WIP: Packageify & Migrate to Py3

.github/workflows/pytest.yml

@@ -0,0 +1,37 @@
+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"]
+
+    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 }}
+
+      # Install any additional dependencies not included in the pyproject.toml file
+      - name: Install additional dependencies
+        run: |
+          pip install '.[tests]'  # Install all dependencies, including test-specific ones
+        shell: bash -l {0}
+
+      # Run pytest on the specified directory
+      - name: Run tests
+        run: |
+          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/flexidot'
+          args: 'format --target-version py310'
+      - uses: stefanzweifel/git-auto-commit-action@v5
+        id: auto-commit-action
+        with:
+          commit_message: 'Style fixes by Ruff'

.gitignore

@@ -0,0 +1,70 @@
+# Mac stuff
+.DS_Store
+
+# Versioning
+src/flexidot/_version.py
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# mypy
+.mypy_cache/

code/README.md → CHANGELOG.md

@@ -1,6 +1,39 @@
 # FlexiDot version changes
 
-![alt text](https://github.com/molbio-dresden/flexidot/blob/master/images/Selfdotplots_banner4.png "FlexiDot self dotplots")
+![alt text](https://github.com/molbio-dresden/flexidot/blob/master/docs/images/Selfdotplots_banner4.png "FlexiDot self dotplots")
+
+## Version 2.0.0
+*Jan 2025*
+
+This release is a major refactor of the Flexidot codebase that migrates to Python 3 and a modern package structure.
+
+**[Faster run time]:**  
+- When comparing a sequence to an identical sequence `find_match_pos_diag()` will recycle kmer counts from the first seq. Saves 33% runtime.
+
+**[New features]:**
+
+- Flexidot and its dependancies are now pip installable - uses Hatch and pyproject.toml
+- Versioning is now managed dynamically using git tags
+- Some basic tests for the core `find_match_pos_diag()` function have been added
+- cmd line options are now managed with argparse
+- Repo includes env yaml to set up conda env for flexidot
+- Check that input files exist
+- Auto cleanup temp files
+- Add action to run pytests
+- Add action to format code with Rust
+- Uses logging module to manage status logging (removed time logging)
+
+**[Changed defaults]:**
+- Several cmd line options have been renamed or have changes to their expected input formatting. See --help.
+- If not using the `--wobble_conversion` option then kmers containing any Ns will be skipped by default.
+- If `--wobble_conversion` is set then `--max_n` determines the max percentage of Ns that will be tolerated in a kmer. Default changed to 10% from hard coded 49%.
+
+**[Bugfixes]:**  
+- Fix depreciation issue with numpy creating an ndarray from ragged nested sequences in `find_match_pos_diag()` Closes issue #15
+- Read files with r instead of rb
+- Fix unicode issue referenced in #10
+
+<br>
 
 ## Version 1.06
 *14.04.2019*