inital working commit

README.md

@@ -1,4 +1,4 @@
-# bio-data-to-db
+# bio-data-to-db: make Uniprot PostgreSQL database
 
 [![image](https://img.shields.io/pypi/v/bio-data-to-db.svg)](https://pypi.python.org/pypi/bio-data-to-db)
 [![PyPI - Downloads](https://img.shields.io/pypi/dm/bio-data-to-db)](https://pypi.python.org/pypi/bio-data-to-db)
@@ -29,7 +29,7 @@ pip install bio-data-to-db
 You can use the command line interface or the python API.
 
 ```bash
-# It will create a table named 'uniprot' in the database.
+# It will create a db 'uniprot' and a table named 'public.uniprot_info' in the database.
 # If you want another name, you can optionally pass it as the last argument.
 bio-data-to-db uniprot create-empty-table 'postgresql://username@localhost:5432/uniprot'
 
@@ -102,3 +102,4 @@ cargo sqlx prepare
 ```
 
 This will make `.sqlx/` directory with the type information for the queries.
+

deps/lock/aarch64-apple-darwin/.requirements.in.sha256

@@ -0,0 +1 @@
+d0208e2c1349ed9b6cb3a691cffd68acaec61a082b24bd824793306fe1d17edb  requirements.in

deps/lock/aarch64-apple-darwin/.requirements_dev.in.sha256

@@ -0,0 +1 @@
+7ee0605e83c97fae896ffe649753e039d808268685d8c71e695169cc617c16ba  requirements_dev.in

deps/lock/aarch64-apple-darwin/requirements.txt

@@ -0,0 +1,45 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile requirements.in -o /home/runner/work/bio-data-to-db/bio-data-to-db/deps/lock/aarch64-apple-darwin/requirements.txt --python-platform aarch64-apple-darwin --python-version 3.10
+click==8.1.7
+    # via typer
+markdown-it-py==3.0.0
+    # via rich
+mdurl==0.1.2
+    # via markdown-it-py
+numpy==2.0.0
+    # via
+    #   pandas
+    #   pyarrow
+pandas==2.2.2
+    # via -r requirements.in
+polars==1.2.0
+    # via -r requirements.in
+psycopg==3.2.1
+    # via -r requirements.in
+psycopg2==2.9.9
+    # via -r requirements.in
+pyarrow==17.0.0
+    # via -r requirements.in
+pygments==2.18.0
+    # via rich
+python-dateutil==2.9.0.post0
+    # via pandas
+pytz==2024.1
+    # via pandas
+rich==13.7.1
+    # via typer
+shellingham==1.5.4
+    # via typer
+six==1.16.0
+    # via python-dateutil
+sqlalchemy==2.0.31
+    # via -r requirements.in
+typer==0.12.3
+    # via -r requirements.in
+typing-extensions==4.12.2
+    # via
+    #   psycopg
+    #   sqlalchemy
+    #   typer
+tzdata==2024.1
+    # via pandas

deps/lock/aarch64-apple-darwin/requirements_dev.txt

@@ -0,0 +1,99 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile requirements_dev.in -o /home/runner/work/bio-data-to-db/bio-data-to-db/deps/lock/aarch64-apple-darwin/requirements_dev.txt --python-platform aarch64-apple-darwin --python-version 3.10
+certifi==2024.7.4
+    # via requests
+charset-normalizer==3.3.2
+    # via requests
+click==8.1.7
+    # via typer
+exceptiongroup==1.2.2
+    # via pytest
+filelock==3.15.4
+    # via huggingface-hub
+fsspec==2024.6.1
+    # via huggingface-hub
+huggingface-hub==0.23.5
+    # via -r requirements_dev.in
+idna==3.7
+    # via requests
+iniconfig==2.0.0
+    # via pytest
+markdown-it-py==3.0.0
+    # via rich
+maturin==1.7.0
+    # via -r requirements_dev.in
+mdurl==0.1.2
+    # via markdown-it-py
+networkx==3.3
+    # via -r requirements_dev.in
+numpy==2.0.0
+    # via
+    #   -r requirements_dev.in
+    #   pandas
+    #   pyarrow
+    #   scipy
+    #   trimesh
+packaging==24.1
+    # via
+    #   huggingface-hub
+    #   pytest
+pandas==2.2.2
+    # via -r requirements.in
+pluggy==1.5.0
+    # via pytest
+polars==1.2.0
+    # via -r requirements.in
+psycopg==3.2.1
+    # via -r requirements.in
+psycopg2==2.9.9
+    # via -r requirements.in
+pyarrow==17.0.0
+    # via -r requirements.in
+pygments==2.18.0
+    # via rich
+pytest==8.2.2
+    # via -r requirements_dev.in
+python-dateutil==2.9.0.post0
+    # via pandas
+pytz==2024.1
+    # via pandas
+pyyaml==6.0.1
+    # via huggingface-hub
+requests==2.32.3
+    # via huggingface-hub
+rich==13.7.1
+    # via
+    #   -r requirements_dev.in
+    #   typer
+ruff==0.5.0
+    # via -r requirements_dev.in
+scipy==1.14.0
+    # via -r requirements_dev.in
+shellingham==1.5.4
+    # via typer
+six==1.16.0
+    # via python-dateutil
+sqlalchemy==2.0.31
+    # via -r requirements.in
+toml==0.10.2
+    # via -r requirements_dev.in
+tomli==2.0.1
+    # via
+    #   maturin
+    #   pytest
+tqdm==4.66.4
+    # via huggingface-hub
+trimesh==4.4.3
+    # via -r requirements_dev.in
+typer==0.12.3
+    # via -r requirements.in
+typing-extensions==4.12.2
+    # via
+    #   huggingface-hub
+    #   psycopg
+    #   sqlalchemy
+    #   typer
+tzdata==2024.1
+    # via pandas
+urllib3==2.2.2
+    # via requests

deps/lock/x86_64-apple-darwin/.requirements.in.sha256

@@ -0,0 +1 @@
+d0208e2c1349ed9b6cb3a691cffd68acaec61a082b24bd824793306fe1d17edb  requirements.in

deps/lock/x86_64-apple-darwin/.requirements_dev.in.sha256

@@ -0,0 +1 @@
+7ee0605e83c97fae896ffe649753e039d808268685d8c71e695169cc617c16ba  requirements_dev.in

deps/lock/x86_64-apple-darwin/requirements.txt

@@ -0,0 +1,47 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile requirements.in -o /home/runner/work/bio-data-to-db/bio-data-to-db/deps/lock/x86_64-apple-darwin/requirements.txt --python-platform x86_64-apple-darwin --python-version 3.10
+click==8.1.7
+    # via typer
+greenlet==3.0.3
+    # via sqlalchemy
+markdown-it-py==3.0.0
+    # via rich
+mdurl==0.1.2
+    # via markdown-it-py
+numpy==2.0.0
+    # via
+    #   pandas
+    #   pyarrow
+pandas==2.2.2
+    # via -r requirements.in
+polars==1.2.0
+    # via -r requirements.in
+psycopg==3.2.1
+    # via -r requirements.in
+psycopg2==2.9.9
+    # via -r requirements.in
+pyarrow==17.0.0
+    # via -r requirements.in
+pygments==2.18.0
+    # via rich
+python-dateutil==2.9.0.post0
+    # via pandas
+pytz==2024.1
+    # via pandas
+rich==13.7.1
+    # via typer
+shellingham==1.5.4
+    # via typer
+six==1.16.0
+    # via python-dateutil
+sqlalchemy==2.0.31
+    # via -r requirements.in
+typer==0.12.3
+    # via -r requirements.in
+typing-extensions==4.12.2
+    # via
+    #   psycopg
+    #   sqlalchemy
+    #   typer
+tzdata==2024.1
+    # via pandas

deps/lock/x86_64-apple-darwin/requirements_dev.txt

@@ -0,0 +1,101 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile requirements_dev.in -o /home/runner/work/bio-data-to-db/bio-data-to-db/deps/lock/x86_64-apple-darwin/requirements_dev.txt --python-platform x86_64-apple-darwin --python-version 3.10
+certifi==2024.7.4
+    # via requests
+charset-normalizer==3.3.2
+    # via requests
+click==8.1.7
+    # via typer
+exceptiongroup==1.2.2
+    # via pytest
+filelock==3.15.4
+    # via huggingface-hub
+fsspec==2024.6.1
+    # via huggingface-hub
+greenlet==3.0.3
+    # via sqlalchemy
+huggingface-hub==0.23.5
+    # via -r requirements_dev.in
+idna==3.7
+    # via requests
+iniconfig==2.0.0
+    # via pytest
+markdown-it-py==3.0.0
+    # via rich
+maturin==1.7.0
+    # via -r requirements_dev.in
+mdurl==0.1.2
+    # via markdown-it-py
+networkx==3.3
+    # via -r requirements_dev.in
+numpy==2.0.0
+    # via
+    #   -r requirements_dev.in
+    #   pandas
+    #   pyarrow
+    #   scipy
+    #   trimesh
+packaging==24.1
+    # via
+    #   huggingface-hub
+    #   pytest
+pandas==2.2.2
+    # via -r requirements.in
+pluggy==1.5.0
+    # via pytest
+polars==1.2.0
+    # via -r requirements.in
+psycopg==3.2.1
+    # via -r requirements.in
+psycopg2==2.9.9
+    # via -r requirements.in
+pyarrow==17.0.0
+    # via -r requirements.in
+pygments==2.18.0
+    # via rich
+pytest==8.2.2
+    # via -r requirements_dev.in
+python-dateutil==2.9.0.post0
+    # via pandas
+pytz==2024.1
+    # via pandas
+pyyaml==6.0.1
+    # via huggingface-hub
+requests==2.32.3
+    # via huggingface-hub
+rich==13.7.1
+    # via
+    #   -r requirements_dev.in
+    #   typer
+ruff==0.5.0
+    # via -r requirements_dev.in
+scipy==1.14.0
+    # via -r requirements_dev.in
+shellingham==1.5.4
+    # via typer
+six==1.16.0
+    # via python-dateutil
+sqlalchemy==2.0.31
+    # via -r requirements.in
+toml==0.10.2
+    # via -r requirements_dev.in
+tomli==2.0.1
+    # via
+    #   maturin
+    #   pytest
+tqdm==4.66.4
+    # via huggingface-hub
+trimesh==4.4.3
+    # via -r requirements_dev.in
+typer==0.12.3
+    # via -r requirements.in
+typing-extensions==4.12.2
+    # via
+    #   huggingface-hub
+    #   psycopg
+    #   sqlalchemy
+    #   typer
+tzdata==2024.1
+    # via pandas
+urllib3==2.2.2
+    # via requests

deps/lock/x86_64-manylinux_2_28/.requirements.in.sha256

@@ -0,0 +1 @@
+d0208e2c1349ed9b6cb3a691cffd68acaec61a082b24bd824793306fe1d17edb  requirements.in

deps/lock/x86_64-manylinux_2_28/.requirements_dev.in.sha256

@@ -0,0 +1 @@
+7ee0605e83c97fae896ffe649753e039d808268685d8c71e695169cc617c16ba  requirements_dev.in

deps/lock/x86_64-manylinux_2_28/requirements.txt

@@ -0,0 +1,47 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile requirements.in -o /home/runner/work/bio-data-to-db/bio-data-to-db/deps/lock/x86_64-manylinux_2_28/requirements.txt --python-platform x86_64-manylinux_2_28 --python-version 3.10
+click==8.1.7
+    # via typer
+greenlet==3.0.3
+    # via sqlalchemy
+markdown-it-py==3.0.0
+    # via rich
+mdurl==0.1.2
+    # via markdown-it-py
+numpy==2.0.0
+    # via
+    #   pandas
+    #   pyarrow
+pandas==2.2.2
+    # via -r requirements.in
+polars==1.2.0
+    # via -r requirements.in
+psycopg==3.2.1
+    # via -r requirements.in
+psycopg2==2.9.9
+    # via -r requirements.in
+pyarrow==17.0.0
+    # via -r requirements.in
+pygments==2.18.0
+    # via rich
+python-dateutil==2.9.0.post0
+    # via pandas
+pytz==2024.1
+    # via pandas
+rich==13.7.1
+    # via typer
+shellingham==1.5.4
+    # via typer
+six==1.16.0
+    # via python-dateutil
+sqlalchemy==2.0.31
+    # via -r requirements.in
+typer==0.12.3
+    # via -r requirements.in
+typing-extensions==4.12.2
+    # via
+    #   psycopg
+    #   sqlalchemy
+    #   typer
+tzdata==2024.1
+    # via pandas