👽 Fix script to look for main branch (was master)

Author: shnizzedy

CONTRIBUTING.md

@@ -1,13 +1,13 @@
 <!-- TOC -->
 
 - [Branches](#branches)
-    - [Versions](#versions)
-        - [`nightly`](#nightly)
-        - [C-PAC release tags](#c-pac-release-tags)
+  - [Versions](#versions)
+    - [`nightly`](#nightly)
+    - [C-PAC release tags](#c-pac-release-tags)
 - [Guidelines](#guidelines)
-    - [Building](#building)
-        - [Let CircleCI build your drafts / works-in-progress](#let-circleci-build-your-drafts--works-in-progress)
-        - [Build locally (C-PAC ≥ v1.8.0)](#build-locally-c-pac-≥-v180)
+  - [Building](#building)
+    - [Let CircleCI build your drafts / works-in-progress](#let-circleci-build-your-drafts--works-in-progress)
+    - [Build locally (C-PAC ≥ v1.8.0)](#build-locally-c-pac-≥-v180)
 - [Flowcharts](#flowcharts)
 - [References and citations](#references-and-citations)
 - [Environment notes](#environment-notes)
@@ -17,7 +17,7 @@
 <a id="markdown-branches" name="branches"></a>
 ## Branches
 
-Please, always base changes on the `source` branch. `master` branch will be overwritten by the CI deployment.
+Please, always base changes on the `source` branch. `main` branch will be overwritten by the CI deployment.
 
 <a id="markdown-versions" name="versions"></a>
 ### Versions
@@ -67,7 +67,7 @@ Steps to build a release:
 * Build environment will match actual docs build environment
 * CircleCI takes ~2 minutes to build
 1. Fork https://github.com/FCP-INDI/fcp-indi.github.io
-1. In your fork's settings, set the GitHub Pages `source` to `master` branch
+1. In your fork's settings, set the GitHub Pages `source` to `main` branch
     ![GitHub Pages settings example screenshot](./images/github-pages-settings-example.png)
 1. Add your project on CircleCI
 1. Merge your draft / work-in-progress into your fork's `source` branch. Make sure you push to your fork and not the main repository's `source` branch.

docs/_sources/conf.py

@@ -159,7 +159,7 @@ def yaml_to_rst(path):
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'
 
-# The master toctree document.
+# The main toctree document.
 master_doc = 'index'
 
 # A list of warning types to suppress arbitrary warning messages.

docs/_sources/developer/index.rst

@@ -1,4 +1,4 @@
-.. CPAC documentation master file, created by
+.. CPAC documentation main file, created by
    sphinx-quickstart on Fri Jun 22 13:46:06 2012.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.

docs/_sources/developer/workflows/cpac_pipeline.rst

@@ -7,7 +7,7 @@ C-PAC Pipeline Construction
 Configuration Object
 ====================
 
-The 'c' variable in cpac_pipeline.py is a `Configuration object <https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/utils/configuration.py>`_, which is an abstract representation used to store the options for the pipeline configuration YAML after it is read in by C-PAC.  Each attribute of the Configuration object is a key from the YAML file, with values mirroring the YAML.
+The 'c' variable in cpac_pipeline.py is a `Configuration object <https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/utils/configuration.py>`_, which is an abstract representation used to store the options for the pipeline configuration YAML after it is read in by C-PAC.  Each attribute of the Configuration object is a key from the YAML file, with values mirroring the YAML.
 
 Strategy Object
 ===============

docs/_sources/developer/workflows/index.rst

@@ -1,4 +1,4 @@
-.. CPAC documentation master file, created by
+.. CPAC documentation main file, created by
    sphinx-quickstart on Fri Jun 22 13:46:06 2012.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.

docs/_sources/index.rst

@@ -1,4 +1,4 @@
-.. CPAC documentation master file, created by
+.. CPAC documentation main file, created by
    sphinx-quickstart on Fri Jun 22 13:46:06 2012.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.

docs/_sources/user/appendix.rst

@@ -40,11 +40,11 @@ A Note About the \*nix Command Line
 
 Overview
 --------
-If you are using Ubuntu (version 12/14) you can download and run `cpac_install.sh <https://github.com/FCP-INDI/C-PAC/blob/master/cpac_install.sh?raw=true>`__ with the following terminal commands as root:
+If you are using Ubuntu (version 12/14) you can download and run `cpac_install.sh <https://github.com/FCP-INDI/C-PAC/blob/main/cpac_install.sh?raw=true>`__ with the following terminal commands as root:
 
 .. code-block:: console
 
-    wget https://github.com/FCP-INDI/C-PAC/blob/master/cpac_install.sh?raw=true
+    wget https://github.com/FCP-INDI/C-PAC/blob/main/cpac_install.sh?raw=true
     mv cpac_install.sh?raw=true cpac_install.sh
     chmod +x cpac_install.sh
     sudo ./cpac_install.sh -r

docs/_sources/user/func.rst

@@ -109,10 +109,10 @@ You can also specify slice timing parameters within the subject list.  If you wi
 
 .. line-block::
   **If all subjects within a site have the same acquisition order:**
-  Use the template :file:`scan_parameters.csv` file available for download `here <https://raw.github.com/FCP-INDI/C-PAC/master/configs/scan_parameters.csv>`__.
+  Use the template :file:`scan_parameters.csv` file available for download `here <https://raw.github.com/FCP-INDI/C-PAC/main/configs/scan_parameters.csv>`__.
 
   **If subjects within a site have different acquisition orders:**
-  Use the template :file:`scan_parameters_multiscan.csv` file available for download `here <https://raw.github.com/FCP-INDI/C-PAC/master/configs/scan_parameters_multiscan.csv>`__.
+  Use the template :file:`scan_parameters_multiscan.csv` file available for download `here <https://raw.github.com/FCP-INDI/C-PAC/main/configs/scan_parameters_multiscan.csv>`__.
 
 Slice Timing information should be entered into these files as follows:
 

docs/_sources/user/index.rst

@@ -1,4 +1,4 @@
-.. C-PAC documentation master file, created by
+.. C-PAC documentation main file, created by
    sphinx-quickstart on Fri Jul 20 16:32:55 2012.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.

docs/_sources/user/pipelines/preconfig.rst

@@ -4,7 +4,7 @@
 default: The Default Pipeline
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Pipeline Configuration YAML: `https://github.com/FCP-INDI/C-PAC/blob/master/dev/docker_data/default_pipeline.yml <https://github.com/FCP-INDI/C-PAC/blob/master/dev/docker_data/default_pipeline.yml>`_
+Pipeline Configuration YAML: `https://github.com/FCP-INDI/C-PAC/blob/main/dev/docker_data/default_pipeline.yml <https://github.com/FCP-INDI/C-PAC/blob/main/dev/docker_data/default_pipeline.yml>`_
 
 **Note:** C-PAC runs this pipeline by default, and it is not necessary to invoke the `--preconfig` flag to run it.
 
@@ -32,7 +32,7 @@ Several different individual level analysis are performed on the fMRI data inclu
 anat-only: Default with Anatomical Preprocessing Only
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Pipeline Configuration YAML: `https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/resources/configs/pipeline_config_anat-only.yml <https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/resources/configs/pipeline_config_anat-only.yml>`_
+Pipeline Configuration YAML: `https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/resources/configs/pipeline_config_anat-only.yml <https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/resources/configs/pipeline_config_anat-only.yml>`_
 
 Based on the preprocessing decisions of the default pipeline, this preconfiguration allows you to immediately kick off a run with only anatomical preprocessing selected. This includes:
 
@@ -43,7 +43,7 @@ Based on the preprocessing decisions of the default pipeline, this preconfigurat
 preproc: Default without Derivatives
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Pipeline Configuration YAML: `https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/resources/configs/pipeline_config_preproc.yml <https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/resources/configs/pipeline_config_preproc.yml>`_
+Pipeline Configuration YAML: `https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/resources/configs/pipeline_config_preproc.yml <https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/resources/configs/pipeline_config_preproc.yml>`_
 
 Based on the preprocessing decisions of the default pipeline, this preconfiguration allows you to preprocess all of your data, without launching into calculation of outputs and data derivatives. This includes:
 
@@ -64,7 +64,7 @@ Functional:
 ndmg: Neurodata's 'ndmg-f' Pipeline
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Pipeline Configuration YAML: `https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/resources/configs/pipeline_config_ndmg.yml <https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/resources/configs/pipeline_config_ndmg.yml>`_
+Pipeline Configuration YAML: `https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/resources/configs/pipeline_config_ndmg.yml <https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/resources/configs/pipeline_config_ndmg.yml>`_
 
 This pipeline is the result of `Neurodata's <https://neurodata.io/>`_ study to converge upon the intersection of pipeline configuration decisions that maximizes discriminability between participants' data, drawing from the connectome graphs produced (labeled 'ndmg_graph' in the C-PAC output directory). This pipeline invokes a minimal set of preprocessing.
 
@@ -77,7 +77,7 @@ Note, the 'ndmg_graph' connectome graph outputs are always produced by C-PAC. Th
 fmriprep-options: fmriprep-Options Pipeline
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Pipeline Configuration YAML: `https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/resources/configs/pipeline_config_fmriprep-options.yml <https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/resources/configs/pipeline_config_fmriprep-options.yml>`_
+Pipeline Configuration YAML: `https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/resources/configs/pipeline_config_fmriprep-options.yml <https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/resources/configs/pipeline_config_fmriprep-options.yml>`_
 
 This pipeline is designed to increase reproducibility with the preprocessing results of the `fmriprep pipeline package <https://fmriprep.readthedocs.io/en/stable/>`_ produced by the `Poldrack Lab at Stanford University <https://poldracklab.stanford.edu/>`_.
 
@@ -87,22 +87,22 @@ This pipeline is designed to increase reproducibility with the preprocessing res
 benchmark-ANTS: C-PAC Benchmark with ANTs Registration
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Pipeline Configuration YAML: `https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/resources/configs/pipeline_config_benchmark-ANTS.yml <https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/resources/configs/pipeline_config_benchmark-ANTS.yml>`_
+Pipeline Configuration YAML: `https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/resources/configs/pipeline_config_benchmark-ANTS.yml <https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/resources/configs/pipeline_config_benchmark-ANTS.yml>`_
 
 The benchmark pipeline has remained mostly unchanged since the project's inception, and is used at the end of each release cycle to ensure the results of C-PAC's key outputs have not changed. It is designed to test a wide range of pipeline options. This pipeline is based on registration-to-template using the ANTs/ITK toolset, as this decision impacts many other aspects of the pipeline further downstream.
 
 benchmark-FNIRT: C-PAC Benchmark with FSL FNIRT Registration
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Pipeline Configuration YAML: `https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/resources/configs/pipeline_config_benchmark-FNIRT.yml <https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/resources/configs/pipeline_config_benchmark-FNIRT.yml>`_
+Pipeline Configuration YAML: `https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/resources/configs/pipeline_config_benchmark-FNIRT.yml <https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/resources/configs/pipeline_config_benchmark-FNIRT.yml>`_
 
 The benchmark pipeline has remained mostly unchanged since the project's inception, and is used at the end of each release cycle to ensure the results of C-PAC's key outputs have not changed. It is designed to test a wide range of pipeline options. This pipeline is based on registration-to-template using the FSL FLIRT & FNIRT, as this decision impacts many other aspects of the pipeline further downstream.
 
 
 Monkey: Default with Monkey Preprocessing 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Pipeline Configuration YAML: `https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/resources/configs/pipeline_config_monkey.yml <https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/resources/configs/pipeline_config_monkey.yml>`_
+Pipeline Configuration YAML: `https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/resources/configs/pipeline_config_monkey.yml <https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/resources/configs/pipeline_config_monkey.yml>`_
 
 This pipeline is based on the work of Xu et al. (2019) and `nhp-ABCD-BIDS-pipeline. <https://zenodo.org/record/3888969#.Xw31IpNKjyU>`_