From 363f34defb2dc3b19825cfb6ec0fdc7d324ade55 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Sun, 8 Aug 2021 15:48:02 +0200 Subject: [PATCH 1/3] style: normalize line ending to LF --- .gitattributes | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 .gitattributes diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..5a6fc2b --- /dev/null +++ b/.gitattributes @@ -0,0 +1,19 @@ +# Set the default behavior, in case people don't have core.autocrlf set. +* text=auto + + +# Explicitly declare text files you want to always be normalized and converted +# to native line endings on checkout. +*.tsv text +*.yml text +*.xml text +*.md text +*.txt text +*.json text +*.rst text + + +# Denote all files that are truly binary and should not be modified. +*.xlsx +*.docx +*.mat From ca5d782b7aa3fc79d71fbae0c90511227f29e9b9 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Sun, 8 Aug 2021 16:00:08 +0200 Subject: [PATCH 2/3] style: add citation --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index aec2978..3b3c2eb 100644 --- a/README.md +++ b/README.md @@ -11,8 +11,7 @@ This repository contains the latest version of Fruitfly-GEM, a fruit fly genome- #### Citation -Manuscript under preparation - + > H. Wang, J. L. Robinson, P. KocabasĖ§, J. Gustafsson, M. Anton, P.-E. Cholley, et al. Genome-scale metabolic network reconstruction of model animals as a platform for translational research. _PNAS_ 118, e2102344118 (2021). [doi.org/10.1073/pnas.2102344118](https://doi.org/10.1073/pnas.2102344118) #### Model Keywords From 1284e782e284776048861c3b3d2abd5f283f51ed Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Sun, 8 Aug 2021 17:37:59 +0200 Subject: [PATCH 3/3] style: rename branches master --> main devel --> develop --- .github/ISSUE_TEMPLATE.md | 6 ++---- .github/PULL_REQUEST_TEMPLATE.md | 2 +- README.md | 4 ++-- 3 files changed, 5 insertions(+), 7 deletions(-) diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md index 60e55f4..1797a08 100644 --- a/.github/ISSUE_TEMPLATE.md +++ b/.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: @@ -17,9 +17,7 @@ ``` **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 *Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE* diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 5c2d4ab..d476a25 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -4,6 +4,6 @@ **I hereby confirm that I have:** - [ ] Tested my code on my own computer for running the model -- [ ] Selected `devel` as a target branch +- [ ] Selected `develop` as a target branch *Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE* diff --git a/README.md b/README.md index 3b3c2eb..e4eac1d 100644 --- a/README.md +++ b/README.md @@ -52,7 +52,7 @@ This repository contains the latest version of Fruitfly-GEM, a fruit fly genome- ### Installation Instructions -* Clone the [master branch](https://github.com/SysBioChalmers/Fruitfly-GEM/tree/master) of this repository, or [download the latest release](https://github.com/SysBioChalmers/Fruitfly-GEM/releases/latest). +* Clone the [main branch](https://github.com/SysBioChalmers/Fruitfly-GEM/tree/main) of this repository, or [download the latest release](https://github.com/SysBioChalmers/Fruitfly-GEM/releases/latest). * Add the directory to your MATLAB path (instructions [here](https://se.mathworks.com/help/matlab/ref/addpath.html?requestedDomain=www.mathworks.com)). @@ -60,7 +60,7 @@ This repository contains the latest version of Fruitfly-GEM, a fruit fly genome- #### Loading/saving the model -`Fruitfly-GEM.mat` (Recommended if on `master` branch) +`Fruitfly-GEM.mat` (Recommended if on `main` branch) * Load and save using the built-in MATLAB `load()` and `save()` functions. `Fruitfly-GEM.xml` (SBML format)