Package with Hatch

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/publish.yml

@@ -0,0 +1,35 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: 
+      - published
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+    - name: Check out the code
+      uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+
+    - name: Install Hatch
+      run: pip install hatch
+
+    - name: Build the package with Hatch
+      run: hatch build
+
+    - name: Publish to PyPI
+      env:
+        HATCH_INDEX_USER: __token__
+        HATCH_INDEX_AUTH: ${{ secrets.TELOCLIP_PYPI_TOKEN }}
+      run: hatch publish

.github/workflows/pytest.yml

@@ -0,0 +1,47 @@
+name: Python Tests
+
+on: [pull_request]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+      # Checkout the latest commit associated with the PR
+      - uses: actions/checkout@v4
+
+      - name: Debug matrix value
+        run: echo "Python version is ${{ matrix.python-version }}"
+
+      # Set up Miniconda
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true  # Optional: update Conda to the latest version
+          python-version: ${{ matrix.python-version }}
+
+      # Create and activate the Conda environment using the environment.yml file
+      - name: Create and activate Conda environment
+        run: |
+          conda env create -f environment.yml -n test-env
+          conda activate test-env
+        shell: bash -l {0}  # Use bash with the login shell to activate Conda
+
+      # Install any additional dependencies not listed in environment.yml
+      - name: Install additional dependencies
+        run: |
+          conda activate test-env
+          pip install '.[tests]'  # Install all dependencies, including test-specific ones
+        shell: bash -l {0}
+
+      # Run pytest on the specified directory
+      - name: Run tests
+        run: |
+          conda activate test-env
+          pytest tests
+        shell: bash -l {0}
+

.github/workflows/ruff.yml

@@ -0,0 +1,23 @@
+name: Ruff Formatting
+on: [pull_request]
+jobs:
+  ruff:
+    if: ${{ github.actor != 'dependabot[bot]' }} # Do not run on commits created by dependabot
+    runs-on: ubuntu-latest
+    permissions:
+      # Give the default GITHUB_TOKEN write permission to commit and push the changed files.
+      contents: write # Allows reading and writing repository contents (e.g., commits)
+      pull-requests: write # Allows reading and writing pull requests
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ github.sha }}
+          token: ${{ secrets.GITHUB_TOKEN }}
+      - uses: chartboost/ruff-action@v1
+        with:
+          src: './src/teloclip'
+          args: 'format --target-version py310'
+      - uses: stefanzweifel/git-auto-commit-action@v5
+        id: auto-commit-action
+        with:
+          commit_message: 'Style fixes by Ruff'

.gitignore

@@ -1,6 +1,9 @@
 # Package notes
 pkg-mgt/
 
+# Mac stuff
+.DS_Store
+
 # Versioning
 src/teloclip/_version.py
 

.gitpod.Dockerfile

@@ -1,20 +1,19 @@
-# Use the Gitpod base image for Python 3.10
-FROM gitpod/workspace-python-3.12
+# Image source code: https://github.com/axonasif/workspace-images/tree/tmp
+# Also see https://github.com/gitpod-io/workspace-images/issues/1071
+FROM axonasif/workspace-base@sha256:8c057b1d13bdfe8c279c68aef8242d32110c8d5310f9a393f9c0417bc61367d9
 
 # Set user
 USER gitpod
 
 # Install Miniconda
-RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-py311_24.1.2-0-Linux-x86_64.sh -O ~/miniconda.sh && \
     /bin/bash ~/miniconda.sh -b -p $HOME/miniconda && \
     rm ~/miniconda.sh
 
 # Add Miniconda to PATH
 ENV PATH="$HOME/miniconda/bin:$PATH"
 
-ENV PYTHONPATH="$HOME/miniconda/bin"
-
-# Initialize conda in bash config fiiles:
+# Initialize conda in bash config files:
 RUN conda init bash
 
 # Set up Conda channels
@@ -25,5 +24,10 @@ RUN conda config --add channels conda-forge && \
 # Set libmamba as solver
 RUN conda config --set solver libmamba
 
-# Remove the undesired location from PATH
-RUN export PATH=$(echo $PATH | tr ':' '\n' | grep -v '/home/gitpod/.pyenv/shims' | tr '\n' ':')
+# Persist ~/ (HOME) and lib
+RUN echo 'create-overlay $HOME /lib' > "$HOME/.runonce/1-home-lib_persist"
+
+# Referenced in `.vscode/settings.json`
+ENV PYTHON_INTERPRETER="$HOME/miniconda/bin/python"
+# Pycharm recognizes this variables
+ENV PYCHARM_PYTHON_PATH="${PYTHON_INTERPRETER}"

.gitpod.yml

@@ -9,13 +9,8 @@ tasks:
       conda env update -n base --file environment.yml
     # Run on every workspace start
     command: |
-      echo 'Installing requirements.txt'
-      pip3 install -r requirements.txt
       echo 'Installing teloclip in interactive mode.'
-      #pip3 install --upgrade setuptools-scm
-      python setup.py --version
-      pip3 install -e .
-      #python3 -m pip install --upgrade build && python3 -m build
+      pip3 install -e ".[tests]"
       echo 'Finished!'
 
 vscode:
@@ -25,4 +20,3 @@ vscode:
     - ms-toolsai.jupyter
     - ms-toolsai.jupyter-keymap
     - oderwat.indent-rainbow
-    - ms-python.black-formatter

README.md

@@ -10,7 +10,7 @@
 <br clear="left"/>
 
 <p align="center">
-  <img src="https://github.com/Adamtaranto/teloclip/blob/2d9628d453e832ac0de15577c6cdde6835fb6417/docs/teloclip_hexlogo.jpg?raw=true" width="180px" title="teloclip_hex"/>
+<img src="https://raw.githubusercontent.com/Adamtaranto/teloclip/main/docs/teloclip_hexlogo.jpg" width="180" height="180" title="teloclip_hex" />
 </p>
 
 <h1>Teloclip</h1>
@@ -103,7 +103,10 @@ Alternatively, [launch a Gitpod Workspace](https://gitpod.io/#https://github.com
 ## Example Usage
 
 Basic use case:
-![teloclip_example](docs/teloclip_example_graphic.png)
+
+<p align="center">
+<img src="https://raw.githubusercontent.com/Adamtaranto/teloclip/main/docs/teloclip_example_graphic.png" title="teloclip_example" />
+</p>
 
 **First index the reference assembly**
 
@@ -337,6 +340,4 @@ Submit feedback to the [Issue Tracker](https://github.com/Adamtaranto/teloclip/i
 
 ## License
 
-Software provided under MIT license.
-
-Teloclip hex-sticker was designed by [@Super_Coleider](www.instagram.com/Super_Coleider).
+Software provided under MIT license.

environment.yml

@@ -1,9 +1,7 @@
-name: teloclip-dev
+name: teloclip
 channels:
   - conda-forge
   - bioconda
-  - defaults
-  - nanoporetech # Has minimap and samtools for Apple Silicon
 dependencies:
   - python >=3.12
   - minimap2
@@ -15,5 +13,4 @@ dependencies:
       #- regex
       #- pysam
       - pytest
-      - build
-      - twine
+      - hatch