From 3224162527f93be9d660a68354e2fc4a12ac2e80 Mon Sep 17 00:00:00 2001
From: Yohsuke Fukai <ysk@yfukai.net>
Date: Mon, 8 Jul 2024 18:59:05 +0900
Subject: [PATCH 1/3] updated pydantic to v2

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index e812014..18a720a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,7 +39,7 @@ scipy = [
 networkx = "^2.6.1"
 pandas = ">=1.3.1,<3.0.0"
 typing-extensions = "^4.1.0"
-pydantic = "^1.10.2"
+pydantic = "^2.0"
 scikit-image = [
     { version = "^0.19.3", python = "<3.11" },
     { version = ">=0.20.0,<1.0.0", python = ">=3.11" }

From 514fc1e1e671040e16ac237836bd41117ab1852b Mon Sep 17 00:00:00 2001
From: Yohsuke Fukai <ysk@yfukai.net>
Date: Wed, 10 Jul 2024 09:46:02 +0900
Subject: [PATCH 2/3] updated lock file

---
 poetry.lock | 574 +++++++++++++++++++++++++++++++---------------------
 1 file changed, 348 insertions(+), 226 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 8790cb5..c24a324 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -11,6 +11,20 @@ files = [
     {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
 ]
 
+[[package]]
+name = "annotated-types"
+version = "0.7.0"
+description = "Reusable constraint types to use with typing.Annotated"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
+    {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
+]
+
+[package.dependencies]
+typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""}
+
 [[package]]
 name = "anyio"
 version = "4.4.0"
@@ -212,23 +226,25 @@ cryptography = "*"
 
 [[package]]
 name = "autodoc-pydantic"
-version = "1.9.1"
+version = "2.1.0"
 description = "Seamlessly integrate pydantic models in your Sphinx documentation."
 optional = false
-python-versions = "<4.0.0,>=3.7.1"
+python-versions = ">=3.8,<4.0.0"
 files = [
-    {file = "autodoc_pydantic-1.9.1-py3-none-any.whl", hash = "sha256:7b7c68ce3720f099ec85b7b8b9bd91414b8873704aa60f75489c2bcfe2d57bb5"},
-    {file = "autodoc_pydantic-1.9.1.tar.gz", hash = "sha256:0443987f1cc2516c8186e85d05a1816a314a19e1433b69a0a4b154f4acca3f9b"},
+    {file = "autodoc_pydantic-2.1.0-py3-none-any.whl", hash = "sha256:9f1f82ee3667589dfa08b21697be8bbd80b15110e838cd765bb1bf3ce1b0ea8f"},
+    {file = "autodoc_pydantic-2.1.0.tar.gz", hash = "sha256:3cf1b973e2f5ff0fbbe9b951c11827b5e32d3409e238f7f5782359426ab8d360"},
 ]
 
 [package.dependencies]
-pydantic = ">=1.5,<2.0.0"
-Sphinx = ">=3.4"
+importlib-metadata = {version = ">1", markers = "python_version <= \"3.8\""}
+pydantic = ">=2.0,<3.0.0"
+pydantic-settings = ">=2.0,<3.0.0"
+Sphinx = ">=4.0"
 
 [package.extras]
 dev = ["coverage (>=7,<8)", "flake8 (>=3,<4)", "pytest (>=7,<8)", "sphinx-copybutton (>=0.4,<0.5)", "sphinx-rtd-theme (>=1.0,<2.0)", "sphinx-tabs (>=3,<4)", "sphinxcontrib-mermaid (>=0.7,<0.8)", "tox (>=3,<4)"]
 docs = ["sphinx-copybutton (>=0.4,<0.5)", "sphinx-rtd-theme (>=1.0,<2.0)", "sphinx-tabs (>=3,<4)", "sphinxcontrib-mermaid (>=0.7,<0.8)"]
-erdantic = ["erdantic (>=0.5,<0.6)"]
+erdantic = ["erdantic (>=0.6,<0.7)"]
 test = ["coverage (>=7,<8)", "pytest (>=7,<8)"]
 
 [[package]]
@@ -300,13 +316,13 @@ css = ["tinycss2 (>=1.1.0,<1.3)"]
 
 [[package]]
 name = "certifi"
-version = "2024.6.2"
+version = "2024.7.4"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2024.6.2-py3-none-any.whl", hash = "sha256:ddc6c8ce995e6987e7faf5e3f1b02b302836a0e5d98ece18392cb1a36c72ad56"},
-    {file = "certifi-2024.6.2.tar.gz", hash = "sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516"},
+    {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"},
+    {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"},
 ]
 
 [[package]]
@@ -752,33 +768,33 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "debugpy"
-version = "1.8.1"
+version = "1.8.2"
 description = "An implementation of the Debug Adapter Protocol for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "debugpy-1.8.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:dda73bf69ea479c8577a0448f8c707691152e6c4de7f0c4dec5a4bc11dee516e"},
-    {file = "debugpy-1.8.1-cp310-cp310-win32.whl", hash = "sha256:3a79c6f62adef994b2dbe9fc2cc9cc3864a23575b6e387339ab739873bea53d0"},
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 ]
 
 [[package]]
@@ -890,69 +906,69 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
 
 [[package]]
 name = "filelock"
-version = "3.15.4"
+version = "3.12.4"
 description = "A platform independent file lock."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "filelock-3.15.4-py3-none-any.whl", hash = "sha256:6ca1fffae96225dab4c6eaf1c4f4f28cd2568d3ec2a44e15a08520504de468e7"},
-    {file = "filelock-3.15.4.tar.gz", hash = "sha256:2207938cbc1844345cb01a5a95524dae30f0ce089eba5b00378295a17e3e90cb"},
+    {file = "filelock-3.12.4-py3-none-any.whl", hash = "sha256:08c21d87ded6e2b9da6728c3dff51baf1dcecf973b768ef35bcbc3447edb9ad4"},
+    {file = "filelock-3.12.4.tar.gz", hash = "sha256:2e6f249f1f3654291606e046b09f1fd5eac39b360664c27f5aad072012f8bcbd"},
 ]
 
 [package.extras]
-docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8.0.1)", "pytest (>=7.4.3)", "pytest-asyncio (>=0.21)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)", "virtualenv (>=20.26.2)"]
-typing = ["typing-extensions (>=4.8)"]
+docs = ["furo (>=2023.7.26)", "sphinx (>=7.1.2)", "sphinx-autodoc-typehints (>=1.24)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.3)", "diff-cover (>=7.7)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest-timeout (>=2.1)"]
+typing = ["typing-extensions (>=4.7.1)"]
 
 [[package]]
 name = "fonttools"
-version = "4.53.0"
+version = "4.53.1"
 description = "Tools to manipulate font files"
 optional = false
 python-versions = ">=3.8"
 files = [
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 mic = ["olefile"]
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+    {file = "pydantic_core-2.20.1-pp39-pypy39_pp73-manylinux_2_5_i686.manylinux1_i686.whl", hash = "sha256:964faa8a861d2664f0c7ab0c181af0bea66098b1919439815ca8803ef136fc4e"},
+    {file = "pydantic_core-2.20.1-pp39-pypy39_pp73-musllinux_1_1_aarch64.whl", hash = "sha256:4dd484681c15e6b9a977c785a345d3e378d72678fd5f1f3c0509608da24f2ac0"},
+    {file = "pydantic_core-2.20.1-pp39-pypy39_pp73-musllinux_1_1_x86_64.whl", hash = "sha256:f6d6cff3538391e8486a431569b77921adfcdef14eb18fbf19b7c0a5294d4e6a"},
+    {file = "pydantic_core-2.20.1-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:a6d511cc297ff0883bc3708b465ff82d7560193169a8b93260f74ecb0a5e08a7"},
+    {file = "pydantic_core-2.20.1.tar.gz", hash = "sha256:26ca695eeee5f9f1aeeb211ffc12f10bcb6f71e2989988fda61dabd65db878d4"},
 ]
 
 [package.dependencies]
-typing-extensions = ">=4.2.0"
+typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
+
+[[package]]
+name = "pydantic-settings"
+version = "2.3.4"
+description = "Settings management using Pydantic"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pydantic_settings-2.3.4-py3-none-any.whl", hash = "sha256:11ad8bacb68a045f00e4f862c7a718c8a9ec766aa8fd4c32e39a0594b207b53a"},
+    {file = "pydantic_settings-2.3.4.tar.gz", hash = "sha256:c5802e3d62b78e82522319bbc9b8f8ffb28ad1c988a99311d04f2a6051fca0a7"},
+]
+
+[package.dependencies]
+pydantic = ">=2.7.0"
+python-dotenv = ">=0.21.0"
 
 [package.extras]
-dotenv = ["python-dotenv (>=0.10.4)"]
-email = ["email-validator (>=1.0.3)"]
+toml = ["tomli (>=2.0.1)"]
+yaml = ["pyyaml (>=6.0.1)"]
 
 [[package]]
 name = "pygments"
@@ -2922,6 +3029,20 @@ files = [
 [package.dependencies]
 six = ">=1.5"
 
+[[package]]
+name = "python-dotenv"
+version = "1.0.1"
+description = "Read key-value pairs from a .env file and set them as environment variables"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "python-dotenv-1.0.1.tar.gz", hash = "sha256:e324ee90a023d808f1959c46bcbc04446a10ced277783dc6ee09987c37ec10ca"},
+    {file = "python_dotenv-1.0.1-py3-none-any.whl", hash = "sha256:f7b63ef50f1b690dddf550d03497b66d609393b40b564ed0d674909a68ebf16a"},
+]
+
+[package.extras]
+cli = ["click (>=5.0)"]
+
 [[package]]
 name = "python-json-logger"
 version = "2.0.7"
@@ -3487,19 +3608,20 @@ files = [
 
 [[package]]
 name = "safety"
-version = "3.2.3"
+version = "3.2.4"
 description = "Checks installed dependencies for known vulnerabilities and licenses."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "safety-3.2.3-py3-none-any.whl", hash = "sha256:cda1e91749f610337a18b7f21f78267c127e44ebbbbcbbd419c83284279a5024"},
-    {file = "safety-3.2.3.tar.gz", hash = "sha256:414154934f1727daf8a6473493944fecb380540c3f00875dc1ae377382f7d83f"},
+    {file = "safety-3.2.4-py3-none-any.whl", hash = "sha256:242ff7ae448d7fb2ea455c90f44e3f2ca45be9c8559b2fe9dfc89617164a0f17"},
+    {file = "safety-3.2.4.tar.gz", hash = "sha256:bac0202016d736a2118057964a0e3983fa20ff2563fd103cac3f3ac1ed3fea11"},
 ]
 
 [package.dependencies]
 Authlib = ">=1.2.0"
 Click = ">=8.0.2"
 dparse = ">=0.6.4b0"
+filelock = ">=3.12.2,<3.13.0"
 jinja2 = ">=3.1.0"
 marshmallow = ">=3.15.0"
 packaging = ">=21.0"
@@ -3780,18 +3902,18 @@ win32 = ["pywin32"]
 
 [[package]]
 name = "setuptools"
-version = "70.1.0"
+version = "70.2.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "setuptools-70.1.0-py3-none-any.whl", hash = "sha256:d9b8b771455a97c8a9f3ab3448ebe0b29b5e105f1228bba41028be116985a267"},
-    {file = "setuptools-70.1.0.tar.gz", hash = "sha256:01a1e793faa5bd89abc851fa15d0a0db26f160890c7102cd8dce643e886b47f5"},
+    {file = "setuptools-70.2.0-py3-none-any.whl", hash = "sha256:b8b8060bb426838fbe942479c90296ce976249451118ef566a5a0b7d8b78fb05"},
+    {file = "setuptools-70.2.0.tar.gz", hash = "sha256:bd63e505105011b25c3c11f753f7e3b8465ea739efddaccef8f0efac2137bac1"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (==1.10.0)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.1)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (==1.10.0)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
 name = "shellingham"
@@ -4146,13 +4268,13 @@ all = ["defusedxml", "fsspec", "imagecodecs (>=2023.1.23)", "lxml", "matplotlib"
 
 [[package]]
 name = "tifffile"
-version = "2024.6.18"
+version = "2024.7.2"
 description = "Read and write TIFF files"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "tifffile-2024.6.18-py3-none-any.whl", hash = "sha256:67299c0445fc47463bbc71f3cb4676da2ab0242b0c6c6542a0680801b4b97d8a"},
-    {file = "tifffile-2024.6.18.tar.gz", hash = "sha256:57e0d2a034bcb6287ea3155d8716508dfac86443a257f6502b57ee7f8a33b3b6"},
+    {file = "tifffile-2024.7.2-py3-none-any.whl", hash = "sha256:5a2ee608c9cc1f2e044d943dacebddc71d4827b6fad150ef4c644b7aefbe2d1a"},
+    {file = "tifffile-2024.7.2.tar.gz", hash = "sha256:02e52e8872c0e9943add686d2fd8bcfb18f0a824760882cf5e35fcbc2c80e32c"},
 ]
 
 [package.dependencies]
@@ -4483,4 +4605,4 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools",
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.8,<3.13"
-content-hash = "4dc2c8c64cfd4af82286d6ef5c7c0008f8ac60cfd5d0cf911c1202ed3cab45fc"
+content-hash = "8f0a001424a39e344d552cc1c819cead85c07b9a3d5f604219a03ecbecd3662d"

From d9a977d622cddc798e489cf70dc458427b454131 Mon Sep 17 00:00:00 2001
From: Yohsuke Fukai <ysk@yfukai.net>
Date: Wed, 10 Jul 2024 10:29:54 +0900
Subject: [PATCH 3/3] mypy ignored failing test

---
 tests/test_tracking.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_tracking.py b/tests/test_tracking.py
index 7c242c9..06c0242 100644
--- a/tests/test_tracking.py
+++ b/tests/test_tracking.py
@@ -317,9 +317,9 @@ def test_gap_closing(shared_datadir: str) -> None:
 
 def test_no_accepting_wrong_argments() -> None:
     with pytest.raises(ValidationError):
-        lt = LapTrack(hogehoge=True)
+        lt = LapTrack(hogehoge=True)  # type: ignore
     with pytest.raises(ValidationError):
-        lt = LapTrack(fugafuga=True)
+        lt = LapTrack(fugafuga=True)  # type: ignore
 
 
 def test_no_accepting_wrong_backend() -> None: