Migrate hatch (#13)

* Use pyproject.toml

* dev env yml

* bump version

* placeholder test

* Init actions

* use scm versioning

* ruff format

* remove rU and remove .ix

* Add blast

* Style fixes by Ruff

---------

Co-authored-by: Adamtaranto <[email protected]>

.github/workflows/publish.yml

@@ -0,0 +1,34 @@
+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@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      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.TIRMITE_PYPI_TOKEN }}
+      run: hatch publish

.github/workflows/pytest.yml

@@ -0,0 +1,35 @@
+
+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"]  # Test with Python 3.8 to the latest available version
+
+    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 Python based on the matrix version
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # Install dependencies, including test dependencies from pyproject.toml
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install '.[tests]'  # Install all dependencies, including test-specific ones
+
+      # Run pytest on the specified directory
+      - name: Run tests
+        run: pytest tests

.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/tirmite'
+          args: 'format --target-version py310'
+      - uses: stefanzweifel/git-auto-commit-action@v5
+        id: auto-commit-action
+        with:
+          commit_message: 'Style fixes by Ruff'

README.md

@@ -65,7 +65,7 @@ Three classes of output are produced:
 
 ### Installing TIRmite
 
-TIRmite requires Python >= v3.6
+TIRmite requires Python >= v3.8
 
 Dependencies:  
   - TIR-pHMM build and search

environment.yml

@@ -0,0 +1,15 @@
+name: tirmite
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python 3.12
+  - "pymummer>=0.10.3"
+  - hmmer
+  - blast
+  - pip
+  - pip:
+      - "biopython>=1.70"
+      - "pandas>=0.20.3"
+      - hatch
+      - pytest

pyproject.toml

@@ -0,0 +1,56 @@
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[project]
+name = "tirmite"
+description = "Map TIR-pHMM models to genomic sequences for annotation of MITES and complete DNA-Transposons."
+readme = "README.md"
+requires-python = ">=3.8"
+license = { text = "MIT" }
+authors = [
+    { name = "Adam Taranto", email = "[email protected]" }
+]
+
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "License :: OSI Approved :: MIT License",
+]
+
+dependencies = ["pandas>=0.20.3", 'biopython>=1.70', "pymummer>=0.10.3",]
+
+dynamic = ["version"]
+
+[project.urls]
+homepage = "https://github.com/adamtaranto/TIRmite"
+documentation = "https://github.com/adamtaranto/TIRmite"
+repository = "https://github.com/adamtaranto/TIRmite"
+
+[project.scripts]
+tirmite="tirmite.cmd_tirmite:main"
+tsplit-LTR="tirmite.cmd_LTR:main"
+tsplit-TIR="tirmite.cmd_TIR:main"
+
+[tool.hatch.build]
+source = "src"
+
+exclude = [
+    "environment.yml",
+    ".github",
+    ".vscode",
+]
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.version.vcs]
+tag-pattern = "v*"  # Git tags starting with 'v' will be used for versioning
+fallback-version = "0.0.0"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "src/tirmite/_version.py"
+
+[project.optional-dependencies]
+tests = ["pytest"]