From d57982e261c84efe3f40f82fa715d0ee92cf6288 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Thu, 13 Feb 2025 21:56:42 +0000
Subject: [PATCH] Update dependency numpy to v2.2.3

---
 poetry.lock    | 365 ++++++++-----------------------------------------
 pyproject.toml |  29 ++--
 2 files changed, 74 insertions(+), 320 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 4c7f94b..14b7978 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -11,21 +11,6 @@ files = [
     {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
 ]
 
-[[package]]
-name = "asttokens"
-version = "3.0.0"
-description = "Annotate AST trees with source code positions"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2"},
-    {file = "asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7"},
-]
-
-[package.extras]
-astroid = ["astroid (>=2,<4)"]
-test = ["astroid (>=2,<4)", "pytest", "pytest-cov", "pytest-xdist"]
-
 [[package]]
 name = "babel"
 version = "2.17.0"
@@ -370,17 +355,6 @@ files = [
 docs = ["ipython", "matplotlib", "numpydoc", "sphinx"]
 tests = ["pytest", "pytest-cov", "pytest-xdist"]
 
-[[package]]
-name = "decorator"
-version = "5.1.1"
-description = "Decorators for Humans"
-optional = false
-python-versions = ">=3.5"
-files = [
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-    {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"},
-]
-
 [[package]]
 name = "deptry"
 version = "0.21.2"
@@ -438,20 +412,6 @@ files = [
 [package.extras]
 test = ["pytest (>=6)"]
 
-[[package]]
-name = "executing"
-version = "2.2.0"
-description = "Get the currently executing AST node of a frame, and other information"
-optional = false
-python-versions = ">=3.8"
-files = [
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-
-[package.extras]
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-
 [[package]]
 name = "filelock"
 version = "3.17.0"
@@ -611,63 +571,6 @@ files = [
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 ]
 
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-description = "IPython: Productive Interactive Computing"
-optional = false
-python-versions = ">=3.10"
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-
-[package.dependencies]
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-decorator = "*"
-exceptiongroup = {version = "*", markers = "python_version < \"3.11\""}
-jedi = ">=0.16"
-matplotlib-inline = "*"
-pexpect = {version = ">4.3", markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\""}
-prompt_toolkit = ">=3.0.41,<3.1.0"
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-stack_data = "*"
-traitlets = ">=5.13.0"
-typing_extensions = {version = ">=4.6", markers = "python_version < \"3.12\""}
-
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-doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "tomli", "typing_extensions"]
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-matplotlib = ["matplotlib"]
-nbconvert = ["nbconvert"]
-nbformat = ["nbformat"]
-notebook = ["ipywidgets", "notebook"]
-parallel = ["ipyparallel"]
-qtconsole = ["qtconsole"]
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-
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-version = "0.19.2"
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-
-[package.extras]
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-testing = ["Django", "attrs", "colorama", "docopt", "pytest (<9.0.0)"]
-
 [[package]]
 name = "jinja2"
 version = "3.1.5"
@@ -916,20 +819,6 @@ python-dateutil = ">=2.7"
 [package.extras]
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-[[package]]
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-version = "0.1.7"
-description = "Inline Matplotlib backend for Jupyter"
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-
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-
 [[package]]
 name = "mergedeep"
 version = "1.3.4"
@@ -1163,66 +1052,66 @@ files = [
 
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 name = "numpy"
-version = "2.2.2"
+version = "2.2.3"
 description = "Fundamental package for array computing in Python"
 optional = false
 python-versions = ">=3.10"
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 ]
 
 [[package]]
@@ -1352,21 +1241,6 @@ files = [
 numpy = ">=1.23.5"
 types-pytz = ">=2022.1.1"
 
-[[package]]
-name = "parso"
-version = "0.8.4"
-description = "A Python Parser"
-optional = false
-python-versions = ">=3.6"
-files = [
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-
-[package.extras]
-qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
-testing = ["docopt", "pytest"]
-
 [[package]]
 name = "pathspec"
 version = "0.12.1"
@@ -1378,20 +1252,6 @@ files = [
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 ]
 
-[[package]]
-name = "pexpect"
-version = "4.9.0"
-description = "Pexpect allows easy control of interactive console applications."
-optional = false
-python-versions = "*"
-files = [
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-]
-
-[package.dependencies]
-ptyprocess = ">=0.5"
-
 [[package]]
 name = "pillow"
 version = "11.1.0"
@@ -1529,45 +1389,6 @@ nodeenv = ">=0.11.1"
 pyyaml = ">=5.1"
 virtualenv = ">=20.10.0"
 
-[[package]]
-name = "prompt-toolkit"
-version = "3.0.50"
-description = "Library for building powerful interactive command lines in Python"
-optional = false
-python-versions = ">=3.8.0"
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-
-[package.dependencies]
-wcwidth = "*"
-
-[[package]]
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-description = "Run a subprocess in a pseudo terminal"
-optional = false
-python-versions = "*"
-files = [
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-
-[[package]]
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-description = "Safely evaluate AST nodes without side effects"
-optional = false
-python-versions = "*"
-files = [
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-]
-
-[package.extras]
-tests = ["pytest"]
-
 [[package]]
 name = "pydantic"
 version = "2.10.6"
@@ -1732,22 +1553,6 @@ pyyaml = "*"
 [package.extras]
 extra = ["pygments (>=2.19.1)"]
 
-[[package]]
-name = "pymupdf"
-version = "1.25.3"
-description = "A high performance Python library for data extraction, analysis, conversion & manipulation of PDF (and other) documents."
-optional = false
-python-versions = ">=3.9"
-files = [
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-    {file = "pymupdf-1.25.3.tar.gz", hash = "sha256:b640187c64c5ac5d97505a92e836da299da79c2f689f3f94a67a37a493492193"},
-]
-
 [[package]]
 name = "pyparsing"
 version = "3.2.1"
@@ -2072,36 +1877,6 @@ files = [
     {file = "six-1.17.0.tar.gz", hash = "sha256:ff70335d468e7eb6ec65b95b99d3a2836546063f63acc5171de367e834932a81"},
 ]
 
-[[package]]
-name = "sniffio"
-version = "1.3.1"
-description = "Sniff out which async library your code is running under"
-optional = false
-python-versions = ">=3.7"
-files = [
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-    {file = "sniffio-1.3.1.tar.gz", hash = "sha256:f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc"},
-]
-
-[[package]]
-name = "stack-data"
-version = "0.6.3"
-description = "Extract data from python stack frames and tracebacks for informative displays"
-optional = false
-python-versions = "*"
-files = [
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-
-[package.dependencies]
-asttokens = ">=2.1.0"
-executing = ">=1.2.0"
-pure-eval = "*"
-
-[package.extras]
-tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
-
 [[package]]
 name = "tomli"
 version = "2.2.1"
@@ -2170,21 +1945,6 @@ virtualenv = ">=20.27.1"
 [package.extras]
 test = ["devpi-process (>=1.0.2)", "pytest (>=8.3.3)", "pytest-mock (>=3.14)"]
 
-[[package]]
-name = "traitlets"
-version = "5.14.3"
-description = "Traitlets Python configuration system"
-optional = false
-python-versions = ">=3.8"
-files = [
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-
-[package.extras]
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-test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.2)", "pytest-mock", "pytest-mypy-testing"]
-
 [[package]]
 name = "types-python-dateutil"
 version = "2.9.0.20241206"
@@ -2319,18 +2079,7 @@ files = [
 [package.extras]
 watchmedo = ["PyYAML (>=3.10)"]
 
-[[package]]
-name = "wcwidth"
-version = "0.2.13"
-description = "Measures the displayed width of unicode strings in a terminal"
-optional = false
-python-versions = "*"
-files = [
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-]
-
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.10,<4.0"
-content-hash = "9af086e594d70faf3e5f37061b19a6c6eb4f6e273b34d012f0e41ec7ea26fe69"
+content-hash = "f0d6b1a0d67607cb0708fa9a9028cfae0a14b8875a2dc8216569e54f2504fa3b"
diff --git a/pyproject.toml b/pyproject.toml
index b0c4aa8..c8dd92c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,14 +1,13 @@
 [tool.poetry]
 name = "biosim_client"
-version = "0.2.2"
+version = "0.0.1"
 description = "This is a library to access biosimulations.org APIs."
 authors = ["Jim Schaff <schaff@uchc.edu>"]
 repository = "https://github.com/biosimulations/biosim-client"
 documentation = "https://jcschaff.github.io/biosim-client/"
 readme = "README.md"
 packages = [
-    {include = "biosim_client"},
-    {include = "tests"},
+  {include = "biosim_client"}
 ]
 
 [tool.poetry.dependencies]
@@ -20,9 +19,6 @@ urllib3 = "^2.2.3"
 typing-extensions = "^4.12.2"
 python-dateutil = "^2.9.0.post0"
 matplotlib = "^3.9.2"
-ipython = "^8.32.0"
-pillow = "^11.1.0"
-pymupdf = "^1.25.3"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^8.0.0"
@@ -33,7 +29,6 @@ pre-commit = "^3.4.0"
 tox = "^4.11.1"
 types-python-dateutil = "^2.9.0.20241003"
 pandas-stubs = "^2.2.3.241009"
-sniffio = "^1.3.1"
 
 [tool.poetry.group.docs.dependencies]
 mkdocs = "^1.4.2"
@@ -46,12 +41,22 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.mypy]
 files = ["biosim_client"]
-exclude = [ "biosim_client/api/simdata/test/*", "biosim_client/api/biosim/test/*"]
-strict = true
+explicit_package_bases = "True"
+disallow_untyped_defs = "True"
+disallow_any_unimported = "True"
+no_implicit_optional = "True"
+check_untyped_defs = "True"
+warn_return_any = "True"
+warn_unused_ignores = "True"
+show_error_codes = "True"
 
 [[tool.mypy.overrides]]
-module = [ "biosim_client.api.*" ]
-disable_error_code = ["no-untyped-def", "no-any-return", "var-annotated", "no-untyped-call", "attr-defined"]
+module = [ "biosim_client.simdata_api.*" ]
+disable_error_code = ["no-untyped-def", "no-any-return", "var-annotated"]
+
+[[tool.mypy.overrides]]
+module = [ "biosim_client.simdata_api.test/*" ]
+disable_error_code = ["return"]
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
@@ -100,7 +105,7 @@ lint.ignore = [
 ]
 
 [tool.ruff.lint.per-file-ignores]
-"biosim_client/api/*" = [
+"biosim_client/simdata_api/*" = [
     "B904",
     "C405",
     "C409",