fix naming of md files to ALL CAPS and add links to Installation and …

…Contribution instructions on github

these will only work properly after merging into main

.github/workflows/changelog.yml

@@ -1,4 +1,4 @@
-# This workflow uses git diff to count the added lines to Changelog.md in a pull request
+# This workflow uses git diff to count the added lines to CHANGELOG.md in a pull request
 # and ensure that it is larger than zero.
 name: Analyze Changelog
 
@@ -18,11 +18,11 @@ jobs:
     - name: Analyze Changelog
       run: |
         git fetch origin main:main
-        NUM_ADDED=`git diff --numstat main Changelog.md | cut -d$'\t' -f1`
+        NUM_ADDED=`git diff --numstat main CHANGELOG.md | cut -d$'\t' -f1`
         if [ "$NUM_ADDED" -gt "0" ]; then
-          echo "$NUM_ADDED lines have been added to Changelog.md"
+          echo "$NUM_ADDED lines have been added to CHANGELOG.md"
           exit 0
         else
-          echo "Nothing has been added to Changelog.md"
+          echo "Nothing has been added to CHANGELOG.md"
           exit 1
         fi

Readme.md → README.md

@@ -12,7 +12,7 @@ A comprehensive Python package for **Non-Negative Matrix Factorization (NMF)** w
 The packages supports multiple optimization backends and can be easily extended to handle application-specific types of transforms.
 
 # General Introduction
-A general introduction to Non-Negative Matrix Factorization and the purpose of this package can be found [here](GeneralIntroduction.md) and on the package's [PyPI page](https://pypi.org/project/tnmf/).
+A general introduction to Non-Negative Matrix Factorization and the purpose of this package can be found [here](doc/GeneralIntroduction.md) and on the package's [PyPI page](https://pypi.org/project/tnmf/).
 
 # Installation
 For using this package, you will at least need Python version 3.6 (or higher).

doc/index.rst

@@ -10,9 +10,11 @@ The packages supports multiple optimization backends and can be easily extended
    :caption: Contents
 
    link_generalintroduction
+   autoapi/index
    link_changelog
    link_license
-   autoapi/index
+   Installation <https://github.com/emdgroup/tnmf/tree/main#installation>
+   Contributing <https://github.com/emdgroup/tnmf/tree/main#contributing>
 
 Indices and tables
 ==================

doc/link_changelog.rst

@@ -1 +1 @@
-.. mdinclude:: ../Changelog.md
+.. mdinclude:: ../CHANGELOG.md

doc/link_generalintroduction.md

@@ -1 +1 @@
-.. mdinclude:: ../GeneralIntroduction.md
+.. mdinclude:: ./GeneralIntroduction.md