Fixed doc

Author: JeanBilheux

README.md

@@ -1,6 +1,7 @@
 # NeutronImagingScripts
 
-This pakcage contains a suite of Python modules and scripts that are critical for the data reduction of Neutron Imaging at Oak Ridge National Laboratory.
+This pakcage contains a suite of Python modules and scripts that are critical for the data reduction of Neutron Imaging 
+at Oak Ridge National Laboratory.
 
 
 ## Overview
@@ -17,7 +18,8 @@ $ pip install NeutronImagingScripts
 
 ### Developers
 For developers, it is __highly__ recommended to setup an isolated virtual environment for this repository.
-After cloning this repository to your local machine, go to the root of this repo and use the follwing commands to install dependencies
+After cloning this repository to your local machine, go to the root of this repo and use the follwing commands to 
+install dependencies
 
 ```bash
 $ pip install -r requirements.txt
@@ -38,41 +40,39 @@ Examples of using this package as a Python module are provided as Jupyter Notebo
 
 #### _Generate Configuration File for Data Reduction_
 To generate the `json` file that is needed for subsequent data reduction, use
+
 ```bash
-$ generate_config.py \
-    IPTS-20267/raw/radiographs \
-    IPTS-20267/raw/ob \
-    IPTS-20267/raw/df \
-    IPTS-20267.json
+$ generate_config.py IPTS-20267/raw/radiographs IPTS-20267/raw/ob IPTS-20267/raw/df IPTS-20267.json
 ```
+
 where 
+
  - `IPTS-20267/raw/radiographs` contains the raw images
  - `IPTS-20267/raw/ob` contains open beam images (white field)
  - `IPTS-20267/raw/df` contains dark field images 
 
 If you would like to have __multiple__ experiment configuration files __nested__ in one `json` file, simply use
+
 ```bash
-$ generate_config.py \
-    IPTS-20267/raw/radiographs,IPTS-20267-2/raw/radiographs \
-    IPTS-20267/raw/ob \
-    IPTS-20267/raw/df \
-    IPTS-20267.json
+$ generate_config.py IPTS-20267/raw/radiographs,IPTS-20267-2/raw/radiographs IPTS-20267/raw/ob IPTS-20267/raw/df IPTS-20267.json
 ```
+
 notice that:
 - You can have more than one folder for raw images, but they need to be within the same string separated by `,`.
 - You can have only __one__ folder for open beam directory
 - You cna have only __one__ folder for dark field directory
 
 The command above will yield a `json` file with the following structure
+
 ```json
-{
-    "IPTS-20267": {"CONFIG_DATA"},
-    "IPTS-20268": {"CONFIG_DATA"}
-}
+ {"IPTS-20267": {"CONFIG_DATA"},
+  "IPTS-20268": {"CONFIG_DATA"}
+ }
 ```
 
 The default tolerance for the categorization with respect to aperture positions is 1mm.
 However, you can change the default value by specify it as below
+
 ```bash
 $ generate_config.py \
     IPTS-20267/raw/radiographs \
@@ -84,18 +84,23 @@ $ generate_config.py \
 #### _MCP Detector correction_
 After installing this package, the scripts located in `scripts` should be visible in your Path.
 Simpy type `mcp_detector_correction.py`, you should see the following
+
 ```bash
 $ mcp_detector_correction.py
 Usage:
     mcp_detector_correction [--skipimg] [--verbose] <input_dir> <output_dir>
     mcp_detector_correction (-h | --help)
     mcp_detector_correction --version
 ```
+
 Therefore, you can process the example data with the following command at the root of this repo
+
 ```bash
 $ mcp_detector_correction.py data tmp
 ```
+
 and you will see the following in your terminal
+
 ```bash
 $ mcp_detector_correction.py data tmp
 Parsing input
@@ -108,6 +113,7 @@ corrected image summary
 	type:	float64
 Writing data to tmp
 ```
+
 > NOTE: make sure you create a `tmp` folder first.
 
 ## Developer Notes

setup.py

@@ -78,6 +78,7 @@ def find_meta(meta):
     setup(
         name=NAME,
         description=find_meta("description"),
+        long_description_content_type="text/markdown",
         license='BSD',
         url=find_meta("url"),
         version=versioneer.get_version(),