From 30405ceb624160ee885c8d677489dac522855211 Mon Sep 17 00:00:00 2001
From: Alexander Berger <alexander.berger@jax.org>
Date: Tue, 5 Dec 2023 12:56:46 -0500
Subject: [PATCH] Updating dependencies and lock file

---
 poetry.lock    | 306 +++++++++++++++++++++++++++++++++++--------------
 pyproject.toml |  22 ++--
 2 files changed, 233 insertions(+), 95 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index d994d0b..3679a7d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -491,43 +491,45 @@ all = ["email-validator (>=1.1.1)", "httpx (>=0.23.0)", "itsdangerous (>=1.1.0)"
 
 [[package]]
 name = "geneweaver-core"
-version = "0.2.0a0"
+version = "0.8.0a0"
 description = "The core of the Jax-Geneweaver Python library"
 optional = false
 python-versions = ">=3.9,<4.0"
 files = [
-    {file = "geneweaver_core-0.2.0a0-py3-none-any.whl", hash = "sha256:71b6cfd2633184541f183a19eeb2aa20add4e11c850fcb956e8fe778418cdf67"},
-    {file = "geneweaver_core-0.2.0a0.tar.gz", hash = "sha256:71d829ba3823feace06c9cf4a548b5761e1409718443feb20b3eb7311ed06824"},
+    {file = "geneweaver_core-0.8.0a0-py3-none-any.whl", hash = "sha256:01a70f8dc9407def33a706cced4e4946de66b10f61e828d69d2b686b39a5a197"},
+    {file = "geneweaver_core-0.8.0a0.tar.gz", hash = "sha256:b4fc0373f3ac21914278a9d9961942deef2130e230ac336d5414591db8f25f2c"},
 ]
 
 [package.dependencies]
+numpy = ">=1.22,<1.24"
 openpyxl = ">=3.1.2,<4.0.0"
+pandas = ">=1.5,<2.1"
 pydantic = {version = ">=1.10.7,<2.0.0", extras = ["dotenv"]}
 
 [[package]]
 name = "geneweaver-db"
-version = "0.1.6a0"
+version = "0.2.0a0"
 description = "Database Interaction Services for GeneWeaver"
 optional = false
 python-versions = ">=3.9,<4.0"
 files = [
-    {file = "geneweaver_db-0.1.6a0-py3-none-any.whl", hash = "sha256:43afdb19bb46c750d668d542b86b4236ce978cdb0318bb3ee22128204c099ee7"},
-    {file = "geneweaver_db-0.1.6a0.tar.gz", hash = "sha256:103e3a95ea65c693ee16f210b61b29bc214e1681fb00f20c4543b35888f0c5a2"},
+    {file = "geneweaver_db-0.2.0a0-py3-none-any.whl", hash = "sha256:9d13bac879d68d3e471e1f795b9f0f71602f61335a1392c60bae33b150f42e6e"},
+    {file = "geneweaver_db-0.2.0a0.tar.gz", hash = "sha256:a595260738bbf85a5d880f9b4c57032b98c5369ecd10a9623524b1b2f737c01e"},
 ]
 
 [package.dependencies]
-geneweaver-core = ">=0.2.0a0,<0.3.0"
-psycopg = {version = ">=3.1.9,<4.0.0", extras = ["binary"]}
+geneweaver-core = ">=0.8.0a0,<0.9.0"
+psycopg = {version = ">=3.1.13,<4.0.0", extras = ["binary"]}
 
 [[package]]
 name = "geneweaver-testing"
-version = "0.0.1b0"
+version = "0.0.3"
 description = "A library to standardize testing of GeneWeaver pacakges."
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
-    {file = "geneweaver_testing-0.0.1b0-py3-none-any.whl", hash = "sha256:29bf5cb790fc5f788eb07bdd4df70a9edbeb9b84f467bce4b6e537b1cada3d47"},
-    {file = "geneweaver_testing-0.0.1b0.tar.gz", hash = "sha256:550b1490a3404357bbaf8dbdb361e3c70efe76f76966b8b03cdcc747c3e8e5e3"},
+    {file = "geneweaver_testing-0.0.3-py3-none-any.whl", hash = "sha256:dd9d04cd9ff6366496a9f66ea3347121d0d810d9748936db736837d6f773d7f5"},
+    {file = "geneweaver_testing-0.0.3.tar.gz", hash = "sha256:e268462ced2d44ad213cae7cb2e669d5c0065e6bf82965730b7d3eb0f0f0e9a8"},
 ]
 
 [package.dependencies]
@@ -824,6 +826,43 @@ files = [
     {file = "mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"},
 ]
 
+[[package]]
+name = "numpy"
+version = "1.23.5"
+description = "NumPy is the fundamental package for array computing with Python."
+optional = false
+python-versions = ">=3.8"
+files = [
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+    {file = "numpy-1.23.5-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:e9f4c4e51567b616be64e05d517c79a8a22f3606499941d97bb76f2ca59f982d"},
+    {file = "numpy-1.23.5-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:7903ba8ab592b82014713c491f6c5d3a1cde5b4a3bf116404e08f5b52f6daf43"},
+    {file = "numpy-1.23.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5e05b1c973a9f858c74367553e236f287e749465f773328c8ef31abe18f691e1"},
+    {file = "numpy-1.23.5-cp310-cp310-win32.whl", hash = "sha256:522e26bbf6377e4d76403826ed689c295b0b238f46c28a7251ab94716da0b280"},
+    {file = "numpy-1.23.5-cp310-cp310-win_amd64.whl", hash = "sha256:dbee87b469018961d1ad79b1a5d50c0ae850000b639bcb1b694e9981083243b6"},
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+    {file = "numpy-1.23.5-cp39-cp39-win_amd64.whl", hash = "sha256:09b7847f7e83ca37c6e627682f145856de331049013853f344f37b0c9690e3df"},
+    {file = "numpy-1.23.5-pp38-pypy38_pp73-macosx_10_9_x86_64.whl", hash = "sha256:abdde9f795cf292fb9651ed48185503a2ff29be87770c3b8e2a14b0cd7aa16f8"},
+    {file = "numpy-1.23.5-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f9a909a8bae284d46bbfdefbdd4a262ba19d3bc9921b1e76126b1d21c3c34135"},
+    {file = "numpy-1.23.5-pp38-pypy38_pp73-win_amd64.whl", hash = "sha256:01dd17cbb340bf0fc23981e52e1d18a9d4050792e8fb8363cecbf066a84b827d"},
+    {file = "numpy-1.23.5.tar.gz", hash = "sha256:1b1766d6f397c18153d40015ddfc79ddb715cabadc04d2d228d4e5a8bc4ded1a"},
+]
+
 [[package]]
 name = "openpyxl"
 version = "3.1.2"
@@ -853,7 +892,6 @@ files = [
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-    {file = "orjson-3.9.2-cp310-none-win32.whl", hash = "sha256:2ae61f5d544030a6379dbc23405df66fea0777c48a0216d2d83d3e08b69eb676"},
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@@ -863,7 +901,6 @@ files = [
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@@ -873,7 +910,6 @@ files = [
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@@ -883,7 +919,6 @@ files = [
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@@ -893,7 +928,6 @@ files = [
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@@ -909,6 +943,73 @@ files = [
     {file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"},
 ]
 
+[[package]]
+name = "pandas"
+version = "2.0.3"
+description = "Powerful data structures for data analysis, time series, and statistics"
+optional = false
+python-versions = ">=3.8"
+files = [
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 ]
 
 [[package]]
@@ -1184,6 +1296,20 @@ pytest = ">=4.6"
 [package.extras]
 testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
 
+[[package]]
+name = "python-dateutil"
+version = "2.8.2"
+description = "Extensions to the standard Python datetime module"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
+files = [
+    {file = "python-dateutil-2.8.2.tar.gz", hash = "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86"},
+    {file = "python_dateutil-2.8.2-py2.py3-none-any.whl", hash = "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9"},
+]
+
+[package.dependencies]
+six = ">=1.5"
+
 [[package]]
 name = "python-dotenv"
 version = "1.0.0"
@@ -1234,6 +1360,17 @@ files = [
 [package.extras]
 dev = ["atomicwrites (==1.2.1)", "attrs (==19.2.0)", "coverage (==6.5.0)", "hatch", "invoke (==1.7.3)", "more-itertools (==4.3.0)", "pbr (==4.3.0)", "pluggy (==1.0.0)", "py (==1.11.0)", "pytest (==7.2.0)", "pytest-cov (==4.0.0)", "pytest-timeout (==2.1.0)", "pyyaml (==5.1)"]
 
+[[package]]
+name = "pytz"
+version = "2023.3.post1"
+description = "World timezone definitions, modern and historical"
+optional = false
+python-versions = "*"
+files = [
+    {file = "pytz-2023.3.post1-py2.py3-none-any.whl", hash = "sha256:ce42d816b81b68506614c11e8937d3aa9e41007ceb50bfdcb0749b921bf646c7"},
+    {file = "pytz-2023.3.post1.tar.gz", hash = "sha256:7b4fddbeb94a1eba4b557da24f19fdf9db575192544270a9101d8509f9f43d7b"},
+]
+
 [[package]]
 name = "pyyaml"
 version = "6.0"
@@ -1506,13 +1643,13 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "uvicorn"
-version = "0.22.0"
+version = "0.24.0.post1"
 description = "The lightning-fast ASGI server."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "uvicorn-0.22.0-py3-none-any.whl", hash = "sha256:e9434d3bbf05f310e762147f769c9f21235ee118ba2d2bf1155a7196448bd996"},
-    {file = "uvicorn-0.22.0.tar.gz", hash = "sha256:79277ae03db57ce7d9aa0567830bbb51d7a612f54d6e1e3e92da3ef24c2c8ed8"},
+    {file = "uvicorn-0.24.0.post1-py3-none-any.whl", hash = "sha256:7c84fea70c619d4a710153482c0d230929af7bcf76c7bfa6de151f0a3a80121e"},
+    {file = "uvicorn-0.24.0.post1.tar.gz", hash = "sha256:09c8e5a79dc466bdf28dead50093957db184de356fcdc48697bad3bde4c2588e"},
 ]
 
 [package.dependencies]
@@ -1522,6 +1659,7 @@ h11 = ">=0.8"
 httptools = {version = ">=0.5.0", optional = true, markers = "extra == \"standard\""}
 python-dotenv = {version = ">=0.13", optional = true, markers = "extra == \"standard\""}
 pyyaml = {version = ">=5.1", optional = true, markers = "extra == \"standard\""}
+typing-extensions = {version = ">=4.0", markers = "python_version < \"3.11\""}
 uvloop = {version = ">=0.14.0,<0.15.0 || >0.15.0,<0.15.1 || >0.15.1", optional = true, markers = "(sys_platform != \"win32\" and sys_platform != \"cygwin\") and platform_python_implementation != \"PyPy\" and extra == \"standard\""}
 watchfiles = {version = ">=0.13", optional = true, markers = "extra == \"standard\""}
 websockets = {version = ">=10.4", optional = true, markers = "extra == \"standard\""}
@@ -1689,4 +1827,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "fd7d68658f669b68f1b10f61315ec59a9c5e5ef5b42b2506ba933a8c955e8e08"
+content-hash = "0ea43acd3f3f058a7640f58d5183d834b88b2da78c07d593beb572892d3d59b5"
diff --git a/pyproject.toml b/pyproject.toml
index 7398b52..cb3e54a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,34 +1,34 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.0.1a0"
+version = "0.0.1a1"
 description = "description"
 authors = ["Jax Computational Sciences <cssc@jax.org>"]
 packages = [
-    {include = "geneweaver/api", from = "src"},
-    {include = "geneweaver/db", from = "src"}
+    {include = "geneweaver/api", from = "src"}
 ]
 
 [tool.poetry.dependencies]
 python = "^3.9"
-geneweaver-core = "^0.2.0a0"
+geneweaver-core = "^0.8.0a0"
 fastapi = {extras = ["all"], version = "^0.99.1"}
-uvicorn = {extras = ["standard"], version = "^0.22.0"}
-geneweaver-db = "^0.1.0a0"
+uvicorn = {extras = ["standard"], version = "^0.24.0"}
+geneweaver-db = "^0.2.0a0"
 psycopg-pool = "^3.1.7"
 requests = "^2.31.0"
 python-jose = {extras = ["cryptography"], version = "^3.3.0"}
 
 [tool.poetry.group.dev.dependencies]
-geneweaver-testing = "^0.0.1b0"
+geneweaver-testing = "^0.0.3"
 pytest-asyncio = "^0.21.0"
 
 [tool.ruff]
 select = ['F', 'E', 'W', 'A', 'C90', 'N', 'B', 'ANN', 'D', 'I', 'ERA', 'PD', 'NPY', 'PT']
 
+[tool.ruff.per-file-ignores]
+"tests/*" = ["ANN001", "ANN201"]
+"src/*" = ["ANN101"]
+"src/geneweaver/api/controller/*" = ["B008"]
+
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
-
-
-
-