ci: move to conventional commits & release-please (#157)

.github/workflows/conventional-prs.yml

@@ -0,0 +1,18 @@
+name: PR
+on:
+  pull_request_target:
+    types:
+      - opened
+      - reopened
+      - edited
+      - synchronize
+
+jobs:
+  title-format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          validateSingleCommit: true

.github/workflows/main.yml

@@ -0,0 +1,91 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches_ignore: []
+
+jobs:
+  cancel-previous:
+    runs-on: ubuntu-latest
+    if: github.ref != 'refs/heads/main'
+    steps:
+      - uses: khan/[email protected]
+        with:
+          workflows: "main.yml"
+        env:
+          GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
+
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+
+      - name: Install Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.8"
+
+      - name: Install dependencies
+        run: |
+            pip install -r requirements/test_black.txt
+            pip freeze
+
+      - name: Run linting tools
+        run: |
+          make lint
+
+      - name: Comment PR
+        if: github.event_name == 'pull_request' && failure()
+        uses: marocchino/[email protected]
+        with:
+          message: 'Please format your code with [black](https://black.readthedocs.io): `make black`.'
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  testing:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version:
+          - '3.8'
+          - '3.9'
+          - '3.10'
+    needs: linting
+    steps:
+      - name: Install Python via conda
+        uses: s-weigand/setup-conda@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+          conda-channels: defaults,bioconda,conda-forge
+
+      - name: Checkout repository
+        uses: actions/checkout@v2
+        with:
+          lfs: true
+
+      - name: Install mamba
+        run: conda install -y mamba==0.27.0
+
+      - name: Prepare environment.yaml file
+        run: >
+          cp environment.yaml /tmp/environment.yaml && sed -i -e
+          's/- python/- python=${{ matrix.python-version }}/'
+          /tmp/environment.yaml
+
+      - name: Update environment using mamba
+        run: mamba env update --name root --file /tmp/environment.yaml
+
+      - name: Save time by installing packages via mamba.
+        run: mamba install -y pysam
+
+      - name: Install dependencies
+        run: |
+            pip install -r requirements/test_black.txt
+            pip freeze
+
+      - name: Run tests
+        run: pytest
+
+      - uses: codecov/codecov-action@v3

.github/workflows/release-please.yml

@@ -0,0 +1,41 @@
+on:
+  push:
+    branches:
+      - main
+
+name: release-please
+
+jobs:
+  release-please:
+    runs-on: ubuntu-latest
+    steps:
+
+      - uses: GoogleCloudPlatform/release-please-action@v2
+        id: release
+        with:
+          release-type: python
+          package-name: cubi-tk
+
+      - uses: actions/checkout@v2
+        if: ${{ steps.release.outputs.release_created }}
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        if: ${{ steps.release.outputs.release_created }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.x'
+
+      - name: Build package
+        if: ${{ steps.release.outputs.release_created }}
+        run: |
+          python -m pip install --upgrade pip
+          python setup.py sdist
+
+      - name: Publish to PyPI
+        if: ${{ steps.release.outputs.release_created }}
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}

CHANGELOG.md

@@ -0,0 +1 @@
+# Changelog

MANIFEST.in

@@ -1,6 +1,6 @@
 include AUTHORS.rst
 include CONTRIBUTING.rst
-include HISTORY.md
+include CHANGELOG.md
 include LICENSE
 include README.md
 

Makefile

@@ -5,29 +5,31 @@ all: black
 black:
 	black -l 100 .
 
-.PHONY: test
-test:
+.PHONY: black-check
+black-check:
 	black -l 100 --check .
 
-.PHONY: pytest
-pytest:
-	pytest .
-
-.PHONY: lint-all
-lint-all: bandit pyflakes pep257
-
-.PHONY: bandit
-bandit:
-	bandit -c bandit.yml -r cubi_tk
-
-.PHONY: pyflakes
-pyflakes:
-	pyflakes cubi_tk tests
+.PHONY: isort
+isort:
+	isort --force-sort-within-sections --profile=black .
 
-.PHONY: pep257
-pep257:
-	pep257
+.PHONY: isort-check
+isort-check:
+	isort --force-sort-within-sections --profile=black --check .
 
 .PHONY: flake8
 flake8:
 	flake8
+
+# .PHONY: mypy
+# mypy: export MYPYPATH=stubs
+# mypy:
+# 	mypy clinvar_this clinvar_api tests
+
+.PHONY: lint
+lint: flake8 isort-check black-check
+# lint: flake8 isort-check black-check mypy
+
+.PHONY: pytest
+pytest:
+	pytest .

README.md

@@ -1,8 +1,4 @@
-![Continuous Integration Status](https://github.com/bihealth/cubi-tk/workflows/CI/badge.svg)
-[![Codacy Badge](https://app.codacy.com/project/badge/Grade/71dd0ea53e444cd0949a00a7025face7)](https://www.codacy.com/gh/bihealth/cubi-tk/dashboard?utm_source=github.com&utm_medium=referral&utm_content=bihealth/cubi-tk&utm_campaign=Badge_Grade)
-[![Codacy Badge](https://app.codacy.com/project/badge/Coverage/71dd0ea53e444cd0949a00a7025face7)](https://www.codacy.com/gh/bihealth/cubi-tk/dashboard?utm_source=github.com&utm_medium=referral&utm_content=bihealth/cubi-tk&utm_campaign=Badge_Coverage)
-[![Coveralls Status](https://coveralls.io/repos/github/bihealth/cubi-tk/badge.svg?branch=master)](https://coveralls.io/github/bihealth/cubi-tk?branch=master)
-[![Documentation Status](https://readthedocs.org/projects/cubi-tk/badge/?version=latest)](https://cubi-tk.readthedocs.io/en/latest/?badge=latest)
+[![CI](https://github.com/bihealth/cubi-tk/actions/workflows/main.yml/badge.svg)](https://github.com/bihealth/cubi-tk/actions/workflows/main.yml)
 [![MIT License](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)
 
 # CUBI Toolkit

cubi_tk/__main__.py

@@ -3,31 +3,32 @@
 
 import argparse
 import logging
+import os
 import sys
 
 import argcomplete
 import logzero
-import os
 from logzero import logger
 
 from cubi_tk import __version__
+
+from .archive import run as run_archive
+from .archive import setup_argparse as setup_argparse_archive
 from .common import run_nocmd
+from .irods import run as run_irods
+from .irods import setup_argparse as setup_argparse_irods
 from .isa_tab import run as run_isa_tab
 from .isa_tab import setup_argparse as setup_argparse_isa_tab
 from .isa_tpl import run as run_isa_tpl
 from .isa_tpl import setup_argparse as setup_argparse_isa_tpl
-from .snappy import run as run_snappy
-from .snappy import setup_argparse as setup_argparse_snappy
-from .sodar import run as run_sodar
-from .sodar import setup_argparse as setup_argparse_sodar
-from .irods import run as run_irods
-from .irods import setup_argparse as setup_argparse_irods
 from .org_raw import run as run_org_raw
 from .org_raw import setup_argparse as setup_argparse_org_raw
 from .sea_snap import run as run_sea_snap
 from .sea_snap import setup_argparse as setup_argparse_sea_snap
-from .archive import run as run_archive
-from .archive import setup_argparse as setup_argparse_archive
+from .snappy import run as run_snappy
+from .snappy import setup_argparse as setup_argparse_snappy
+from .sodar import run as run_sodar
+from .sodar import setup_argparse as setup_argparse_sodar
 
 
 def setup_argparse_only():  # pragma: nocover

cubi_tk/archive/common.py

@@ -1,14 +1,14 @@
 """``cubi-tk archive``: common features"""
 
 import argparse
-import attr
 import json
 import os
+from pathlib import Path
 import subprocess
 import sys
 import typing
 
-from pathlib import Path
+import attr
 
 
 @attr.s(frozen=True, auto_attribs=True)