From 2f716ca0c2930ab80c74346608311a8afef2fca1 Mon Sep 17 00:00:00 2001
From: Akio Taniguchi <13254278+astropenguin@users.noreply.github.com>
Date: Wed, 19 Mar 2025 04:23:51 +0000
Subject: [PATCH 01/11] #25 Update project dependencies

---
 .devcontainer/Dockerfile        |   11 -
 .devcontainer/devcontainer.json |   47 +-
 poetry.lock                     | 3229 +++++++++++++++----------------
 pyproject.toml                  |   54 +-
 4 files changed, 1623 insertions(+), 1718 deletions(-)
 delete mode 100644 .devcontainer/Dockerfile

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
deleted file mode 100644
index 27405f5..0000000
--- a/.devcontainer/Dockerfile
+++ /dev/null
@@ -1,11 +0,0 @@
-FROM python:3.10-slim
-
-ENV PATH=$PATH:/root/.local/bin
-ENV POETRY_VIRTUALENVS_CREATE=false
-ENV POETRY_VERSION=1.2.0
-
-RUN apt-get update \
-    && apt-get install -y curl gcc git tk-dev \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* \
-    && curl -sSL https://install.python-poetry.org | python -
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index a48b762..acbc737 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,26 +1,35 @@
 {
     "name": "fmflow",
-    "build": {
-        "context": "..",
-        "dockerfile": "Dockerfile"
+    "image":"python:3.12",
+    "containerEnv": {
+        "POETRY_VIRTUALENVS_CREATE": "false"
     },
-    "postCreateCommand": "poetry install",
-    "extensions": [
-        "github.vscode-pull-request-github",
-        "mhutchie.git-graph",
-        "ms-python.python",
-        "streetsidesoftware.code-spell-checker",
-        "tamasfe.even-better-toml"
+    "runArgs": [
+        "--name=fmflow"
     ],
-    "settings": {
-        "files.insertFinalNewline": true,
-        "files.trimTrailingWhitespace": true,
-        "python.formatting.provider": "black",
-        "python.languageServer": "Pylance",
-        "[python]": {
-            "editor.formatOnSave": true,
-            "editor.insertSpaces": true,
-            "editor.tabSize": 4
+    "onCreateCommand": "pip install poetry==1.8.5",
+    "postCreateCommand": "poetry install",
+    "customizations": {
+        "vscode": {
+            "extensions": [
+                "github.vscode-pull-request-github",
+                "mhutchie.git-graph",
+                "ms-python.black-formatter",
+                "ms-python.python",
+                "streetsidesoftware.code-spell-checker",
+                "tamasfe.even-better-toml"
+            ],
+            "settings": {
+                "files.insertFinalNewline": true,
+                "files.trimTrailingWhitespace": true,
+                "[python]": {
+                    "editor.defaultFormatter": "ms-python.black-formatter",
+                    "editor.formatOnSave": true,
+                    "editor.insertSpaces": true,
+                    "editor.tabSize": 4,
+                    "python.languageServer": "Pylance"
+                }
+            }
         }
     }
 }
diff --git a/poetry.lock b/poetry.lock
index c60a627..8006591 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,378 +1,701 @@
-[[package]]
-name = "alabaster"
-version = "0.7.12"
-description = "A configurable sidebar-enabled Sphinx theme"
-category = "dev"
-optional = false
-python-versions = "*"
-
-[[package]]
-name = "appnope"
-version = "0.1.3"
-description = "Disable App Nap on macOS >= 10.9"
-category = "dev"
-optional = false
-python-versions = "*"
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
 
 [[package]]
-name = "astropy"
-version = "4.3.1"
-description = "Astronomy and astrophysics core library"
-category = "main"
+name = "accessible-pygments"
+version = "0.0.5"
+description = "A collection of accessible pygments styles"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.9"
+files = [
+    {file = "accessible_pygments-0.0.5-py3-none-any.whl", hash = "sha256:88ae3211e68a1d0b011504b2ffc1691feafce124b845bd072ab6f9f66f34d4b7"},
+    {file = "accessible_pygments-0.0.5.tar.gz", hash = "sha256:40918d3e6a2b619ad424cb91e556bd3bd8865443d9f22f1dcdf79e33c8046872"},
+]
 
 [package.dependencies]
-importlib-metadata = {version = "*", markers = "python_version == \"3.7\""}
-numpy = ">=1.17"
-pyerfa = ">=1.7.3"
+pygments = ">=1.5"
 
 [package.extras]
-all = ["PyYAML (>=3.13)", "asdf (>=2.6)", "beautifulsoup4", "bleach", "bottleneck", "certifi", "dask[array]", "h5py", "html5lib", "ipython (>=4.2)", "jplephem", "matplotlib (>=3.0,!=3.4.0)", "mpmath", "pandas", "pytest", "pytz", "scipy (>=1.1)", "sortedcontainers"]
-docs = ["PyYAML (>=3.13)", "matplotlib (>=3.1,!=3.4.0)", "packaging", "pytest", "scipy (>=1.1)", "sphinx (<4)", "sphinx-astropy (>=1.3)", "sphinx-changelog (>=1.1.0)"]
-test = ["coverage", "ipython (>=4.2)", "objgraph", "packaging", "pytest-astropy (>=0.8)", "pytest-xdist", "sgp4 (>=2.3)", "skyfield (>=1.20)"]
+dev = ["pillow", "pkginfo (>=1.10)", "playwright", "pre-commit", "setuptools", "twine (>=5.0)"]
+tests = ["hypothesis", "pytest"]
+
+[[package]]
+name = "alabaster"
+version = "0.7.16"
+description = "A light, configurable Sphinx theme"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"},
+    {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
+]
 
 [[package]]
 name = "astropy"
-version = "5.1"
+version = "6.1.7"
 description = "Astronomy and astrophysics core library"
-category = "main"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.10"
+files = [
+    {file = "astropy-6.1.7-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:be954c5f7707a089609053665aeb76493b79e5c4753c39486761bc6d137bf040"},
+    {file = "astropy-6.1.7-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:b5e48df5ab2e3e521e82a7233a4b1159d071e64e6cbb76c45415dc68d3b97af1"},
+    {file = "astropy-6.1.7-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:55c78252633c644361e2f7092d71f80ef9c2e6649f08d97711d9f19af514aedc"},
+    {file = "astropy-6.1.7-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:985e5e74489d23f1a11953b6b283fccde3f46cb6c68fee4f7228e5f6d8350ba9"},
+    {file = "astropy-6.1.7-cp310-cp310-musllinux_1_2_x86_64.whl", hash = "sha256:dc2ea28ed41a3d92c39b1481d9c5be016ae58d68f144f3fd8cecffe503525bab"},
+    {file = "astropy-6.1.7-cp310-cp310-win32.whl", hash = "sha256:4e4badadd8dfa5dca08fd86e9a50a3a91af321975859f5941579e6b7ce9ba199"},
+    {file = "astropy-6.1.7-cp310-cp310-win_amd64.whl", hash = "sha256:8d7f6727689288ee08fc0a4a297fc7e8089d01718321646bd00fea0906ad63dc"},
+    {file = "astropy-6.1.7-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:09edca01276ee63f7b2ff511da9bfb432068ba3242e27ef27d76e5a171087b7e"},
+    {file = "astropy-6.1.7-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:072f62a67992393beb016dc80bee8fb994fda9aa69e945f536ed8ac0e51291e6"},
+    {file = "astropy-6.1.7-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:b2706156d3646f9c9a7fc810475d8ab0df4c717beefa8326552576a0f8ddca20"},
+    {file = "astropy-6.1.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:fcd99e627692f8e58bb3097d330bfbd109a22e00dab162a67f203b0a0601ad2c"},
+    {file = "astropy-6.1.7-cp311-cp311-musllinux_1_2_x86_64.whl", hash = "sha256:b0ebbcb637b2e9bcb73011f2b7890d7a3f5a41b66ccaad7c28f065e81e28f0b2"},
+    {file = "astropy-6.1.7-cp311-cp311-win32.whl", hash = "sha256:192b12ede49cd828362ab1a6ede2367fe203f4d851804ec22fa92e009a524281"},
+    {file = "astropy-6.1.7-cp311-cp311-win_amd64.whl", hash = "sha256:3cac64bcdf570c947019bd2bc96711eeb2c7763afe192f18c9551e52a6c296b2"},
+    {file = "astropy-6.1.7-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:f2a8bcbb1306052cc38c9eed2c9331bfafe2582b499a7321946abf74b26eb256"},
+    {file = "astropy-6.1.7-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:eaf88878684f9d31aff36475c90d101f4cff22fdd4fd50098d9950fd56994df7"},
+    {file = "astropy-6.1.7-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1cb8cd231e53556e4eebe0393ea95a8cea6b2ff4187c95ac4ff8b17e7a8da823"},
+    {file = "astropy-6.1.7-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5ad36334d138a4f71d6fdcf225a98ad1dad6c343da4362d5a47a71f5c9da3ca9"},
+    {file = "astropy-6.1.7-cp312-cp312-musllinux_1_2_x86_64.whl", hash = "sha256:dd731c526869d0c68507be7b31dd10871b7c44d310bb5495476505560c83cd33"},
+    {file = "astropy-6.1.7-cp312-cp312-win32.whl", hash = "sha256:662bacd7ae42561e038cbd85eea3b749308cf3575611a745b60f034d3350c97a"},
+    {file = "astropy-6.1.7-cp312-cp312-win_amd64.whl", hash = "sha256:5b4d02a98a0bf91ff7fd4ef0bd0ecca83c9497338cb88b61ec9f971350688222"},
+    {file = "astropy-6.1.7-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:fbeaf04427987c0c6fa2e579eb40011802b06fba6b3a7870e082d5c693564e1b"},
+    {file = "astropy-6.1.7-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:ab6e88241a14185b9404b02246329185b70292984aa0616b20a0628dfe4f4ebb"},
+    {file = "astropy-6.1.7-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a0529c75565feaabb629946806b4763ae7b02069aeff4c3b56a69e8a9e638500"},
+    {file = "astropy-6.1.7-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9c5ec347631da77573fc729ba04e5d89a3bc94500bf6037152a2d0f9965ae1ce"},
+    {file = "astropy-6.1.7-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:dc496f87aaccaa5c6624acc985b8770f039c5bbe74b120c8ed7bad3698e24e1b"},
+    {file = "astropy-6.1.7-cp313-cp313-win32.whl", hash = "sha256:b1e01d534383c038dbf8664b964fa4ea818c7419318830d3c732c750c64115c6"},
+    {file = "astropy-6.1.7-cp313-cp313-win_amd64.whl", hash = "sha256:af08cf2b0368f1ea585eb26a55d99a2de9e9b0bd30aba84b5329059c3ec33590"},
+    {file = "astropy-6.1.7.tar.gz", hash = "sha256:a405ac186306b6cb152e6df2f7444ab8bd764e4127d7519da1b3ae4dd65357ef"},
+]
 
 [package.dependencies]
-numpy = ">=1.18"
+astropy-iers-data = ">=0.2024.10.28.0.34.7"
+numpy = ">=1.23"
 packaging = ">=19.0"
-pyerfa = ">=2.0"
+pyerfa = ">=2.0.1.1"
 PyYAML = ">=3.13"
 
 [package.extras]
-all = ["asdf (>=2.10.0)", "beautifulsoup4", "bleach", "bottleneck", "certifi", "dask[array]", "h5py", "html5lib", "ipython (>=4.2)", "jplephem", "matplotlib (>=3.1,!=3.4.0,!=3.5.2)", "mpmath", "pandas", "pyarrow (>=5.0.0)", "pytest (>=7.0)", "pytz", "scipy (>=1.3)", "sortedcontainers", "typing-extensions (>=3.10.0.1)"]
-docs = ["Jinja2 (<3.1)", "matplotlib (>=3.1,!=3.4.0,!=3.5.2)", "pytest (>=7.0)", "scipy (>=1.3)", "sphinx (<4)", "sphinx-astropy (>=1.6)", "sphinx-changelog (>=1.1.0)"]
-recommended = ["matplotlib (>=3.1,!=3.4.0,!=3.5.2)", "scipy (>=1.3)"]
-test = ["pytest (>=7.0)", "pytest-astropy (>=0.10)", "pytest-astropy-header (>=0.2.1)", "pytest-doctestplus (>=0.12)", "pytest-xdist"]
-test_all = ["coverage", "ipython (>=4.2)", "objgraph", "pytest (>=7.0)", "pytest-astropy (>=0.9)", "pytest-astropy-header (>=0.2.1)", "pytest-doctestplus (>=0.12)", "pytest-xdist", "sgp4 (>=2.3)", "skyfield (>=1.20)"]
+all = ["asdf-astropy (>=0.3)", "astropy[recommended]", "astropy[typing]", "beautifulsoup4", "bleach", "bottleneck", "certifi", "dask[array]", "fsspec[http] (>=2023.4.0)", "h5py", "html5lib", "ipython (>=4.2)", "jplephem", "mpmath", "pandas", "pre-commit", "pyarrow (>=7.0.0)", "pytest (>=7.0)", "pytz", "s3fs (>=2023.4.0)", "sortedcontainers"]
+docs = ["Jinja2 (>=3.1.3)", "astropy[recommended]", "matplotlib (>=3.9.1)", "numpy (<2.0)", "pytest (>=7.0)", "sphinx", "sphinx-astropy[confv2] (>=1.9.1)", "sphinx-changelog (>=1.2.0)", "sphinx_design", "sphinxcontrib-globalsubs (>=0.1.1)", "tomli"]
+recommended = ["matplotlib (>=3.5.0,!=3.5.2)", "scipy (>=1.8)"]
+test = ["pytest (>=7.0)", "pytest-astropy (>=0.10)", "pytest-astropy-header (>=0.2.1)", "pytest-doctestplus (>=0.12)", "pytest-xdist", "threadpoolctl"]
+test-all = ["array-api-strict", "astropy[test]", "coverage[toml]", "ipython (>=4.2)", "objgraph", "sgp4 (>=2.3)", "skyfield (>=1.20)"]
+typing = ["typing_extensions (>=4.0.0)"]
 
 [[package]]
-name = "asttokens"
-version = "2.0.8"
-description = "Annotate AST trees with source code positions"
-category = "dev"
+name = "astropy-iers-data"
+version = "0.2025.3.17.0.34.53"
+description = "IERS Earth Rotation and Leap Second tables for the astropy core package"
 optional = false
-python-versions = "*"
-
-[package.dependencies]
-six = "*"
+python-versions = ">=3.8"
+files = [
+    {file = "astropy_iers_data-0.2025.3.17.0.34.53-py3-none-any.whl", hash = "sha256:8006784932c625121c091f7b069b3fb4d0f471f63fe5b1e740d6d8f9f75171f7"},
+    {file = "astropy_iers_data-0.2025.3.17.0.34.53.tar.gz", hash = "sha256:646f050d4af4772ac5a0181fd133a452118ca5b4485af69ebe371ff51129ea28"},
+]
 
 [package.extras]
-test = ["astroid (<=2.5.3)", "pytest"]
+docs = ["pytest"]
+test = ["hypothesis", "pytest", "pytest-remotedata"]
 
 [[package]]
-name = "attrs"
-version = "22.1.0"
-description = "Classes Without Boilerplate"
-category = "dev"
+name = "asttokens"
+version = "3.0.0"
+description = "Annotate AST trees with source code positions"
 optional = false
-python-versions = ">=3.5"
+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]
-dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"]
-docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"]
-tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"]
-tests_no_zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"]
+astroid = ["astroid (>=2,<4)"]
+test = ["astroid (>=2,<4)", "pytest", "pytest-cov", "pytest-xdist"]
 
 [[package]]
-name = "Babel"
-version = "2.10.3"
+name = "babel"
+version = "2.17.0"
 description = "Internationalization utilities"
-category = "dev"
 optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-pytz = ">=2015.7"
+python-versions = ">=3.8"
+files = [
+    {file = "babel-2.17.0-py3-none-any.whl", hash = "sha256:4d0b53093fdfb4b21c92b5213dba5a1b23885afa8383709427046b21c366e5f2"},
+    {file = "babel-2.17.0.tar.gz", hash = "sha256:0c54cffb19f690cdcc52a3b50bcbf71e07a808d1c80d549f2459b9d2cf0afb9d"},
+]
 
-[[package]]
-name = "backcall"
-version = "0.2.0"
-description = "Specifications for callback functions passed in to an API"
-category = "dev"
-optional = false
-python-versions = "*"
+[package.extras]
+dev = ["backports.zoneinfo", "freezegun (>=1.0,<2.0)", "jinja2 (>=3.0)", "pytest (>=6.0)", "pytest-cov", "pytz", "setuptools", "tzdata"]
 
 [[package]]
 name = "beautifulsoup4"
-version = "4.11.1"
+version = "4.13.3"
 description = "Screen-scraping library"
-category = "dev"
 optional = false
-python-versions = ">=3.6.0"
+python-versions = ">=3.7.0"
+files = [
+    {file = "beautifulsoup4-4.13.3-py3-none-any.whl", hash = "sha256:99045d7d3f08f91f0d656bc9b7efbae189426cd913d830294a15eefa0ea4df16"},
+    {file = "beautifulsoup4-4.13.3.tar.gz", hash = "sha256:1bd32405dacc920b42b83ba01644747ed77456a65760e285fbc47633ceddaf8b"},
+]
 
 [package.dependencies]
 soupsieve = ">1.2"
+typing-extensions = ">=4.0.0"
 
 [package.extras]
+cchardet = ["cchardet"]
+chardet = ["chardet"]
+charset-normalizer = ["charset-normalizer"]
 html5lib = ["html5lib"]
 lxml = ["lxml"]
 
 [[package]]
 name = "black"
-version = "22.8.0"
+version = "25.1.0"
 description = "The uncompromising code formatter."
-category = "dev"
 optional = false
-python-versions = ">=3.6.2"
+python-versions = ">=3.9"
+files = [
+    {file = "black-25.1.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:759e7ec1e050a15f89b770cefbf91ebee8917aac5c20483bc2d80a6c3a04df32"},
+    {file = "black-25.1.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:0e519ecf93120f34243e6b0054db49c00a35f84f195d5bce7e9f5cfc578fc2da"},
+    {file = "black-25.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:055e59b198df7ac0b7efca5ad7ff2516bca343276c466be72eb04a3bcc1f82d7"},
+    {file = "black-25.1.0-cp310-cp310-win_amd64.whl", hash = "sha256:db8ea9917d6f8fc62abd90d944920d95e73c83a5ee3383493e35d271aca872e9"},
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 graphite = ["lz4 (>=1.7.4.2)"]
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 pathops = ["skia-pathops (>=0.5.0)"]
 plot = ["matplotlib"]
 repacker = ["uharfbuzz (>=0.23.0)"]
 symfont = ["sympy"]
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 ufo = ["fs (>=2.2.0,<3)"]
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 [[package]]
 name = "idna"
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+version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
-category = "dev"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
+files = [
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-[package.extras]
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-python-versions = "*"
-
-[[package]]
-name = "ipython"
-version = "7.34.0"
-description = "IPython: Productive Interactive Computing"
-category = "dev"
+version = "2.0.0"
+description = "brain-dead simple config-ini parsing"
 optional = false
 python-versions = ">=3.7"
-
-[package.dependencies]
-appnope = {version = "*", markers = "sys_platform == \"darwin\""}
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-traitlets = ">=4.2"
-
-[package.extras]
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-kernel = ["ipykernel"]
-nbconvert = ["nbconvert"]
-nbformat = ["nbformat"]
-notebook = ["ipywidgets", "notebook"]
-parallel = ["ipyparallel"]
-qtconsole = ["qtconsole"]
-test = ["ipykernel", "nbformat", "nose (>=0.10.1)", "numpy (>=1.17)", "pygments", "requests", "testpath"]
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+]
 
 [[package]]
 name = "ipython"
-version = "8.5.0"
+version = "8.34.0"
 description = "IPython: Productive Interactive Computing"
-category = "dev"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.10"
+files = [
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-appnope = {version = "*", markers = "sys_platform == \"darwin\""}
-backcall = "*"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 decorator = "*"
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-pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
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-traitlets = ">=5"
+stack_data = "*"
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+typing_extensions = {version = ">=4.6", markers = "python_version < \"3.12\""}
 
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+version = "0.19.2"
 description = "An autocompletion tool for Python that can be used for text editors."
-category = "dev"
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 python-versions = ">=3.6"
+files = [
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 [package.dependencies]
-parso = ">=0.8.0,<0.9.0"
+parso = ">=0.8.4,<0.9.0"
 
 [package.extras]
-qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
-testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<7.0.0)"]
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+testing = ["Django", "attrs", "colorama", "docopt", "pytest (<9.0.0)"]
 
 [[package]]
-name = "Jinja2"
-version = "3.1.2"
+name = "jinja2"
+version = "3.1.6"
 description = "A very fast and expressive template engine."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
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+]
 
 [package.dependencies]
 MarkupSafe = ">=2.0"
@@ -382,328 +705,763 @@ i18n = ["Babel (>=2.7)"]
 
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-tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
+docs = ["furo", "olefile", "sphinx (>=8.1)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinxext-opengraph"]
+fpx = ["olefile"]
+mic = ["olefile"]
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+typing = ["typing-extensions"]
+xmp = ["defusedxml"]
 
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-version = "2.5.2"
-description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "dev"
+version = "4.3.6"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
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-python-versions = ">=3.7"
+python-versions = ">=3.8"
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+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=8.3.2)", "pytest-cov (>=5)", "pytest-mock (>=3.14)"]
+type = ["mypy (>=1.11.2)"]
 
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-category = "dev"
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-python-versions = ">=3.6"
-
-[package.dependencies]
-importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
+python-versions = ">=3.8"
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+]
 
 [package.extras]
 dev = ["pre-commit", "tox"]
@@ -711,11 +1469,14 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
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-version = "3.0.31"
+version = "3.0.50"
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-category = "dev"
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-python-versions = ">=3.6.2"
+python-versions = ">=3.8.0"
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+]
 
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@@ -724,397 +1485,553 @@ wcwidth = "*"
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-category = "dev"
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+files = [
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 [package.extras]
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+standalone = ["Sphinx (>=5)"]
+test = ["defusedxml (>=0.7.1)", "pytest"]
 
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-category = "dev"
+version = "2.0.0"
+description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
+files = [
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+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "stack-data"
-version = "0.5.0"
+version = "0.6.3"
 description = "Extract data from python stack frames and tracebacks for informative displays"
-category = "dev"
 optional = false
 python-versions = "*"
+files = [
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 [package.dependencies]
-asttokens = "*"
-executing = "*"
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+executing = ">=1.2.0"
 pure-eval = "*"
 
 [package.extras]
@@ -1122,1160 +2039,168 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
 
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+python-versions = ">=3.9"
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 [[package]]
 name = "tqdm"
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 description = "Fast, Extensible Progress Meter"
-category = "main"
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
+python-versions = ">=3.7"
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 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [package.extras]
-dev = ["py-make (>=0.1.0)", "twine", "wheel"]
+dev = ["nbval", "pytest (>=6)", "pytest-asyncio (>=0.24)", "pytest-cov", "pytest-timeout"]
+discord = ["requests"]
 notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
 
 [[package]]
 name = "traitlets"
-version = "5.3.0"
-description = ""
-category = "dev"
+version = "5.14.3"
+description = "Traitlets Python configuration system"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
+files = [
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 [package.extras]
-test = ["pre-commit", "pytest"]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
+test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.2)", "pytest-mock", "pytest-mypy-testing"]
 
 [[package]]
-name = "typed-ast"
-version = "1.5.4"
-description = "a fork of Python 2 and 3 ast modules with type comment support"
-category = "dev"
+name = "typing-extensions"
+version = "4.12.2"
+description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
+files = [
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+]
 
 [[package]]
-name = "typing-extensions"
-version = "4.3.0"
-description = "Backported and Experimental Type Hints for Python 3.7+"
-category = "main"
+name = "tzdata"
+version = "2025.1"
+description = "Provider of IANA time zone data"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=2"
+files = [
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+    {file = "tzdata-2025.1.tar.gz", hash = "sha256:24894909e88cdb28bd1636c6887801df64cb485bd593f2fd83ef29075a81d694"},
+]
 
 [[package]]
 name = "urllib3"
-version = "1.26.12"
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 description = "HTTP library with thread-safe connection pooling, file post, and more."
-category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, <4"
+python-versions = ">=3.9"
+files = [
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 [package.extras]
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-secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
-socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+h2 = ["h2 (>=4,<5)"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "wcwidth"
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+version = "0.2.13"
 description = "Measures the displayed width of unicode strings in a terminal"
-category = "dev"
 optional = false
 python-versions = "*"
+files = [
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+]
 
 [[package]]
 name = "xarray"
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-description = "N-D labeled arrays and datasets in Python"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-
-[package.dependencies]
-importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
-numpy = ">=1.18"
-pandas = ">=1.1"
-typing-extensions = {version = ">=3.7", markers = "python_version < \"3.8\""}
-
-[package.extras]
-accel = ["bottleneck", "numbagg", "scipy"]
-complete = ["bottleneck", "cfgrib", "cftime", "dask[complete]", "fsspec", "h5netcdf", "matplotlib", "nc-time-axis", "netCDF4", "numbagg", "pooch", "pydap", "rasterio", "scipy", "seaborn", "zarr"]
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-io = ["cfgrib", "cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap", "rasterio", "scipy", "zarr"]
-parallel = ["dask[complete]"]
-viz = ["matplotlib", "nc-time-axis", "seaborn"]
-
-[[package]]
-name = "xarray"
-version = "2022.6.0"
+version = "2025.1.2"
 description = "N-D labeled arrays and datasets in Python"
-category = "main"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.10"
+files = [
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-packaging = ">=20.0"
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+pandas = ">=2.1"
 
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-io = ["cfgrib", "cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap", "rasterio", "scipy", "zarr"]
+accel = ["bottleneck", "flox", "numba (>=0.54)", "numbagg", "opt_einsum", "scipy"]
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 parallel = ["dask[complete]"]
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-
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-category = "main"
-optional = false
-python-versions = ">=3.7"
-
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+viz = ["cartopy", "matplotlib", "nc-time-axis", "seaborn"]
 
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+lock-version = "2.0"
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+content-hash = "cb535a9295a44187a90696c3c258fc2ee53d75e0179699d115f4b75b87d5ab6b"
diff --git a/pyproject.toml b/pyproject.toml
index b0bc274..16b791a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,44 +10,26 @@ homepage = "https://github.com/fmlo-dev/fmflow/"
 documentation = "https://fmlo-dev.github.io/fmflow/"
 
 [tool.poetry.dependencies]
-python = "^3.7"
-astropy = [
-    { version = ">=4.3, <5.0", python = ">=3.7, <3.8" },
-    { version = "^5.0", python = ">=3.8, <3.11" },
-]
-matplotlib = "^3.2"
-netcdf4 = "^1.6"
-numba = "^0.56"
-numpy = [
-    { version = ">=1.21, <1.22", python = ">=3.7, <3.8" },
-    { version = "^1.22", python = ">=3.8, <3.11" },
-]
-pyyaml = "^6.0"
-scikit-learn = [
-    { version = ">=1.0, <1.1", python = ">=3.7, <3.8" },
-    { version = "^1.1", python = ">=3.8, <3.11" },
-]
-scipy = [
-    { version = ">=1.7, <1.8", python = ">=3.7, <3.8" },
-    { version = "^1.8", python = ">=3.8, <3.11" },
-]
-tqdm = "^4.64"
-xarray = [
-    { version = ">=0.20, <0.21", python = ">=3.7, <3.8" },
-    { version = ">=0.21, <2023", python = ">=3.8, <3.11" },
-]
+python = ">=3.10, <3.14"
+astropy = ">=6, <8"
+matplotlib = "^3"
+netcdf4 = "^1"
+numba = "^0.60"
+numpy = "^2"
+pyyaml = "^6"
+scikit-learn = "^1"
+scipy = "^1"
+tqdm = "^4"
+xarray = ">=2024, <2026"
 
 [tool.poetry.group.dev.dependencies]
-black = "^22.8"
-ipython = [
-    { version = ">=7.34, <8.0", python = ">=3.7, <3.8" },
-    { version = "^8.0", python = ">=3.8, <3.11" },
-]
-myst-parser = "^0.18"
-pydata-sphinx-theme = "^0.9"
-pyright = "^1.1"
-pytest = "^7.1"
-sphinx = "^5.1"
+black = "^25"
+ipython = "^8"
+myst-parser = "^3"
+pydata-sphinx-theme = "^0.15"
+pyright = "^1"
+pytest = "^8"
+sphinx = "^7"
 
 [build-system]
 requires = ["poetry-core"]

From 32145330dce8a06a81f0f2c0b3b2395ebfd5cd75 Mon Sep 17 00:00:00 2001
From: Akio Taniguchi <13254278+astropenguin@users.noreply.github.com>
Date: Wed, 19 Mar 2025 04:25:09 +0000
Subject: [PATCH 02/11] #25 Format codes by the latest Black formatter

---
 fmflow/fits/aste/functions.py   | 2 +-
 fmflow/fits/nro45m/functions.py | 1 +
 fmflow/models/__init__.py       | 1 +
 3 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/fmflow/fits/aste/functions.py b/fmflow/fits/aste/functions.py
index 6fb0262..9f94d29 100644
--- a/fmflow/fits/aste/functions.py
+++ b/fmflow/fits/aste/functions.py
@@ -268,7 +268,7 @@ def eof(f):
             data["arraydata"][on] *= np.mean(data["dalpha"][on])
 
         ## apply ZERO and coeff. to R data
-        for (r, sky) in zip(rs, skys):
+        for r, sky in zip(rs, skys):
             data["arraydata"][r] -= data["arraydata"][zero]
             data["arraydata"][r] *= data["dbeta"][sky]
 
diff --git a/fmflow/fits/nro45m/functions.py b/fmflow/fits/nro45m/functions.py
index 38dfa50..8e3e3bf 100644
--- a/fmflow/fits/nro45m/functions.py
+++ b/fmflow/fits/nro45m/functions.py
@@ -34,6 +34,7 @@
 CONF_ANTENNA = get_data("fmflow", "data/nro45m_antennalog.yaml")
 BAR_FORMAT = "{l_bar}{bar}| {n_fmt}/{total_fmt} [{elapsed}<{remaining}]"
 
+
 # functions
 def fromnro45m(fmlolog, backendlog, antennalog=None, byteorder="<"):
     """Read logging data of NRO45m and merge them into a FITS object.
diff --git a/fmflow/models/__init__.py b/fmflow/models/__init__.py
index 8050eb7..7b5692a 100644
--- a/fmflow/models/__init__.py
+++ b/fmflow/models/__init__.py
@@ -1,5 +1,6 @@
 # coding: utf-8
 
+
 # base model
 class BaseModel(object):
     def __init__(self, params, logger=None):

From e81f48387a3e088903b1beb1f868a3922053a51a Mon Sep 17 00:00:00 2001
From: Akio Taniguchi <13254278+astropenguin@users.noreply.github.com>
Date: Wed, 19 Mar 2025 04:27:52 +0000
Subject: [PATCH 03/11] #25 Use raw strings for regex patterns

---
 fmflow/fits/aste/functions.py   | 4 ++--
 fmflow/fits/nro45m/functions.py | 2 +-
 fmflow/utils/fits/functions.py  | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/fmflow/fits/aste/functions.py b/fmflow/fits/aste/functions.py
index 9f94d29..fd960da 100644
--- a/fmflow/fits/aste/functions.py
+++ b/fmflow/fits/aste/functions.py
@@ -287,7 +287,7 @@ def eof(f):
     tforms = map(fm.utils.ctype_to_tform, ctypes, shapes)
     fmts = OrderedDict(item for item in zip(names, tforms))
 
-    num = re.findall("\d+", fmts.pop("iary_data"))[0]
+    num = re.findall(r"\d+", fmts.pop("iary_data"))[0]
     fmts["arraydata"] = "{}E".format(num)
     fmts["starttime"] = "A26"
     fmts["arrayid"] = fmts.pop("cary_name")
@@ -339,7 +339,7 @@ def make_obsinfo_mac(hdus):
     header["object"] = obsinfo["cobj_name"]
     header["ra"] = obsinfo["dsrc_pos"][0][0]
     header["dec"] = obsinfo["dsrc_pos"][1][0]
-    header["equinox"] = float(re.findall("\d+", obsinfo["cepoch"])[0])
+    header["equinox"] = float(re.findall(r"\d+", obsinfo["cepoch"])[0])
 
     data = OrderedDict()
     data["arrayid"] = np.unique(datinfo["arrayid"])
diff --git a/fmflow/fits/nro45m/functions.py b/fmflow/fits/nro45m/functions.py
index 8e3e3bf..a078be0 100644
--- a/fmflow/fits/nro45m/functions.py
+++ b/fmflow/fits/nro45m/functions.py
@@ -335,7 +335,7 @@ def make_obsinfo_sam45(hdus):
     header["object"] = obsinfo["cobj_name"]
     header["ra"] = obsinfo["dsrc_pos"][0][0]
     header["dec"] = obsinfo["dsrc_pos"][1][0]
-    header["equinox"] = float(re.findall("\d+", obsinfo["cepoch"])[0])
+    header["equinox"] = float(re.findall(r"\d+", obsinfo["cepoch"])[0])
 
     data = OrderedDict()
     arrayids = np.unique(datinfo["arrayid"])
diff --git a/fmflow/utils/fits/functions.py b/fmflow/utils/fits/functions.py
index 704a5cb..2edef51 100644
--- a/fmflow/utils/fits/functions.py
+++ b/fmflow/utils/fits/functions.py
@@ -52,7 +52,7 @@ def ctype_to_tform(ctype, shape=None):
         return count + "B"
     # character
     elif re.search("s", ctype):
-        num = re.findall("\d+", ctype)[0]
+        num = re.findall(r"\d+", ctype)[0]
         return count + "A{}".format(num)
     # otherwise
     else:
@@ -94,7 +94,7 @@ def dtype_to_tform(dtype, shape=None):
         return count + "D"
     # character or Unicode
     elif re.search("S|U", dtype):
-        num = re.findall("\d+", dtype)[0]
+        num = re.findall(r"\d+", dtype)[0]
         return count + "A{}".format(num)
     # otherwise
     else:

From 39792197bcc87744588e57aed7bdb5f1e5d67f89 Mon Sep 17 00:00:00 2001
From: Akio Taniguchi <13254278+astropenguin@users.noreply.github.com>
Date: Wed, 19 Mar 2025 04:28:35 +0000
Subject: [PATCH 04/11] #25 Use SafeLoader for loading YAML files

---
 fmflow/fits/aste/functions.py       | 12 ++++++------
 fmflow/fits/nro45m/functions.py     | 12 ++++++------
 fmflow/models/atmosphere/classes.py |  4 ++--
 3 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/fmflow/fits/aste/functions.py b/fmflow/fits/aste/functions.py
index fd960da..c0fb485 100644
--- a/fmflow/fits/aste/functions.py
+++ b/fmflow/fits/aste/functions.py
@@ -91,7 +91,7 @@ def read_fmlolog(fmlolog):
     fmlolog = Path(fmlolog).expanduser()
 
     # read fmlolog
-    fmts = yaml.load(CONF_FMLOLOG, Loader=yaml.BaseLoader)
+    fmts = yaml.load(CONF_FMLOLOG, Loader=yaml.SafeLoader)
     names, dtypes, units = list(map(list, zip(*fmts)))
     tforms = list(map(fm.utils.dtype_to_tform, dtypes))
 
@@ -123,7 +123,7 @@ def read_antennalog(antennalog):
     antennalog = Path(antennalog).expanduser()
 
     # read antennalog
-    fmts = yaml.load(CONF_ANTENNA, Loader=yaml.BaseLoader)
+    fmts = yaml.load(CONF_ANTENNA, Loader=yaml.SafeLoader)
     names, dtypes, units = list(map(list, zip(*fmts)))
     tforms = list(map(fm.utils.dtype_to_tform, dtypes))
 
@@ -174,7 +174,7 @@ def check_backend(backendlog, byteorder):
     # path
     backendlog = Path(backendlog).expanduser()
 
-    com = yaml.load(CONF_BACKEND_COM, Loader=yaml.BaseLoader)
+    com = yaml.load(CONF_BACKEND_COM, Loader=yaml.SafeLoader)
     head = fm.utils.CStructReader(com["head"], IGNORED_KEY, byteorder)
     ctl = fm.utils.CStructReader(com["ctl"], IGNORED_KEY, byteorder)
 
@@ -203,8 +203,8 @@ def read_backendlog_mac(backendlog, byteorder):
     # path
     backendlog = Path(backendlog).expanduser()
 
-    com = yaml.load(CONF_BACKEND_COM, Loader=yaml.BaseLoader)
-    mac = yaml.load(CONF_BACKEND_MAC, Loader=yaml.BaseLoader)
+    com = yaml.load(CONF_BACKEND_COM, Loader=yaml.SafeLoader)
+    mac = yaml.load(CONF_BACKEND_MAC, Loader=yaml.SafeLoader)
     head = fm.utils.CStructReader(com["head"], IGNORED_KEY, byteorder)
     ctl = fm.utils.CStructReader(com["ctl"], IGNORED_KEY, byteorder)
     obs = fm.utils.CStructReader(mac["obs"], IGNORED_KEY, byteorder)
@@ -324,7 +324,7 @@ def make_obsinfo_mac(hdus):
     p = fm.utils.DatetimeParser()
     flag = np.array(obsinfo["iary_usefg"], dtype=bool)
 
-    fmts = yaml.load(CONF_OBSINFO, Loader=yaml.BaseLoader)
+    fmts = yaml.load(CONF_OBSINFO, Loader=yaml.SafeLoader)
     names, dtypes, units = list(map(list, zip(*fmts)))
     tforms = list(map(fm.utils.dtype_to_tform, dtypes))
 
diff --git a/fmflow/fits/nro45m/functions.py b/fmflow/fits/nro45m/functions.py
index a078be0..79f6c93 100644
--- a/fmflow/fits/nro45m/functions.py
+++ b/fmflow/fits/nro45m/functions.py
@@ -89,7 +89,7 @@ def read_fmlolog(fmlolog):
     fmlolog = Path(fmlolog).expanduser()
 
     # read fmlolog
-    fmts = yaml.load(CONF_FMLOLOG, Loader=yaml.BaseLoader)
+    fmts = yaml.load(CONF_FMLOLOG, Loader=yaml.SafeLoader)
     names, dtypes, units = list(map(list, zip(*fmts)))
     tforms = list(map(fm.utils.dtype_to_tform, dtypes))
 
@@ -121,7 +121,7 @@ def read_antennalog(antennalog):
     antennalog = Path(antennalog).expanduser()
 
     # read antennalog
-    fmts = yaml.load(CONF_ANTENNA, Loader=yaml.BaseLoader)
+    fmts = yaml.load(CONF_ANTENNA, Loader=yaml.SafeLoader)
     names, dtypes, units = list(map(list, zip(*fmts)))
     tforms = list(map(fm.utils.dtype_to_tform, dtypes))
 
@@ -172,7 +172,7 @@ def check_backend(backendlog, byteorder):
     # path
     backendlog = Path(backendlog).expanduser()
 
-    com = yaml.load(CONF_BACKEND_COM, Loader=yaml.BaseLoader)
+    com = yaml.load(CONF_BACKEND_COM, Loader=yaml.SafeLoader)
     head = fm.utils.CStructReader(com["head"], IGNORED_KEY, byteorder)
     ctl = fm.utils.CStructReader(com["ctl"], IGNORED_KEY, byteorder)
 
@@ -201,8 +201,8 @@ def read_backendlog_sam45(backendlog, byteorder):
     # path
     backendlog = Path(backendlog).expanduser()
 
-    com = yaml.load(CONF_BACKEND_COM, Loader=yaml.BaseLoader)
-    sam = yaml.load(CONF_BACKEND_SAM, Loader=yaml.BaseLoader)
+    com = yaml.load(CONF_BACKEND_COM, Loader=yaml.SafeLoader)
+    sam = yaml.load(CONF_BACKEND_SAM, Loader=yaml.SafeLoader)
     head = fm.utils.CStructReader(com["head"], IGNORED_KEY, byteorder)
     ctl = fm.utils.CStructReader(com["ctl"], IGNORED_KEY, byteorder)
     obs = fm.utils.CStructReader(sam["obs"], IGNORED_KEY, byteorder)
@@ -320,7 +320,7 @@ def make_obsinfo_sam45(hdus):
     p = fm.utils.DatetimeParser()
     flag = np.array(obsinfo["iary_usefg"], dtype=bool)
 
-    fmts = yaml.load(CONF_OBSINFO, Loader=yaml.BaseLoader)
+    fmts = yaml.load(CONF_OBSINFO, Loader=yaml.SafeLoader)
     names, dtypes, units = list(map(list, zip(*fmts)))
     tforms = list(map(fm.utils.dtype_to_tform, dtypes))
 
diff --git a/fmflow/models/atmosphere/classes.py b/fmflow/models/atmosphere/classes.py
index 41e6f2b..fd5f4de 100644
--- a/fmflow/models/atmosphere/classes.py
+++ b/fmflow/models/atmosphere/classes.py
@@ -26,8 +26,8 @@
 C = constants.c.value
 AMCMD = ["am", "-"]
 AMDATA = get_data("fmflow", "data/am.yaml")
-AMCONFIG = yaml.load(AMDATA, Loader=yaml.BaseLoader)["config"]
-AMLAYERS = yaml.load(AMDATA, Loader=yaml.BaseLoader)["layers"]
+AMCONFIG = yaml.load(AMDATA, Loader=yaml.SafeLoader)["config"]
+AMLAYERS = yaml.load(AMDATA, Loader=yaml.SafeLoader)["layers"]
 
 
 # classes

From 7fd92a2dce4bfdcdecc0734719e34328a7814f65 Mon Sep 17 00:00:00 2001
From: Akio Taniguchi <13254278+astropenguin@users.noreply.github.com>
Date: Wed, 19 Mar 2025 04:36:56 +0000
Subject: [PATCH 05/11] #25 Update workflows

---
 .../workflows/{gh-pages.yml => gh-pages.yaml} | 18 +++++-----
 .github/workflows/pypi.yaml                   | 22 ++++++++++++
 .github/workflows/pypi.yml                    | 20 -----------
 .github/workflows/tests.yaml                  | 34 +++++++++++++++++++
 .github/workflows/tests.yml                   | 33 ------------------
 README.md                                     |  2 +-
 6 files changed, 66 insertions(+), 63 deletions(-)
 rename .github/workflows/{gh-pages.yml => gh-pages.yaml} (51%)
 create mode 100644 .github/workflows/pypi.yaml
 delete mode 100644 .github/workflows/pypi.yml
 create mode 100644 .github/workflows/tests.yaml
 delete mode 100644 .github/workflows/tests.yml

diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yaml
similarity index 51%
rename from .github/workflows/gh-pages.yml
rename to .github/workflows/gh-pages.yaml
index 14ef1a7..ab94182 100644
--- a/.github/workflows/gh-pages.yml
+++ b/.github/workflows/gh-pages.yaml
@@ -12,16 +12,16 @@ jobs:
     env:
       POETRY_VIRTUALENVS_CREATE: false
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
-      - name: Install project dependencies
-        run: pip install poetry && poetry install
-      - name: Build docs
-        run: docs/build
-      - name: Deploy docs
-        uses: peaceiris/actions-gh-pages@v3
+          python-version: "3.1jj
+      - uses: abatilo/actions-poetry@v3
+        with:
+          poetry-version: "1.8.5"
+      - run: poetry install
+      - run: docs/build
+      - uses: peaceiris/actions-gh-pages@v3
         with:
           force_orphan: true
           github_token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml
new file mode 100644
index 0000000..22e742a
--- /dev/null
+++ b/.github/workflows/pypi.yaml
@@ -0,0 +1,22 @@
+name: PyPI
+
+on:
+  release:
+    types:
+      - created
+
+jobs:
+  job:
+    name: PyPI
+    runs-on: ubuntu-latest
+    env:
+      POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - uses: abatilo/actions-poetry@v3
+        with:
+          poetry-version: "1.8.5"
+      - run: poetry publish --build
diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
deleted file mode 100644
index 64e7b3e..0000000
--- a/.github/workflows/pypi.yml
+++ /dev/null
@@ -1,20 +0,0 @@
-name: PyPI
-
-on:
-  release:
-    types:
-      - created
-
-jobs:
-  job:
-    name: PyPI
-    runs-on: ubuntu-latest
-    env:
-      POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-        with:
-          python-version: "3.10"
-      - name: Publish package to PyPI
-        run: pip install poetry && poetry publish --build
diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
new file mode 100644
index 0000000..7fa18ca
--- /dev/null
+++ b/.github/workflows/tests.yaml
@@ -0,0 +1,34 @@
+name: Tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  job:
+    name: Test (Python ${{ matrix.python }})
+    runs-on: ubuntu-latest
+    env:
+      POETRY_VIRTUALENVS_CREATE: false
+    strategy:
+      fail-fast: false
+      matrix:
+        python: ["3.10", "3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+      - uses: abatilo/actions-poetry@v3
+        with:
+          poetry-version: "1.8.5"
+      - run: poetry install
+      - run: black --check docs fmflow tests
+      - run: pytest -v tests
+      - run: docs/build
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
deleted file mode 100644
index 524a282..0000000
--- a/.github/workflows/tests.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-name: Tests
-
-on:
-  push:
-    branches:
-      - main
-  pull_request:
-    branches:
-      - main
-
-jobs:
-  job:
-    name: Test (Python ${{ matrix.python }})
-    runs-on: ubuntu-latest
-    env:
-      POETRY_VIRTUALENVS_CREATE: false
-    strategy:
-      fail-fast: false
-      matrix:
-        python: ["3.7", "3.8", "3.9", "3.10"]
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python }}
-      - name: Install project dependencies
-        run: pip install poetry && poetry install
-      - name: Test code's formatting (Black)
-        run: black --check docs tests fmflow
-      - name: Test code's execution (pytest)
-        run: pytest -v tests
-      - name: Test docs' building (Sphinx)
-        run: docs/build
diff --git a/README.md b/README.md
index 791039a..586f87e 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,6 @@
 [![Python](https://img.shields.io/pypi/pyversions/fmflow?label=Python&color=cornflowerblue&style=flat-square)](https://pypi.org/project/fmflow/)
 [![Downloads](https://img.shields.io/pypi/dm/fmflow?label=Downloads&color=cornflowerblue&style=flat-square)](https://pepy.tech/project/fmflow)
 [![DOI](https://img.shields.io/badge/DOI-10.5281/zenodo.3433962-cornflowerblue?style=flat-square)](https://doi.org/10.5281/zenodo.3433962)
-[![Tests](https://img.shields.io/github/workflow/status/fmlo-dev/fmflow/Tests?label=Tests&style=flat-square)](https://github.com/fmlo-dev/fmflow/actions)
+[![Tests](https://img.shields.io/github/actions/workflow/status/fmlo-dev/fmflow/tests.yaml?label=Tests&style=flat-square)](https://github.com/fmlo-dev/fmflow/actions)
 
 Data analysis package for FMLO

From 51b2d4242555ffca8c36257c5dc342e67ae734f0 Mon Sep 17 00:00:00 2001
From: Akio Taniguchi <13254278+astropenguin@users.noreply.github.com>
Date: Wed, 19 Mar 2025 04:37:18 +0000
Subject: [PATCH 06/11] #25 Fix wrong import path

---
 fmflow/models/astrosignal/classes.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/fmflow/models/astrosignal/classes.py b/fmflow/models/astrosignal/classes.py
index 025335d..ccd91ef 100644
--- a/fmflow/models/astrosignal/classes.py
+++ b/fmflow/models/astrosignal/classes.py
@@ -14,7 +14,8 @@
 from .. import BaseModel
 from scipy.interpolate import interp1d
 from scipy.optimize import curve_fit, OptimizeWarning
-from scipy.signal import convolve, gaussian, savgol_filter
+from scipy.signal import convolve, savgol_filter
+from scipy.signal.windows import gaussian
 
 warnings.simplefilter("ignore", OptimizeWarning)
 

From f4f887d7d2f107748b9081fe6fb7a7cefbaa2ac5 Mon Sep 17 00:00:00 2001
From: Akio Taniguchi <13254278+astropenguin@users.noreply.github.com>
Date: Wed, 19 Mar 2025 04:41:38 +0000
Subject: [PATCH 07/11] #25 Add extra datetime formats

---
 fmflow/utils/datetime/classes.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/fmflow/utils/datetime/classes.py b/fmflow/utils/datetime/classes.py
index cbe4994..6546353 100644
--- a/fmflow/utils/datetime/classes.py
+++ b/fmflow/utils/datetime/classes.py
@@ -12,9 +12,13 @@
     "%y%m%d%H%M%S",
     "%y%m%d%H%M%S.",
     "%y%m%d%H%M%S.%f",
+    "%y%m%d%H%M%S\x00",
+    "%y%m%d%H%M%S\x00%f",
     "%Y%m%d%H%M%S",
     "%Y%m%d%H%M%S.",
     "%Y%m%d%H%M%S.%f",
+    "%Y%m%d%H%M%S\x00",
+    "%Y%m%d%H%M%S\x00%f",
     ISO_8601,
 ]
 

From 3beaf1d91d91d5db18e0eb84aa2a3dd2b1ef868a Mon Sep 17 00:00:00 2001
From: Akio Taniguchi <13254278+astropenguin@users.noreply.github.com>
Date: Wed, 19 Mar 2025 04:46:04 +0000
Subject: [PATCH 08/11] #25 Add off-source data processing in reading SAM45
 logging

---
 fmflow/fits/nro45m/functions.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/fmflow/fits/nro45m/functions.py b/fmflow/fits/nro45m/functions.py
index 79f6c93..d3a8a1f 100644
--- a/fmflow/fits/nro45m/functions.py
+++ b/fmflow/fits/nro45m/functions.py
@@ -256,6 +256,7 @@ def eof(f):
 
         ## slices of each scantype
         ons = fm.utils.slicewhere(flag & (data["scantype"] == b"ON"))
+        offs = fm.utils.slicewhere(flag & (data["scantype"] == b"OFF"))
         rs = fm.utils.slicewhere(flag & (data["scantype"] == b"R"))
         skys = fm.utils.slicewhere(flag & (data["scantype"] == b"SKY"))
         zero = fm.utils.slicewhere(flag & (data["scantype"] == b"ZERO"))[0]
@@ -264,6 +265,10 @@ def eof(f):
         for on in ons:
             data["arraydata"][on] -= data["arraydata"][zero]
 
+        ## apply ZERO to OFF data
+        for off in offs:
+            data["arraydata"][off] -= data["arraydata"][zero]
+
         ## apply ZERO and ifatt to R data
         for r in rs:
             data["arraydata"][r] -= data["arraydata"][zero]

From 299ef47d1be148972d003101612be257f33d13bd Mon Sep 17 00:00:00 2001
From: Akio Taniguchi <13254278+astropenguin@users.noreply.github.com>
Date: Wed, 19 Mar 2025 04:47:59 +0000
Subject: [PATCH 09/11] =?UTF-8?q?#25=20Update=20package=20version=20(0.4.0?=
 =?UTF-8?q?=20=E2=86=92=200.5.0)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 CITATION.cff           | 2 +-
 fmflow/__init__.py     | 2 +-
 pyproject.toml         | 2 +-
 tests/test_metadata.py | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index 2c30f26..0274de7 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -3,7 +3,7 @@ message: "If you use this software, please cite it as below."
 
 title: "fmflow"
 abstract: "Data analysis package for FMLO"
-version: 0.4.0
+version: 0.5.0
 date-released: 2022-09-09
 license: "MIT"
 doi: "10.5281/zenodo.3433962"
diff --git a/fmflow/__init__.py b/fmflow/__init__.py
index bcd400f..6f4a545 100644
--- a/fmflow/__init__.py
+++ b/fmflow/__init__.py
@@ -1,6 +1,6 @@
 # coding: utf-8
 
-__version__ = "0.4.0"
+__version__ = "0.5.0"
 __author__ = "Akio Taniguchi"
 
 from . import utils
diff --git a/pyproject.toml b/pyproject.toml
index 16b791a..674dc88 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fmflow"
-version = "0.4.0"
+version = "0.5.0"
 description = "Data analysis package for FMLO"
 authors = ["Akio Taniguchi <taniguchi@a.phys.nagoya-u.ac.jp>"]
 keywords = ["astronomy", "radio-astronomy", "data-analysis", "fmlo"]
diff --git a/tests/test_metadata.py b/tests/test_metadata.py
index 4ada5b6..64ec502 100644
--- a/tests/test_metadata.py
+++ b/tests/test_metadata.py
@@ -3,7 +3,7 @@
 
 def test_version():
     """Make sure the version is valid."""
-    assert fm.__version__ == "0.4.0"
+    assert fm.__version__ == "0.5.0"
 
 
 def test_author():

From 3362f2cf93f87cf28c20ba38e4fea5809f12d912 Mon Sep 17 00:00:00 2001
From: Akio Taniguchi <13254278+astropenguin@users.noreply.github.com>
Date: Wed, 19 Mar 2025 04:49:08 +0000
Subject: [PATCH 10/11] #25 Update project description

---
 CITATION.cff   | 4 ++--
 LICENSE        | 2 +-
 pyproject.toml | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index 0274de7..184186d 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -4,12 +4,12 @@ message: "If you use this software, please cite it as below."
 title: "fmflow"
 abstract: "Data analysis package for FMLO"
 version: 0.5.0
-date-released: 2022-09-09
+date-released: 2025-03-19
 license: "MIT"
 doi: "10.5281/zenodo.3433962"
 url: "https://github.com/fmlo-dev/fmflow"
 authors:
   - given-names: "Akio"
     family-names: "Taniguchi"
-    affiliation: "Nagoya University"
+    affiliation: "Kitami Institute of Technology"
     orcid: "https://orcid.org/0000-0002-9695-6183"
diff --git a/LICENSE b/LICENSE
index 1a5d9c0..cbb82ea 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2017-2022 Akio Taniguchi
+Copyright (c) 2017-2025 Akio Taniguchi
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/pyproject.toml b/pyproject.toml
index 674dc88..fd7fd22 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,7 +2,7 @@
 name = "fmflow"
 version = "0.5.0"
 description = "Data analysis package for FMLO"
-authors = ["Akio Taniguchi <taniguchi@a.phys.nagoya-u.ac.jp>"]
+authors = ["Akio Taniguchi <taniguchi.akio@gmail.com>"]
 keywords = ["astronomy", "radio-astronomy", "data-analysis", "fmlo"]
 license = "MIT"
 readme = "README.md"

From c23adc1d9eeb9020c2884cb1ea09fa11ac3bfab6 Mon Sep 17 00:00:00 2001
From: Akio Taniguchi <13254278+astropenguin@users.noreply.github.com>
Date: Wed, 19 Mar 2025 04:58:08 +0000
Subject: [PATCH 11/11] #25 Update project dependencies

---
 .github/workflows/gh-pages.yaml | 2 +-
 .github/workflows/tests.yaml    | 2 +-
 poetry.lock                     | 6 +++---
 pyproject.toml                  | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/gh-pages.yaml b/.github/workflows/gh-pages.yaml
index ab94182..c6bfcf6 100644
--- a/.github/workflows/gh-pages.yaml
+++ b/.github/workflows/gh-pages.yaml
@@ -15,7 +15,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.1jj
+          python-version: "3.12
       - uses: abatilo/actions-poetry@v3
         with:
           poetry-version: "1.8.5"
diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
index 7fa18ca..3e460cc 100644
--- a/.github/workflows/tests.yaml
+++ b/.github/workflows/tests.yaml
@@ -17,7 +17,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.10", "3.11", "3.12", "3.13"]
+        python: ["3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
         with:
diff --git a/poetry.lock b/poetry.lock
index 8006591..29cccee 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand.
 
 [[package]]
 name = "accessible-pygments"
@@ -2202,5 +2202,5 @@ viz = ["cartopy", "matplotlib", "nc-time-axis", "seaborn"]
 
 [metadata]
 lock-version = "2.0"
-python-versions = ">=3.10, <3.14"
-content-hash = "cb535a9295a44187a90696c3c258fc2ee53d75e0179699d115f4b75b87d5ab6b"
+python-versions = ">=3.10, <3.13"
+content-hash = "35238350d5c51f7db3a22a9ebc204591c48d50248ad00229d393d263b04e36c7"
diff --git a/pyproject.toml b/pyproject.toml
index fd7fd22..2000b58 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,7 +10,7 @@ homepage = "https://github.com/fmlo-dev/fmflow/"
 documentation = "https://fmlo-dev.github.io/fmflow/"
 
 [tool.poetry.dependencies]
-python = ">=3.10, <3.14"
+python = ">=3.10, <3.13"
 astropy = ">=6, <8"
 matplotlib = "^3"
 netcdf4 = "^1"