chore: change branch names

.github/issue_template.md

@@ -7,7 +7,7 @@
 
 
 #### Current feature/value/output:
-*How the reaction/metabolite/gene/simulation actually looks in the `master` branch. PLEASE DELETE THIS LINE.*
+*How the reaction/metabolite/gene/simulation actually looks in the `main` branch. PLEASE DELETE THIS LINE.*
 
 
 #### Reproducing these results:
@@ -18,6 +18,6 @@
 
 **I hereby confirm that I have:**
 - [ ] Tested my code with [all requirements](https://github.com/SysBioChalmers/yeast-GEM#required-software---user) for running the model
-- [ ] Done this analysis in the `master` branch of the repository
+- [ ] Done this analysis in the `main` branch of the repository
 - [ ] Checked that a similar issue does not exist already
 - [ ] If needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/yeast-GEM) about the issue

.github/pull_request_template.md

@@ -4,5 +4,5 @@
 **I hereby confirm that I have:**
 
 - [ ] Tested my code with [all requirements](https://github.com/SysBioChalmers/yeast-GEM#required-software---contributor) for running the model
-- [ ] Selected `devel` as a target branch (top left drop-down menu)
+- [ ] Selected `develop` as a target branch (top left drop-down menu)
 - [ ] If needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/yeast-GEM) about this PR

.github/workflows/yaml-validation.yml

@@ -2,9 +2,9 @@ name: YAML validation
 
 on:
   push:
-    branches: [ devel ]
+    branches: [ develop ]
   pull_request:
-    branches: [ master, devel ]
+    branches: [ main, develop ]
 
 jobs:
   yaml-validation:

README.md

@@ -1,4 +1,3 @@
- @@ -0,0 +1,94 @@
 # yeast-GEM: The consensus genome-scale metabolic model of _Saccharomyces cerevisiae_
 
 [![DOI](https://zenodo.org/badge/52777598.svg)](https://zenodo.org/badge/latestdoi/52777598) [![GitHub version](https://badge.fury.io/gh/sysbiochalmers%2Fyeast-gem.svg)](https://badge.fury.io/gh/sysbiochalmers%2Fyeast-gem) [![Join the chat at https://gitter.im/SysBioChalmers/yeast-GEM](https://badges.gitter.im/SysBioChalmers/yeast-GEM.svg)](https://gitter.im/SysBioChalmers/yeast-GEM?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)[![Memote history](https://github.com/SysBioChalmers/yeast-GEM/workflows/Memote%20history/badge.svg)](https://sysbiochalmers.github.io/yeast-GEM/history_report.html)
@@ -65,12 +64,12 @@ This is because `results.db` (the database that stores all memote results) is tr
 * [Gurobi Optimizer](http://www.gurobi.com/registration/download-reg) for any simulations.
 
 ### Installation instructions
-* For users: Clone it from [`master`](https://github.com/SysBioChalmers/yeast-GEM) in the Github repo, or just download [the latest release](https://github.com/SysBioChalmers/yeast-GEM/releases). If you work in python, please create an environment with all requirements:
+* For users: Clone it from [`main`](https://github.com/SysBioChalmers/yeast-GEM) in the Github repo, or just download [the latest release](https://github.com/SysBioChalmers/yeast-GEM/releases). If you work in python, please create an environment with all requirements:
   ```bash
   pip install -r requirements/requirements.txt  # installs all dependencies
   touch .env                                    # creates a .env file for locating the root
   ```
-* For contributors: Fork it to your Github account, and create a new branch from [`devel`](https://github.com/SysBioChalmers/yeast-GEM/tree/devel).
+* For contributors: Fork it to your Github account, and create a new branch from [`develop`](https://github.com/SysBioChalmers/yeast-GEM/tree/develop).
 
 ## Usage
 
@@ -95,7 +94,7 @@ Make sure to load/save the model with the corresponding wrapper functions!
 
 ## Contributing
 
-Contributions are always welcome! Please read the [contributions guideline](https://github.com/SysBioChalmers/yeast-GEM/blob/master/.github/CONTRIBUTING.md) to get started.
+Contributions are always welcome! Please read the [contributions guideline](https://github.com/SysBioChalmers/yeast-GEM/blob/main/.github/CONTRIBUTING.md) to get started.
 
 ## Contributors
 

code/deprecated/otherChanges/convertYmn2FBC2.m

@@ -17,7 +17,7 @@
 % So the last SBML2-compatible COBRA version can be downloaded from
 % https://github.com/opencobra/cobratoolbox/tree/10f98a0ab834118c6dfb943970c38d68c7e1ae70
 % 
-% The whole idea of the script is to load curated Yeast 7.6 from 'master'
+% The whole idea of the script is to load curated Yeast 7.6 from 'main'
 % branch, then load SBML3 format model from
 % https://sourceforge.net/projects/yeast/files/, add the missing
 % annotation to the former model, do some final changes and export it to

code/increaseVersion.m

@@ -1,7 +1,7 @@
 function increaseVersion(bumpType)
 % increaseVersion
 %   Upgrades the model to a new version. Run this function after merging
-%   changes to the master branch for making a new release.
+%   changes to the main branch for making a new release.
 %
 %   bumpType    One of the following 3 strings: "major", "minor" or
 %               "patch", indicating the type of increase of version to be
@@ -13,10 +13,10 @@ function increaseVersion(bumpType)
 %   Usage: increaseVersion(bumpType)
 %
 
-%Check if in master:
+%Check if in main:
 currentBranch = git('rev-parse --abbrev-ref HEAD');
-if ~strcmp(currentBranch,'master')
-    error('ERROR: not in master')
+if ~strcmp(currentBranch,'main')
+    error('ERROR: not in main')
 end
 
 %Bump version number:
@@ -77,8 +77,8 @@ function increaseVersion(bumpType)
     end
 end
 if change
-    error(['Some files are changing from devel. To fix, first update devel, ' ...
-        'then merge to master, and try again.'])
+    error(['Some files are changing from develop. To fix, first update develop, ' ...
+        'then merge to main, and try again.'])
 end
 
 %Allow .mat & .xlsx storage:

code/missingFields/mapIDsViaMNXref.m

@@ -35,9 +35,9 @@
 % order to load data structure from RAVEN repository since the data is
 % stored in raven toolbox.
 %since right now, MNX reference structure only exist in the RAVEN branch:
-%origin/feat/add_MetaNetX, we need to switch devel branch to that branch, load
+%origin/feat/add_MetaNetX, we need to switch develop branch to that branch, load
 %the file and switch back.
-%remember when this branch is merged to the master branch, change codes
+%remember when this branch is merged to the main branch, change codes
 %below.
 IDfile = 'ravenCobraWrapper.m';
 currentPath = pwd;
@@ -69,8 +69,8 @@
 end
 cd external/MetaNetX/
 load('MNXref.mat');
-% swich back to the master branch of RAVEN
-git checkout master
+% swich back to the main branch of RAVEN
+git checkout main
 cd(currentPath);
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

model/yeast-GEM.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" level="3" version="1" fbc:required="false" groups:required="false">
-  <model metaid="yeastGEM.xml" id="M_yeastGEM_devel" name="The Consensus Genome-Scale Metabolic Model of Yeast" fbc:strict="true">
+  <model metaid="yeastGEM.xml" id="M_yeastGEM_develop" name="The Consensus Genome-Scale Metabolic Model of Yeast" fbc:strict="true">
     <listOfUnitDefinitions>
       <unitDefinition id="mmol_per_gDW_per_hr">
         <listOfUnits>

model/yeast-GEM.yml

@@ -1,7 +1,7 @@
 ---
 !!omap
 - metaData:
-    id: "yeastGEM_devel"
+    id: "yeastGEM_develop"
     name: "The Consensus Genome-Scale Metabolic Model of Yeast"
     date: "2021-06-15"
 - metabolites: