Project restructure WIP

.github/workflows/test.yml

@@ -0,0 +1,24 @@
+name: Testing
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8, 3.9, "3.10"]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Dependencies
+        run: |
+          pip install .[test]
+      - name: 🧪 - Testing
+        run: |
+          pytest -v

.gitignore

@@ -1 +1,82 @@
 cluster_uploader_wrapper.py
+
+#IntelliJ project structure files
+*.iml
+*.xml
+.idea/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.pytest_cache/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Rope project settings
+.ropeproject
+
+# VSCode
+.vscode/
+
+# Ruff
+.ruff_cache/

.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort (python)
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.286
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix, --show-fixes]

LICENSE.md

@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright 2017-2022 EMBL-EBI
+   Copyright 2017-2024 EMBL-EBI
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

genomeuploader/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.0.1" # TODO: pin the correct version