Deploy 0117eb6 to gh-pages

.github/ISSUE_TEMPLATE/feature-request.yml

@@ -0,0 +1,38 @@
+name: Feature request
+description: Request a new feature
+labels: "enhancement"
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thank you for taking the time to let us know what gget is missing!
+  - type: dropdown
+    id: request-type
+    attributes:
+      label: Request type
+      description: Are you requesting the extension of an existing module or a new module?
+      options:
+        - Extension of existing module
+        - New module
+    validations:
+      required: true
+  - type: textarea
+    id: description
+    attributes:
+      label: Request description
+      description: Please describe your request.
+      placeholder: Include links to references/databases if applicable.
+    validations:
+      required: true
+  - type: textarea
+    id: command
+    attributes:
+      label: Example command
+      description: Please provide an example command as you envision it.
+      render: shell
+  - type: textarea
+    id: command-output
+    attributes:
+      label: Example return value
+      description: Please describe what the above-mentioned command should return.
+      placeholder: What is the most important information? Which format would be most useful?

.github/ISSUE_TEMPLATE/issue_report.yml

@@ -0,0 +1,73 @@
+name: Issue / Bug Report
+description: Create a report to help us improve
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thank you for taking the time to fill out this report and help us improve! :)
+  - type: textarea
+    id: what-happened
+    attributes:
+      label: What happened?
+      description: Please provide a clear and concise description of what the issue is.
+    validations:
+      required: true
+  - type: textarea
+    id: version
+    attributes:
+      label: gget version
+      description: Which version of gget are you using?
+      placeholder: 0.27.2
+    validations:
+      required: true
+  - type: dropdown
+    id: os
+    attributes:
+      label: Operating System (OS)
+      description: Which Operating System (OS) did you use?
+      multiple: true
+      options:
+        - Linux
+        - macOS
+        - Windows
+        - Other (please specify above)
+        - Not applicable
+    validations:
+      required: true
+  - type: dropdown
+    id: interface
+    attributes:
+      label: User interface
+      description: Did the problem occur when calling gget from the command-line or Python? (Select all that apply.)
+      multiple: true
+      options:
+        - Command-line
+        - Python
+        - Google Colab (please include a shareable link above)
+        - R (please specify Python wrapper above)
+        - Not applicable
+    validations:
+      required: true
+  - type: dropdown
+    id: m1
+    attributes:
+      label: Are you using a computer with an Apple M1 chip?
+      description: We are asking this because the M1 chip has been causing [problems](https://github.com/pachterlab/gget/issues/30) for some `gget alphafold` dependencies.
+      options:
+        - Not M1
+        - M1
+        - Not applicable
+    validations:
+      required: true
+  - type: textarea
+    id: command
+    attributes:
+      label: What is the exact command that was run?
+      description: Please copy-paste the gget command that caused the problem.
+      render: shell
+  - type: textarea
+    id: command-output
+    attributes:
+      label: Which output/error did you get?
+      description: Please copy-paste the complete output/error returned by the command entered above.
+      render: shell

.github/workflows/ci.yml

@@ -0,0 +1,31 @@
+name: CI
+
+on:
+  schedule:
+    - cron: "0 16 * * 1,4"
+  push:
+    paths:
+    - 'gget/**'
+    - 'tests/**'
+
+jobs:
+  build:
+    runs-on: ubuntu-22.04
+    strategy:
+      fail-fast: false
+      matrix:
+        python: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
+        os: ['ubuntu-22.04']
+    name: Test on Python ${{ matrix.python }}
+    steps:
+      - name: Checkout branch
+        uses: actions/checkout@main
+      - name: Setup python
+        uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python }}
+          architecture: x64
+      - name: Install dependencies
+        run: pip install -r requirements.txt && pip install -r dev-requirements.txt
+      - name: Run tests
+        run: coverage run -m pytest -ra -v tests && coverage report --omit=main.py,tests*

.github/workflows/deploy.yml

@@ -0,0 +1,36 @@
+name: Deploy
+on:
+  push:
+    branches:
+    - main
+
+    paths:
+    - 'docs/**'
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+    - name: Install mdbook
+      run: |
+        mkdir mdbook
+        curl -sSL https://github.com/rust-lang/mdBook/releases/download/v0.4.34/mdbook-v0.4.34-x86_64-unknown-linux-gnu.tar.gz | tar -xz --directory=./mdbook
+        echo `pwd`/mdbook >> $GITHUB_PATH
+    - name: Deploy GitHub Pages
+      run: |
+        cd docs/
+        mdbook build
+        git worktree add gh-pages
+        git config user.name "Deploy from CI"
+        git config user.email ""
+        cd gh-pages
+        # Delete the ref to avoid keeping history.
+        git update-ref -d refs/heads/gh-pages
+        rm -rf *
+        mv ../book/* .
+        git add .
+        git commit -m "Deploy $GITHUB_SHA to gh-pages"
+        git push --force --set-upstream origin gh-pages

.github/workflows/traffic.yml

@@ -0,0 +1,33 @@
+name: Traffic
+on:
+  schedule: 
+    # Runs every week
+    - cron: "0 0 */7 * *"
+
+jobs:
+  # This workflow stores repository traffic and clones past the default 2 week period
+  traffic:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    steps:
+    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+    - uses: actions/checkout@v2
+      with:
+        ref: "traffic"
+
+    # Calculates traffic and clones and stores them in a CSV file
+    # This workflow is based on https://github.com/marketplace/actions/repository-traffic
+    - name: GitHub traffic 
+      uses: sangonzal/[email protected]
+      env:
+        TRAFFIC_ACTION_TOKEN: ${{ secrets.TRAFFIC_ACTION_TOKEN }} 
+
+    # Commits files to traffic branch
+    - name: Commit changes
+      uses: EndBug/add-and-commit@v4
+      with:
+        author_name: Laura Luebbert
+        message: "GitHub traffic"
+        add: "./traffic/*"
+        ref: "traffic"

.gitignore

@@ -0,0 +1,142 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Mac OS file that stores custom attributes of its containing folder
+.DS_Store
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+/gget/elm_files/
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# PyCharm
+/.idea/
+
+# mdbook documentation
+/docs/book/
+
+# Scratch directory
+/scratch/