From f51e0203e706d1b1b8900d229e2e4198b4af04cf Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Fri, 25 Oct 2024 23:26:06 +0200 Subject: [PATCH] Fix #80, which is a temporary fix until the hyperspy developers fix #71 on their side --- dev-requirements.txt | 174 +++++++++++++++++++++++-------------------- pyproject.toml | 3 +- 2 files changed, 97 insertions(+), 80 deletions(-) diff --git a/dev-requirements.txt b/dev-requirements.txt index 933ddb7..2cb5fda 100644 --- a/dev-requirements.txt +++ b/dev-requirements.txt @@ -1,6 +1,6 @@ # This file was autogenerated by uv via the following command: # uv pip compile --extra=dev --extra=docs --output-file=dev-requirements.txt pyproject.toml -anyio==4.4.0 +anyio==4.6.2.post1 # via # httpx # jupyter-server @@ -16,7 +16,7 @@ asciitree==0.3.3 # via zarr ase==3.23.0 # via pynxtools -asteval==1.0.2 +asteval==1.0.5 # via lmfit asttokens==2.4.1 # via stack-data @@ -34,18 +34,18 @@ beautifulsoup4==4.12.3 # via nbconvert bleach==6.1.0 # via nbconvert -build==1.2.1 +build==1.2.2.post1 # via pip-tools certifi==2024.8.30 # via # httpcore # httpx # requests -cffi==1.17.0 +cffi==1.17.1 # via argon2-cffi-bindings cfgv==3.4.0 # via pre-commit -charset-normalizer==3.3.2 +charset-normalizer==3.4.0 # via requests click==8.1.7 # via @@ -57,7 +57,7 @@ click==8.1.7 # pynxtools click-default-group==1.2.4 # via pynxtools -cloudpickle==3.0.0 +cloudpickle==3.1.0 # via dask colorama==0.4.6 # via mkdocs-material @@ -67,18 +67,18 @@ comm==0.2.2 # ipywidgets contourpy==1.3.0 # via matplotlib -coverage==7.6.1 +coverage==7.6.4 # via pytest-cov cycler==0.12.1 # via matplotlib -dask==2024.8.1 +dask==2024.10.0 # via # hyperspy # kikuchipy # orix # pyxem # rosettasciio -debugpy==1.8.5 +debugpy==1.8.7 # via ipykernel decorator==5.1.1 # via @@ -86,26 +86,26 @@ decorator==5.1.1 # ipython defusedxml==0.7.1 # via nbconvert -diffpy-structure==3.2.0 +diffpy-structure==3.2.3 # via # diffsims # kikuchipy # orix -diffsims==0.6.0 +diffsims==0.6.1 # via # kikuchipy # pyxem -dill==0.3.8 +dill==0.3.9 # via # hyperspy # lmfit -distlib==0.3.8 +distlib==0.3.9 # via virtualenv entrypoints==0.4 # via ipyparallel -executing==2.0.1 +executing==2.1.0 # via stack-data -fabio==2024.4.0 +fabio==2024.9.0 # via # pyfai # silx @@ -113,27 +113,27 @@ fasteners==0.19 # via zarr fastjsonschema==2.20.0 # via nbformat -filelock==3.15.4 +filelock==3.16.1 # via virtualenv flatdict==4.0.1 # via pynxtools-em (pyproject.toml) -fonttools==4.53.1 +fonttools==4.54.1 # via matplotlib fqdn==1.5.1 # via jsonschema -fsspec==2024.6.1 +fsspec==2024.10.0 # via # dask # hyperspy ghp-import==2.1.0 # via mkdocs -greenlet==3.0.3 +greenlet==3.1.1 # via sqlalchemy h11==0.14.0 # via httpcore -h5grove==2.2.0 +h5grove==2.3.0 # via jupyterlab-h5web -h5py==3.11.0 +h5py==3.12.1 # via # fabio # h5grove @@ -149,17 +149,22 @@ h5py==3.11.0 # silx hdf5plugin==5.0.0 # via fabio -httpcore==1.0.5 +hjson==3.1.0 + # via + # mkdocs-macros-plugin + # super-collections +httpcore==1.0.6 # via httpx httpx==0.27.2 # via jupyterlab hyperspy==1.7.6 # via + # pynxtools-em (pyproject.toml) # kikuchipy # pyxem -identify==2.6.0 +identify==2.6.1 # via pre-commit -idna==3.8 +idna==3.10 # via # anyio # httpx @@ -173,7 +178,7 @@ imageio==2.27.0 # nionswift-io # nionui # scikit-image -importlib-metadata==8.4.0 +importlib-metadata==8.5.0 # via # hyperspy # pynxtools @@ -187,7 +192,7 @@ ipykernel==6.29.5 # jupyterlab ipyparallel==8.8.0 # via hyperspy -ipython==8.27.0 +ipython==8.29.0 # via # hyperspy # ipykernel @@ -221,11 +226,11 @@ jsonschema==4.23.0 # jupyter-events # jupyterlab-server # nbformat -jsonschema-specifications==2023.12.1 +jsonschema-specifications==2024.10.1 # via jsonschema jupyter==1.1.1 # via pynxtools-em (pyproject.toml) -jupyter-client==8.6.2 +jupyter-client==8.6.3 # via # ipykernel # ipyparallel @@ -263,7 +268,7 @@ jupyterlab==4.2.5 # pynxtools-em (pyproject.toml) # jupyter # notebook -jupyterlab-h5web==12.2.0 +jupyterlab-h5web==12.3.0 # via pynxtools-em (pyproject.toml) jupyterlab-pygments==0.3.0 # via nbconvert @@ -275,7 +280,7 @@ jupyterlab-widgets==3.0.13 # via ipywidgets kikuchipy==0.10.0 # via pynxtools-em (pyproject.toml) -kiwisolver==1.4.5 +kiwisolver==1.4.7 # via matplotlib lazy-loader==0.4 # via scikit-image @@ -298,7 +303,7 @@ markdown==3.7 # pymdown-extensions markdown-include==0.8.1 # via pynxtools-em (pyproject.toml) -markupsafe==2.1.5 +markupsafe==3.0.2 # via # jinja2 # mkdocs @@ -326,7 +331,7 @@ mergedeep==1.3.4 # pynxtools mistune==3.0.2 # via nbconvert -mkdocs==1.6.0 +mkdocs==1.6.1 # via # pynxtools-em (pyproject.toml) # mkdocs-macros-plugin @@ -335,9 +340,9 @@ mkdocs-click==0.8.1 # via pynxtools-em (pyproject.toml) mkdocs-get-deps==0.2.0 # via mkdocs -mkdocs-macros-plugin==1.0.5 +mkdocs-macros-plugin==1.3.6 # via pynxtools-em (pyproject.toml) -mkdocs-material==9.5.33 +mkdocs-material==9.5.42 # via pynxtools-em (pyproject.toml) mkdocs-material-extensions==1.3.1 # via @@ -345,7 +350,7 @@ mkdocs-material-extensions==1.3.1 # mkdocs-material mpmath==1.3.0 # via sympy -mypy==1.11.2 +mypy==1.13.0 # via pynxtools-em (pyproject.toml) mypy-extensions==1.0.0 # via mypy @@ -364,7 +369,7 @@ nbformat==5.10.4 # nbconvert nest-asyncio==1.6.0 # via ipykernel -networkx==3.3 +networkx==3.4.2 # via scikit-image niondata==15.6.3 # via @@ -398,7 +403,7 @@ numba==0.60.0 # orix # pyxem # sparse -numcodecs==0.13.0 +numcodecs==0.13.1 # via zarr numexpr==2.10.1 # via @@ -411,6 +416,7 @@ numpy==1.26.4 # ase # contourpy # dask + # diffpy-structure # diffsims # fabio # h5grove @@ -427,9 +433,9 @@ numpy==1.26.4 # numba # numcodecs # numexpr - # numpy-quaternion # orix # pandas + # pycifrw # pyfai # pynxtools # pyxem @@ -444,14 +450,12 @@ numpy==1.26.4 # xarray # xraydb # zarr -numpy-quaternion==2023.0.4 - # via orix -orix==0.12.1.post0 +orix==0.13.2 # via # diffsims # kikuchipy # pyxem -orjson==3.10.7 +orjson==3.10.10 # via h5grove overrides==7.7.0 # via jupyter-server @@ -467,6 +471,7 @@ packaging==24.1 # lazy-loader # matplotlib # mkdocs + # mkdocs-macros-plugin # nbconvert # pint # pooch @@ -477,7 +482,7 @@ packaging==24.1 # xraydb paginate==0.5.7 # via mkdocs-material -pandas==2.2.2 +pandas==2.2.3 # via # pynxtools # xarray @@ -488,7 +493,9 @@ parso==0.8.4 partd==1.4.2 # via dask pathspec==0.12.1 - # via mkdocs + # via + # mkdocs + # mkdocs-macros-plugin pexpect==4.9.0 # via ipython pillow==10.0.1 @@ -508,7 +515,7 @@ pip==24.2 # via pip-tools pip-tools==7.4.1 # via pynxtools-em (pyproject.toml) -platformdirs==4.2.2 +platformdirs==4.3.6 # via # jupyter-core # mkdocs-get-deps @@ -517,21 +524,23 @@ platformdirs==4.2.2 # xraydb pluggy==1.5.0 # via pytest +ply==3.11 + # via pycifrw pooch==1.8.2 # via # kikuchipy # orix -pre-commit==3.8.0 +pre-commit==4.0.1 # via pynxtools-em (pyproject.toml) prettytable==3.11.0 # via hyperspy -prometheus-client==0.20.0 +prometheus-client==0.21.0 # via jupyter-server -prompt-toolkit==3.0.47 +prompt-toolkit==3.0.48 # via # ipython # jupyter-console -psutil==6.0.0 +psutil==6.1.0 # via # diffsims # ipykernel @@ -543,9 +552,13 @@ ptyprocess==0.7.0 # terminado pure-eval==0.2.3 # via stack-data +pycifrw==4.4.6 + # via + # diffpy-structure + # orix pycparser==2.22 # via cffi -pyfai==2024.5.0 +pyfai==2024.9.0 # via pyxem pygments==2.18.0 # via @@ -553,17 +566,17 @@ pygments==2.18.0 # jupyter-console # mkdocs-material # nbconvert -pymdown-extensions==10.9 +pymdown-extensions==10.11.2 # via mkdocs-material -pynxtools==0.7.0 +pynxtools==0.7.4 # via pynxtools-em (pyproject.toml) -pyparsing==3.1.4 +pyparsing==3.2.0 # via matplotlib -pyproject-hooks==1.1.0 +pyproject-hooks==1.2.0 # via # build # pip-tools -pytest==8.3.2 +pytest==8.3.3 # via # pynxtools-em (pyproject.toml) # pytest-cov @@ -587,7 +600,7 @@ python-dateutil==2.9.0.post0 # rosettasciio python-json-logger==2.0.7 # via jupyter-events -pytz==2024.1 +pytz==2024.2 # via # nionswift # pandas @@ -621,7 +634,7 @@ referencing==0.35.1 # jsonschema # jsonschema-specifications # jupyter-events -regex==2024.7.24 +regex==2024.9.11 # via mkdocs-material requests==2.32.3 # via @@ -650,7 +663,7 @@ scikit-image==0.22.0 # hyperspy # kikuchipy # pyxem -scikit-learn==1.5.1 +scikit-learn==1.5.2 # via # kikuchipy # pyxem @@ -672,11 +685,11 @@ scipy==1.14.1 # xraydb send2trash==1.8.3 # via jupyter-server -setuptools==74.0.0 +setuptools==75.2.0 # via # jupyterlab # pip-tools -silx==2.1.1 +silx==2.1.2 # via pyfai six==1.16.0 # via @@ -693,15 +706,17 @@ soupsieve==2.6 # via beautifulsoup4 sparse==0.15.4 # via hyperspy -sqlalchemy==2.0.32 +sqlalchemy==2.0.36 # via xraydb stack-data==0.6.3 # via ipython structlog==24.4.0 # via pynxtools-em (pyproject.toml) -sympy==1.13.2 +super-collections==0.5.3 + # via mkdocs-macros-plugin +sympy==1.13.3 # via hyperspy -termcolor==2.4.0 +termcolor==2.5.0 # via mkdocs-macros-plugin terminado==0.18.1 # via @@ -709,14 +724,14 @@ terminado==0.18.1 # jupyter-server-terminals threadpoolctl==3.5.0 # via scikit-learn -tifffile==2024.8.28 +tifffile==2024.9.20 # via # h5grove # hyperspy # scikit-image -tinycss2==1.3.0 +tinycss2==1.4.0 # via nbconvert -toolz==0.12.1 +toolz==1.0.0 # via # dask # hyperspy @@ -763,20 +778,21 @@ transforms3d==0.4.2 # via # diffsims # pyxem -types-python-dateutil==2.9.0.20240821 +types-python-dateutil==2.9.0.20241003 # via arrow -types-pytz==2024.1.0.20240417 +types-pytz==2024.2.0.20241003 # via pynxtools-em (pyproject.toml) -types-pyyaml==6.0.12.20240808 +types-pyyaml==6.0.12.20240917 # via pynxtools-em (pyproject.toml) -types-requests==2.32.0.20240712 +types-requests==2.32.0.20241016 # via pynxtools-em (pyproject.toml) typing-extensions==4.12.2 # via # h5grove # mypy + # orix # sqlalchemy -tzdata==2024.1 +tzdata==2024.2 # via pandas tzlocal==5.2 # via @@ -786,15 +802,15 @@ uncertainties==3.2.2 # via lmfit uri-template==1.3.0 # via jsonschema -urllib3==2.2.2 +urllib3==2.2.3 # via # requests # types-requests -uv==0.4.0 +uv==0.4.27 # via pynxtools-em (pyproject.toml) -virtualenv==20.26.3 +virtualenv==20.27.0 # via pre-commit -watchdog==5.0.0 +watchdog==5.0.3 # via mkdocs wcwidth==0.2.13 # via @@ -812,13 +828,13 @@ wheel==0.44.0 # via pip-tools widgetsnbextension==4.0.13 # via ipywidgets -xarray==2024.7.0 +xarray==2024.10.0 # via pynxtools -xmltodict==0.13.0 +xmltodict==0.14.2 # via pynxtools-em (pyproject.toml) xraydb==4.5.4 # via pynxtools-em (pyproject.toml) -zarr==2.18.2 +zarr==2.18.3 # via hyperspy -zipp==3.20.1 +zipp==3.20.2 # via importlib-metadata diff --git a/pyproject.toml b/pyproject.toml index d486669..bd7ca8a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,7 +23,8 @@ classifiers = [ ] dependencies = [ "pint==0.17", - "pynxtools>=0.7.0", + "pynxtools>=0.7.0,<=0.7.4", + "hyperspy==1.7.6", "rosettasciio>=0.6", "kikuchipy>=0.9.0", "pyxem>=0.16.0",