Updated docs

Makefile

@@ -4,7 +4,7 @@ lint:
 pyinstaller:
 	cd specfiles && pyinstaller --noconfirm Mint.spec ../scripts/Mint.py
 
-docs:
+doc:
 	mkdocs build && mkdocs gh-deploy
 
 devel:

docs/developer-notes.md

@@ -6,30 +6,18 @@
     cd specfiles && pyinstaller --noconfirm Mint.spec ..\scripts\Mint.py
 
 ## Documentation deployment
-
     mkdocs build && mkdocs gh-deploy
 
 ## Example NGINX config
 
-    location /mint/ {
-        client_max_body_size    10G;
-        proxy_pass       http://localhost:9999;
-        #rewrite ^/mint/(.*) /$1 break;
+To run Mint on a remote server you need to setup a remote proxy. 
 
-        proxy_http_version 1.1;
-        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
-        proxy_set_header Host $host;
-        proxy_set_header Upgrade $http_upgrade;
-        proxy_set_header Connection "upgrade";
-        proxy_read_timeout 86400;
+    server {
+        ...
+        location / {
+            proxy_pass              http://localhost:8080;
+            client_max_body_size    100G;
+            proxy_set_header        X-Forwarded-Proto https;
+            proxy_set_header        Host $host;
+        }
     }
-
-Then start MINT with `--serve-path='\mint\'`.
-
-
-## Additional packages
-
-To run tests and code optimization you need the
-following packages:
-
-    conda install flake8 pytest mkdocs

docs/gui.md

@@ -48,18 +48,18 @@ Note that _mzXML_ and _mzML_ files will be deleted after convertion.
 Metadata for the individual files can be edited in the `Metadata` tab. This data can be used to group results e.g. by batch or by label as well as types.
 You want to edit metadata table to:
 
-## Peaklist
+## Targetlists
 
 - Import peaklist from CSV file or add new peaks manually
 - Rename peaks definitions or change parameters
 - Delete peak definitions
 
-![Peaklist](image/peaklist.png "Peaklist")
+![Targetlists](image/peaklist.png "Peaklist")
 
-Peaklists are collection of peak definitions for the extraction of MS intensities beloning to individual metabolites. 
-Peaklists can be provided as Excel or CSV files. Peaklists are explained in more detail [here](peaklists.md).
-Files can be uploaded via the drag and drop area or the selection tool. The peaklist can be edited in place or
-with the peak optimization tools.
+Targetlists are collection of peak definitions for the extraction of MS intensities beloning to individual metabolites. 
+Targetlists can be provided as Excel or CSV files. Targetlists are explained in more detail [here](targets.md).
+Files can be uploaded via the drag and drop area or the selection tool. The targetlists can be edited in place or
+with the optimization tools.
 
 ## Add Metabolites
 
@@ -117,7 +117,7 @@ When the results tables are present the results can be explored with the followi
 The generated results can be downloaded with the `DOWNLOAD` button.
 
 
-# Analysis
+## Analysis
 
 After running MINT the results can be downloaed or analysed using the provided tools.
 For quality control purposes histograms and boxplots can be generated in the 

docs/index.md

@@ -17,5 +17,3 @@ Check out the [Quickstart](quickstart.md) to jump right into it.
 ## What is it all about?
 What problem is MINT solving? Check out the [background](background.md) section.
 
-## How to use the Python API?
-Go to the [Jupyter](jupyter.md) section.

mkdocs.yml

@@ -1,5 +1,5 @@
-site_name: MINT
-site_url: https://github.com/sorenwacker/ms-mint
+site_name: ms-mint GUI
+site_url: https://github.com/lewisresearchgroup/ms-mint-app
 site_author: Soren Wacker 
 nav:
   - Home: 'index.md'
@@ -8,20 +8,20 @@ nav:
   - Installation: 'install.md'
   - GUI: 'gui.md'
   - Targets: 'targets.md'
-  #- Peak detection: 'peak-detection.md'
-  #- Python: 'python.md'
-  - Jupyter: 'jupyter.md'
   - Developer Notes: 'developer-notes.md'
   - Gallery: 'gallery.md'
 extra:
   analytics:
     provider: google
-    propertyl: UA-207276128-1
+    property: G-F718PR80XX
   consent:
     title: Cookie consent
     description: > 
-
+  
       We use cookies to recognize your repeated visits and preferences, as well
       as to measure the effectiveness of our documentation and whether users
       find what they're searching for. With your consent, you're helping us to
-      make our documentation better.
+      make our documentation better.
+theme:
+  name: material
+