Merge branch 'master' into factor_value_lists

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,30 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Load Altamisa in Python or use via the CLI.
+2. Run this code '...'
+3. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Output**
+Provide console output to help explain your problem.
+
+**System information (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Python version
+
+**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: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. E. g.: 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 about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,12 @@
+<!--
+
+NOTE: In most cases, you should create an issue first, and only then
+a pull request. Please see the contribution guidelines for
+further information. In particular related to conventional
+commit messages.
+
+The title should have the following format:
+
+  <type>: description (#<issue>)
+
+-->

.github/workflows/ci.yml

@@ -13,36 +13,34 @@ jobs:
           - '3.9'
           - '3.10'
           - '3.11'
+          - '3.12'
 
     steps:
-      - name: Install Python via conda.
-        uses: s-weigand/setup-conda@v1
+      - name: Install Python
+        uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
-          conda-channels: defaults,bioconda,conda-forge
+          python-version: "${{ matrix.python-version }}"
+
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           lfs: true
-      - name: Install mamba.
-        run: conda install -y mamba
+
       - name: Install test dependencies via pip
         run: pip install -r requirements/test_black.txt
+
+      - name: Lint
+        run: make lint
+
       - name: Run tests
-        run: pytest
-      - name: Create text report
-        run: coverage report
-      - name: Create XML report for codacy
-        run: coverage xml
-      - name: Coveralls
-        uses: AndreMiras/coveralls-python-action@develop
-      - name: Run codacy-coverage-reporter
-        uses: codacy/codacy-coverage-reporter-action@master
+        run: |
+          make test
+          coverage report
+          coverage xml
+
+      - name: Upload Python coverage reports to Codecov
+        uses: codecov/codecov-action@v3
         with:
-          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
-          coverage-reports: coverage.xml
-        if: ${{ matrix.python-version == '3.7' }}
-      - name: Check style with black
-        run: make black-check
-      - name: Check style with flake8
-        run: flake8 .
+          flags: python
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.readthedocs.yaml

@@ -0,0 +1,22 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# We recommend specifying your dependencies to enable reproducible builds:
+# https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+  - requirements: requirements/develop.txt

CODEOWNERS

@@ -0,0 +1 @@
+*            @sellth @mkuhring @holtgrewe

MANIFEST.in

@@ -11,6 +11,7 @@ recursive-exclude * *.py[co]
 recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
 
 include versioneer.py
-include vcfpy/_version.py
+include altamisa/_version.py
+include altamisa/py.typed
 
 include requirements.txt requirements/*.txt

Makefile

@@ -1,21 +1,59 @@
-.PHONY: default black flake8 test test-v test-vv
+.PHONY: default
+default: help
 
-default: black flake8
+.PHONY: help
+help:
+	@echo "make help         - show this help"
+	@echo "make lint         - run all linting"
+	@echo "make format       - run all formatting"
+	@echo "make lint-isort   - run isort linting"
+	@echo "make format-isort - run isort formatting"
+	@echo "make lint-black   - run black linting"
+	@echo "make format-black - run black formatting"
+	@echo "make lint-flake8  - run flake8 linting"
+	@echo "make lint-pyright - run pyright linting"
+	@echo "make test         - run all tests"
+	@echo "make test-v       - run all tests with verbose output"
+	@echo "make test-vv      - run all tests with very verbose output"
 
-black:
-	black -l 100 --exclude "versioneer.py|_version.py" .
+.PHONY: lint
+lint: lint-isort lint-black lint-flake8 lint-pyright
+
+.PHONY: format
+format: format-isort format-black
+
+.PHONY: lint-isort
+lint-isort:
+	isort --check-only --diff --force-sort-within-sections --profile=black .
+
+.PHONY: format-isort
+format-isort:
+	isort --force-sort-within-sections --profile=black .
 
-black-check:
+.PHONY: lint-black
+lint-black:
 	black -l 100 --exclude "versioneer.py|_version.py" --check .
 
-flake8:
+.PHONY: format-black
+format-black:
+	black -l 100 --exclude "versioneer.py|_version.py" .
+
+.PHONY: lint-flake8
+lint-flake8:
 	flake8 .
 
+.PHONY: lint-pyright
+lint-pyright:
+	pyright
+
+.PHONY: test
 test:
 	pytest
 
+.PHONY: test-v
 test-v:
 	pytest -v
 
+.PHONY: test-vv
 test-vv:
 	pytest -vv

README.md

@@ -1,9 +1,7 @@
 [![PyPI version](https://badge.fury.io/py/altamisa.svg)](https://badge.fury.io/py/altamisa)
+[![codecov](https://codecov.io/gh/bihealth/altamisa/graph/badge.svg?token=R5GXUKCUYJ)](https://codecov.io/gh/bihealth/altamisa)
 [![Install with Bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io)
 ![Continuous Integration Status](https://github.com/bihealth/altamisa/workflows/CI/badge.svg)
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/a853a56253604aa7ab87d2bcdcd9da51)](https://www.codacy.com/app/bihealth/altamisa?utm_source=github.com&utm_medium=referral&utm_content=bihealth/altamisa&utm_campaign=Badge_Grade)
-[![Coverage Badge](https://api.codacy.com/project/badge/Coverage/a853a56253604aa7ab87d2bcdcd9da51)](https://www.codacy.com/app/bihealth/altamisa?utm_source=github.com&utm_medium=referral&utm_content=bihealth/altamisa&utm_campaign=Badge_Coverage)
-[![Coverage Status](https://coveralls.io/repos/github/bihealth/altamisa/badge.svg?branch=master)](https://coveralls.io/github/bihealth/altamisa?branch=master)
 [![Documentation Status](https://readthedocs.org/projects/altamisa/badge/?version=latest)](https://altamisa.readthedocs.io/en/latest/?badge=latest)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.01610/status.svg)](https://doi.org/10.21105/joss.01610)
 [![MIT License](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)

altamisa/_version.py

@@ -12,12 +12,12 @@
 """Git implementation of _version.py."""
 
 import errno
+import functools
 import os
 import re
 import subprocess
 import sys
 from typing import Any, Callable, Dict, List, Optional, Tuple
-import functools
 
 
 def get_keywords() -> Dict[str, str]: