From b3c36fd0e29855bf5e077d172351bd3c8327da1e Mon Sep 17 00:00:00 2001
From: llegregam <legregam@insa-toulouse.fr>
Date: Mon, 4 Mar 2024 09:54:06 +0100
Subject: [PATCH 1/4] Handle spaces when verifying input data

---
 physiofit/base/io.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/physiofit/base/io.py b/physiofit/base/io.py
index e4653c2..1f84309 100644
--- a/physiofit/base/io.py
+++ b/physiofit/base/io.py
@@ -166,6 +166,9 @@ def _verify_data(data: DataFrame):
                 f"The column {x} contains only null or NA values"
             )
 
+        # To avoid errors when concatenating dataframes for the final summary
+        data["experiments"] = data["experiments"].str.replace(pat=" ", repl="_")
+
     @staticmethod
     def get_model_list():
         model_dir = Path(__file__).parent / "models"

From 335a1757aa9f9d5021aeb1c69d55aafccf4f40c8 Mon Sep 17 00:00:00 2001
From: llegregam <legregam@insa-toulouse.fr>
Date: Mon, 4 Mar 2024 09:54:27 +0100
Subject: [PATCH 2/4] Update pyproject.toml & lockfile

---
 poetry.lock    | 1213 +++++++++++++++++++++++-------------------------
 pyproject.toml |    2 +-
 2 files changed, 590 insertions(+), 625 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 45884f7..13b3e3e 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -13,13 +13,13 @@ files = [
 
 [[package]]
 name = "altair"
-version = "5.1.2"
+version = "5.2.0"
 description = "Vega-Altair: A declarative statistical visualization library for Python."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "altair-5.1.2-py3-none-any.whl", hash = "sha256:7219708ec33c152e53145485040f428954ed15fd09b2a2d89e543e6d111dae7f"},
-    {file = "altair-5.1.2.tar.gz", hash = "sha256:e5f52a71853a607c61ce93ad4a414b3d486cd0d46ac597a24ae8bd1ac99dd460"},
+    {file = "altair-5.2.0-py3-none-any.whl", hash = "sha256:8c4888ad11db7c39f3f17aa7f4ea985775da389d79ac30a6c22856ab238df399"},
+    {file = "altair-5.2.0.tar.gz", hash = "sha256:2ad7f0c8010ebbc46319cc30febfb8e59ccf84969a201541c207bc3a4fa6cf81"},
 ]
 
 [package.dependencies]
@@ -32,8 +32,8 @@ toolz = "*"
 typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
-dev = ["anywidget", "black (<24)", "hatch", "ipython", "m2r", "mypy", "pandas-stubs", "pyarrow (>=11)", "pytest", "pytest-cov", "ruff", "types-jsonschema", "types-setuptools", "vega-datasets", "vegafusion[embed] (>=1.4.0)", "vl-convert-python (>=0.14.0)"]
-doc = ["docutils", "geopandas", "jinja2", "myst-parser", "numpydoc", "pillow (>=9,<10)", "pydata-sphinx-theme", "scipy", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinxext-altair"]
+dev = ["anywidget", "geopandas", "hatch", "ipython", "m2r", "mypy", "pandas-stubs", "pyarrow (>=11)", "pytest", "pytest-cov", "ruff (>=0.1.3)", "types-jsonschema", "types-setuptools", "vega-datasets", "vegafusion[embed] (>=1.4.0)", "vl-convert-python (>=1.1.0)"]
+doc = ["docutils", "jinja2", "myst-parser", "numpydoc", "pillow (>=9,<10)", "pydata-sphinx-theme (>=0.14.1)", "scipy", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinxext-altair"]
 
 [[package]]
 name = "appnope"
@@ -48,20 +48,21 @@ files = [
 
 [[package]]
 name = "asttokens"
-version = "2.4.0"
+version = "2.4.1"
 description = "Annotate AST trees with source code positions"
 optional = false
 python-versions = "*"
 files = [
-    {file = "asttokens-2.4.0-py2.py3-none-any.whl", hash = "sha256:cf8fc9e61a86461aa9fb161a14a0841a03c405fa829ac6b202670b3495d2ce69"},
-    {file = "asttokens-2.4.0.tar.gz", hash = "sha256:2e0171b991b2c959acc6c49318049236844a5da1d65ba2672c4880c1c894834e"},
+    {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"},
+    {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"},
 ]
 
 [package.dependencies]
 six = ">=1.12.0"
 
 [package.extras]
-test = ["astroid", "pytest"]
+astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
+test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
 
 [[package]]
 name = "attrs"
@@ -83,13 +84,13 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte
 
 [[package]]
 name = "babel"
-version = "2.13.1"
+version = "2.14.0"
 description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Babel-2.13.1-py3-none-any.whl", hash = "sha256:7077a4984b02b6727ac10f1f7294484f737443d7e2e66c5e4380e41a3ae0b4ed"},
-    {file = "Babel-2.13.1.tar.gz", hash = "sha256:33e0952d7dd6374af8dbf6768cc4ddf3ccfefc244f9986d4074704f2fbd18900"},
+    {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
+    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
 ]
 
 [package.dependencies]
@@ -175,13 +176,13 @@ css = ["tinycss2 (>=1.1.0,<1.3)"]
 
 [[package]]
 name = "blinker"
-version = "1.6.3"
+version = "1.7.0"
 description = "Fast, simple object-to-object and broadcast signaling"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "blinker-1.6.3-py3-none-any.whl", hash = "sha256:296320d6c28b006eb5e32d4712202dbcdcbf5dc482da298c2f44881c43884aaa"},
-    {file = "blinker-1.6.3.tar.gz", hash = "sha256:152090d27c1c5c722ee7e48504b02d76502811ce02e1523553b4cf8c8b3d3a8d"},
+    {file = "blinker-1.7.0-py3-none-any.whl", hash = "sha256:c3f865d4d54db7abc53758a01601cf343fe55b84c1de4e3fa910e420b438d5b9"},
+    {file = "blinker-1.7.0.tar.gz", hash = "sha256:e6820ff6fa4e4d1d8e2747c2283749c3f547e4fee112b98555cdcdae32996182"},
 ]
 
 [[package]]
@@ -197,13 +198,13 @@ files = [
 
 [[package]]
 name = "certifi"
-version = "2023.7.22"
+version = "2023.11.17"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"},
-    {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
+    {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
+    {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
 ]
 
 [[package]]
@@ -283,101 +284,101 @@ files = [
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.1"
+version = "3.3.2"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7.0"
 files = [
-    {file = "charset-normalizer-3.3.1.tar.gz", hash = "sha256:d9137a876020661972ca6eec0766d81aef8a5627df628b664b234b73396e727e"},
-    {file = "charset_normalizer-3.3.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:8aee051c89e13565c6bd366813c386939f8e928af93c29fda4af86d25b73d8f8"},
-    {file = "charset_normalizer-3.3.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:352a88c3df0d1fa886562384b86f9a9e27563d4704ee0e9d56ec6fcd270ea690"},
-    {file = "charset_normalizer-3.3.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:223b4d54561c01048f657fa6ce41461d5ad8ff128b9678cfe8b2ecd951e3f8a2"},
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 [[package]]
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+version = "0.2.0"
 description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
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-python-versions = ">=3.6"
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 test = ["pytest"]
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 [[package]]
 name = "contourpy"
@@ -561,13 +560,13 @@ files = [
 
 [[package]]
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+version = "0.3.8"
 description = "Distribution utilities"
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 python-versions = "*"
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 [[package]]
@@ -583,13 +582,13 @@ files = [
 
 [[package]]
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+version = "1.2.0"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
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 [package.extras]
@@ -597,13 +596,13 @@ test = ["pytest (>=6)"]
 
 [[package]]
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-version = "2.0.0"
+version = "2.0.1"
 description = "Get the currently executing AST node of a frame, and other information"
 optional = false
-python-versions = "*"
+python-versions = ">=3.5"
 files = [
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 [package.extras]
@@ -611,13 +610,13 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth
 
 [[package]]
 name = "fastjsonschema"
-version = "2.18.1"
+version = "2.19.0"
 description = "Fastest Python implementation of JSON schema"
 optional = false
 python-versions = "*"
 files = [
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 [package.extras]
@@ -625,75 +624,75 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
 
 [[package]]
 name = "filelock"
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+version = "3.13.1"
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 python-versions = ">=3.8"
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+typing = ["typing-extensions (>=4.8)"]
 
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 lxml = ["lxml (>=4.0,<5)"]
 pathops = ["skia-pathops (>=0.5.0)"]
 plot = ["matplotlib"]
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 symfont = ["sympy"]
 type1 = ["xattr"]
 ufo = ["fs (>=2.2.0,<3)"]
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 woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 
 [[package]]
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 [[package]]
 name = "idna"
-version = "3.4"
+version = "3.6"
 description = "Internationalized Domain Names in Applications (IDNA)"
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 python-versions = ">=3.5"
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 [[package]]
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 [package.dependencies]
@@ -807,13 +806,13 @@ files = [
 
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 [package.dependencies]
@@ -915,13 +914,13 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
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+version = "4.20.0"
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 [package.dependencies]
@@ -938,28 +937,28 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[package]]
 name = "jsonschema-specifications"
-version = "2023.7.1"
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 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.extras]
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 [package.dependencies]
@@ -1278,7 +1277,6 @@ packaging = ">=20.0"
 pillow = ">=6.2.0"
 pyparsing = ">=2.3.1"
 python-dateutil = ">=2.7"
-setuptools_scm = ">=7"
 
 [[package]]
 name = "matplotlib-inline"
@@ -1318,13 +1316,13 @@ files = [
 
 [[package]]
 name = "nbclient"
-version = "0.8.0"
+version = "0.9.0"
 description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
 optional = false
 python-versions = ">=3.8.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -1340,13 +1338,13 @@ test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=
 
 [[package]]
 name = "nbconvert"
-version = "7.9.2"
+version = "7.13.0"
 description = "Converting Jupyter Notebooks"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1373,7 +1371,7 @@ docs = ["ipykernel", "ipython", "myst-parser", "nbsphinx (>=0.2.12)", "pydata-sp
 qtpdf = ["nbconvert[qtpng]"]
 qtpng = ["pyqtwebengine (>=5.15)"]
 serve = ["tornado (>=6.1)"]
-test = ["flaky", "ipykernel", "ipywidgets (>=7)", "pytest", "pytest-dependency"]
+test = ["flaky", "ipykernel", "ipywidgets (>=7.5)", "pytest"]
 webpdf = ["playwright"]
 
 [[package]]
@@ -1512,8 +1510,8 @@ files = [
 [package.dependencies]
 numpy = [
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     {version = ">=1.23.2", markers = "python_version >= \"3.11\""},
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 ]
 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
@@ -1584,13 +1582,13 @@ testing = ["docopt", "pytest (<6.0.0)"]
 
 [[package]]
 name = "pexpect"
-version = "4.8.0"
+version = "4.9.0"
 description = "Pexpect allows easy control of interactive console applications."
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 python-versions = "*"
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 ]
 
 [package.dependencies]
@@ -1687,13 +1685,13 @@ files = [
 
 [[package]]
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+version = "4.1.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 optional = false
-python-versions = ">=3.7"
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 [package.extras]
@@ -1747,13 +1745,13 @@ files = [
 
 [[package]]
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+version = "3.0.43"
 description = "Library for building powerful interactive command lines in Python"
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 python-versions = ">=3.7.0"
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 [package.dependencies]
@@ -1761,49 +1759,47 @@ wcwidth = "*"
 
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 [package.dependencies]
@@ -2243,110 +2247,110 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"]
 
 [[package]]
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+version = "0.15.2"
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 [[package]]
@@ -2387,44 +2391,6 @@ dev = ["click", "doit (>=0.36.0)", "flake8", "mypy", "pycodestyle", "pydevtool",
 doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-design (>=0.2.0)"]
 test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
 
-[[package]]
-name = "setuptools"
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-optional = false
-python-versions = ">=3.8"
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-[package.extras]
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-
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-tomli = {version = ">=1", markers = "python_version < \"3.11\""}
-typing-extensions = "*"
-
-[package.extras]
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-rich = ["rich"]
-test = ["build", "pytest", "rich", "wheel"]
-
 [[package]]
 name = "six"
 version = "1.16.0"
@@ -2664,13 +2630,13 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
 
 [[package]]
 name = "streamlit"
-version = "1.27.2"
+version = "1.29.0"
 description = "A faster way to build and share data apps"
 optional = false
 python-versions = ">=3.8, !=3.9.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -2768,33 +2734,33 @@ files = [
 
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-version = "6.3.3"
+version = "6.4"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
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 python-versions = ">= 3.8"
 files = [
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 ]
 
 [[package]]
 name = "tox"
-version = "4.11.3"
+version = "4.11.4"
 description = "tox is a generic virtualenv management and test command line tool"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2815,28 +2781,28 @@ testing = ["build[virtualenv] (>=0.10)", "covdefaults (>=2.3)", "detect-test-pol
 
 [[package]]
 name = "traitlets"
-version = "5.12.0"
+version = "5.14.0"
 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,<7.5)", "pytest-mock", "pytest-mypy-testing"]
 
 [[package]]
 name = "typing-extensions"
-version = "4.8.0"
+version = "4.9.0"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
@@ -2870,18 +2836,17 @@ devenv = ["check-manifest", "pytest (>=4.3)", "pytest-cov", "pytest-mock (>=3.3)
 
 [[package]]
 name = "urllib3"
-version = "2.0.7"
+version = "2.1.0"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 [package.extras]
 brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
-secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
 
@@ -2909,19 +2874,19 @@ tooling-extras = ["pyaml (>=23.7.0)", "pypandoc-binary (>=1.11)", "pytest (>=7.4
 
 [[package]]
 name = "virtualenv"
-version = "20.24.6"
+version = "20.25.0"
 description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.24.6-py3-none-any.whl", hash = "sha256:520d056652454c5098a00c0f073611ccbea4c79089331f60bf9d7ba247bb7381"},
-    {file = "virtualenv-20.24.6.tar.gz", hash = "sha256:02ece4f56fbf939dbbc33c0715159951d6bf14aaf5457b092e4548e1382455af"},
+    {file = "virtualenv-20.25.0-py3-none-any.whl", hash = "sha256:4238949c5ffe6876362d9c0180fc6c3a824a7b12b80604eeb8085f2ed7460de3"},
+    {file = "virtualenv-20.25.0.tar.gz", hash = "sha256:bf51c0d9c7dd63ea8e44086fa1e4fb1093a31e963b86959257378aef020e1f1b"},
 ]
 
 [package.dependencies]
 distlib = ">=0.3.7,<1"
 filelock = ">=3.12.2,<4"
-platformdirs = ">=3.9.1,<4"
+platformdirs = ">=3.9.1,<5"
 
 [package.extras]
 docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
@@ -2968,13 +2933,13 @@ watchmedo = ["PyYAML (>=3.10)"]
 
 [[package]]
 name = "wcwidth"
-version = "0.2.8"
+version = "0.2.12"
 description = "Measures the displayed width of unicode strings in a terminal"
 optional = false
 python-versions = "*"
 files = [
-    {file = "wcwidth-0.2.8-py2.py3-none-any.whl", hash = "sha256:77f719e01648ed600dfa5402c347481c0992263b81a027344f3e1ba25493a704"},
-    {file = "wcwidth-0.2.8.tar.gz", hash = "sha256:8705c569999ffbb4f6a87c6d1b80f324bd6db952f5eb0b95bc07517f4c1813d4"},
+    {file = "wcwidth-0.2.12-py2.py3-none-any.whl", hash = "sha256:f26ec43d96c8cbfed76a5075dac87680124fa84e0855195a6184da9c187f133c"},
+    {file = "wcwidth-0.2.12.tar.gz", hash = "sha256:f01c104efdf57971bcb756f054dd58ddec5204dd15fa31d6503ea57947d97c02"},
 ]
 
 [[package]]
@@ -3006,4 +2971,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<3.9.7 || >3.9.7,<3.12"
-content-hash = "e4c7f0f80a2c32e3437444122643bcf93feeb108f23d40ba6c57e4e34250ec06"
+content-hash = "a2db77c06bcea369e534a31bbafdd09f838ff59a80314c6e50dbf65cbf3eb643"
diff --git a/pyproject.toml b/pyproject.toml
index f59ab50..f39797c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -14,7 +14,7 @@ python = ">=3.8,<3.9.7 || >3.9.7,<3.12"
 pandas = "^2.0.1"
 numpy = "^1.24.2"
 scipy = "^1.10.1"
-streamlit = "^1.20.0"
+streamlit = "^1.27.0"
 matplotlib = "^3.7.1"
 pyyaml = "^6.0"
 

From 84d2ca6b116de04a7e2891fd7b8f3c68f39904cb Mon Sep 17 00:00:00 2001
From: llegregam <legregam@insa-toulouse.fr>
Date: Mon, 4 Mar 2024 09:59:20 +0100
Subject: [PATCH 3/4] Added missing parameters in docstrings

---
 physiofit/base/io.py | 68 +++++++++++++++++++++-----------------------
 1 file changed, 33 insertions(+), 35 deletions(-)

diff --git a/physiofit/base/io.py b/physiofit/base/io.py
index 1f84309..95d9f00 100644
--- a/physiofit/base/io.py
+++ b/physiofit/base/io.py
@@ -11,9 +11,6 @@
 import matplotlib.pyplot as plt
 import numpy as np
 
-# Switch matplotlib logger to higher level to not get debug logs in root logger
-logging.getLogger("matplotlib").setLevel(logging.WARNING)
-
 from matplotlib.backends.backend_pdf import PdfPages
 from pandas import DataFrame, read_csv, concat
 import yaml
@@ -22,9 +19,13 @@
 from physiofit.base.fitter import PhysioFitter
 from physiofit.models.base_model import StandardDevs, Bounds
 
+# Switch matplotlib logger to higher level to not get debug logs in root logger
+logging.getLogger("matplotlib").setLevel(logging.WARNING)
+
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.DEBUG)
 
+
 class IoHandler:
     """
     Input/Output class that handles the former and initializes the
@@ -68,7 +69,7 @@ def read_data(data: str) -> DataFrame:
         try:
             if isinstance(data, str):
                 data_path = Path(data).resolve()
-            # .dat file type for galaxy implementation
+                # .dat file type for galaxy implementation
                 if data_path.suffix in [".txt", ".tsv", ".dat"]:
                     data = read_csv(str(data_path), sep="\t")
                 elif data_path.suffix == ".csv":
@@ -129,7 +130,6 @@ def read_model(self, model_file):
 
         return model_class
 
-
     @staticmethod
     def _verify_data(data: DataFrame):
         """
@@ -163,8 +163,8 @@ def _verify_data(data: DataFrame):
                 )
             if all(data[x].isnull()) or all(data[x].isna()):
                 raise ValueError(
-                f"The column {x} contains only null or NA values"
-            )
+                    f"The column {x} contains only null or NA values"
+                )
 
         # To avoid errors when concatenating dataframes for the final summary
         data["experiments"] = data["experiments"].str.replace(pat=" ", repl="_")
@@ -185,7 +185,7 @@ def get_model_list():
                 model = model_class(df)
                 print(model.model_name)
         return
-        
+
     def get_models(self, data=None):
         """
         Read modules containing the different models and add them to models attribute
@@ -240,7 +240,7 @@ def read_yaml(yaml_file: str | bytes) -> ConfigParser:
             raise IOError(
                 f"Error while reading yaml configuration file {yaml_file}. "
                 f"\nTraceback:\n\n{e}"
-                )
+            )
         return config_parser
 
     def initialize_fitter(self, data: pd.DataFrame, **kwargs) -> PhysioFitter:
@@ -266,11 +266,11 @@ def initialize_fitter(self, data: pd.DataFrame, **kwargs) -> PhysioFitter:
 
         if "sd" not in kwargs:
             fitter.sd.update(
-                {"X" : 0.2}
+                {"X": 0.2}
             )
             for col in self.data.columns[2:]:
                 fitter.sd.update(
-                    {col : 0.2}
+                    {col: 0.2}
                 )
 
         fitter.initialize_sd_matrix()
@@ -281,7 +281,6 @@ def initialize_fitter(self, data: pd.DataFrame, **kwargs) -> PhysioFitter:
 
         return fitter
 
-
     def output_pdf(self, fitter: PhysioFitter, export_path: str | Path = None):
         """
         Handle the creation and output of a pdf file containing fit results as
@@ -343,13 +342,13 @@ def output_recap(self, export_path: str, galaxy=False):
         else:
             final_df.to_csv(f"{str(Path(export_path))}/summary.csv")
 
-
-    def output_report(self, fitter, export_path: str |list = None):
+    def output_report(self, fitter, export_path: str | list = None):
         """
         Handle creation and export of the report containing stats from monte
         carlo analysis of optimization parameters
 
-        :param export_paths: list of paths to export the stats and fluxes. [0]
+        :param fitter: PhysioFitter object containing results from the optimization of parameters
+        :param export_path: list of paths to export the stats and fluxes. [0]
                              is for stats and [1] for fluxes.
         """
 
@@ -459,6 +458,7 @@ def plot_data(self, fitter, display: bool = False):
         """
         Plot the data
 
+        :param fitter: PhysioFitter object after optimization of parameters has been executed
         :param display: should plots be displayed
         """
 
@@ -536,7 +536,6 @@ def _add_sd_area(self, element: str, ax: plt.Axes):
 
 
 class ConfigParser:
-
     allowed_keys = ["model", "sds", "mc", "iterations"]
 
     def __init__(
@@ -564,7 +563,6 @@ def __init__(
                 f"Number of iterations must be an integer: Detected input: {self.mc}, type: {type(self.iterations)}"
             )
 
-
     @classmethod
     def from_file(cls, yaml_file):
 
@@ -584,9 +582,9 @@ def from_file(cls, yaml_file):
             return ConfigParser(
                 path_to_data=data["path_to_data"],
                 selected_model=data["model"],
-                sds = data["sds"],
-                mc = data["mc"],
-                iterations = data["iterations"]
+                sds=data["sds"],
+                mc=data["mc"],
+                iterations=data["iterations"]
             )
         except KeyError:
             return ConfigParser(
@@ -601,13 +599,13 @@ def from_galaxy(cls, galaxy_yaml):
         pass
 
     def get_kwargs(self):
-        return  {
-            "path_to_data" : self.path_to_data,
-            "model" : self.model,
-            "mc" : self.mc,
-            "iterations" : self.iterations,
-            "sd" : self.sds
-            }
+        return {
+            "path_to_data": self.path_to_data,
+            "model": self.model,
+            "mc": self.mc,
+            "iterations": self.iterations,
+            "sd": self.sds
+        }
 
     def update_model(self, model):
 
@@ -621,15 +619,15 @@ def export_config(self, export_path):
 
         with open(fr"{export_path}/config_file.yml", "w") as file:
             data = {
-                "model" : {
-                    "model_name" : self.model.model_name,
-                    "parameters_to_estimate" : self.model.parameters_to_estimate,
-                    "bounds" : {name : f"{bounds[0], bounds[1]}" for name, bounds in self.model.bounds.items()}
+                "model": {
+                    "model_name": self.model.model_name,
+                    "parameters_to_estimate": self.model.parameters_to_estimate,
+                    "bounds": {name: f"{bounds[0], bounds[1]}" for name, bounds in self.model.bounds.items()}
                 },
-                "sds" : dict(self.sds),
-                "mc" : self.mc,
-                "iterations" : self.iterations,
-                "path_to_data" : str(self.path_to_data)
+                "sds": dict(self.sds),
+                "mc": self.mc,
+                "iterations": self.iterations,
+                "path_to_data": str(self.path_to_data)
             }
             yaml.safe_dump(
                 data,

From 187270cfc3372773785f3fe96b9616cdaf3f6d78 Mon Sep 17 00:00:00 2001
From: llegregam <legregam@insa-toulouse.fr>
Date: Mon, 4 Mar 2024 10:18:36 +0100
Subject: [PATCH 4/4] updated dependencies (patch for security reasons)

---
 poetry.lock    | 1055 +++++++++++++++++++++++++-----------------------
 pyproject.toml |    2 +
 2 files changed, 544 insertions(+), 513 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 13b3e3e..752eb52 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -37,13 +37,13 @@ doc = ["docutils", "jinja2", "myst-parser", "numpydoc", "pillow (>=9,<10)", "pyd
 
 [[package]]
 name = "appnope"
-version = "0.1.3"
+version = "0.1.4"
 description = "Disable App Nap on macOS >= 10.9"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 files = [
-    {file = "appnope-0.1.3-py2.py3-none-any.whl", hash = "sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"},
-    {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"},
+    {file = "appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c"},
+    {file = "appnope-0.1.4.tar.gz", hash = "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee"},
 ]
 
 [[package]]
@@ -66,21 +66,22 @@ test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
 
 [[package]]
 name = "attrs"
-version = "23.1.0"
+version = "23.2.0"
 description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
-    {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
+    {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
+    {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
 ]
 
 [package.extras]
 cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[docs,tests]", "pre-commit"]
+dev = ["attrs[tests]", "pre-commit"]
 docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
 tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
+tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "babel"
@@ -140,19 +141,22 @@ tzdata = ["tzdata"]
 
 [[package]]
 name = "beautifulsoup4"
-version = "4.12.2"
+version = "4.12.3"
 description = "Screen-scraping library"
 optional = false
 python-versions = ">=3.6.0"
 files = [
-    {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"},
-    {file = "beautifulsoup4-4.12.2.tar.gz", hash = "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da"},
+    {file = "beautifulsoup4-4.12.3-py3-none-any.whl", hash = "sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed"},
+    {file = "beautifulsoup4-4.12.3.tar.gz", hash = "sha256:74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051"},
 ]
 
 [package.dependencies]
 soupsieve = ">1.2"
 
 [package.extras]
+cchardet = ["cchardet"]
+chardet = ["chardet"]
+charset-normalizer = ["charset-normalizer"]
 html5lib = ["html5lib"]
 lxml = ["lxml"]
 
@@ -187,24 +191,24 @@ files = [
 
 [[package]]
 name = "cachetools"
-version = "5.3.2"
+version = "5.3.3"
 description = "Extensible memoizing collections and decorators"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "cachetools-5.3.2-py3-none-any.whl", hash = "sha256:861f35a13a451f94e301ce2bec7cac63e881232ccce7ed67fab9b5df4d3beaa1"},
-    {file = "cachetools-5.3.2.tar.gz", hash = "sha256:086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2"},
+    {file = "cachetools-5.3.3-py3-none-any.whl", hash = "sha256:0abad1021d3f8325b2fc1d2e9c8b9c9d57b04c3932657a72465447332c24d945"},
+    {file = "cachetools-5.3.3.tar.gz", hash = "sha256:ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105"},
 ]
 
 [[package]]
 name = "certifi"
-version = "2023.11.17"
+version = "2024.2.2"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
-    {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
+    {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
+    {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"},
 ]
 
 [[package]]
@@ -408,13 +412,13 @@ files = [
 
 [[package]]
 name = "comm"
-version = "0.2.0"
+version = "0.2.1"
 description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "comm-0.2.0-py3-none-any.whl", hash = "sha256:2da8d9ebb8dd7bfc247adaff99f24dce705638a8042b85cb995066793e391001"},
-    {file = "comm-0.2.0.tar.gz", hash = "sha256:a517ea2ca28931c7007a7a99c562a0fa5883cfb48963140cf642c41c948498be"},
+    {file = "comm-0.2.1-py3-none-any.whl", hash = "sha256:87928485c0dfc0e7976fd89fc1e187023cf587e7c353e4a9b417555b44adf021"},
+    {file = "comm-0.2.1.tar.gz", hash = "sha256:0bc91edae1344d39d3661dcbc36937181fdaddb304790458f8b044dbc064b89a"},
 ]
 
 [package.dependencies]
@@ -511,29 +515,33 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "debugpy"
-version = "1.8.0"
+version = "1.8.1"
 description = "An implementation of the Debug Adapter Protocol for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "debugpy-1.8.0-cp310-cp310-macosx_11_0_x86_64.whl", hash = "sha256:7fb95ca78f7ac43393cd0e0f2b6deda438ec7c5e47fa5d38553340897d2fbdfb"},
-    {file = "debugpy-1.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ef9ab7df0b9a42ed9c878afd3eaaff471fce3fa73df96022e1f5c9f8f8c87ada"},
-    {file = "debugpy-1.8.0-cp310-cp310-win32.whl", hash = "sha256:a8b7a2fd27cd9f3553ac112f356ad4ca93338feadd8910277aff71ab24d8775f"},
-    {file = "debugpy-1.8.0-cp310-cp310-win_amd64.whl", hash = "sha256:5d9de202f5d42e62f932507ee8b21e30d49aae7e46d5b1dd5c908db1d7068637"},
-    {file = "debugpy-1.8.0-cp311-cp311-macosx_11_0_universal2.whl", hash = "sha256:ef54404365fae8d45cf450d0544ee40cefbcb9cb85ea7afe89a963c27028261e"},
-    {file = "debugpy-1.8.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:60009b132c91951354f54363f8ebdf7457aeb150e84abba5ae251b8e9f29a8a6"},
-    {file = "debugpy-1.8.0-cp311-cp311-win32.whl", hash = "sha256:8cd0197141eb9e8a4566794550cfdcdb8b3db0818bdf8c49a8e8f8053e56e38b"},
-    {file = "debugpy-1.8.0-cp311-cp311-win_amd64.whl", hash = "sha256:a64093656c4c64dc6a438e11d59369875d200bd5abb8f9b26c1f5f723622e153"},
-    {file = "debugpy-1.8.0-cp38-cp38-macosx_11_0_x86_64.whl", hash = "sha256:b05a6b503ed520ad58c8dc682749113d2fd9f41ffd45daec16e558ca884008cd"},
-    {file = "debugpy-1.8.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:3c6fb41c98ec51dd010d7ed650accfd07a87fe5e93eca9d5f584d0578f28f35f"},
-    {file = "debugpy-1.8.0-cp38-cp38-win32.whl", hash = "sha256:46ab6780159eeabb43c1495d9c84cf85d62975e48b6ec21ee10c95767c0590aa"},
-    {file = "debugpy-1.8.0-cp38-cp38-win_amd64.whl", hash = "sha256:bdc5ef99d14b9c0fcb35351b4fbfc06ac0ee576aeab6b2511702e5a648a2e595"},
-    {file = "debugpy-1.8.0-cp39-cp39-macosx_11_0_x86_64.whl", hash = "sha256:61eab4a4c8b6125d41a34bad4e5fe3d2cc145caecd63c3fe953be4cc53e65bf8"},
-    {file = "debugpy-1.8.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:125b9a637e013f9faac0a3d6a82bd17c8b5d2c875fb6b7e2772c5aba6d082332"},
-    {file = "debugpy-1.8.0-cp39-cp39-win32.whl", hash = "sha256:57161629133113c97b387382045649a2b985a348f0c9366e22217c87b68b73c6"},
-    {file = "debugpy-1.8.0-cp39-cp39-win_amd64.whl", hash = "sha256:e3412f9faa9ade82aa64a50b602544efcba848c91384e9f93497a458767e6926"},
-    {file = "debugpy-1.8.0-py2.py3-none-any.whl", hash = "sha256:9c9b0ac1ce2a42888199df1a1906e45e6f3c9555497643a85e0bf2406e3ffbc4"},
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+    {file = "fonttools-4.49.0.tar.gz", hash = "sha256:ebf46e7f01b7af7861310417d7c49591a85d99146fc23a5ba82fdb28af156321"},
+]
+
+[package.extras]
+all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "pycairo", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=15.1.0)", "xattr", "zopfli (>=0.1.4)"]
 graphite = ["lz4 (>=1.7.4.2)"]
 interpolatable = ["munkres", "pycairo", "scipy"]
-lxml = ["lxml (>=4.0,<5)"]
+lxml = ["lxml (>=4.0)"]
 pathops = ["skia-pathops (>=0.5.0)"]
 plot = ["matplotlib"]
 repacker = ["uharfbuzz (>=0.23.0)"]
@@ -719,20 +727,20 @@ smmap = ">=3.0.1,<6"
 
 [[package]]
 name = "gitpython"
-version = "3.1.40"
+version = "3.1.42"
 description = "GitPython is a Python library used to interact with Git repositories"
 optional = false
 python-versions = ">=3.7"
 files = [
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-    {file = "GitPython-3.1.40.tar.gz", hash = "sha256:22b126e9ffb671fdd0c129796343a02bf67bf2994b35449ffc9321aa755e18a4"},
+    {file = "GitPython-3.1.42-py3-none-any.whl", hash = "sha256:1bf9cd7c9e7255f77778ea54359e54ac22a72a5b51288c457c881057b7bb9ecd"},
+    {file = "GitPython-3.1.42.tar.gz", hash = "sha256:2d99869e0fef71a73cbd242528105af1d6c1b108c60dfabd994bf292f76c3ceb"},
 ]
 
 [package.dependencies]
 gitdb = ">=4.0.1,<5"
 
 [package.extras]
-test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-instafail", "pytest-subtests", "pytest-sugar"]
+test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre-commit", "pytest (>=7.3.1)", "pytest-cov", "pytest-instafail", "pytest-mock", "pytest-sugar"]
 
 [[package]]
 name = "idna"
@@ -758,13 +766,13 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "6.11.0"
+version = "7.0.1"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "importlib_metadata-7.0.1-py3-none-any.whl", hash = "sha256:4805911c3a4ec7c3966410053e9ec6a1fecd629117df5adee56dfc9432a1081e"},
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 ]
 
 [package.dependencies]
@@ -777,13 +785,13 @@ testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs
 
 [[package]]
 name = "importlib-resources"
-version = "6.1.1"
+version = "6.1.2"
 description = "Read resources from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_resources-6.1.1-py3-none-any.whl", hash = "sha256:e8bf90d8213b486f428c9c39714b920041cb02c184686a3dee24905aaa8105d6"},
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+    {file = "importlib_resources-6.1.2.tar.gz", hash = "sha256:308abf8474e2dba5f867d279237cd4076482c3de7104a40b41426370e891549b"},
 ]
 
 [package.dependencies]
@@ -791,7 +799,7 @@ zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff", "zipp (>=3.17)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)", "zipp (>=3.17)"]
 
 [[package]]
 name = "iniconfig"
@@ -806,13 +814,13 @@ files = [
 
 [[package]]
 name = "ipykernel"
-version = "6.27.1"
+version = "6.29.3"
 description = "IPython Kernel for Jupyter"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -826,7 +834,7 @@ matplotlib-inline = ">=0.1"
 nest-asyncio = "*"
 packaging = "*"
 psutil = "*"
-pyzmq = ">=20"
+pyzmq = ">=24"
 tornado = ">=6.1"
 traitlets = ">=5.4.0"
 
@@ -835,7 +843,7 @@ cov = ["coverage[toml]", "curio", "matplotlib", "pytest-cov", "trio"]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "trio"]
 pyqt5 = ["pyqt5"]
 pyside6 = ["pyside6"]
-test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio", "pytest-cov", "pytest-timeout"]
+test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.23.5)", "pytest-cov", "pytest-timeout"]
 
 [[package]]
 name = "ipython"
@@ -897,13 +905,13 @@ testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
 
 [[package]]
 name = "jinja2"
-version = "3.1.2"
+version = "3.1.3"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "Jinja2-3.1.3.tar.gz", hash = "sha256:ac8bd6544d4bb2c9792bf3a159e80bba8fda7f07e81bc3aed565432d5925ba90"},
 ]
 
 [package.dependencies]
@@ -914,13 +922,13 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "jsonschema"
-version = "4.20.0"
+version = "4.21.1"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "jsonschema-4.21.1.tar.gz", hash = "sha256:85727c00279f5fa6bedbe6238d2aa6403bedd8b4864ab11207d07df3cc1b2ee5"},
 ]
 
 [package.dependencies]
@@ -937,13 +945,13 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[package]]
 name = "jsonschema-specifications"
-version = "2023.11.2"
+version = "2023.12.1"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -975,13 +983,13 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt
 
 [[package]]
 name = "jupyter-core"
-version = "5.5.1"
+version = "5.7.1"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
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 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -1143,127 +1151,127 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
 [[package]]
 name = "markupsafe"
-version = "2.1.3"
+version = "2.1.5"
 description = "Safely add untrusted strings to HTML/XML markup."
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.dependencies]
@@ -1416,13 +1424,13 @@ traitlets = ">=5"
 
 [[package]]
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+version = "1.6.0"
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 [[package]]
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 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
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 [[package]]
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 docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-removed-in", "sphinxext-opengraph"]
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 tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
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 name = "pkgutil-resolve-name"
@@ -1685,28 +1711,28 @@ files = [
 
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 ]
 
 [package.extras]
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 [[package]]
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 [[package]]
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 [[package]]
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-version = "1.29.0"
+version = "1.31.1"
 description = "A faster way to build and share data apps"
 optional = false
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 [package.dependencies]
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 cachetools = ">=4.0,<6"
 click = ">=7.0,<9"
 gitpython = ">=3.0.7,<3.1.19 || >3.1.19,<4"
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 numpy = ">=1.19.3,<2"
 packaging = ">=16.8,<24"
 pandas = ">=1.3.0,<3"
 pillow = ">=7.1.0,<11"
 protobuf = ">=3.20,<5"
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 pydeck = ">=0.8.0b4,<1"
 python-dateutil = ">=2.7.3,<3"
 requests = ">=2.27,<3"
@@ -2723,13 +2749,13 @@ files = [
 
 [[package]]
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 [[package]]
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 [package.dependencies]
-cachetools = ">=5.3.1"
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 chardet = ">=5.2"
 colorama = ">=0.4.6"
-filelock = ">=3.12.3"
-packaging = ">=23.1"
-platformdirs = ">=3.10"
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+packaging = ">=23.2"
+platformdirs = ">=4.1"
 pluggy = ">=1.3"
 pyproject-api = ">=1.6.1"
 tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""}
-virtualenv = ">=20.24.3"
+virtualenv = ">=20.25"
 
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 [[package]]
 name = "traitlets"
-version = "5.14.0"
+version = "5.14.1"
 description = "Traitlets Python configuration system"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.extras]
@@ -2796,24 +2822,24 @@ test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,
 
 [[package]]
 name = "typing-extensions"
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+version = "4.10.0"
 description = "Backported and Experimental Type Hints for Python 3.8+"
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 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
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+version = "2024.1"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
 files = [
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 ]
 
 [[package]]
@@ -2836,17 +2862,18 @@ devenv = ["check-manifest", "pytest (>=4.3)", "pytest-cov", "pytest-mock (>=3.3)
 
 [[package]]
 name = "urllib3"
-version = "2.1.0"
+version = "2.2.1"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.extras]
 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)"]
 
@@ -2874,13 +2901,13 @@ tooling-extras = ["pyaml (>=23.7.0)", "pypandoc-binary (>=1.11)", "pytest (>=7.4
 
 [[package]]
 name = "virtualenv"
-version = "20.25.0"
+version = "20.25.1"
 description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -2894,38 +2921,40 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess
 
 [[package]]
 name = "watchdog"
-version = "3.0.0"
+version = "4.0.0"
 description = "Filesystem events monitoring"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -2933,13 +2962,13 @@ watchmedo = ["PyYAML (>=3.10)"]
 
 [[package]]
 name = "wcwidth"
-version = "0.2.12"
+version = "0.2.13"
 description = "Measures the displayed width of unicode strings in a terminal"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [[package]]
@@ -2971,4 +3000,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<3.9.7 || >3.9.7,<3.12"
-content-hash = "a2db77c06bcea369e534a31bbafdd09f838ff59a80314c6e50dbf65cbf3eb643"
+content-hash = "31de9eeb3d22fe50589b7d15c16ca8f6998d57bd4f50008e50a4903a65665c22"
diff --git a/pyproject.toml b/pyproject.toml
index f39797c..3952faa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,6 +17,8 @@ scipy = "^1.10.1"
 streamlit = "^1.27.0"
 matplotlib = "^3.7.1"
 pyyaml = "^6.0"
+pillow = "^10.2.0"
+pyarrow = "^14.0.1"
 
 [tool.poetry.group.dev.dependencies]
 ipykernel = "^6.21.3"