chore: migrate to pyproject.toml

.github/workflows/ci.yml

@@ -9,39 +9,35 @@ jobs:
     strategy:
       matrix:
         python-version:
-          - 3.6
-          - 3.7
-          - 3.8
           - 3.9
 
     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
+        uses: actions/checkout@v4
         with:
           lfs: true
-      - name: Install test dependencies via pip
-        run: pip install -r requirements/test_black.txt
-      - 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
+      - name: Setup conda conda.
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          conda-channels: conda-forge,bioconda
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
         with:
-          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
-          coverage-reports: coverage.xml
-        if: ${{ matrix.python-version == '3.7' && (github.ref == 'refs/heads/main') }}
-      - name: Check style with black
-        run: black --check --line-length 100 .
-        if: ${{ matrix.python-version < '3.9' }}
-      - name: Check style with flake8
-        run: flake8 .
+          # Install a specific version of uv and enable caching.
+          version: "0.5.16"
+          enable-cache: true
+
+      - name: Set up Python
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Run tests
+        run: uv run pytest
+
+      - name: Check formatting
+        run: uv run ruff format --check
+
+      - name: Lint
+        run: uv run ruff check

MANIFEST.in

@@ -2,15 +2,14 @@ include AUTHORS.rst
 include CONTRIBUTING.rst
 include HISTORY.rst
 include LICENSE
-include README.rst
+include README.md
+
+graft src
 
 recursive-include tests requirements *
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 
 recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
 
-include versioneer.py
-recursive-include sodar_cli *.py
-
 include requirements.txt requirements/*.txt

Makefile

@@ -1,37 +1,15 @@
 .PHONY: all
-all: black
+all: format lint pytest
 
-.PHONY: black
-black:
-	black -l 100 .
+.PHONY: format
+format:
+	uv run ruff format .
 
-.PHONY: test
-test:
-	black -l 100 --check .
+.PHONY: lint
+lint:
+	uv run ruff check .
 
 .PHONY: pytest
 pytest:
-	pytest .
+	uv run pytest
 
-.PHONY: lint-all
-lint-all: bandit pyflakes pep257 prospector
-
-.PHONY: bandit
-bandit:
-	bandit -c bandit.yml -r sodar_cli
-
-.PHONY: pyflakes
-pyflakes:
-	pyflakes sodar_cli tests
-
-.PHONY: pep257
-pep257:
-	pep257
-
-.PHONY: flake8
-flake8:
-	flake8
-
-.PHONY: prospector
-prospector:
-	prospector

README.md

@@ -0,0 +1,57 @@
+[![Continuous Integration Status](https://github.com/bihealth/sodar-cli/workflows/CI/badge.svg)](https://github.com/bihealth/sodar-cli/actions)
+
+[![image](https://app.codacy.com/project/badge/Grade/0bf5c6d8a91e4a7380676672e466525d)](https://www.codacy.com/gh/bihealth/sodar-cli/dashboard?utm_source=github.com&utm_medium=referral&utm_content=bihealth/sodar-cli&utm_campaign=Badge_Grade)
+
+[![image](https://app.codacy.com/project/badge/Coverage/0bf5c6d8a91e4a7380676672e466525d)](https://www.codacy.com/gh/bihealth/sodar-cli/dashboard?utm_source=github.com&utm_medium=referral&utm_content=bihealth/sodar-cli&utm_campaign=Badge_Coverage)
+
+[![image](https://coveralls.io/repos/github/bihealth/sodar-cli/badge.svg?branch=main)](https://coveralls.io/github/bihealth/sodar-cli?branch=main)
+
+[![MIT License](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)
+
+# SODAR CLI
+
+Command line interface for [SODAR
+Server](https://github.com/bihealth/sodar-server).
+
+## Getting Started
+
+-   [SODAR Homepage](https://www.cubi.bihealth.org/software/sodar/)
+-   [Manual](https://sodar-server.readthedocs.io/en/latest/)
+
+## SODAR Repositories
+
+[sodar-server](https://github.com/bihealth/sodar-server)
+
+:   SODAR web server for meta and mass data management.
+
+[sodar-taskflow](https://github.com/bihealth/sodar-taskflow)
+
+:   Helper component for running tasks with rollback functionality.
+
+## Installation
+
+``` bash
+$ git clone [email protected]:bihealth/sodar-cli.git
+$ cd sodar-cli
+$ conda create -n sodar-cli python=3.7
+$ conda activate sodar-cli
+$ pip install -e .
+$ cat >~/.sodarrc.toml <<EOF
+[global]
+
+# URL to SODAR server.
+sodar_server_url = "https://sodar.example.com/"
+# API token to use for SODAR API.
+sodar_api_token = "XXX"
+EOF
+```
+
+## Releasing
+
+``` bash
+$ $EDITOR HISTORY.rst
+$ git tag ...
+$ rm -rf dist
+$ python setup.py sdist
+$ twine upload dist/*.tar.gz
+```

docs/conf.py

@@ -55,9 +55,9 @@
 master_doc = "index"
 
 # General information about the project.
-project = u"SODAR CLI"
-copyright = u"2020-2021 CUBI - Core Unit Bioinformatics, Berlin Institute of Health"
-author = u"Manuel Holtgrewe"
+project = "SODAR CLI"
+copyright = "2020-2021 CUBI - Core Unit Bioinformatics, Berlin Institute of Health"
+author = "Manuel Holtgrewe"
 
 # The version info for the project you're documenting, acts as replacement
 # for |version| and |release|, also used in various other places throughout
@@ -133,15 +133,21 @@
 # (source start file, target name, title, author, documentclass
 # [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, "sodar_cli.tex", u"SODAR CLI Documentation", u"Core Unit Bioinformatics", "manual")
+    (
+        master_doc,
+        "sodar_cli.tex",
+        "SODAR CLI Documentation",
+        "Core Unit Bioinformatics",
+        "manual",
+    )
 ]
 
 
 # -- Options for manual page output ------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "sodar_cli", u"SODAR CLI Documentation", [author], 1)]
+man_pages = [(master_doc, "sodar_cli", "SODAR CLI Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------
@@ -153,7 +159,7 @@
     (
         master_doc,
         "sodar_cli",
-        u"SODAR CLI Documentation",
+        "SODAR CLI Documentation",
         author,
         "sodar_cli",
         "One line description of project.",