pythoncharmers-meta 0.6.0__tar.gz → 0.6.1__tar.gz

{pythoncharmers_meta-0.6.0 → pythoncharmers_meta-0.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pythoncharmers-meta
-Version: 0.6.0
+Version: 0.6.1
 Summary: Meta package with dependencies for Python Charmers training courses
 License-File: LICENSE
 Requires-Python: >=3.10
@@ -68,6 +68,13 @@ Requires-Dist: streamlit>=1.45.0; extra == 'analytics'
 Requires-Dist: tables>=3.10.1; extra == 'analytics'
 Requires-Dist: textblob>=0.19.0; extra == 'analytics'
 Requires-Dist: textdistance[levenshtein]>=4.6.3; extra == 'analytics'
+Provides-Extra: bio
+Requires-Dist: anndata>=0.11.4; extra == 'bio'
+Requires-Dist: biopython>=1.85; extra == 'bio'
+Requires-Dist: paramiko>=3.5.1; extra == 'bio'
+Requires-Dist: pooch>=1.8.2; extra == 'bio'
+Requires-Dist: scanpy>=1.11.2; extra == 'bio'
+Requires-Dist: tqdm>=4.67.1; extra == 'bio'
 Provides-Extra: db
 Requires-Dist: duckdb>=1.1.3; extra == 'db'
 Requires-Dist: ibis-framework[duckdb,polars,sqlite]>=10.5.0; extra == 'db'

{pythoncharmers_meta-0.6.0 → pythoncharmers_meta-0.6.1}/pyproject.toml

@@ -1,199 +1,197 @@
 [project]
 name = "pythoncharmers-meta"
-version = "0.6.0"
+version = "0.6.1"
 description = "Meta package with dependencies for Python Charmers training courses"
 readme = "README.md"
 requires-python = ">=3.10"
 dependencies = [
+    "black>=24.8.0",
+    "diskcache>=5.6.3",
+    "humanize>=4.10.0",
+    "hvplot>=0.10.0",
     "ipython>=8.12.3",
-    "polars[excel,graph,numpy,plot,pyarrow,pydantic,style,timezone]>=1.29.0",
+    "isort>=5.13.2",
+    "keyring>=25.4.1",
+    "keyrings-cryptfile>=1.3.9",
+    "llm>=0.26",
+    "loguru>=0.7.2",
+    "logzero>=1.7.0",
+    "lxml>=5.3.0",
     "matplotlib>=3.9.2",
-    "plotly>=5.24.0,!=6.0.*",
-    "pandas[aws,compression,computation,consortium-standard,excel,feather,fss,hdf5,html,output-formatting,parquet,plot,sql-other,xml]>=2.2.3",
-    "numexpr>=2.10.1",
+    "more-itertools>=10.6.0",
     "mypy>=1.11.2",
-    "loguru>=0.7.2",
-    "psutil>=6.0.0",
-    "streamlit>=1.45.0",
-    "schedule>=1.2.2",
-    "requests>=2.32.3",
-    "hvplot>=0.10.0",
-    # Numba requires NumPy 2.1 or less:
+    "natural>=0.2.0",
+    "nbformat>=5.10.4",
+    "numba>=0.61.2",
+    "numexpr>=2.10.1",
     "numpy<2.3.0",
-    "black>=24.8.0",
-    "isort>=5.13.2",
-    "toolz>=0.12.1",
-    "logzero>=1.7.0",
-    # "sqlalchemy>=2.0.35",
     "openpyxl>=3.1.5",
-    "natural>=0.2.0",
+    "pandas[aws,compression,computation,consortium-standard,excel,feather,fss,hdf5,html,output-formatting,parquet,plot,sql-other,xml]>=2.2.3",
     "parse>=1.20.2",
-    "humanize>=4.10.0",
-    "keyrings-cryptfile>=1.3.9",
-    "keyring>=25.4.1",
-    "diskcache>=5.6.3",
-    "lxml>=5.3.0",
+    "plotly>=5.24.0,!=6.0.*",
+    "polars[excel,graph,numpy,plot,pyarrow,pydantic,style,timezone]>=1.29.0",
+    "psutil>=6.0.0",
     "pydantic>=2.9.2",
     "pytest>=8.3.5",
-    "more-itertools>=10.6.0",
-    "ruff>=0.11.1",
+    "requests>=2.32.3",
     "rich>=13.9.4",
+    "ruff>=0.11.1",
+    "schedule>=1.2.2",
+    "streamlit>=1.45.0",
+    "toolz>=0.12.1",
     "tqdm>=4.67.1",
-    "numba>=0.61.2",
-    "llm>=0.26",
-    "nbformat>=5.10.4",
+    # "sqlalchemy>=2.0.35",
 ]
 
 [project.optional-dependencies]
 gis = [
-    "rasterio>=1.3.11",
-    "xarray>=2024.9.0",
-    "geopandas>=1.0.1",
-    "folium>=0.17.0",
-    "shapely>=2.0.6",
-    "datashader>=0.16.3",
-    "fiona>=1.10.0",
     "cartopy>=0.23.0",
-    "pyproj>=3.6.1",
-    "pysal>=24.7",
-    "rioxarray>=0.17.0",
-    "scikit-image>=0.24.0",
-    "netcdf4>=1.7.1.post2",
-    "networkx>=3.3",
+    "cftime>=1.6.4",
+    "contextily>=1.6.2",
     "dask-image>=2024.5.3",
+    "datashader>=0.16.3",
+    "descartes>=1.1.0",
+    "fiona>=1.10.0",
+    "folium>=0.17.0",
+    "geoalchemy>=0.7.2",
+    "geopandas>=1.0.1",
+    "geopy>=2.4.1",
     "graphviz>=0.20.3",
-    "zarr>=2.18.3",
     "h5netcdf>=1.3.0",
-    "pydap>=3.5",
-    "scipy>=1.15",
-    "cftime>=1.6.4",
     "iris>=1.0.7",
+    "netcdf4>=1.7.1.post2",
+    "networkx>=3.3",
     "pint>=0.24.3",
     "psycopg2-binary>=2.9.10",
-    "geoalchemy>=0.7.2",
-    "geopy>=2.4.1",
-    "contextily>=1.6.2",
-    "descartes>=1.1.0",
     "pydantic-geojson>=0.2.0",
+    "pydap>=3.5",
+    "pyproj>=3.6.1",
+    "pysal>=24.7",
+    "rasterio>=1.3.11",
+    "rioxarray>=0.17.0",
+    "scikit-image>=0.24.0",
+    "scipy>=1.15",
+    "shapely>=2.0.6",
+    "xarray>=2024.9.0",
+    "zarr>=2.18.3",
 ]
 ml = [
-    "scikit-learn>=1.6.1",
-    "yellowbrick>=1.5",
-    "xgboost>=2.1.1",
     "eli5>=0.15.0",
+    "joblib>=1.4.2",
     "pyod>=2.0.5",
-    "textdistance[Levenshtein]>=4.6.3",
+    "scikit-learn>=1.6.1",
     "skorch>=1.0.0",
-    "joblib>=1.4.2",
+    "textdistance[Levenshtein]>=4.6.3",
+    "xgboost>=2.1.1",
+    "yellowbrick>=1.5",
 ]
 web = [
-    "flask>=3.0.3",
-    "httpx>=0.27.2",
-    "fastapi>=0.115.8",
     "alembic>=1.13.2",
-    "django>=5.1.1",
+    "beautifulsoup4>=4.13.3",
     "cryptography>=43.0.0",
+    "django>=5.1.1",
+    "fastapi>=0.115.8",
+    "flask>=3.0.3",
+    "httpx>=0.27.2",
+    "jinja2>=3.1.5",
     "passlib>=1.7.4",
-    "sqlalchemy>=2.0.35",
     "scrapy>=2.12.0",
-    "beautifulsoup4>=4.13.3",
-    "jinja2>=3.1.5",
+    "sqlalchemy>=2.0.35",
 ]
 analytics = [
-    "duckdb>=1.1.3",
-    "ibis-framework[duckdb,polars,sqlite]>=10.5.0",
-    "pandas[aws,compression,computation,consortium-standard,excel,feather,fss,hdf5,html,output-formatting,parquet,plot,spss,sql-other,xml]>=2.2.3",
-    # "sqlalchemy[asyncio]>=2.0.35",
-    "numba>=0.61.0",
-    "matplotlib>=3.9.2",
-    "scipy>=1.15.2",
-    "statsmodels>=0.14.4",
-    "seaborn>=0.13.2",
-    "fastexcel>=0.12.1",
+    "altair>=5.4.1",
+    "bokeh>=3.4.3",
+    "bottleneck>=1.4.0",
     "connectorx>=0.4.1",
     "dask>=2025.2.0",
+    "distributed>=2024.9.1",
+    "duckdb>=1.1.3",
+    "fastexcel>=0.12.1",
+    "formulaic>=1.1.1",
+    "glum>=3.1.2",
+    "graphviz>=0.20.3",
+    "holoviews>=1.19.1",
     "hvplot>=0.10.0",
+    "ibis-framework[duckdb,polars,sqlite]>=10.5.0",
+    "matplotlib>=3.9.2",
     "networkx>=3.3",
-    "holoviews>=1.19.1",
-    "bokeh>=3.4.3",
+    "numba>=0.61.0",
+    "pandas[aws,compression,computation,consortium-standard,excel,feather,fss,hdf5,html,output-formatting,parquet,plot,spss,sql-other,xml]>=2.2.3",
+    "pandera[mypy,pandas,polars]>=0.24.0",
     "pyod>=2.0.5",
-    "tables>=3.10.1",
-    "altair>=5.4.1",
-    "bottleneck>=1.4.0",
-    "graphviz>=0.20.3",
-    "distributed>=2024.9.1",
-    "streamlit>=1.45.0",
-    "glum>=3.1.2",
     "scikit-learn>=1.6.1",
-    "formulaic>=1.1.1",
+    "scipy>=1.15.2",
+    "seaborn>=0.13.2",
+    "statsmodels>=0.14.4",
+    "streamlit>=1.45.0",
+    "tables>=3.10.1",
     "textblob>=0.19.0",
     "textdistance[Levenshtein]>=4.6.3",
-    "pandera[mypy,pandas,polars]>=0.24.0",
+    # "sqlalchemy[asyncio]>=2.0.35",
 ]
 scieng = [
-    "pooch>=1.8.2",
-    "h5py>=3.11.0",
-    "duckdb>=1.1.3",
-    "pandas[aws,compression,computation,consortium-standard,excel,feather,fss,hdf5,html,output-formatting,parquet,plot,sql-other,xml]>=2.2.3",
-    "numba>=0.61.0",
-    "scipy>=1.15.2",
-    "statsmodels>=0.14.4",
-    "seaborn>=0.13.2",
-    "fastexcel>=0.12.1",
+    "altair>=5.4.1",
+    "bokeh>=3.4.3",
+    "bottleneck>=1.4.0",
     "connectorx>=0.4.1",
-    "pint>=0.24.3",
-    "scikit-image>=0.24.0",
+    "dask-image>=2024.5.3",
     "dask>=2025.2.0",
-    "matplotlib>=3.9.2",
+    "distributed>=2024.9.1",
+    "duckdb>=1.1.3",
+    "fastexcel>=0.12.1",
+    "formulaic>=1.1.1",
+    "glum>=3.1.2",
+    "graphviz>=0.20.3",
+    "h5py>=3.11.0",
+    "holoviews>=1.19.1",
     "hvplot>=0.10.0",
+    "matplotlib>=3.9.2",
     "networkx>=3.3",
-    "dask-image>=2024.5.3",
-    "holoviews>=1.19.1",
-    "bokeh>=3.4.3",
-    "streamlit>=1.45.0",
+    "numba>=0.61.0",
+    "pandas[aws,compression,computation,consortium-standard,excel,feather,fss,hdf5,html,output-formatting,parquet,plot,sql-other,xml]>=2.2.3",
+    "pint>=0.24.3",
+    "pooch>=1.8.2",
     "pyod>=2.0.5",
+    "scikit-image>=0.24.0",
+    "scipy>=1.15.2",
+    "seaborn>=0.13.2",
+    "statsmodels>=0.14.4",
+    "streamlit>=1.45.0",
+    "sympy>=1.13.3",
     "tables>=3.10.1",
-    "graphviz>=0.20.3",
-    "altair>=5.4.1",
-    "bottleneck>=1.4.0",
-    "graphviz>=0.20.3",
     "zarr>=2.18.3",
-    "distributed>=2024.9.1",
-    "glum>=3.1.2",
-    "formulaic>=1.1.1",
-    "sympy>=1.13.3",
 ]
 net = [
-    "pandas[aws,fss]>=2.2.3",
-    "cryptography>=43.0.0",
-    "networkx>=3.3",
-    "psutil>=6.0.0",
-    "textfsm>=1.1.3",
-    "pyshark>=0.6",
-    "pyzmq>=26.2.0",
-    "aiopath>=0.6.11",
+    "aiobotocore>=2.15.1",
+    "aiofile>=3.9.0",
     "aiofiles>=24.1.0",
+    "aiometer>=0.5.0",
+    "aiopath>=0.6.11",
     "anyio>=3.7.1",
-    "httpx>=0.27.2",
-    "s3fs>=2024.9.0",
-    "aiobotocore>=2.15.1",
+    "boto3>=1.36.3",
+    "botocore>=1.36.3",
+    "celery>=5.4.0",
+    "cryptography>=43.0.0",
+    "dask>=2025.2.0",
     "distributed>=2024.9.1",
     "fastapi>=0.115.8",
-    "uvicorn>=0.34.0",
+    "ftputil>=5.1.0",
+    "httpx>=0.27.2",
     "locust>=2.33.2",
-    "aiometer>=0.5.0",
-    "unsync>=1.4.0",
-    "pathos>=0.3.3",
-    "celery>=5.4.0",
-    "redis>=5.2.1",
-    "pytest-repeat>=0.9.3",
-    "aiofile>=3.9.0",
-    "botocore>=1.36.3",
-    "boto3>=1.36.3",
+    "networkx>=3.3",
+    "pandas[aws,fss]>=2.2.3",
     "passlib>=1.7.4",
-    "ftputil>=5.1.0",
-    "dask>=2025.2.0",
+    "pathos>=0.3.3",
     "polars[async,fsspec]>=1.29.0",
+    "psutil>=6.0.0",
+    "pyshark>=0.6",
+    "pytest-repeat>=0.9.3",
+    "pyzmq>=26.2.0",
+    "redis>=5.2.1",
+    "s3fs>=2024.9.0",
+    "textfsm>=1.1.3",
+    "unsync>=1.4.0",
+    "uvicorn>=0.34.0",
 ]
 dl = [
     "dataset>=1.5.2",
@@ -213,39 +211,47 @@ dl = [
     "yellowbrick>=1.5",
 ]
 testing = [
-    "memory-profiler>=0.61.0",
-    "line-profiler>=4.1.3",
+    "bandit>=1.8.3",
+    "black>=25.1.0",
+    "dodgy>=0.2.1",
+    "flake8-async>=25.3.1",
+    "flake8-import-order>=0.18.2",
+    "flake8>=7.1.2",
+    "gprof2dot>=2024.6.6",
     "hypothesis>=6.129.4",
+    "isort>=6.0.0",
+    "line-profiler>=4.1.3",
+    "memory-profiler>=0.61.0",
+    "mkdocs>=1.6.1",
+    "py-spy>=0.4.0",
     "pycodestyle>=2.12.1",
+    "pyinstrument>=5.0.1",
     "pylint>=3.3.6",
-    "pytest>=8.3.5",
+    "pyt>=1.0.5",
     "pytest-cov>=6.0.0",
     "pytest-repeat>=0.9.3",
     "pytest-xdist>=3.6.1",
-    "sphinx>=8.1.3",
-    "mkdocs>=1.6.1",
-    "flake8-async>=25.3.1",
-    "flake8-import-order>=0.18.2",
-    "isort>=6.0.0",
-    "bandit>=1.8.3",
-    "dodgy>=0.2.1",
-    "pyt>=1.0.5",
-    "black>=25.1.0",
-    "flake8>=7.1.2",
+    "pytest>=8.3.5",
     "scalene>=1.5.51",
     "snakeviz>=2.2.2",
-    "py-spy>=0.4.0",
-    "pyinstrument>=5.0.1",
-    "gprof2dot>=2024.6.6",
+    "sphinx>=8.1.3",
 ]
 db = [
-    "pandas[sql-other]>=2.2.3",
-    "redis>=5.2.1",
-    "sqlalchemy>=2.0.38",
     "duckdb>=1.1.3",
     "ibis-framework[duckdb,polars,sqlite]>=10.5.0",
-    "pyodbc>=5.2.0",
+    "pandas[sql-other]>=2.2.3",
     "polars[database]>=1.29.0",
+    "pyodbc>=5.2.0",
+    "redis>=5.2.1",
+    "sqlalchemy>=2.0.38",
+]
+bio = [
+    "anndata>=0.11.4",
+    "biopython>=1.85",
+    "paramiko>=3.5.1",
+    "pooch>=1.8.2",
+    "scanpy>=1.11.2",
+    "tqdm>=4.67.1",
 ]
 
 [build-system]

{pythoncharmers_meta-0.6.0 → pythoncharmers_meta-0.6.1}/uv.lock

@@ -348,6 +348,25 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/26/99/fc813cd978842c26c82534010ea849eee9ab3a13ea2b74e95cb9c99e747b/amqp-5.3.1-py3-none-any.whl", hash = "sha256:43b3319e1b4e7d1251833a93d672b4af1e40f3d632d479b98661a95f117880a2", size = 50944, upload-time = "2024-11-12T19:55:41.782Z" },
 ]
 
+[[package]]
+name = "anndata"
+version = "0.11.4"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "array-api-compat" },
+    { name = "exceptiongroup", marker = "python_full_version < '3.11'" },
+    { name = "h5py" },
+    { name = "natsort" },
+    { name = "numpy" },
+    { name = "packaging" },
+    { name = "pandas" },
+    { name = "scipy" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/6e/bb/895fa2e9f8cd6d1c058aa90759da715037d0f11e23713e692537555549d7/anndata-0.11.4.tar.gz", hash = "sha256:4ce08d09d2ccb5f37d32790363bbcc7fc1b79863842296ae4badfaf48c736e24", size = 541143, upload-time = "2025-03-26T11:38:54.566Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/0a/4b/ab615fea52e34579d5c6c7dba86b4f9d7f3cdb6a170b348ec49f34cf4355/anndata-0.11.4-py3-none-any.whl", hash = "sha256:fefebb1480316dfa5a23924aa9f74781d447484421bb0c788b0b2ca5e3b339d2", size = 144472, upload-time = "2025-03-26T11:38:52.547Z" },
+]
+
 [[package]]
 name = "annotated-types"
 version = "0.7.0"
@@ -413,6 +432,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/5a/e4/bf8034d25edaa495da3c8a3405627d2e35758e44ff6eaa7948092646fdcc/argon2_cffi_bindings-21.2.0-cp38-abi3-macosx_10_9_universal2.whl", hash = "sha256:e415e3f62c8d124ee16018e491a009937f8cf7ebf5eb430ffc5de21b900dad93", size = 53104, upload-time = "2021-12-01T09:09:31.335Z" },
 ]
 
+[[package]]
+name = "array-api-compat"
+version = "1.12.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/8d/bd/9fa5c7c5621698d5632cc852a79fbbdc28024462c9396698e5fdcb395f37/array_api_compat-1.12.0.tar.gz", hash = "sha256:585bc615f650de53ac24b7c012baecfcdd810f50df3573be47e6dd9fa20df974", size = 99883, upload-time = "2025-05-16T08:49:59.897Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/e0/b1/0542e0cab6f49f151a2d7a42400f84f706fc0b64e85dc1f56708b2e9fd37/array_api_compat-1.12.0-py3-none-any.whl", hash = "sha256:a0b4795b6944a9507fde54679f9350e2ad2b1e2acf4a2408a098cdc27f890a8b", size = 58156, upload-time = "2025-05-16T08:49:58.129Z" },
+]
+
 [[package]]
 name = "asciitree"
 version = "0.3.3"
@@ -530,6 +558,64 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/88/85/db74b9233e0aa27ec96891045c5e920a64dd5cbccd50f8e64e9460f48d35/bandit-1.8.3-py3-none-any.whl", hash = "sha256:28f04dc0d258e1dd0f99dee8eefa13d1cb5e3fde1a5ab0c523971f97b289bcd8", size = 129078, upload-time = "2025-02-17T05:24:54.068Z" },
 ]
 
+[[package]]
+name = "bcrypt"
+version = "4.3.0"
+source = { registry = "https://pypi.org/simple" }
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