Merge pull request #189 from cgat-developers/AC-docchange

Ac docchange

README.md

@@ -1,29 +1,18 @@
 
 ![CGAT-core](https://github.com/cgat-developers/cgat-core/blob/master/docs/img/CGAT_logo.png)
 ----------------------------------------
+![Licence](https://img.shields.io/github/license/cgat-developers/cgat-core.svg)
+![Conda](https://img.shields.io/conda/v/bioconda/cgatcore.svg)
+![Build Status](https://github.com/cgat-developers/cgat-core/actions/workflows/cgatcore_python.yml/badge.svg)
 
-<p align="left">
-	<a href="https://readthedocs.org/projects/cgat-core/badge/?version=latest", alt="Documentation">
-		<img src="https://readthedocs.org/projects/cgat-core/badge/?version=latest" /></a>
-	<a href="https://travis-ci.org/cgat-developers/cgat-core", alt="Travis">
-		<img src="https://img.shields.io/travis/cgat-developers/cgat-core.svg" /></a>
-	<a href="https://twitter.com/cgat_oxford?lang=en", alt="Twitter followers">
-		<img src="https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter" /></a>
-	<a href="https://twitter.com/cgat_oxford?lang=en", alt="Twitter followers">
-		<img src="https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter" /></a>
-</p>
 
 ----------------------------------------
 
 CGAT-core is a workflow management system that allows users to quickly and reproducibly build scalable
 data analysis pipelines. CGAT-core is a set of libraries and helper functions used to enable researchers
 to design and build computational workflows for the analysis of large-scale data-analysis. 
 
-Documentation for CGAT-core can be accessed at [read the docs](http://cgat-core.readthedocs.io/en/latest/) 
-
-Used in combination with CGAT-apps, we have demonstrated the functionality of our
-flexible implementation using a set of well documented, easy to install and easy to use workflows, 
-called [CGAT-flow](https://github.com/cgat-developers/cgat-flow) ([Documentation](https://www.cgat.org/downloads/public/cgatpipelines/documentation/)).
+Documentation for CGAT-core can be accessed [here](https://cgat-developers.github.io/cgat-core/) 
 
 CGAT-core is open-sourced, powerful and user-friendly, and has been continually developed 
 as a Next Generation Sequencing (NGS) workflow management system over the past 10 years.
@@ -32,19 +21,7 @@ as a Next Generation Sequencing (NGS) workflow management system over the past 1
 Installation
 ============
 
-The following sections describe how to install the [cgatcore](https://cgat-core.readthedocs.io/en/latest/index.html) framework. For instructions on how to install
-our other repos, CGAT-apps (scripts) and CGAT-flow (workflows/pipelines), please follow these instructions [here](https://www.cgat.org/downloads/public/cgatpipelines/documentation/InstallingPipelines.html).
+The following sections describe how to install the [cgatcore](https://cgat-developers.github.io/cgat-core/) framework. 
 
 The preferred method to install the cgatcore is using conda, by following the instructions on [read the docs](https://cgat-core.readthedocs.io/en/latest/getting_started/Installation.html). However, there are a few other methods to install cgatcore, including pip and our own bash script installer.
 
-Linux vs OS X
-=============
-
-* ulimit works as expected in Linux but it does not have an effect on OS X. [Disabled](https://github.com/cgat-developers/cgat-core/commit/d4d9b9fb75525873b291028a622aac70c44a5065) ulimit tests for OS X.
-
-* ssh.connect times out in OSX. Exception [caught](https://github.com/cgat-developers/cgat-core/commit/d4d9b9fb75525873b291028a622aac70c44a5065)
-
-* Linux uses /proc/meminfo and OS X uses [vm_stat](https://github.com/cgat-developers/cgat-core/compare/bb1c75df8f42...575f0699b326)
-
-* Currently our testing framework is broken for OSX, however we are working to fix this. However, we dont envisage any issues running the code at present.
-

docs/index.md

@@ -2,7 +2,7 @@
 
 ![Licence](https://img.shields.io/github/license/cgat-developers/cgat-core.svg)
 ![Conda](https://img.shields.io/conda/v/bioconda/cgatcore.svg)
-[![Documentation Status](https://readthedocs.org/projects/cgat-core/badge/?version=latest)]()
+![Build Status](https://github.com/cgat-developers/cgat-core/actions/workflows/cgatcore_python.yml/badge.svg)
 
 Welcome to the CGAT-core documentation! CGAT-core is a workflow management system designed to support the rapid development of scalable, reproducible data analysis pipelines. It is built upon a flexible and user-friendly set of libraries and functions tailored for large-scale data analysis.
 

mkdocs.yml

@@ -41,11 +41,11 @@ nav:
   - Core Functions:
     - Pipeline: function_doc/pipeline.md
     - Core:
-      - Experiment: function_doc/core/experiment.md
-      - csv2db: function_doc/core/csv2db.md
-      - Database: function_doc/core/database.md
-      - IOTools: function_doc/core/iotools.md
-      - Logfile: function_doc/core/logfile.md
+      - Experiment: function_doc/experiment.md
+      - csv2db: function_doc/csv2db.md
+      - Database: function_doc/database.md
+      - IOTools: function_doc/iotools.md
+      - Logfile: function_doc/logfile.md
   - Project Info:
     - Contributing: project_info/contributing.md
     - How to Contribute: project_info/how_to_contribute.md