Project Files - Team Charter and Git Repository

This project will use both Microsoft TEAMS and git to organize your files and communications.

TEAMS FOLDER Use this folder to store your team organizational documents. This includes the team charter, meeting minutes, NDA/IP agreements, Weekly 3x3 Reports etc, report drafts.
Git Repository Use this folder to track your teams code. We expect all teams to use good software management practices when dealing with code and a good version control system is key.

1. Teams Folder

Your instructor should have already created a folder for your team. Organize this folder in a way that makes sense to you. However, you must include files to help the instructors (and your teammates) navigate the folder and quickly find what you need.

This week we just need you to create a folder for your signed NDA/IP agreements as well as a complete “Team Charter” document from the in-class activity on Wednesday. As the semester moves forward the structure of your folder should look something like:

TEAM NAME
    TEAMNAME_TeamCharter.docx
    REPORTS
        Weekly3x3
            20230125-3x3.docx
        MeetingNptes
            20230123-Weeky_meeting.docx
    Deliverables
        20230129-Propoal.docx
        20230319-Closed_Loop_Video.mpeg4
    TeamMember_files
        Name1
        Name2
        Name3
    NDA Files
        DataFile1.csv
        DataFile2.csv

DO NOT use spaces in file names

When you name all of the files and folders inside of a team directory, please DO NOT include spaces in the folder or file names. Although all modern computer’s have ways to accept names with spaces do not use them. Instead use underscores (_) or CamleCase (No spaces and capital letters at the beginning of each word in the name). Avoiding spaces in your names will Always save time in the long run.

Points will be taken off if files and folders have spaces in the names.

NDA Signatures

If your project requires an NDA or IP agreement. Please make a copy of the PDF form for your project and sign the agreements. The form that is required for your team is in your project team drive. Sign the document and put a pdf copy in a folder named “Signed_agreements” with your files named “MSUNetID_ProjectSponsor_IP.pdf” and “MSUNETID_ProjectSPonsor_IP.pdf”. For example, I would save mine as “colbrydi_Valve_IP.pdf” and “colbrydi_Valve_NDA.pdf”.

This is an Official document so it is important that you make it look professional. Some guidelines to consider:

Remove all yellow highlighting. It is there to show you what you need to edit.
Fill out everything you can except the stuff the company will need to fill out.
Type everything in except the signature. Do not write information in with a pen.
If there is a underline space make sure what you type in is also underlined.
It is preferred that you actually sign by overlaying a picture of your signature but you can also print out the document, sign it and then scan it.
If you use a scanned signature make sure you can’t easily tell when looking at the final PDF. Use a completely white background on your signature. Insert the signature “Underneath” the text so that the singing lines look right.
Clean up the spacing so it fits reasonably on the pages. Don’t leave dangling lines on extra pages.

The following video may be helpful if you are confused. Note this video is from last semester so the way we are organizing files is different. The first part about D2L can be ignored (we are using Teams). The rest of the video takes you step by step through me signing the document.

Direct Link to video

Team Charter

Create a word document, give it a clear name and add it to your Team directory. This will be a “living” document which means it will change as your team grows. Remember that we drafted this document in class on Wednesday. To start make sure it includes the following:

Members and roles
Team Purpose and goals
Expected outcomes
Ground rules
Instructions/URL for accessing the git repository (See below).

For more information about the motivation behind a team charter see the following link:

Creating a Team Charter

2. Git Repository

Create a git repository and share it with your classmates and instructors. This repository will be used for the remainder of the course to track all of your code developed for this project. By the end of the semester your repository will have a structure similar to the following:

ProjectName/
    .gitignore
    docs/
         package_name/
              module1.html
              module2.html
         images/
              image1.jpg
    environments.yml
    Examples/
          datafile1.csv
          datafile2.tiff
          datafile3.xls
    Figures/
          Generate_Figure1.ipynb
          Generate_Figure2.ipynb
          Generate_Figure3.ipynb
    LICENSE.txt
    makefile
    package_name/
          __init__.py
          module1.py
          module2.py
          test/
              __init__.py
              test_module1.py
              test_module2.py
    README.md
    setup.py

Projects structure will vary. The important part is that repositories are well documented so that it is easy to navigate. You must follow the guidelines shown out in this document.

Examples

Here is an example projects you can download from a different course with a similar structure. Note these may have had slightly different expectation and assignment goals relative to your project but are still good representation of the types of projects that would be acceptable for this course. Projects shared with permission by former students:

Even more projects (may require logging into MSU GitLab to access:

Basic git INSTRUCTIONS

For this milestone we only need to set up the basic structure with the following. To start, please keep the files simple and do not include files that do not add something to the project (see “what not to include” below):

ProjectName/
    .gitignore
    LICENSE.txt
    README.md

Here is a description of each of these:

ProjectName - The top level folder is the short name of your team. Give your project a short and memorable name. An ideal name should be descriptive and have meaning to people who may be interested in using your software. A poor name only has meaning to your team. For example, DO NOT USE CMSE495 NOR YOUR NAME in the the name. Instead try to pick a name that relates to your project or what you think your project will do. Although we can change the name later it is much easier if we pick a good name to start.
- README.md - This is a description of your git repository written in Markdown. For now this file can just contain your team member names.
- .gitignore - There are a lot of files that are inappropriate to include in a git repository (more information below) the “Git Ignore” file helps by telling Git that you never want to use these files. There are plenty of examples for good .gitignore files for Python projects on the Internet. Try to include one that makes sense (you can update it as the semester goes on).
- LICENSE - Use this file to describe your license (See section below).

HINT: Many of you may find this git template helpful.

If you need help figuring out how to set up your git repository there are a ton of tutorials online. For example here is a good one:

Github learning lab

If you continue to need help go see your instructors.

The following video are instructions specifically for how to use the MSU Gitlab. We will be using the MSU gitlab for all projects because it allows us to best maintain file permissions. If you have a completely opensource project with no NDA or IP agreement you are also allowed to post on Github or other public spaces:

Some of you may get some sort of “Authentication” error when trying to use git on a windows machine (especially if you have your computer already set up to use github). If that is the case, the following video may help you set up an SSH key on your windows machine.

Direct Link to Windows SSH key generation video

As you update and change the files in your repository you will need to push those changes to gitlab. The following instructions walk you though this process:

What not to include (building a .gitignore file)

First thing we want to teach is is that not everything should go into a git repository. i.e. we do not want to bloat our repository with unwanted files. The git repository works best with Text files that represent “source” code and not compiled or generated code. Here are some basic guidelines of what not to include:

.ipynb_checkpoint - These folders are generated when you run jupyter notebooks. They are “temporary” compiled folders that will change each time you run your notebook and should not be included in your repository.
__pychache__ - Similar to .ipynb_checkpoint folders these folders are often generated when running python scripts and should not be included in your repository.
Other “Temporary” files - Temporary files are generated by all types of software and often start with a special characters such as the dot (.) or the tilde (~). For example many text editors generate temporary files to save a document in case of a program crash. Do not include temporary files in your repository.
Compiled Code - Programs such as C and FORTRAN must compile their code to an executable in order to run on your computer. These compiled codes are not editable and should be left out of your repository. Instead it is better to include instructions for compiling the source code as part of your repository.
Program Output - Do not include any program output in your repository (unless for very specific reasons such as documentation, testing, or figures in your final report). Assume that any output that can be generated by the source code should not be included with the source code (it is redundant).

A good rule of thumb is that if you did not generate the file and/or do not know what it is you probably do NOT want to include it in your repository.

WARNING do not blindly add all files to your repository with the * (star) syntax. This is bad practice. For example do NOT do the following:

~~git add *~~

Other files to avoid

In addition to the above files it is good to avoid any type of “Binary” file (with a few exceptions). As stated early, git works best with text files so it can easily track changes. Some example binary files to avoid include:

Large Data files Although it is good to include a few example inputs to your software, avoid using entire datasets. It is best to store these files someplace else (ex. Teams folder).
Non-Text formats such as Word, Excel or PowerPoint documents should be avoided. These tend to change each time they are opened even if the core text does not change. it is better to use an alternative text example.

Note: one exception to the above rules are image files (ex jpg or png) that are used to help markdown or in the documentation. It is typically okay to include these since they tend to get included only once and do not change much as the project evolves.

.gitignore file

The .gitignore (read “dot git ignore”) file is used to help keep unwanted files out of your project. Each line .gitignore file are filenames you want git to ignore. For example, based on what we said above, a good place to start on your .gitignore file would be the following two lines:

.ipynbcheckpoint
__pychache__

What should go into a .gitignore depends a lot on the type of project. However, you don’t need to invent these from scratch. For example, you could just copy the .gitignore file from the course repository or find one on the internet.

README.md file

Make sure your git repository has a README.md file. This file is very important as it will be the first place everyone will look when they first get your repository. Write this as if someone in the future stumbles across your folder. Include a brief description of the class, the sponsor, the project and the goals of this repository. Link to any installation instructions or getting started instructions. It is important that this file guides readers to the rest of the repository.

Jupyter notebook files in git repositories

Turns out that Jupyter notebook files and git repositories work very poorly together. Jupyter notebook files are a unique combination of source and program generated information. So, every time you run a jupyter file it can add output cells which make git think you you changed something important. In many cases it is just a few numbers or some output text. When you run the git status command it always looks like jupyter notebook files have changed even when they have not changed.

A good rule of thumb is to clear all of the output files before committing any changes to jupyter notebook files.

Open the jupyter notebook file
Select “Reset Kernel and clear output” from the menu
Save the notebook file.
Do your “git add” and “git commit” commands

The following video goes though why we have to treat jupyter notebooks this way:

Direct Link

Licensing file

As authors of software it is important to let people know how they can use our software. If your project has an NDA or IP agreement you must copy/paste/edit wording from those file as your LICENSE agreement. Please ask during class if you are not sure.

The following article is a great resource for learning the types of terminology and logic used when talking about software License.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002598
https://creativecommons.org/licenses/

Creative commons license

Include a ./LICENSE test file in your top directory. Select which license to use using the following website:

https://choosealicense.com/

Copy and paste your chosen license file into a file named ./LICENSE

The following articles are a great resource for learning the types of terminology and logic used when talking about software License.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002598
https://choosealicense.com/
https://creativecommons.org/licenses/

Make sure you talk to your instructors to know what type of license is appropriate for your project given. What license you use may also depend on the NDA and IP agreement made with you and the sponsor.

Include a ./LICENSE.txt test file in your top directory.

Working with files professionally

Anytime you are working with files you need to pay attention to what you are doing. Pay attention to whom you will be sharing files and keep things clean and professional. Points will be taken off for unprofessional files.

Consider the following guidelines.

Use Filenames that make sense

Make sure the contents of the files are clear. If something is associated with a specific date then would like to use the following format:

YYYYMMDD-TEAM-Contents.ext

YYYY - Year file (ex, 2023)
MM - Two diget Month (ex. 01 for January)
DD - Two diget Day (ex. 09 )
TEAM - Short team name (if not obvious in context.
Contents - Content of the file.

DO NOT use spaces in file names

I said this above and I will say it again.

When you name all of the files and folders inside of a repository, it is important that your names DO NOT include spaces. Although all modern computer’s have ways to accept names with spaces do not use them. Instead use underscores (_) or CamleCase (No spaces and capital letters at the beginning of each word in the name). Avoiding spaces in your names will Alaways save time in the long run.

Always Use Relative Paths

In your code there are two basic ways to determine the location of a folder inside your computer; Relative Paths and Absolute Paths. A relative path is a path starting from your current directory and an absolute path is is a path starting from your computer’s “root” directory.

Relative paths typically start with a single dot (.), representing the current directory, or two double dots (..) representing the current directories parent folder.
Absolute paths typically start at the global root directory (/) on a Linux or Mac machine or with a drive label (ex C:) on a windows machine.

ALWAYS use relative paths in your git repository. This ensures that others will be able to use your software if they download it onto their computer. For example:

Good: ./data/  or ../data/ is a relative path to a child directory or sibling directory called data. 
Bad (not acceptable): C:/research/data or /mnt/home/data are absolute paths to a data directory

Turning Everything in

Make sure your instructors and classmates have the correct permissions to access, clone your repositories and provide the full git command/instructions in your team charter.

Your instructor will evaluate your assignment by reviewing the following:

Review of team charter
Checking pdfs of NDA and IP agreements (if required)
Forking and cloning your repository
Reviewing of your git log
Review of your repository README file
Checking your License file
Checking for reasonable .gitignore file

You will be graded on how well directions were followed and the professionalism of the submission.

Written by Dr. Dirk Colbry, Michigan State University
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.