Merge pull request #46 from AllenCell/downgrade-pdm

Downgrade pdm

.github/actions/pdm/action.yml

@@ -7,6 +7,6 @@ runs:
       uses: pdm-project/setup-pdm@c050bdcb2405837648035b6678c75609d53a749f
       with:
         python-version: "3.9"
-        version: 2.17.1
+        version: 2.12.2
         # Cache all dependencies installed from pdm.lock
         cache: true

requirements/linux/requirements.txt

@@ -8,8 +8,6 @@ aicsshparam==0.1.7
 aiohttp==3.9.3
 aiosignal==1.3.1
 annotated-types==0.6.0
-annoy==1.17.3
-appnope==0.1.3; platform_system == "Darwin"
 argon2-cffi==23.1.0
 argon2-cffi-bindings==21.2.0
 argparse==1.4.0
@@ -18,24 +16,21 @@ astropy==5.2.2
 asttokens==2.4.1
 async-timeout==4.0.3; python_version < "3.11"
 attrs==23.2.0
-av==11.0.0
+av==12.3.0
 backoff==1.11.1
 beautifulsoup4==4.12.3
-bigtree==0.16.1
-bioio==1.0.2
-bioio-base==1.0.1
+bigtree==0.19.3
+bioio==1.0.3
+bioio-base==1.0.4
 bioio-ome-zarr==1.0.1
 bleach==6.1.0
-bokeh==3.1.1
 botocore==1.34.32
 certifi==2023.11.17
 cffi==1.16.0
 charset-normalizer==3.3.2
 click==8.1.7
 cloudpickle==3.0.0
-colorama==0.4.6; sys_platform == "win32" or platform_system == "Windows"
-colorcet==3.0.1
-colorizer-data @ git+https://github.com/allen-cell-animated/[email protected]
+colorizer-data @ git+https://github.com/allen-cell-animated/[email protected]
 colour-science==0.4.4
 comm==0.2.1
 contourpy==1.1.1
@@ -52,7 +47,7 @@ exceptiongroup==1.2.0; python_version < "3.11"
 executing==2.0.1
 fasteners==0.19
 fastjsonschema==2.19.1
-fire==0.5.0
+fire==0.6.0
 fonttools==4.47.2
 frozenlist==1.4.1
 fsspec==2023.6.0
@@ -61,25 +56,17 @@ imagecodecs==2023.3.16
 imageio==2.27.0
 imageio-ffmpeg==0.4.9
 importlib-metadata==7.0.1
-importlib-resources==6.1.1; python_version < "3.10"
+importlib-resources==6.1.1; python_version < "3.10" or sys_platform != "emscripten"
 iniconfig==2.0.0
-ipydatawidgets==4.3.2
-ipykernel==6.29.0
-ipympl==0.9.3
+ipykernel==6.29.5
 ipython==8.18.1
 ipython-genutils==0.2.0
-ipywidgets==7.8.1
-itk==5.3.0
-itk-core==5.3.0
-itk-filtering==5.3.0
-itk-io==5.3.0
-itk-meshtopolydata==0.10.0
-itk-numerics==5.3.0
-itk-registration==5.3.0
-itk-segmentation==5.3.0
-itkwidgets==0.32.6
+ipywidgets==8.1.3
+itkwasm==1.0b175
+itkwasm-downsample==1.3.0
+itkwasm-downsample-wasi==1.3.0; sys_platform != "emscripten"
 jedi==0.19.1
-Jinja2==3.1.3
+jinja2==3.1.3
 jmespath==1.0.1
 joblib==1.3.2
 jsonpickle==2.2.0
@@ -90,84 +77,67 @@ jupyter-client==8.6.0
 jupyter-console==6.6.3
 jupyter-core==5.7.1
 jupyterlab-pygments==0.3.0
-jupyterlab-widgets==1.1.7; python_version >= "3.6"
+jupyterlab-widgets==3.0.11
 kiwisolver==1.4.5
 labkey==1.4.1
 lazy-loader==0.3
-linkify-it-py==2.0.2
 lkaccess==1.4.25
-llvmlite==0.41.1
 locket==1.0.0
 lxml==4.9.4
 lxml-stubs==0.5.1
-markdown==3.5.2
 markdown-it-py==3.0.0
 markupsafe==2.1.4
 marshmallow==3.21.1
-matplotlib==3.7.4
+matplotlib==3.9.1
 matplotlib-inline==0.1.6
-mdit-py-plugins==0.4.0
 mdurl==0.1.2
 mistune==3.0.2
-moviepy==1.0.3
 msgpack==1.0.7
 multidict==6.0.4
-mypy==1.8.0
+mypy==1.11.0
 mypy-extensions==1.0.0
 nbclient==0.9.0
 nbconvert==7.14.2
 nbformat==5.9.2
 nest-asyncio==1.6.0
 networkx==3.1
+ngff-zarr==0.8.5
 notebook==6.4.13
-numba==0.58.1
 numcodecs==0.12.1
-numpy==1.23.5
+numpy==1.26.4
 ome-types==0.5.1.post1
 ome-zarr==0.8.3
-opencv-python-headless==4.10.0.82
-opencv-stubs==0.0.8
+opencv-python-headless==4.10.0.84
+opencv-stubs==0.0.10
 packaging==23.2
-pacmap==0.7.2
-pandas==1.5.1
-pandas-stubs==2.0.1.230501
+pandas==1.5.3
+pandas-stubs==2.2.2.240603
 pandocfilters==1.5.1
-panel==1.2.3
-param==2.0.2
 parso==0.8.3
 partd==1.4.1
-pathlib==1.0.1
-patsy==0.5.6
 pexpect==4.9.0; sys_platform != "win32"
 pillow==10.2.0
 platformdirs==4.2.0
-plotly==5.18.0
-pluggy==1.4.0
+pluggy==1.5.0
 pooch==1.8.0
-proglog==0.1.10
 prometheus-client==0.19.0
 prompt-toolkit==3.0.43
 psutil==5.9.8
 ptyprocess==0.7.0; sys_platform != "win32" or os_name != "nt"
 pure-eval==0.2.2
 pyaml==20.4.0
-pyarrow==15.0.0
+pyarrow==17.0.0
 pycparser==2.21
-pyct==0.5.0
 pydantic==2.6.0
 pydantic-compat==0.1.2
 pydantic-core==2.16.1
 pyerfa==2.0.0.3
 pygments==2.17.2
 pyparsing==3.1.1
 pyshtools==4.10
-pytest==8.0.0
+pytest==8.3.2
 python-dateutil==2.8.2
 pytz==2023.4
-pyviz-comms==3.0.1
-PyWavelets==1.4.1
-pywin32==306; sys_platform == "win32" and platform_python_implementation != "PyPy"
-pywinpty==2.0.12; os_name == "nt"
 PyYAML==6.0.1
 pyzmq==25.1.2
 qtconsole==5.5.1
@@ -176,21 +146,22 @@ referencing==0.33.0
 rehash==1.0.1
 requests==2.31.0
 resource-backed-dask-array==0.1.0
+rich==13.7.1
+rich-argparse==1.5.2
 rpds-py==0.17.1
 s3fs==0.4.2
-scikit-image==0.21.0
-scikit-learn==1.3.2
-scipy==1.10.1
+scikit-image==0.22.0
+scikit-learn==1.5.1
+scipy==1.13.1
 seaborn==0.13.2
 semver==3.0.2
 Send2Trash==1.8.2
 setuptools==69.0.3
-shapely==2.0.2
+shapely==2.0.5
 six==1.16.0
 sortedcontainers==2.4.0
 soupsieve==2.5
 stack-data==0.6.3
-statsmodels==0.14.1
 tblib==3.0.0
 tenacity==8.1.0
 termcolor==2.4.0
@@ -201,42 +172,39 @@ tinycss2==1.2.1
 tomli==2.0.1; python_version < "3.11"
 toolz==0.12.1
 tornado==6.4
-tqdm==4.66.1
+tqdm==4.66.4
 traitlets==5.6.0
-traittypes==0.2.1
-types-colorama==0.4.15.20240205
-types-decorator==5.1.8.20240106
+types-colorama==0.4.15.20240311
+types-decorator==5.1.8.20240310
 types-docutils==0.20.0.20240227
-types-jsonschema==4.21.0.20240118
-types-openpyxl==3.1.0.20240301
-types-Pillow==10.2.0.20240213
-types-psutil==5.9.5.20240205
-types-pycurl==7.45.2.20240106
-types-Pygments==2.17.0.20240106
+types-jsonschema==4.23.0.20240712
+types-openpyxl==3.1.5.20240719
+types-Pillow==10.2.0.20240520
+types-psutil==6.0.0.20240621
+types-pycurl==7.45.3.20240421
+types-Pygments==2.18.0.20240506
 types-pytz==2024.1.0.20240203
-types-PyYAML==6.0.12.12
+types-PyYAML==6.0.12.20240724
 types-Send2Trash==1.8.2.7
 types-setuptools==69.1.0.20240223
-types-six==1.16.21.20240301
+types-six==1.16.21.20240513
 types-termcolor==1.1.6.2
-types-tqdm==4.66.0.20240106
+types-tqdm==4.66.0.20240417
 typing-extensions==4.9.0
 typing-inspect==0.9.0
-uc-micro-py==1.0.2
 urllib3==1.26.18
 vtk==9.3.0
-vtk-osmesa==9.3.0
+vtk-osmesa==9.3.1
+wasmtime==23.0.0; sys_platform != "emscripten"
 wcwidth==0.2.13
 webencodings==0.5.1
-widgetsnbextension==3.6.6
+widgetsnbextension==4.0.11
 wrapt==1.16.0
 xarray==2023.1.0
 xmlschema==3.0.1
 xsdata==24.1
-xyzservices==2023.10.1
 yarl==1.9.4
 zarr==2.15.0
 zict==3.0.0
 zipp==3.17.0
-zstandard==0.22.0
 --extra-index-url https://wheels.vtk.org