00. Create repository
01. clone it locally
git clone [email protected]:free-cortex/framework.git
cd framework
git init
03. Create a pdfs branch for the pdf files (see more).
git checkout -b pdfs
rm -rf * README.md .github .gitignore *swp ~.git .idea
git add -A
git commit -m 'clean pdfs branch'
git push origin pdfs
02. create .gitignore
Download and edit .gitignore
# Ignored paths and directories
## pycharm project path
.idea
## vim temporal files
**/*.swp
## temporal TeX files
**/*.aux
**/*.fdb_latexmk
**/*.fls
**/*.log
**/*.nav
**/slides/main.pdf
**/*.snm
**/*.synctex.gz
**/*.toc
**/*.vrb
**/slides/_minted-main/*.*
01 Create a deploy key with ssh-keygen -m PEM -t rsa -b 4096 -C "[email protected]" 🔗
🔗
02. Add a new secret variable called DEPLOY_KEY in
https://github.com/$PROJECT_NAME/$REPO_NAME/settings/secrets/actions where DEPLOY_KEY is taken from id_rsa using
xclip -selection clipboard < ~/.ssh/id_rsa
which looks like:
-----BEGIN RSA PRIVATE KEY-----
...
-----END RSA PRIVATE KEY-----
- Don't forget to "Adding your SSH key to the ssh-agent" and be authentified 🔗
eval "$(ssh-agent -s)"
ssh-add ~/.ssh/id_rsa
ssh -T [email protected]
03. Create github action workflow
.github/workflow/*.yml and then create main.yml
mkdir -p .github/workflows
cd .github/workflows && wget https://raw.githubusercontent.com/free-cortex/framework/main/.github/workflows/template.yml
mv template.yml $DESIRED_NAME.yml
- Setting up variables for pdf documents and keys in .github/workflows/main.yml.
See this template.yml as example.
Edit
template.ymlby changing branches and repository name.
04. Commit genesis in the main branch using CI-CV for CV (or no capital flags for CI build) in the commit
git add .
git commit -m "genesis commit CI-CV"
git branch -M main
git remote add origin [email protected]:free-cortex/framework.git
git push -u origin main
00. Raise a new issue
01. checkout and pull main
git checkout main
git pull
02. create a new branch
git checkout -b $ISSUENUMBER-$BRANCHNAME
03. Create github action workflow
.github/workflow/*.yml and then create main.yml
mkdir -p .github/workflows
cd .github/workflows && wget https://raw.githubusercontent.com/free-cortex/framework/main/.github/workflows/template.yml
mv template.yml $DESIRED_NAME.yml
- Setting up variables for pdf documents and keys in
.github/workflows/*.yml. For instance,
name: Compiling-TeX-$BRANCHNAME
on:
push:
branches:
- main
- 05-$BRANCHNAME
jobs:
build:
if: "contains(github.event.head_commit.message, 'CI-$BRANCHNAME')"
See this template.yml as example.
04. commit genesis and add path/files and push them
git add -A
git commit -m ':fire: genesis of $BRANCHNAME [skip branches]'
git push origin $ISSUENUMBER-$BRANCHNAME
- Edit README for new actions and readme icons
## Slides
[](https://github.com/free-cortex/framework/actions) [](https://github.com/free-cortex/framework/blob/pdfs/slides.pdf)
05. Create pull request
Title: [WIP] Drafting $BRANCHNAME
Content: Resolves #$ISSUENUMBER
If CI is successful, tex file will be built [here](https://github.com/free-cortex/framework/blob/pdfs/$PDFFILE.pdf)
06. keep making commit until the issue is sorted out
git add -A
git commit -m ':fire: genesis of $BRANCHNAME'
git push origin $ISSUENUMBER-$BRANCHNAME
You can add capital CI and the type of document for its CI build or nothing
See workflows *.yml
mkdir -p $HOME/Downloads/latex && cd $HOME/Downloads/latex
wget http://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gz
tar -xf install-tl-unx.tar.gz
rm install-tl-unx.tar.gz
cd $HOME
echo '# Setting PATH of the TeX Live binaries'
echo 'export PATH=/usr/local/texlive/2020/bin/x86_64-linux/:$PATH'
In your terminal:
cd ~/unt-manuscript-2021/journal-of-imaging-2021/manuscript-tex
make clean && make && make view
make clean
Use Git Bash to set up SSH keys
-
Install TexLive at TEXDIR C:/texlive/2020;
- (run it anyway)
- Disk space 7293 MB
- Tex Live Installer might take few minutes (90mins ish) as ~4056 packages are installed.
-
"When installation is complete, you will have to restart Windows, and then you can run the TEX programs from a command prompt." 🔗
-
Install Cygwin (Get that Linux feeling - on Windows)
04.01 Download and run setup-x86_64.exe
Install it from the internet
04.02 Running installation
* Location: C:\cygwin64
* Use System Proxy Settings
* Choose a mirror
* Make sure to select the latest installers of: make, vim, evince.
04.03 Add these lines your .bashrc (vim .bashrc)
* alias cdc='cd /cygdrive/c'
* ll = 'ls -la'
* export C=/cygdrive/c
04.04 Close and open Cygwin
04.05 Accessing your files
cd /cygdrive/c/Users/$USERNAME/UNT/gift-surg/unt-manuscript-2021/journal-of-imaging-2021/manuscript-tex -
Install make in GitBASH
Keep in mind you can easy add make, but it doesn't come packaged with all the standard UNIX build toolchain--so you will have to ensure those are installed and on your PATH, or you will encounter endless error messages.
ref05.01 Go to https://sourceforge.net/projects/ezwinports/
05.02 Download make-4.1-2-without-guile-w32-bin.zip (get the version without guile).
05.03 Extract zip.
05.04 Copy the contents to your Git\mingw64\ merging the folders, but do NOT overwrite/replace any existing files
- Open Gitbash and go to
cd
~/.../unt-manuscript-2021/journals/ieee-tbe-2021/manuscript-tex - clean project, make project and open pdf
make clean && make && explorer main.pdf- commit changes
- add
CITBEanywhere in your commit message for ci tex build
- Open Cygwin64
- Go to with
cd /cygdrive/c/Users/$USERNAME/UNT/$MAIN_REPO/$REPONAME/$JOURNAL/manuscript-tex - Built, clean and view
make- cygstart.exe main.pdf #to view pdf
make clean
- commit changes
- add
CITEXanywhere in the commit message, when you do not build tex files with github action.
- add
- Checkout branch
origin/#NumberOfIssue-#BranchName - Click on the blue arrow (Ctrt+T) and choose
merge in coming changes into the current branch- 02.01 If one accidentally forgot to pull latest commits creating error when pushing files, one can do
git reset --hard HEAD~1. For this case, be sure to copy your progress in a different file and put it back once you update the latest commits.
- 02.01 If one accidentally forgot to pull latest commits creating error when pushing files, one can do
- Make your changes and commit with a message adding CITEX.
⚠️ User would try to avoid working on the same file as it might create conflicts (recommended to have a chat).
To create figures using vector files with inkscape, the following template is used
where vectors path has svg files, drawing-vNN.svg where NN is the number of version,
reference for other images and versions for png or pdf outputs. See one example of
the path organisation:
.
├── Makefile
├── README.md
├── references
│ └── README.md
├── vectors
│ └── drawing-v00.svg
│ └── drawing-v01.svg
└── versions
├── drawing-v00.png
├── drawing-v01.png
└── README.md
When creating a new version, modify /vectors/drawing-v00.svg
and use the latest version for instance, a copy of v02 to create for instance v03.
Type the following in the terminal
make
mv versions/drawing.png versions/drawing-vNN.png #todo: add this in the makefile
open /svgpath/drawing.svg with inkscape using the explorer to make modifications (use explorer . in Cygwin)
Then go to the menu File>Export PNG image... export the figure.
In such window select path and filename to be, for instance, /versions/drawing-v03.png and click Export as.
To avoid any conflicts when two persons are working in the same file such as references.
references_blurs.bib contains any potential references that can then be moved to
a particular section references such as references_introduction.bib.
It is recommended to have a plan and continuous communication in the first stages
of drafting the papers.
One way to avoid keeping PDF files version in the repository (as this mainly build a pdf of the current tex and images) is to go to a particular commit to then build the PDF of such commit. For example,
$ git checkout $CURRENT_BRANCH #(e.g. manuscript-for-ipcai2021) # change to manuscript branch
$ git log --oneline # show history of commit hashes
da1949a (HEAD -> manuscript-for-ipcai2021) Merge branch 'manuscript-for-ipcai2021' of https://github.com/gift-surg/us-needle-tracking-verification into manuscript-for-ipcai2021
.
.
.
aa81cbe update gitignore to ignore TexStudio files
a07dca0 adds workflow for figures [skip mdpi2021] (see further discussion at #51)
$ git checkout a07dca0 # change to that version
$ cd .../manuscript-exe/ && make clean && make && evince main.pdf # build your pdf output (instead of evince, `cygstart.exe main.pdf #to view pdf in windows`)
$ git checkout da1949a #HEAD -> manuscript-for-ipcai2021) # going back to the latest commit
$ git log --oneline
38246bc (HEAD -> manuscript-for-ipcai2021, origin/manuscript-for-ipcai2021) refactors methods and materials sections and adds legacy figure for signal processing pipeline
ed519ca adds figure v00 for coordinate systems
8279905 cosmetic changes to title, author list, and acknowledgements
$ git stash list #This will list down all your stashes.
$ git stash save "my-save"
$ git pull
$ git log --oneline
51a8ede (HEAD -> manuscript-for-ipcai2021, origin/manuscript-for-ipcai2021) Fix image size.
b2fb176 Change phrasing and add guidelines for sig proc part.
$ git stash list #This will list down all your stashes.
$ git stash pop stash@{n} #To apply a stash and remove it from the stash stack, type:
Where n is the index of the stashed change.
See the following comments to-rebase-local-branch-onto-remote-master using the terminal ref
git checkout main
git pull origin main
git checkout RB
git rebase main
git push --force origin RB