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python package for PEPSE project

Project description

pepsepy Module Repository

Table of Contents

This simple project is an example repo for Python projects.

Learn more

git clone

cd pepsepy

python install [--record files.txt]


Command line instructions

Git global setup git config --global "Van Long Lê" git config --global ""

Create a new repository git clone cd pepsepy touch git add git commit -m "add README" git push -u origin master

Existing folder cd existing_folder git init git remote add origin git add . git commit -m "Initial commit" git push -u origin master

Existing Git repository cd existing_repo git remote rename origin old-origin git remote add origin git push -u origin --all git push -u origin --tags

Create master branch and push it to server

git init

git remote add origin

Make changes ...

git add files folders

git commit -m "messages"

git push origin master


Create a new branch

git checkout -b pepseday2019

add and commit

git push -u origin new_branch: push to server

invite new collaborators

For new collaborators:

git clone

git checkout --track origin/pepseday2019

make changes

git add . && git commit

git fetch or git pull

solve conflicts

git push -u origin pepseday2019

The conflicts comme here

git push -u [--set-upstream] origin pepseday2019

The next step is to see how to merge pepseday2019 to master

Case: work on pepseday2019, the work is done and readay to merge it backt to master

(--rebase will get the changes from master and could overwrite changes other people made)

The goal is to keep pepseday2019 branch updated with the things happening in master and later could merge them back into master No, rebase never overwrite, it just trying to achieve a cleaner history, by reattach (or fake) the history to the late point of the master. (it undoes the commits from the branch pepseday2019, then applies the commit backt to )

Git Branching - Rebasing

In Git, there are two main ways to integrate changes from one branch into another: the merge and the rebase.

The easiest way to integrate the branches, as we’ve already covered, is the merge command. It performs a three-way merge between the two latest branch snapshots (C3 and C4) and the most recent common ancestor of the two (C2), creating a new snapshot (and commit).


Basic Branching and Merging

Simple workflow
  1. Do some work on a website (git add, git commit)
  2. Create a branch for a new user story you're working on (git checkout -b new_branch)
  3. Do some work in that branch (git commit -a -m 'added a new footer [issue 53]')

At this stage, you’ll receive a call that another issue is critical and you need a hotfix. You’ll do the following:

Note: when you’ve been working on part of your project, things are in a messy state and you want to switch branches for a bit to work on something else. The problem is, you don’t want to do a commit of half-done work just so you can get back to this point later. The answer to this issue is the git stash command.

git status

Changes to be commited

git stash
Saved working directory and index state

git status
# On branch master
nothing to commit, working directory clean

At this point, you can switch branches and do work elsewhere; your changes are stored on your stack. To see which stashes you’ve stored, you can use git stash list:

git stash list

git stash apply (most recent) or git stash apply stash@{2} (specific stash)

  1. Switch to your production (git checkout master)
  2. Create a branch to add hotfix (git checkout -b hotfix)
  3. After it is tested, merge the hotfix branch, and push to production (git commit -a -m 'fixed the broken email address')
  4. Switch back to your original user story and continue working (git checkout master, git merge hotfix)

After your super-important fix is deployed, you’re ready to switch back to the work you were doing before you were interrupted. However, first you’ll delete the hotfix branch, because you no longer need it — the master branch points at the same place. You can delete it with the -d option to git branch:

git branch -d hotfix

Now you can switch back to your work-in-progress branch on issue #53 and continue working on it.

git checkout iss53
vim index.html
git commit -a -m 'finished the new footer [issue 53]'

It is worth noting here that the work you did on your hotfix branch is not contained in the files in your iss53 branch. If you need to pull it in, you can merge your master branch into your iss53 branch by running git merge master, or you can wait to integrate those changes untill you decide to pull the iss53 branch back into master later

The issue #53 is commplete and ready to be merged into your master branch.

git checkout master
git merge iss53
Basic merge conflicts

For resolving the merge conflict, you can run git mergetool, which files up an appropriate visual merge tool and walks you through the conflicts

Basic rebasing

There is another way to integrate the branches: you can take the patch of the change that was introduced

If you want to learn more about files, check out this repository <>_.

Structure of the Repository

  • requirements.txt
  • pepsepy/
  • pepsepy/
  • pepsepy/
  • docs/
  • docs/


python install or python install --record files.txt : To record a list of installed files

Install using pip


Linux: xargs rm -rf < files.txt or cat files.txt | xargs rm -rf Windows: using Powershell Get-Content files.txt | ForEach-Object {Remove-Item $_ -Recurse -Force} Then delete also the containing directory: ~/Programs/anaconda/.../pepsepy


  • merge pepseday2019 to master
  • create release entries
  • create changelog
  • create wiki
  • create
  • create gitlab CI/CD

GitLab CI/CD: GitLab Continuous Integration

The continuous methodologies of software development are based on automating the execution of scripts to minimize the chance of introducing errors while developing applications. They require less human intervention or event no intervention at all, from the develoment of new code until its deployment.

It involves continuously building, testing, and deploying code changes at every small iteration, reducing the chance of developing new code cased on bugged or failed previous versions

Continuous Integration

Developers push code changes every day, multiple times a day. For every push to the repository, you can create a set of scripts to build and test your application automatically, decreasing the chance of introducing errors to your app.

This practice is known as Continuous Integration; for every change submitted to an application - even to development branches - it’s built and tested automatically and continuously, ensuring the introduced changes pass all tests, guidelines, and code compliance standards you established for your app.

Continuous Delivery

Continuous Delivery is a step beyond Continuous Integration. Your application is not only built and tested at every code change pushed to the codebase, but, as an additional step, it’s also deployed continuously, though the deployments are triggered manually.

This method ensures the code is checked automatically but requires human intervention to manually and strategically trigger the deployment of the changes.

Continuous Deployment

Continuous Deployment is also a further step beyond Continuous Integration, similar to Continuous Delivery. The difference is that instead of deploying your application manually, you set it to be deployed automatically. It does not require human intervention at all to have your application deployed.

  • GitLab's built-in tool for sofware development using continuous methodology
    • Continuous integration (CI)
    • Continuous delivery and deployment (CD)


How GitLab CI/CD (or travis CI) works

To use GitLab CI/CD, all you need is an application codebase hosted in a Git repository, and for your build, test, and deployment scripts to be specified in a file called .gitlab-ci.yml, located in the root path of your repository.

In this file, you can define the scripts you want to run, define include and cache dependencies, choose commands you want to run in sequence and those you want to run in parallel, define where you want to deploy your app, and specify whether you will want to run the scripts automatically or trigger any of them manually. Once you’re familiar with GitLab CI/CD you can add more advanced steps into the configuration file.

To add scripts to that file, you’ll need to organize them in a sequence that suits your application and are in accordance with the tests you wish to perform. To visualize the process, imagine that all the scripts you add to the configuration file are the same as the commands you run on a terminal in your computer.

Once you’ve added your .gitlab-ci.yml configuration file to your repository, GitLab will detect it and run your scripts with the tool called GitLab Runner, which works similarly to your terminal.

The scripts are grouped into jobs, and together they compose a pipeline. A minimalist example of .gitlab-ci.yml file could contain:


- apt-get install rubygems ruby-dev -y



    - ruby --version

The before_script attribute would install the dependencies for your app before running anything, and a job called run-test would print the Ruby version of the current system. Both of them compose a pipeline triggered at every push to any branch of the repository.

GitLab CI/CD not only executes the jobs you’ve set, but also shows you what’s happening during execution, as you would see in your terminal:




Git - taging

delete local tag '12345'

git tag -d 12345

delete remote tag '12345' (eg, GitHub version too)

git push origin :refs/tags/12345

alternative approach

git push --delete origin tagName

git tag -d tagName

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