Add uv support with pyproject.toml

- Create pyproject.toml with all dependencies from requirements.txt
- Configure for Python >=3.11
- Include standalone scripts via script-files
- Set README.org content-type for proper packaging
- Enable uv sync and uv run workflows

client/qldbtools/bin/mc-db-populate-minio

@@ -3,6 +3,13 @@
     mc-db-refine-info) and push the databases it lists to the mrvacommander minio
     DB.
 """
+# /// script
+# dependencies = [
+#   "pandas",
+#   "numpy",
+#   "minio",
+# ]
+# ///
 import argparse
 import qldbtools.utils as utils
 import logging

client/qldbtools/pyproject.toml

@@ -0,0 +1,138 @@
+[project]
+name = "qldbtools"
+version = "0.1.0"
+description = "A Python package for selecting sets of CodeQL databases to work on"
+authors = [
+    {name = "Michael Hohn", email = "hohn@github.com"}
+]
+readme = {file = "README.org", content-type = "text/plain"}
+requires-python = ">=3.11"
+dependencies = [
+    "annotated-types>=0.7.0",
+    "anyio>=4.4.0",
+    "appnope>=0.1.4",
+    "argon2-cffi>=23.1.0",
+    "argon2-cffi-bindings>=21.2.0",
+    "arrow>=1.3.0",
+    "asttokens>=2.4.1",
+    "async-lru>=2.0.4",
+    "attrs>=24.2.0",
+    "babel>=2.16.0",
+    "beautifulsoup4>=4.12.3",
+    "bleach>=6.1.0",
+    "blinker>=1.9.0",
+    "certifi>=2024.7.4",
+    "cffi>=1.17.0",
+    "charset-normalizer>=3.3.2",
+    "click>=8.1.7",
+    "comm>=0.2.2",
+    "debugpy>=1.8.5",
+    "decorator>=5.1.1",
+    "defusedxml>=0.7.1",
+    "executing>=2.0.1",
+    "fastapi>=0.115.5",
+    "fastjsonschema>=2.20.0",
+    "flask>=3.1.0",
+    "fqdn>=1.5.1",
+    "h11>=0.14.0",
+    "httpcore>=1.0.5",
+    "httpx>=0.27.0",
+    "idna>=3.7",
+    "ipykernel>=6.29.5",
+    "ipython>=8.26.0",
+    "isoduration>=20.11.0",
+    "itsdangerous>=2.2.0",
+    "jedi>=0.19.1",
+    "jinja2>=3.1.4",
+    "json5>=0.9.25",
+    "jsonpointer>=3.0.0",
+    "jsonschema>=4.23.0",
+    "jsonschema-specifications>=2023.12.1",
+    "jupyter-events>=0.10.0",
+    "jupyter-lsp>=2.2.5",
+    "jupyter-client>=8.6.2",
+    "jupyter-core>=5.7.2",
+    "jupyter-server>=2.14.2",
+    "jupyter-server-terminals>=0.5.3",
+    "jupyterlab>=4.2.4",
+    "jupyterlab-pygments>=0.3.0",
+    "jupyterlab-server>=2.27.3",
+    "lckr-jupyterlab-variableinspector",
+    "markupsafe>=2.1.5",
+    "matplotlib-inline>=0.1.7",
+    "minio==7.2.8",
+    "mistune>=3.0.2",
+    "nbclient>=0.10.0",
+    "nbconvert>=7.16.4",
+    "nbformat>=5.10.4",
+    "nest-asyncio>=1.6.0",
+    "notebook-shim>=0.2.4",
+    "numpy>=2.1.0",
+    "overrides>=7.7.0",
+    "packaging>=24.1",
+    "pandas>=2.2.2",
+    "pandocfilters>=1.5.1",
+    "parso>=0.8.4",
+    "pexpect>=4.9.0",
+    "platformdirs>=4.2.2",
+    "plumbum>=1.9.0",
+    "prometheus-client>=0.20.0",
+    "prompt-toolkit>=3.0.47",
+    "psutil>=6.0.0",
+    "ptyprocess>=0.7.0",
+    "pure-eval>=0.2.3",
+    "pycparser>=2.22",
+    "pycryptodome>=3.20.0",
+    "pydantic>=2.10.2",
+    "pydantic-core>=2.27.1",
+    "pygments>=2.18.0",
+    "python-dateutil>=2.9.0.post0",
+    "python-json-logger>=2.0.7",
+    "pytz>=2024.1",
+    "pyyaml>=6.0.2",
+    "pyzmq>=26.1.1",
+    "referencing>=0.35.1",
+    "requests>=2.32.3",
+    "rfc3339-validator>=0.1.4",
+    "rfc3986-validator>=0.1.1",
+    "rpds-py>=0.20.0",
+    "send2trash>=1.8.3",
+    "six>=1.16.0",
+    "sniffio>=1.3.1",
+    "soupsieve>=2.6",
+    "stack-data>=0.6.3",
+    "starlette>=0.41.3",
+    "terminado>=0.18.1",
+    "tinycss2>=1.3.0",
+    "tornado>=6.4.1",
+    "traitlets>=5.14.3",
+    "types-python-dateutil>=2.9.0.20240821",
+    "typing-extensions>=4.12.2",
+    "tzdata>=2024.1",
+    "uri-template>=1.3.0",
+    "urllib3>=2.2.2",
+    "uvicorn>=0.32.1",
+    "wcwidth>=0.2.13",
+    "webcolors>=24.8.0",
+    "webencodings>=0.5.1",
+    "websocket-client>=1.8.0",
+    "werkzeug>=3.1.3",
+]
+
+[build-system]
+requires = ["setuptools>=75.5.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+packages = ["qldbtools"]
+script-files = [
+    "bin/mc-db-generate-selection",
+    "bin/mc-db-initial-info",
+    "bin/mc-db-populate-minio",
+    "bin/mc-db-refine-info",
+    "bin/mc-db-unique",
+    "bin/mc-db-view-info",
+    "bin/mc-hepc-init",
+    "bin/mc-hepc-serve",
+    "bin/mc-rows-from-mrva-list",
+]