Merge branch 'develop' into main

.github/workflows/create-release-and-deploy.yml

@@ -0,0 +1,39 @@
+name: Create release and deploy
+run-name: ${{ github.actor }} is releasing ${{ github.ref }}
+on: 
+  push:
+    tags:
+      - "v.*"
+
+permissions:
+  contents: write
+
+jobs: 
+  build-sqlite-db:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build SQLite DB
+        run: cat flumut_db.sql | sqlite3 src/flumut_db_data/flumut_db.sqlite
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.x'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build
+
+      - name: Create release
+        uses: softprops/action-gh-release@v2
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          files: 
+            src/flumut_db_data/flumut_db.sqlite
+            dist/*
+
+

.gitignore

@@ -0,0 +1,165 @@
+# FluMutDB specific
+flumut_db_data
+
+# 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/
+share/python-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/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

README.md

@@ -1,3 +1,3 @@
 # FluMutDb
 
-THis repository contains the database for FluMut
+This repository contains the database for FluMut

pyproject.toml

@@ -0,0 +1,41 @@
+[build-system]
+requires = ["setuptools>=61.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "flumut_db"
+description = "Utility module for FluMut database"
+requires-python = ">=3.7"
+dependencies = [
+    "importlib-resources >= 1.3",
+]
+authors = [
+    {name = "Edoardo Giussani", email = "[email protected]"},
+    {name = "Alessandro Sartori", email = "[email protected]"},
+]
+dynamic = ["version"]
+
+[project.readme]
+file = "README.md"
+content-type = "text/markdown"
+
+[project.license]
+file = "LICENSE"
+content-type = "text-markdown"
+
+[project.urls]
+Home-page = "https://github.com/izsvenezie-virology/FluMutDb"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+namespaces = true
+
+[tool.setuptools.package-data]
+flumut_db_data = ["flumut_db.sqlite"]
+
+[tool.setuptools.dynamic]
+version = {file= ["version.txt"]}

src/flumut_db.py

@@ -0,0 +1,19 @@
+import sqlite3
+from urllib.request import urlretrieve
+from importlib_resources import files
+
+_DB_FILE = files('flumut_db_data').joinpath('flumut_db.sqlite')
+
+def get_db_file() -> str:
+    return _DB_FILE
+
+def update_db_file():
+    url = 'https://github.com/izsvenezie-virology/FluMutDB/releases/latest/download/FluMutDB.sqlite3'
+    _ = urlretrieve(url, _DB_FILE)
+
+def get_db_version():
+    connection = sqlite3.connect(_DB_FILE)
+    cursor = connection.cursor()
+    major, minor, date = cursor.execute('SELECT * FROM db_version').fetchone()
+    connection.close()
+    return major, minor, date

version.txt

@@ -0,0 +1 @@
+5.0