rename main branch

rinikerlab · Jul 20, 2023 · 6f66fb1 · 6f66fb1
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diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
@@ -3,10 +3,10 @@ name: CI
 on:
   push:
     branches:
-      - "master"
+      - "main"
   pull_request:
     branches:
-      - "master"
+      - "main"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.ref }}"

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -2,9 +2,9 @@ name: "CodeQL"
 
 on:
   push:
-    branches: [ "master" ]
+    branches: [ "main" ]
   pull_request:
-    branches: [ "master" ]
+    branches: [ "main" ]
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.ref }}"

diff --git a/README.md b/README.md
@@ -6,8 +6,8 @@ Welcome to Ensembler
 ==============================
 
 [//]: # (Badges)
-[![GitHub Actions Build Status](https://github.com/rinikerlab/ensembler/workflows/CI/badge.svg)](https://github.com/rinikerlab/ensembler/actions?query=branch%3Amaster+workflow%3ACI)
-[![codecov](https://codecov.io/gh/rinikerlab/Ensembler/branch/master/graph/badge.svg)](https://codecov.io/gh/rinikerlab/Ensembler/branch/master)
+[![GitHub Actions Build Status](https://github.com/rinikerlab/ensembler/workflows/CI/badge.svg)](https://github.com/rinikerlab/ensembler/actions?query=branch%3Amain+workflow%3ACI)
+[![codecov](https://codecov.io/gh/rinikerlab/Ensembler/branch/main/graph/badge.svg)](https://codecov.io/gh/rinikerlab/Ensembler/branch/main)
 [![Documentation](https://img.shields.io/badge/Documentation-here-white.svg)](https://rinikerlab.github.io/Ensembler/index.html)
 
 ## Description
@@ -17,8 +17,8 @@ There is an article about Ensembler in JCIM, check it out: https://doi.org/10.10
 
 **Quick Start to Simulations:**
 
-[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/rinikerlab/Ensembler/blob/master/examples/Tutorial_Simulations.ipynb)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/rinikerlab/Ensembler/master?filepath=examples%2FTutorial_Simulations.ipynb)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/rinikerlab/Ensembler/blob/main/examples/Tutorial_Simulations.ipynb)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/rinikerlab/Ensembler/main?filepath=examples%2FTutorial_Simulations.ipynb)
 
 ## Contents
 The full documentation can be found here:  https://rinikerlab.github.io/Ensembler/
@@ -87,36 +87,36 @@ In the following links you can find more features of Ensembler.
 
 Potentials: 
 
-[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/rinikerlab/Ensembler/blob/master/examples/Tutorial_Potentials.ipynb)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/rinikerlab/Ensembler/master?filepath=examples%2FTutorial_Potentials.ipynb)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/rinikerlab/Ensembler/blob/main/examples/Tutorial_Potentials.ipynb)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/rinikerlab/Ensembler/main?filepath=examples%2FTutorial_Potentials.ipynb)
 
 Simulations: 
 
-[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/rinikerlab/Ensembler/blob/master/examples/Tutorial_Simulations.ipynb)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/rinikerlab/Ensembler/master?filepath=examples%2FTutorial_Simulations.ipynb)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/rinikerlab/Ensembler/blob/main/examples/Tutorial_Simulations.ipynb)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/rinikerlab/Ensembler/main?filepath=examples%2FTutorial_Simulations.ipynb)
 
 ### Examples
 Examples are advanced jupyter notebooks, covering a specific topic, going deeper into the methodology and having nice visualizations.
 
 Enhanced Sampling: 
 
-[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/rinikerlab/Ensembler/blob/master/examples/Example_EnhancedSampling.ipynb)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/rinikerlab/Ensembler/master?filepath=examples%2FExample_EnhancedSampling.ipynb)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/rinikerlab/Ensembler/blob/main/examples/Example_EnhancedSampling.ipynb)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/rinikerlab/Ensembler/main?filepath=examples%2FExample_EnhancedSampling.ipynb)
 
 Free Energy Calculations: 
 
-[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/rinikerlab/Ensembler/blob/master/examples/Example_FreeEnergyCalculationSimulation.ipynb)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/rinikerlab/Ensembler/master?filepath=examples%2FExample_FreeEnergyCalculationSimulation.ipynb)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/rinikerlab/Ensembler/blob/main/examples/Example_FreeEnergyCalculationSimulation.ipynb)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/rinikerlab/Ensembler/main?filepath=examples%2FExample_FreeEnergyCalculationSimulation.ipynb)
 
 Interactive ConveyorBelt: 
 
-[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/rinikerlab/Ensembler/blob/master/examples/Example_ConveyorBelt.ipynb)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/rinikerlab/Ensembler/master?filepath=examples%2FExample_ConveyorBelt.ipynb)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/rinikerlab/Ensembler/blob/main/examples/Example_ConveyorBelt.ipynb)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/rinikerlab/Ensembler/main?filepath=examples%2FExample_ConveyorBelt.ipynb)
 
 EDS-Potentials: 
 
-[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/rinikerlab/Ensembler/blob/master/examples/Example_EDS.ipynb)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/rinikerlab/Ensembler/master?filepath=examples%2FExample_EDS.ipynb)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/rinikerlab/Ensembler/blob/main/examples/Example_EDS.ipynb)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/rinikerlab/Ensembler/main?filepath=examples%2FExample_EDS.ipynb)
 
 
 
@@ -134,20 +134,14 @@ There are many ways to get the Ensembler package.
 
   * If you want to use Ensembler, see the example notebooks or develop Ensembler - but not install the package:
     Add the path to the Ensembler repository; the requirements needed for the package can be used like in the following examples:
-
-    * PIP:
-
-            git clone https://github.com/rinikerlab/Ensembler.git
-            cd Ensembler
-            pip install .
 
     * Anaconda:
 
             git clone https://github.com/rinikerlab/Ensembler.git
             cd Ensembler
             conda create -n Ensembler --file devtools/conda-envs/environment_unix.yml
             conda activate Ensembler
-            pip install .
+            conda develop ${PWD}
 
 For windows, we also provide the required files in the same folders:
   * devtools/pip_requirements/requirements_windows.txt