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Merge pull request #15 from pepkit/device_login
First release 🥳
2 parents 3655f16 + 4af98bd commit 3087c52

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‎.github/workflows/black.yml

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name: Lint
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on:
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pull_request:
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branches: [main]
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jobs:
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lint:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: actions/setup-python@v2
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- uses: psf/black@stable

‎.github/workflows/pytest-windows.yml

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name: Run pytests windows
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on:
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push:
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branches: [dev]
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pull_request:
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branches: [main, dev]
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jobs:
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pytest:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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python-version: ["3.10"]
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os: [windows-latest]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install all dependencies
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run: pip install -r requirements/requirements-all.txt
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- name: Install test dependencies
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run: pip install -r requirements/requirements-test.txt
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- name: Install package
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run: python -m pip install .
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- name: Run pytest tests
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run: pytest tests -v

‎.github/workflows/pytest.yml

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name: Run pytests
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on:
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push:
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branches: [dev]
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pull_request:
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branches: [main, dev]
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jobs:
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pytest:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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python-version: ["3.8", "3.11"]
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os: [ubuntu-20.04]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install all dependencies
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run: if [ -f requirements/requirements-all.txt ]; then pip install -r requirements/requirements-all.txt; fi
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- name: Install test dependencies
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run: if [ -f requirements/requirements-test.txt ]; then pip install -r requirements/requirements-test.txt; fi
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- name: Install package
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run: python -m pip install .
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- name: Run pytest tests
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run: pytest tests -v

‎.github/workflows/python-publish.yml

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# This workflows will upload a Python Package using Twine when a release is created
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# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
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name: Upload Python Package
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on:
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release:
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types: [created]
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jobs:
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deploy:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: '3.x'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install setuptools wheel twine
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- name: Build and publish
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env:
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TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
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TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
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run: |
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python setup.py sdist bdist_wheel
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twine upload dist/*

‎LICENSE.txt

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Copyright 2023 Nathan Sheffield
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Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎MANIFEST.in

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include requirements/*
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include README.md
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include pephubclient/pephub_oauth/*

‎Makefile

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lint:
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black . && isort . && flake8
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# black should be last in the list, as it lint the code. Tests can fail if order will be different
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flake8 && isort . && black .
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run-coverage:
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coverage run -m pytest

‎README.md

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# `PEPHubClient`
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`PEPHubClient` is a tool to provide Python and CLI interface for `pephub`.
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Authorization is based on `OAuth` with using GitHub.
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[![PEP compatible](https://pepkit.github.io/img/PEP-compatible-green.svg)](https://pepkit.github.io)
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![Run pytests](https://github.com/pepkit/pephubclient/workflows/Run%20pytests/badge.svg)
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[![pypi-badge](https://img.shields.io/pypi/v/pephubclient)](https://pypi.org/project/pephubclient)
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[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
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The authorization process is slightly complex and needs more explanation.
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The explanation will be provided based on two commands:
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`PEPHubClient` is a tool to provide Python API and CLI for [PEPhub](https://pephub.databio.org).
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`pephubclient` features:
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1) `push` (upload) projects)
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2) `pull` (download projects)
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## 1. `pephubclient login`
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To authenticate itself user must execute `pephubclient login` command (1).
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Command triggers the process of authenticating with GitHub.
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`PEPHubClient` sends the request for user and device verification codes (2), and
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GitHub responds with the data (3). Next, if user is not logged in, GitHub
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asks for login (4), user logs in (5) and then GitHub asks to input
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verification code (6) that is shown to user in the CLI.
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After inputting the correct verification code (7), `PEPHubClient`
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sends the request to GitHub and asks about access token (8), which is then
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provided by GitHub based on data from authentication (9).
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![](static/pephubclient_login.png)
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Additionally, our client supports pephub authorization.
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The authorization process is based on pephub device authorization protocol.
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To upload projects or to download private projects, user must be authorized through pephub.
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To login, use the `login` argument; to logout, use `logout`.
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## 2. `pephubclient pull project/name:tag`
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![](static/pephubclient_pull.png)
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----
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```text
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$ phc --help
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Usage: pephubclient [OPTIONS] COMMAND [ARGS]...
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╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────╮
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│ --version -v │
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│ --install-completion Install completion for the current shell. │
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│ --show-completion Show completion for the current shell, to copy it or customize the │
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│ installation. │
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│ --help Show this message and exit. │
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╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
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╭─ Commands ──────────────────────────────────────────────────────────────────────────────────────────────────────╮
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│ login Login to PEPhub │
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│ logout Logout │
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│ pull Download and save project locally. │
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│ push Upload/update project in PEPhub │
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╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
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```
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```text
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$ phc pull --help
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Usage: pephubclient pull [OPTIONS] PROJECT_REGISTRY_PATH
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Download and save project locally.
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╭─ Arguments ─────────────────────────────────────────────────────────────────────────────────────────────────────╮
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│ * project_registry_path TEXT [default: None] [required] │
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╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
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╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────╮
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│ --force --no-force Overwrite project if it exists. [default: no-force] │
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│ --help Show this message and exit. │
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╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
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```
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```text
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$ phc push --help
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Usage: pephubclient push [OPTIONS] CFG
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Upload/update project in PEPhub
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╭─ Arguments ─────────────────────────────────────────────────────────────────────────────────────────────────────╮
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│ * cfg TEXT Project config file (YAML) or sample table (CSV/TSV)with one row per sample to constitute │
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│ project │
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│ [default: None] │
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│ [required] │
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╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
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╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────╮
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│ * --namespace TEXT Project namespace [default: None] [required] │
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│ * --name TEXT Project name [default: None] [required] │
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│ --tag TEXT Project tag [default: None] │
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│ --force --no-force Force push to the database. Use it to update, or upload project. │
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│ [default: no-force] │
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│ --is-private --no-is-private Upload project as private. [default: no-is-private] │
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│ --help Show this message and exit. │
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╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
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```

‎docs/changelog.md

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# Changelog
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This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
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## [0.1.0] - 2023-04-16
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### Added
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- First release

‎error_handling/constants.py

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‎error_handling/error_handler.py

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‎error_handling/models.py

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‎github_oauth_client/constants.py

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