Cobra is a project creation and management tool for python and git. It creates a conda environment and a github repository based on your requirements.
You can use the base conda to install cobra.
conda config --set auto_activate_base true
You have three different options to install cobra. Just always keep in mind that the python version need to be > 3.5.
If your pip path is pointing to the pip3 you can also you just pip.
pip3 install cobra-projects
Then execute the command
cobra --install
and follow the instructions.
- Download the sourcecode from github.
- Move into the cobra root directory (folder which contains the setup.py file)
cd cobra - Install it
pip install .
Then execute the command
cobra --install
and follow the instructions.
If you have to re-install or uninstall cobra:
- Delete the access token from your github page (Settings -> Developer settings -> Personal access tokens -> delete (cobra)
rm -rf ~/.cobrapip3/pip uninstall cobra-projects
usage: cobra [-h] [--install] [--test] [--clear] {create,list,remove} ...
Project creation (cobra) command line tool
positional arguments:
{create,list,remove} The different functions of cobra
create Create a new cobra project
list Lists all existing cobra projects
remove Remove a cobra project
optional arguments:
-h, --help show this help message and exit
--install Start the installation wizard.
--test Puts cobra into testing mode
--clear Clears all user files
To create a new project you can use the create command.
The minimum requirements is the -n parameter to give the project a name.
You can also lik the project with already existing conda environments or github repos.
CARE:
The -gh, --git-hook command is in beta. This command exports before each git commit the conda environment.
usage: cobra create [-h] -n PROJECT_NAME [-p PYTHON_VERSION] [-r REPO_NAME]
[-c CONDA_NAME] [-gh]
optional arguments:
-h, --help show this help message and exit
-n PROJECT_NAME, --project-name PROJECT_NAME
Name of the project
-p PYTHON_VERSION, --python-version PYTHON_VERSION
Python version for the project. Default: 3.5
-r REPO_NAME, --repo-name REPO_NAME
If you already have a github repo for the project.
Enter the repo name.
-c CONDA_NAME, --conda-name CONDA_NAME
If you already have a conda environment for the
project. Enter the name.
-gh, --git-hook Install a pre-commit git hook which updates the conda
environment file before you commit. This is just
working, if the current environment is the
environment of the project!
This command lists all the cobra project with some additional information.
usage: cobra list [-h]
optional arguments:
-h, --help show this help message and exit
After some time you want to remove a project from your system. This you can do with the remove command. The remove command with out additional options will just delete the cobra project from the system but not the files, environment or the repository. If you want to remove the the files, environment or repository use the below shown parameters.
usage: cobra remove [-h] -n NAME [-r] [-c] [-f] [-a]
optional arguments:
-h, --help show this help message and exit
-n NAME, --name NAME Name of the cobra project to remove
-r, --repo Also removes the remote repository
-c, --conda Also removes the conda environment from the system
-f, --folder Also removes the local folder
-a, --remove-all Remove everything (repo, folder, conda)
To do testing you have to create the conda environment test_environment.yml and activate it:
conda env create -f test_environment.yml
conda activate cobra_dev
Then you can test the whole program including test coverage (htmlcov/index.html) with:
tox
@inproceedings{voegtlin2020cobra,
address = {Online},
author = {Voegtlin, Lars and Pondenkandath, Vinaychandran and Ingold, Rolf},
title = {{Cobra: A CLI Tool To Create And Share Reproducible Projects}},
booktitle = {2020 7th Swiss Conference on Data Science (SDS)},
year = {2020},
month = {jun},
}
- Create repo with template
- Create conda Dockerfile
- Automatically build docker container and push it to dockerhub
![dependabot[bot] avatar](https://avatars.githubusercontent.com/in/29110?v=4 "dependabot[bot]")
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