From c36b0b35ed0eeef986c112c6982b82491b6aaedb Mon Sep 17 00:00:00 2001
From: Thomas Grandjean <tgrandje@gmail.com>
Date: Fri, 20 Sep 2024 17:27:19 +0200
Subject: [PATCH] Reset cartiflette with new dependencies for docker image
 (#99)

* Update poetry dependencies with python-calamine
---
 poetry.lock      | 425 +++++++++++++++++++++++++++++++++--------------
 pyproject.toml   |   6 +-
 requirements.txt |  10 --
 3 files changed, 300 insertions(+), 141 deletions(-)
 delete mode 100644 requirements.txt

diff --git a/poetry.lock b/poetry.lock
index 7e35d29..bd121c5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -285,6 +285,30 @@ files = [
     {file = "async_timeout-4.0.3-py3-none-any.whl", hash = "sha256:7405140ff1230c310e51dc27b3145b9092d659ce68ff733fb0cefe3ee42be028"},
 ]
 
+[[package]]
+name = "asyncssh"
+version = "2.17.0"
+description = "AsyncSSH: Asynchronous SSHv2 client and server library"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "asyncssh-2.17.0-py3-none-any.whl", hash = "sha256:70bfe4081793255b0115f7a72efd92d5bad8562639302531223bb00188db9747"},
+    {file = "asyncssh-2.17.0.tar.gz", hash = "sha256:3b159c105aa388c1e2245c4faf483f540ada8cad99402281119100166e5edb3c"},
+]
+
+[package.dependencies]
+cryptography = ">=39.0"
+typing-extensions = ">=4.0.0"
+
+[package.extras]
+bcrypt = ["bcrypt (>=3.1.3)"]
+fido2 = ["fido2 (>=0.9.2)"]
+gssapi = ["gssapi (>=1.2.0)"]
+libnacl = ["libnacl (>=1.4.2)"]
+pkcs11 = ["python-pkcs11 (>=0.7.0)"]
+pyopenssl = ["pyOpenSSL (>=23.0.0)"]
+pywin32 = ["pywin32 (>=227)"]
+
 [[package]]
 name = "atomicwrites"
 version = "1.4.1"
@@ -358,46 +382,6 @@ files = [
 docs = ["furo", "jaraco.packaging (>=9.3)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 testing = ["jaraco.test", "pytest (!=8.0.*)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)"]
 
-[[package]]
-name = "bcrypt"
-version = "4.2.0"
-description = "Modern password hashing for your software and your servers"
-optional = false
-python-versions = ">=3.7"
-files = [
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-    {file = "bcrypt-4.2.0.tar.gz", hash = "sha256:cf69eaf5185fd58f268f805b505ce31f9b9fc2d64b376642164e9244540c1221"},
-]
-
-[package.extras]
-tests = ["pytest (>=3.2.1,!=3.3.0)"]
-typecheck = ["mypy"]
-
 [[package]]
 name = "beautifulsoup4"
 version = "4.12.3"
@@ -1204,6 +1188,23 @@ files = [
     {file = "defusedxml-0.7.1.tar.gz", hash = "sha256:1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69"},
 ]
 
+[[package]]
+name = "deprecated"
+version = "1.2.14"
+description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "Deprecated-1.2.14-py2.py3-none-any.whl", hash = "sha256:6fac8b097794a90302bdbb17b9b815e732d3c4720583ff1b198499d78470466c"},
+    {file = "Deprecated-1.2.14.tar.gz", hash = "sha256:e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3"},
+]
+
+[package.dependencies]
+wrapt = ">=1.10,<2"
+
+[package.extras]
+dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
+
 [[package]]
 name = "diff-match-patch"
 version = "20230430"
@@ -2875,56 +2876,47 @@ files = [
 
 [[package]]
 name = "numpy"
-version = "2.0.2"
+version = "1.26.4"
 description = "Fundamental package for array computing in Python"
 optional = false
 python-versions = ">=3.9"
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 windows-terminal = ["colorama (>=0.4.6)"]
 
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 [package.extras]
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+]
+
 [[package]]
 name = "python-dateutil"
 version = "2.9.0.post0"
@@ -4231,6 +4350,17 @@ files = [
     {file = "pytz-2024.2.tar.gz", hash = "sha256:2aa355083c50a0f93fa581709deac0c9ad65cca8a9e9beac660adcbd493c798a"},
 ]
 
+[[package]]
+name = "pyuca"
+version = "1.2"
+description = "a Python implementation of the Unicode Collation Algorithm"
+optional = false
+python-versions = "*"
+files = [
+    {file = "pyuca-1.2-py2.py3-none-any.whl", hash = "sha256:abaa12e1bd2c7c68ca8396ff8383bc0654a739cef3ae68fd7af58bf29af0a91e"},
+    {file = "pyuca-1.2.tar.gz", hash = "sha256:8a382fe74627f08c0d18908c0713ca4a20aad5385f077579e56208beea2893b2"},
+]
+
 [[package]]
 name = "pywin32"
 version = "306"
@@ -4612,13 +4742,13 @@ qtpy = "*"
 
 [[package]]
 name = "qtconsole"
-version = "5.5.2"
+version = "5.6.0"
 description = "Jupyter Qt console"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "qtconsole-5.5.2-py3-none-any.whl", hash = "sha256:42d745f3d05d36240244a04e1e1ec2a86d5d9b6edb16dbdef582ccb629e87e0b"},
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+    {file = "qtconsole-5.6.0-py3-none-any.whl", hash = "sha256:c36e0d497a473b67898b96dd38666e645e4594019244263da7b409b84fa2ebb5"},
+    {file = "qtconsole-5.6.0.tar.gz", hash = "sha256:4c82120a3b53a3d36e3f76e6a1a26ffddf4e1ce2359d56a19889c55e1d73a436"},
 ]
 
 [package.dependencies]
@@ -4627,7 +4757,6 @@ jupyter-client = ">=4.1"
 jupyter-core = "*"
 packaging = "*"
 pygments = "*"
-pyzmq = ">=17.1"
 qtpy = ">=2.4.0"
 traitlets = "<5.2.1 || >5.2.1,<5.2.2 || >5.2.2"
 
@@ -5206,17 +5335,19 @@ test = ["pytest"]
 
 [[package]]
 name = "spyder"
-version = "5.5.6"
+version = "6.0.0"
 description = "The Scientific Python Development Environment"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
+aiohttp = ">=3.9.3"
 applaunchservices = {version = ">=0.3.0", markers = "platform_system == \"Darwin\""}
+asyncssh = ">=2.14.0,<3.0.0"
 atomicwrites = ">=1.2.0"
 chardet = ">=2.0.0"
 cloudpickle = ">=0.5.0"
@@ -5231,58 +5362,62 @@ jsonschema = ">=3.2.0"
 keyring = ">=17.0.0"
 nbconvert = ">=4.0"
 numpydoc = ">=0.6.0"
-paramiko = {version = ">=2.4.0", markers = "platform_system == \"Windows\""}
 parso = ">=0.7.0,<0.9.0"
 pexpect = ">=4.4.0"
 pickleshare = ">=0.4"
 psutil = ">=5.3"
+pygithub = ">=2.3.0"
 pygments = ">=2.0"
 pylint = ">=3.1,<4"
 pylint-venv = ">=3.0.2"
 pyls-spyder = ">=0.4.0"
-pyqt5 = ">=5.10,<5.16"
-pyqtwebengine = ">=5.10,<5.16"
+pyqt5 = ">=5.15,<5.16"
+pyqtwebengine = ">=5.15,<5.16"
 python-lsp-black = ">=2.0.0,<3.0.0"
 python-lsp-server = {version = ">=1.12.0,<1.13.0", extras = ["all"]}
+pyuca = ">=1.2"
 pyxdg = {version = ">=0.26", markers = "platform_system == \"Linux\""}
 pyzmq = ">=24.0.0"
 qdarkstyle = ">=3.2.0,<3.3.0"
 qstylizer = ">=0.2.2"
 qtawesome = ">=1.3.1,<1.4.0"
-qtconsole = ">=5.5.1,<5.6.0"
-qtpy = ">=2.1.0"
+qtconsole = ">=5.6.0,<5.7.0"
+qtpy = ">=2.4.0"
 rtree = ">=0.9.7"
 setuptools = ">=49.6.0"
 sphinx = ">=0.6.6"
-spyder-kernels = ">=2.5.2,<2.6.0"
+spyder-kernels = ">=3.0.0,<3.1.0"
+superqt = ">=0.6.2,<1.0.0"
 textdistance = ">=4.2.0"
 three-merge = ">=0.1.1"
 watchdog = ">=0.10.3"
+yarl = ">=1.9.4"
 
 [package.extras]
 test = ["coverage", "cython", "flaky", "matplotlib", "pandas", "pillow", "pytest (<8.0)", "pytest-cov", "pytest-lazy-fixture", "pytest-mock", "pytest-order", "pytest-qt", "pytest-timeout", "pywin32", "pyyaml", "scipy", "sympy"]
 
 [[package]]
 name = "spyder-kernels"
-version = "2.5.2"
+version = "3.0.0"
 description = "Jupyter kernels for Spyder's console"
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
 files = [
-    {file = "spyder_kernels-2.5.2-py2.py3-none-any.whl", hash = "sha256:1c95bc09ca20f54c981e7d923708df85c6d6583f683e23923e10d524628bc000"},
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+    {file = "spyder_kernels-3.0.0-py3-none-any.whl", hash = "sha256:f0fc98fa3feafc2e0a99f305a5d6b5f614849b2c0cfb851c1dd9a553d9f45660"},
+    {file = "spyder_kernels-3.0.0.tar.gz", hash = "sha256:3d316ea04802ed1feb366405cca03df2349dc9e35ad8653538d2fe48c0e9417f"},
 ]
 
 [package.dependencies]
 cloudpickle = "*"
-ipykernel = {version = ">=6.29.3,<7", markers = "python_version >= \"3.8\""}
+ipykernel = ">=6.29.3,<7"
 ipython = {version = ">=8.13.0,<8.17.1 || >8.17.1,<9", markers = "python_version > \"3.8\""}
-jupyter-client = {version = ">=7.4.9,<9", markers = "python_version >= \"3\""}
-pyzmq = {version = ">=24.0.0", markers = "python_version >= \"3\""}
+jupyter-client = ">=7.4.9,<9"
+pyxdg = {version = ">=0.26", markers = "platform_system == \"Linux\""}
+pyzmq = ">=24.0.0"
 wurlitzer = {version = ">=1.0.3", markers = "platform_system != \"Windows\""}
 
 [package.extras]
-test = ["cython", "dask[distributed]", "django", "flaky", "matplotlib", "mock", "numpy", "pandas", "pillow", "pytest", "pytest-cov", "scipy", "xarray"]
+test = ["cython", "dask[distributed]", "django", "flaky", "h5py", "matplotlib", "mock", "numpy", "pandas", "pillow", "pydicom", "pytest", "pytest-cov", "scipy", "xarray"]
 
 [[package]]
 name = "stack-data"
@@ -5303,6 +5438,38 @@ pure-eval = "*"
 [package.extras]
 tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
 
+[[package]]
+name = "superqt"
+version = "0.6.7"
+description = "Missing widgets and components for PyQt/PySide"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "superqt-0.6.7-py3-none-any.whl", hash = "sha256:4300a0e38c4dd36ae06d1e33dc75e33d238252251c43311cc45da52888476223"},
+    {file = "superqt-0.6.7.tar.gz", hash = "sha256:af80d5687ec75df6c3e54119ee895e42f79742ed326684c79425414b5c20f1e3"},
+]
+
+[package.dependencies]
+pygments = ">=2.4.0"
+qtpy = ">=1.1.0"
+typing-extensions = ">=3.7.4.3,<3.10.0.0 || >3.10.0.0"
+
+[package.extras]
+cmap = ["cmap (>=0.1.1)"]
+dev = ["ipython", "mypy", "pdbpp", "pre-commit", "pydocstyle", "rich", "ruff", "types-pygments"]
+docs = ["cmap", "mkdocs-macros-plugin", "mkdocs-material", "mkdocstrings[python]", "pint"]
+font-fa5 = ["fonticon-fontawesome5"]
+font-fa6 = ["fonticon-fontawesome6"]
+font-mi6 = ["fonticon-materialdesignicons6"]
+font-mi7 = ["fonticon-materialdesignicons7"]
+iconify = ["pyconify (>=0.1.4)"]
+pyqt5 = ["pyqt5"]
+pyqt6 = ["pyqt6 (<6.7)"]
+pyside2 = ["pyside2"]
+pyside6 = ["pyside6 (!=6.5.0,!=6.5.1,!=6.6.2)"]
+quantity = ["pint"]
+test = ["cmap", "numpy", "pint", "pyconify", "pytest", "pytest-cov", "pytest-qt"]
+
 [[package]]
 name = "tabulate"
 version = "0.9.0"
@@ -5961,4 +6128,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "8067d669ec0f895864efa03341f1e9e7e5fc499ede671b3b26e6540ac85b4cbf"
+content-hash = "0b196747c921e35e3de1c87bddab9066905b72039e1b263e90f2268a4c6ac483"
diff --git a/pyproject.toml b/pyproject.toml
index 380ef8b..5499279 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,7 @@ python = "^3.9"
 requests = "^2.28.2"
 py7zr = "^0.20.4"
 geopandas = "^1.0.1"
-openpyxl = "^3.1.1"
+openpyxl = "^3.1.5"
 s3fs = "^2023.3.0"
 PyYAML = "^6.0"
 xlrd = "^2.0.1"
@@ -31,13 +31,15 @@ pyarrow = "^17.0.0"
 diskcache = "^5.6.3"
 urllib3 = "<2"
 retrying = "^1.3.4"
+pandas = "^2.2.2"
+python-calamine = "^0.2.3"
 
 
 [tool.poetry.group.dev.dependencies]
 PyQt5 = {version = "^5.15", markers = "sys_platform == 'win32'"}
 PyQt5-Qt5 = {version = "5.15.2", markers = "sys_platform == 'win32'"}
 PyQtWebEngine-Qt5 = {version = "5.15.2", markers = "sys_platform == 'win32'"}
-spyder = "^5.4.2"
+spyder = "^6.0.0"
 pytest = "^8.1.1"
 
 [build-system]
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index f5fec62..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-pyarrow>=15.0
-geopandas>=1.0.1
-openpyxl
-PyYAML
-py7zr
-requests
-s3fs
-topojson
-tqdm
-xlrd
\ No newline at end of file