Switching to main branch

Dockerfile.env

@@ -19,8 +19,8 @@ RUN git clone https://aur.archlinux.org/miniconda3.git /home/nonroot/downloads/m
 RUN cd /home/nonroot/downloads/miniconda3 && makepkg -scri --noconfirm
 RUN echo "[ -f /opt/miniconda3/etc/profile.d/conda.sh ] && source /opt/miniconda3/etc/profile.d/conda.sh" >> ~/.bashrc && source ~/.bashrc
 
-RUN wget -P /home/nonroot/downloads/ https://raw.githubusercontent.com/euxhenh/cellar/master/env.yml && \
-        wget -P /home/nonroot/downloads/ https://raw.githubusercontent.com/euxhenh/cellar/master/install_Rdeps.py
+RUN wget -P /home/nonroot/downloads/ https://raw.githubusercontent.com/euxhenh/cellar/main/env.yml && \
+        wget -P /home/nonroot/downloads/ https://raw.githubusercontent.com/euxhenh/cellar/main/install_Rdeps.py
 
 # Create conda environment
 ENV PATH /opt/miniconda3/bin:$PATH

README.rst

@@ -5,13 +5,13 @@
 .. |PythonVersion| image:: https://img.shields.io/badge/python-3.7%20%7C%203.8%20%7C%203.9-blue
 .. _PythonVersion: https://img.shields.io/badge/python-3.7%20%7C%203.8%20%7C%203.9-blue
 .. |MITLicense| image:: https://img.shields.io/badge/License-MIT-blue
-.. _MITLicense: https://raw.githubusercontent.com/euxhenh/cellar/master/LICENSE.txt
+.. _MITLicense: https://raw.githubusercontent.com/euxhenh/cellar/main/LICENSE.txt
 .. |Website| image:: https://img.shields.io/website-up-down-green-red/http/shields.io
 .. _Website: https://data.test.hubmapconsortium.org/app/cellar
 
 .. |PythonMinVersion| replace:: 3.7
 
-.. image:: https://raw.githubusercontent.com/euxhenh/cellar/master/assets/cellar-logo.png
+.. image:: https://raw.githubusercontent.com/euxhenh/cellar/main/assets/cellar-logo.png
   :width: 400
   :target: https://data.test.hubmapconsortium.org/app/cellar
 

docs/docs/dependencies.md

@@ -13,7 +13,7 @@ in a conda environment.
 
 ---
 
-View Cellar's [conda environment](https://github.com/euxhenh/cellar/blob/master/env.yml) for a full list of libraries and their
+View Cellar's [conda environment](https://github.com/euxhenh/cellar/blob/main/env.yml) for a full list of libraries and their
 versions. Below we describe only the libraries that Cellar depends on
 explicitly.
 
@@ -39,7 +39,7 @@ explicitly.
 
 NOTE: We prefer to install R (r-base) via conda as seen above.
 The few remaining R libraries can be installed
-by using the [install_Rdeps.py](https://github.com/euxhenh/cellar/blob/master/install_Rdeps.py) script while inside the conda environment.
+by using the [install_Rdeps.py](https://github.com/euxhenh/cellar/blob/main/install_Rdeps.py) script while inside the conda environment.
 
 ---
 

docs/index.md

@@ -52,9 +52,9 @@ An alternative to a Docker installation is to create a local
 [conda](https://docs.conda.io/en/latest/) virtual environment
 with all the required dependencies. If you do not have conda installed, please
 follow these [instructions](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) first. Assuming conda is now available, follow the steps below.
-1. Download Cellar's [conda environment](https://github.com/euxhenh/cellar/blob/master/env.yml) yml file
+1. Download Cellar's [conda environment](https://github.com/euxhenh/cellar/blob/main/env.yml) yml file
 ```bash
-$ wget https://raw.githubusercontent.com/euxhenh/cellar/master/env.yml
+$ wget https://raw.githubusercontent.com/euxhenh/cellar/main/env.yml
 ```
 2. Install the conda environment
 ```bash
@@ -65,9 +65,9 @@ This will create an environment named `cellar`.
 ```bash
 $ conda activate cellar
 ```
-4. Download the [install_Rdeps.py](https://github.com/euxhenh/cellar/blob/master/install_Rdeps.py) script
+4. Download the [install_Rdeps.py](https://github.com/euxhenh/cellar/blob/main/install_Rdeps.py) script
 ```bash
-$ wget https://raw.githubusercontent.com/euxhenh/cellar/master/install_Rdeps.py
+$ wget https://raw.githubusercontent.com/euxhenh/cellar/main/install_Rdeps.py
 ```
 5. Install R dependencies
 ```bash
@@ -100,4 +100,4 @@ A preprint is available on [bioRxiv](https://www.biorxiv.org/content/10.1101/202
 
 ### License
 
-Cellar is distributed by an [MIT license](https://github.com/euxhenh/cellar/blob/master/LICENSE.txt).
+Cellar is distributed by an [MIT license](https://github.com/euxhenh/cellar/blob/main/LICENSE.txt).