Merge pull request #7 from ArpiarSaundersLab/dev

duckdb version updated to latest v1.2.2

Author: kennypavan

README.md

@@ -8,6 +8,7 @@
 	<a href="https://github.com/ArpiarSaundersLab/annsql/tree/main/tests"><img src="https://img.shields.io/badge/build-passing-brightgreen"></a>
 	<a href="https://img.shields.io/github/v/release/ArpiarSaundersLab/annsql"><img src="https://img.shields.io/github/v/release/ArpiarSaundersLab/annsql"></a>
 	<a href="https://static.pepy.tech/badge/annsql/month"><img src="https://static.pepy.tech/badge/annsql/month"></a>
+	<a href="https://static.pepy.tech/badge/annsql"><img src="https://static.pepy.tech/badge/annsql"></a>
 </p>
 
 <br>
@@ -126,7 +127,7 @@ asql.plot_umap(color_by="leiden_clusters", annotate=True)
 
 
 ## Reference
-AnnSQL: A Python SQL-based package for large-scale single-cell genomics analysis on a laptop<br />
+AnnSQL: A Python SQL-based package for fast large-scale single-cell genomics analysis using minimal computational resources<br />
 Kenny Pavan, Arpiar Saunders<br />
 bioRxiv 2024.11.02.621676; [doi: https://doi.org/10.1101/2024.11.02.621676](https://www.biorxiv.org/content/10.1101/2024.11.02.621676)
 

docs/cite.md

@@ -1,5 +1,5 @@
 # Citation
 
-AnnSQL: A Python SQL-based package for large-scale single-cell genomics analysis on a laptop<br />
+AnnSQL: A Python SQL-based package for fast large-scale single-cell genomics analysis using minimal computational resources<br />
 Kenny Pavan, Arpiar Saunders<br />
 bioRxiv 2024.11.02.621676; [doi: https://doi.org/10.1101/2024.11.02.621676](https://www.biorxiv.org/content/10.1101/2024.11.02.621676)

requirements.txt

@@ -1,104 +1,194 @@
-anndata==0.10.9
-AnnSQL @ file:///home/kenny/Documents/OHSU/Projects/AnnSql/dist/AnnSQL-0.9.4-py3-none-any.whl#sha256=f2ef75f08d4b932600dd8801d74973bd8b8045203a4278cfb9bcaa8e9b4fd70f
+agate==1.9.1
+anndata==0.11.1
+annotated-types==0.7.0
+anyio==4.8.0
 array_api_compat==1.9.1
 asttokens==2.4.1
+attrs==24.3.0
 autocommand==2.2.2
+babel==2.16.0
 backports.tarfile==1.2.0
+beautifulsoup4==4.13.3
+bio==1.7.1
+biopython==1.85
+biothings_client==0.4.1
+bleach==6.2.0
 build==1.2.2.post1
 certifi==2024.8.30
 cffi==1.17.1
 charset-normalizer==3.4.0
+click==8.1.8
+colorama==0.4.6
 comm==0.2.2
-contourpy==1.3.0
+contourpy==1.3.1
 cryptography==43.0.3
 cycler==0.12.1
+daff==1.3.46
+dbt-adapters==1.13.2
+dbt-common==1.14.0
+dbt-core==1.9.1
+dbt-duckdb==1.9.1
+dbt-extractor==0.5.1
+dbt-semantic-interfaces==0.7.4
 debugpy==1.8.5
 decorator==5.1.1
+deepdiff==7.0.1
+defusedxml==0.7.1
 docutils==0.21.2
-duckdb==1.1.2
+duckdb==1.2.2
 e==1.4.5
 executing==2.1.0
+fastjsonschema==2.21.1
 fonttools==4.54.1
+gffpandas==1.2.0
+ghp-import==2.1.0
+gprofiler-official==1.0.0
+griffe==1.5.7
+h11==0.14.0
 h5py==3.12.1
+httpcore==1.0.7
+httpx==0.28.1
 idna==3.10
-importlib_metadata==8.0.0
+igraph==0.11.8
+importlib-metadata==6.11.0
 importlib_resources==6.4.0
 inflect==7.3.1
 ipykernel==6.29.5
 ipython==8.27.0
+isodate==0.6.1
 jaraco.classes==3.4.0
 jaraco.context==5.3.0
 jaraco.functools==4.0.1
 jaraco.text==3.12.1
 jedi==0.19.1
 jeepney==0.8.0
+Jinja2==3.1.5
 joblib==1.4.2
+jsonschema==4.23.0
+jsonschema-specifications==2024.10.1
 jupyter_client==8.6.2
 jupyter_core==5.7.2
+jupyterlab_pygments==0.3.0
+jupytext==1.16.7
 keyring==25.5.0
 kiwisolver==1.4.7
+leather==0.4.0
 legacy-api-wrap==1.4
+leidenalg==0.10.2
 llvmlite==0.43.0
+Markdown==3.7
 markdown-it-py==3.0.0
+MarkupSafe==3.0.2
+mashumaro==3.14
 matplotlib==3.9.2
 matplotlib-inline==0.1.7
+mdit-py-plugins==0.4.2
 mdurl==0.1.2
 memory-profiler==0.61.0
+mergedeep==1.3.4
+mistune==3.1.2
+mkdocs==1.6.1
+mkdocs-autorefs==1.4.0
+mkdocs-get-deps==0.2.0
+mkdocs-jupyter==0.25.1
+mkdocs-material==9.6.5
+mkdocs-material-extensions==1.3.1
+mkdocstrings==0.28.2
+mkdocstrings-python==1.16.2
 more-itertools==10.3.0
+msgpack==1.1.0
+mygene==3.2.2
 natsort==8.4.0
+nbclient==0.10.2
+nbconvert==7.16.6
+nbformat==5.10.4
 nest-asyncio==1.6.0
 networkx==3.4.2
 nh3==0.2.18
 numba==0.60.0
 numpy==2.0.2
-packaging==24.1
+ordered-set==4.1.0
+packaging==24.2
+paginate==0.5.7
 pandas==2.2.3
+pandocfilters==1.5.1
+parsedatetime==2.6
 parso==0.8.4
-patsy==0.5.6
+pathlib==1.0.1
+pathspec==0.12.1
+patsy==1.0.1
 pexpect==4.9.0
 pillow==11.0.0
 pkginfo==1.10.0
 platformdirs==4.2.2
+polars==1.21.0
+pooch==1.8.2
 prompt_toolkit==3.0.47
-psutil==6.0.0
+protobuf==5.29.3
+psutil==6.1.0
 ptyprocess==0.7.0
 pure_eval==0.2.3
-pyarrow==17.0.0
+pyarrow==18.0.0
 pycparser==2.22
+pydantic==2.10.5
+pydantic_core==2.27.2
 Pygments==2.18.0
+pymdown-extensions==10.14.3
 pynndescent==0.5.13
 pyparsing==3.2.0
 pyproject_hooks==1.2.0
+pysam==0.22.1
 python-dateutil==2.9.0.post0
+python-slugify==8.0.4
+pytimeparse==1.1.8
 pytz==2024.2
+PyYAML==6.0.2
+pyyaml_env_tag==0.1
 pyzmq==26.2.0
 readme_renderer==44.0
+referencing==0.36.1
+regex==2024.11.6
 requests==2.32.3
 requests-toolbelt==1.0.0
 rfc3986==2.0.0
 rich==13.9.3
-scanpy==1.10.3
+rpds-py==0.22.3
+rpy2==3.5.17
+scanpy==1.10.4
 scikit-learn==1.5.2
+scikit-network==0.33.1
 scipy==1.14.1
+scReadSim==1.4.1
 seaborn==0.13.2
 SecretStorage==3.3.3
 session_info==1.0.0
 setuptools==74.1.2
 six==1.16.0
+sniffio==1.3.1
+snowplow-tracker==1.0.4
+soupsieve==2.6
+sqlparse==0.5.3
 stack-data==0.6.3
 statsmodels==0.14.4
 stdlib-list==0.11.0
+text-unidecode==1.3
+texttable==1.7.0
 threadpoolctl==3.5.0
+tinycss2==1.4.0
 tomli==2.0.1
 tornado==6.4.1
-tqdm==4.66.6
+tqdm==4.67.0
 traitlets==5.14.3
 twine==5.1.1
 typeguard==4.3.0
+types-requests==2.32.0.20241016
 typing_extensions==4.12.2
 tzdata==2024.2
+tzlocal==5.2
 umap-learn==0.5.7
 urllib3==2.2.3
+watchdog==6.0.0
 wcwidth==0.2.13
+webencodings==0.5.1
 wheel==0.43.0
 zipp==3.19.2

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
 	name='AnnSQL',
-	version='v1.0.1',
+	version='v1.0.2',
 	author="Kenny Pavan",
 	author_email="pavan@ohsu.edu",
 	description="A Python SQL tool for converting Anndata objects to a relational DuckDb database. Methods are included for querying and basic single-cell preprocessing (experimental). ",
@@ -22,7 +22,7 @@
 	],
 	install_requires=[
 		'scanpy>=1.10.3',
-		'duckdb>=1.1.2',
+		'duckdb>=1.2.2',
 		'memory-profiler>=0.61.0',
 		'psutil>=6.0.0',
 		'pyarrow>=17.0.0',