remove uneeded dependencies

This commit is contained in:
Valentin Boettcher 2023-03-23 10:21:38 -04:00
parent dfce04ac0d
commit 2ffb1b5e77
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GPG key ID: E034E12B7AF56ACE
4 changed files with 26 additions and 279 deletions

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@ -1,13 +1,7 @@
import numpy as np
import scipy as sc
import matplotlib.pyplot as plt
from numpy.typing import ArrayLike
from scipy import signal
from skimage.transform import resize
from skimage.filters import hessian
from skimage.morphology import skeletonize
import itertools
from scipy.interpolate import splrep, BSpline
def load_data(data_file: str) -> np.ndarray:

View file

@ -23,6 +23,7 @@
pyright
python310Packages.jupyter
black
poetry
];
};
};

294
poetry.lock generated
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@ -4,7 +4,7 @@
name = "appnope"
version = "0.1.3"
description = "Disable App Nap on macOS >= 10.9"
category = "main"
category = "dev"
optional = false
python-versions = "*"
files = [
@ -12,29 +12,11 @@ files = [
{file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"},
]
[[package]]
name = "asteval"
version = "0.9.29"
description = "Safe, minimalistic evaluator of python expression using ast module"
category = "main"
optional = false
python-versions = ">=3.7"
files = [
{file = "asteval-0.9.29-py3-none-any.whl", hash = "sha256:134e42fc4790582f2f926999e59abb444fb491046ba396836962268aad8a68a5"},
{file = "asteval-0.9.29.tar.gz", hash = "sha256:ab98c61ba9394149c774ae7861497e9c32580301aa693ca19746997216c31fab"},
]
[package.extras]
all = ["Sphinx", "build", "coverage", "pytest", "pytest-cov", "twine"]
dev = ["build", "twine"]
doc = ["Sphinx"]
test = ["coverage", "pytest", "pytest-cov"]
[[package]]
name = "asttokens"
version = "2.2.1"
description = "Annotate AST trees with source code positions"
category = "main"
category = "dev"
optional = false
python-versions = "*"
files = [
@ -52,7 +34,7 @@ test = ["astroid", "pytest"]
name = "backcall"
version = "0.2.0"
description = "Specifications for callback functions passed in to an API"
category = "main"
category = "dev"
optional = false
python-versions = "*"
files = [
@ -64,7 +46,7 @@ files = [
name = "colorama"
version = "0.4.6"
description = "Cross-platform colored terminal text."
category = "main"
category = "dev"
optional = false
python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
files = [
@ -163,7 +145,7 @@ files = [
name = "decorator"
version = "5.1.1"
description = "Decorators for Humans"
category = "main"
category = "dev"
optional = false
python-versions = ">=3.5"
files = [
@ -175,7 +157,7 @@ files = [
name = "executing"
version = "1.2.0"
description = "Get the currently executing AST node of a frame, and other information"
category = "main"
category = "dev"
optional = false
python-versions = "*"
files = [
@ -212,54 +194,11 @@ ufo = ["fs (>=2.2.0,<3)"]
unicode = ["unicodedata2 (>=15.0.0)"]
woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
[[package]]
name = "future"
version = "0.18.3"
description = "Clean single-source support for Python 3 and 2"
category = "main"
optional = false
python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
files = [
{file = "future-0.18.3.tar.gz", hash = "sha256:34a17436ed1e96697a86f9de3d15a3b0be01d8bc8de9c1dffd59fb8234ed5307"},
]
[[package]]
name = "imageio"
version = "2.26.0"
description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats."
category = "main"
optional = false
python-versions = ">=3.7"
files = [
{file = "imageio-2.26.0-py3-none-any.whl", hash = "sha256:1a4fdb820abc52ba0f08e770ee46293c334908e8d53217808d9d888f993b1df2"},
{file = "imageio-2.26.0.tar.gz", hash = "sha256:169f1642cdb723133fe8fe901887f4f1b39bc036458c4664f1f9d256226ced35"},
]
[package.dependencies]
numpy = "*"
pillow = ">=8.3.2"
[package.extras]
all-plugins = ["astropy", "av", "imageio-ffmpeg", "psutil", "tifffile"]
all-plugins-pypy = ["av", "imageio-ffmpeg", "psutil", "tifffile"]
build = ["wheel"]
dev = ["black", "flake8", "fsspec[github]", "invoke", "pytest", "pytest-cov"]
docs = ["numpydoc", "pydata-sphinx-theme", "sphinx (<6)"]
ffmpeg = ["imageio-ffmpeg", "psutil"]
fits = ["astropy"]
full = ["astropy", "av", "black", "flake8", "fsspec[github]", "gdal", "imageio-ffmpeg", "invoke", "itk", "numpydoc", "psutil", "pydata-sphinx-theme", "pytest", "pytest-cov", "sphinx (<6)", "tifffile", "wheel"]
gdal = ["gdal"]
itk = ["itk"]
linting = ["black", "flake8"]
pyav = ["av"]
test = ["fsspec[github]", "invoke", "pytest", "pytest-cov"]
tifffile = ["tifffile"]
[[package]]
name = "ipython"
version = "8.11.0"
description = "IPython: Productive Interactive Computing"
category = "main"
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
@ -298,7 +237,7 @@ test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pa
name = "jedi"
version = "0.18.2"
description = "An autocompletion tool for Python that can be used for text editors."
category = "main"
category = "dev"
optional = false
python-versions = ">=3.6"
files = [
@ -318,7 +257,7 @@ testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
name = "jupyter-core"
version = "5.3.0"
description = "Jupyter core package. A base package on which Jupyter projects rely."
category = "main"
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
@ -413,46 +352,6 @@ files = [
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]
[[package]]
name = "lazy-loader"
version = "0.1"
description = "lazy_loader"
category = "main"
optional = false
python-versions = ">=3.7"
files = [
{file = "lazy_loader-0.1-py3-none-any.whl", hash = "sha256:623bd4831a40ce659d74472af40a58d016f2a5a047685409affbc2ba5c044641"},
{file = "lazy_loader-0.1.tar.gz", hash = "sha256:77ce7f2737ebabf9c0ff73b4a99c947876d74d24c2f026544e32246ecca5feca"},
]
[package.extras]
lint = ["pre-commit (>=2.20)"]
test = ["codecov (>=2.1)", "pytest (>=7.1)", "pytest-cov (>=3.0)"]
[[package]]
name = "lmfit"
version = "1.1.0"
description = "Least-Squares Minimization with Bounds and Constraints"
category = "main"
optional = false
python-versions = ">=3.7"
files = [
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]
[package.dependencies]
asteval = ">=0.9.28"
numpy = ">=1.19"
scipy = ">=1.6"
uncertainties = ">=3.1.4"
[package.extras]
all = ["Pillow", "Sphinx", "build", "cairosvg", "check-wheel-contents", "codecov", "corner", "coverage", "dill", "emcee (>=3.0.0)", "flaky", "jupyter-sphinx (>=0.2.4)", "matplotlib", "numdifftools", "pandas", "pre-commit", "pycairo", "pytest", "pytest-cov", "sphinx-gallery (>=0.10)", "sphinxcontrib-svg2pdfconverter", "sympy", "twine"]
dev = ["build", "check-wheel-contents", "pre-commit", "twine"]
doc = ["Pillow", "Sphinx", "cairosvg", "corner", "dill", "emcee (>=3.0.0)", "jupyter-sphinx (>=0.2.4)", "matplotlib", "numdifftools", "pandas", "pycairo", "sphinx-gallery (>=0.10)", "sphinxcontrib-svg2pdfconverter", "sympy"]
test = ["codecov", "coverage", "flaky", "pytest", "pytest-cov"]
[[package]]
name = "matplotlib"
version = "3.7.1"
@ -519,7 +418,7 @@ python-dateutil = ">=2.7"
name = "matplotlib-inline"
version = "0.1.6"
description = "Inline Matplotlib backend for Jupyter"
category = "main"
category = "dev"
optional = false
python-versions = ">=3.5"
files = [
@ -530,25 +429,6 @@ files = [
[package.dependencies]
traitlets = "*"
[[package]]
name = "networkx"
version = "3.0"
description = "Python package for creating and manipulating graphs and networks"
category = "main"
optional = false
python-versions = ">=3.8"
files = [
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{file = "networkx-3.0.tar.gz", hash = "sha256:9a9992345353618ae98339c2b63d8201c381c2944f38a2ab49cb45a4c667e412"},
]
[package.extras]
default = ["matplotlib (>=3.4)", "numpy (>=1.20)", "pandas (>=1.3)", "scipy (>=1.8)"]
developer = ["mypy (>=0.991)", "pre-commit (>=2.20)"]
doc = ["nb2plots (>=0.6)", "numpydoc (>=1.5)", "pillow (>=9.2)", "pydata-sphinx-theme (>=0.11)", "sphinx (==5.2.3)", "sphinx-gallery (>=0.11)", "texext (>=0.6.7)"]
extra = ["lxml (>=4.6)", "pydot (>=1.4.2)", "pygraphviz (>=1.10)", "sympy (>=1.10)"]
test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"]
[[package]]
name = "numpy"
version = "1.24.2"
@ -603,7 +483,7 @@ files = [
name = "parso"
version = "0.8.3"
description = "A Python Parser"
category = "main"
category = "dev"
optional = false
python-versions = ">=3.6"
files = [
@ -619,7 +499,7 @@ testing = ["docopt", "pytest (<6.0.0)"]
name = "pexpect"
version = "4.8.0"
description = "Pexpect allows easy control of interactive console applications."
category = "main"
category = "dev"
optional = false
python-versions = "*"
files = [
@ -634,7 +514,7 @@ ptyprocess = ">=0.5"
name = "pickleshare"
version = "0.7.5"
description = "Tiny 'shelve'-like database with concurrency support"
category = "main"
category = "dev"
optional = false
python-versions = "*"
files = [
@ -737,7 +617,7 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa
name = "platformdirs"
version = "3.1.1"
description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
category = "main"
category = "dev"
optional = false
python-versions = ">=3.7"
files = [
@ -753,7 +633,7 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2.1)", "pytes
name = "prompt-toolkit"
version = "3.0.38"
description = "Library for building powerful interactive command lines in Python"
category = "main"
category = "dev"
optional = false
python-versions = ">=3.7.0"
files = [
@ -768,7 +648,7 @@ wcwidth = "*"
name = "ptyprocess"
version = "0.7.0"
description = "Run a subprocess in a pseudo terminal"
category = "main"
category = "dev"
optional = false
python-versions = "*"
files = [
@ -780,7 +660,7 @@ files = [
name = "pure-eval"
version = "0.2.2"
description = "Safely evaluate AST nodes without side effects"
category = "main"
category = "dev"
optional = false
python-versions = "*"
files = [
@ -795,7 +675,7 @@ tests = ["pytest"]
name = "pygments"
version = "2.14.0"
description = "Pygments is a syntax highlighting package written in Python."
category = "main"
category = "dev"
optional = false
python-versions = ">=3.6"
files = [
@ -836,49 +716,11 @@ files = [
[package.dependencies]
six = ">=1.5"
[[package]]
name = "pywavelets"
version = "1.4.1"
description = "PyWavelets, wavelet transform module"
category = "main"
optional = false
python-versions = ">=3.8"
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category = "dev"
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[package.dependencies]
imageio = ">=2.4.1"
lazy_loader = ">=0.1"
networkx = ">=2.8"
numpy = ">=1.21.1"
packaging = ">=20.0"
pillow = ">=9.0.1"
PyWavelets = ">=1.1.1"
scipy = {version = ">=1.8", markers = "python_version > \"3.9\""}
tifffile = ">=2019.7.26"
[package.extras]
build = ["Cython (>=0.29.24)", "build", "meson-python (>=0.13.0rc0)", "ninja", "numpy (>=1.21.1)", "packaging (>=20)", "pythran", "setuptools (>=67)", "wheel"]
data = ["pooch (>=1.3.0)"]
default = ["PyWavelets (>=1.1.1)", "imageio (>=2.4.1)", "lazy_loader (>=0.1)", "networkx (>=2.8)", "numpy (>=1.21.1)", "packaging (>=20.0)", "pillow (>=9.0.1)", "scipy (>=1.8)", "scipy (>=1.8,<1.9.2)", "tifffile (>=2019.7.26)"]
developer = ["pre-commit", "rtoml"]
docs = ["dask[array] (>=2022.9.2)", "ipywidgets", "kaleido", "matplotlib (>=3.6)", "myst-parser", "numpydoc (>=1.5)", "pandas (>=1.5)", "plotly (>=5.10)", "pooch (>=1.6)", "pytest-runner", "scikit-learn", "seaborn (>=0.11)", "sphinx (>=5.2)", "sphinx-copybutton", "sphinx-gallery (>=0.11)", "tifffile (>=2022.8.12)"]
optional = ["SimpleITK", "astropy (>=3.1.2)", "cloudpickle (>=0.2.1)", "dask[array] (>=1.0.0,!=2.17.0)", "matplotlib (>=3.3)", "pooch (>=1.3.0)", "pyamg"]
test = ["asv", "codecov", "matplotlib (>=3.3)", "pooch (>=1.3.0)", "pytest (>=5.2.0)", "pytest-cov (>=2.7.0)", "pytest-faulthandler", "pytest-localserver"]
[[package]]
name = "scipy"
version = "1.10.1"
@ -1004,7 +795,7 @@ files = [
name = "stack-data"
version = "0.6.2"
description = "Extract data from python stack frames and tracebacks for informative displays"
category = "main"
category = "dev"
optional = false
python-versions = "*"
files = [
@ -1020,29 +811,11 @@ pure-eval = "*"
[package.extras]
tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
[[package]]
name = "tifffile"
version = "2023.3.15"
description = "Read and write TIFF files"
category = "main"
optional = false
python-versions = ">=3.8"
files = [
{file = "tifffile-2023.3.15-py3-none-any.whl", hash = "sha256:0ad708d0d5a45d068444e9036a20f1f8a237da008e35cc9cbc69bbb5602d6987"},
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]
[package.dependencies]
numpy = "*"
[package.extras]
all = ["defusedxml", "fsspec", "imagecodecs (>=2023.1.23)", "lxml", "matplotlib", "zarr"]
[[package]]
name = "traitlets"
version = "5.9.0"
description = "Traitlets Python configuration system"
category = "main"
category = "dev"
optional = false
python-versions = ">=3.7"
files = [
@ -1054,32 +827,11 @@ files = [
docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"]
[[package]]
name = "uncertainties"
version = "3.1.7"
description = "Transparent calculations with uncertainties on the quantities involved (aka error propagation); fast calculation of derivatives"
category = "main"
optional = false
python-versions = "*"
files = [
{file = "uncertainties-3.1.7-py2.py3-none-any.whl", hash = "sha256:4040ec64d298215531922a68fa1506dc6b1cb86cd7cca8eca848fcfe0f987151"},
{file = "uncertainties-3.1.7.tar.gz", hash = "sha256:80111e0839f239c5b233cb4772017b483a0b7a1573a581b92ab7746a35e6faab"},
]
[package.dependencies]
future = "*"
[package.extras]
all = ["nose", "numpy", "sphinx"]
docs = ["sphinx"]
optional = ["numpy"]
tests = ["nose", "numpy"]
[[package]]
name = "wcwidth"
version = "0.2.6"
description = "Measures the displayed width of unicode strings in a terminal"
category = "main"
category = "dev"
optional = false
python-versions = "*"
files = [
@ -1090,4 +842,4 @@ files = [
[metadata]
lock-version = "2.0"
python-versions = ">=3.10,<3.12"
content-hash = "ced817d683c629812123afdb11927679ccdbec449228aa3ac607e659c69ebd64"
content-hash = "1f354255f14417846edfccd27f5e4ef9d5a5d29cd73a4428c415a8b7b32e9d1b"

View file

@ -9,10 +9,10 @@ readme = "README.md"
python = ">=3.10,<3.12"
scipy = "^1.10.1"
matplotlib = "^3.7.1"
lmfit = "^1.1.0"
[tool.poetry.group.dev.dependencies]
ipython = "^8.11.0"
jupyter-core = "^5.3.0"
scikit-image = "^0.20.0"
[build-system]