Use markdown table on results website (#122)

* Use markdown table in jupyterbook

* Update link to markdown database

* Use https instead of http

* Rename the markdown file to match header

* Fix typo

* Update contribution table url

Author: notZaki

.github/workflows/convert_csv.yml

@@ -27,17 +27,17 @@ jobs:
         pip install wheel pytest
         pip install -r notebooks/requirements.txt
         pip install .
-
     - name: Test with pytest
       run: |
         pytest .
-
     # Build the book
+    - name: Convert contributors csv to md
+      run: |
+        python doc/convert_to_md.py
     - name: Build the book
       run: |
         jupyter-book build notebooks/
         touch notebooks/_build/html/.nojekyll
-
     - name: Re-organize files
       run: |
         mkdir out

.github/workflows/jupyterbook.yml

@@ -5,8 +5,8 @@
 
 
 
-- [code database with links to source code](doc/code_contributions_record.md)
-- [test-results website](http://osipi.org/DCE-DSC-MRI_TestResults)
+- [code database with links to source code](https://osipi.org/DCE-DSC-MRI_TestResults/overview_of_code_collection.html)
+- [test-results website](https://osipi.org/DCE-DSC-MRI_TestResults)
 
 The ISMRM Open Science Initiative for Perfusion Imaging ([OSIPI](https://www.osipi.org/)) aims to promote the sharing of perfusion imaging software in order to reduce duplication, improve reproducibility and speed up translation. This **DCE-DSC-MRI_CodeCollection** code library is maintained by [Taskforce 2.3](https://www.osipi.org/task-force-2-3/) of OSIPI and aims to collect, test and share open-source perfusion imaging code for use in research and software development. Code contributions can include modules covering one or more steps within the image processing pipeline, for example T1 mapping, converting signal to concentration and pharmacokinetic modelling. A further aim of OSIPI is to develop a fully tested and harmonised code library, drawing on the contributions within this repository.
 
@@ -43,4 +43,4 @@ The results of the validated code are published on the [test-results website](ht
 
 
 
-This is an ongoing project, we welcome new contributions. If you would like to contribute to the OSIPI initiative please email the contacts listed on our [website](https://www.osipi.org/task-force-2-3/).
+This is an ongoing project, we welcome new contributions. If you would like to contribute to the OSIPI initiative please email the contacts listed on our [website](https://www.osipi.org/task-force-2-3/).

README.md

@@ -1,5 +1,7 @@
 import pandas as pd
 
 df = pd.read_csv('doc/code_contributions_record.csv')
-with open('doc/code_contributions_record.md', 'w') as md:
-    df.to_markdown(buf=md, index=False)
+md = df.to_markdown(index=False).replace("(../", "(https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/tree/develop/")
+with open('notebooks/overview_of_code_collection.md', 'w') as f:
+    f.write("# Overview of code collection\n\n")
+    f.write(md)

doc/code_contributions_record.md

@@ -4,7 +4,7 @@
 format: jb-article
 root: intro.md
 sections:
-- file: contributors.ipynb
+- file: overview_of_code_collection.md
 - file: DCE.md
   sections:
     - file: T1mapping.md