@ -3,7 +3,7 @@ language: python
 python:
   - "3.5"
   - "3.6"
-  - "3.7-dev"
+  #- "3.7-dev" # fails due to datrie build failure (snakemake dependency)
 # command to install dependencies
 install:
   - pip install -r requirements.txt
@@ -11,3 +11,4 @@ install:
 # command to run tests
 script:
   - pytest
+

README.md

@@ -1,6 +1,6 @@
 # 2019-snakemake-cli
 
-[![travis](https://img.shields.io/travis/charlesreid1/2019-snakemake-cli.svg)](https://travis-ci.org/charlesreid1/2019-snakemake-cli.svg)
+[![travis](https://img.shields.io/travis/charlesreid1/2019-snakemake-cli.svg)](https://travis-ci.org/charlesreid1/2019-snakemake-cli)
 [![license](https://img.shields.io/github/license/charlesreid1/2019-snakemake-cli.svg)](https://github.com/charlesreid1/2019-snakemake-cli/blob/master/LICENSE)
 
 An example of a Snakemake command line interface
@@ -18,7 +18,7 @@ a command line tool called `bananas`.
 This runs through the installation and usage 
 of 2019-snakemake-cli.
 
-## Installing banana
+## Installing bananas
 
 Start by setting up a virtual environment,
 and install the required packages into the
@@ -37,13 +37,13 @@ python setup.py build install
 Now you can run
 
 ```
-which banana
+which bananas
 ```
 
-and you should see `bananas` in your Python 
-distribution's `bin/` directory.
+and you should see `bananas` in your virtual 
+environment's `bin/` directory.
 
-## Running banana
+## Running bananas
 
 Move to the `test/` directory and run the tests
 with the provided config and params files.
@@ -66,7 +66,7 @@ Run the goodbye workflow with Beth params:
 
 ```
 rm -f goodbye.txt
-./run workflow-goodbye params-beth
+bananas workflow-goodbye params-beth
 ```
 
 # Details
@@ -80,3 +80,10 @@ An alternative arrangement would be for users
 to provide a Snakefile via rules in the working
 directory, or via a Github URL or a remote URL.
 
+# Tags
+
+* `v1.0` - initial version, [ctb/2018-snakemake-cli](https://github.com/ctb/2018-snakemake-cli)
+
+* `v2.0` - Snakemake workflow bundled as installable Python package, Snakefile bundled with
+  Python package, command line interface provided to wrap Snakemake API call
+

requirements-to-freeze.txt

@@ -8,7 +8,7 @@ gitdb2==2.0.5
 GitPython==2.1.11
 idna==2.8
 jsonschema==2.6.0
-PyYAML==3.13
+PyYAML>=4.2b1
 ratelimiter==1.2.0.post0
 requests==2.21.0
 smmap2==2.0.5