Some dependencies' newer versions break the code

[piyueh]

Haven't had time to check which dependencies break the code. For those who just need a working environment, use the following YAML to create the environment:

channels:
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - alsa-lib=1.2.3.2=h166bdaf_0
  - aom=3.3.0=h27087fc_1
  - appdirs=1.4.4=pyh9f0ad1d_0
  - argon2-cffi=21.3.0=pyhd8ed1ab_0
  - argon2-cffi-bindings=21.2.0=py39hb9d737c_2
  - astroid=2.11.4=py39hf3d152e_0
  - asttokens=2.0.5=pyhd8ed1ab_0
  - attrs=21.4.0=pyhd8ed1ab_0
  - backcall=0.2.0=pyh9f0ad1d_0
  - backports=1.0=py_2
  - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
  - beautifulsoup4=4.11.1=pyha770c72_0
  - bleach=5.0.0=pyhd8ed1ab_0
  - brotli=1.0.9=h166bdaf_7
  - brotli-bin=1.0.9=h166bdaf_7
  - bzip2=1.0.8=h7f98852_4
  - c-ares=1.18.1=h7f98852_0
  - ca-certificates=2022.6.15=ha878542_0
  - cached-property=1.5.2=hd8ed1ab_1
  - cached_property=1.5.2=pyha770c72_1
  - certifi=2022.6.15=py39hf3d152e_0
  - cffi=1.15.0=py39h4bc2ebd_0
  - cftime=1.6.0=py39hd257fcd_1
  - colorama=0.4.4=pyh9f0ad1d_0
  - cudatoolkit=11.5.1=hcf5317a_10
  - cudnn=8.2.1.32=h86fa8c9_0
  - cupy=10.4.0=py39hc3c280e_0
  - curl=7.83.0=h2283fc2_0
  - cutensor=1.5.0.3=h12f7317_2
  - cycler=0.11.0=pyhd8ed1ab_0
  - dbus=1.13.6=h5008d03_3
  - debugpy=1.6.0=py39h5a03fae_0
  - decorator=5.1.1=pyhd8ed1ab_0
  - defusedxml=0.7.1=pyhd8ed1ab_0
  - dill=0.3.4=pyhd8ed1ab_0
  - double-conversion=3.2.0=h9c3ff4c_0
  - eigen=3.4.0=h4bd325d_0
  - entrypoints=0.4=pyhd8ed1ab_0
  - executing=0.8.3=pyhd8ed1ab_0
  - expat=2.4.8=h27087fc_0
  - fastrlock=0.8=py39h5a03fae_2
  - ffmpeg=4.4.1=hd7ab26d_2
  - flake8=4.0.1=pyhd8ed1ab_2
  - flit-core=3.7.1=pyhd8ed1ab_0
  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
  - font-ttf-inconsolata=3.000=h77eed37_0
  - font-ttf-source-code-pro=2.038=h77eed37_0
  - font-ttf-ubuntu=0.83=hab24e00_0
  - fontconfig=2.14.0=h8e229c2_0
  - fonts-conda-ecosystem=1=0
  - fonts-conda-forge=1=0
  - fonttools=4.33.3=py39hb9d737c_0
  - freetype=2.10.4=h0708190_1
  - gettext=0.19.8.1=h73d1719_1008
  - giflib=5.2.1=h36c2ea0_2
  - gl2ps=1.4.2=h0708190_0
  - glew=2.1.0=h9c3ff4c_2
  - gmp=6.2.1=h58526e2_0
  - gnutls=3.6.13=h85f3911_1
  - gst-plugins-base=1.20.2=hcf0ee16_0
  - gstreamer=1.20.2=hd4edc92_0
  - h5py=3.6.0=mpi_openmpi_py39hb889842_0
  - hdf4=4.2.15=h10796ff_3
  - hdf5=1.12.1=mpi_openmpi_h41b9b70_4
  - icu=69.1=h9c3ff4c_0
  - imageio=2.19.0=pyhcf75d05_1
  - importlib-metadata=4.11.3=py39hf3d152e_1
  - importlib_resources=5.7.1=pyhd8ed1ab_0
  - iniconfig=1.1.1=pyh9f0ad1d_0
  - ipycanvas=0.12.0=pyhd8ed1ab_0
  - ipyevents=2.0.1=pyhd8ed1ab_0
  - ipykernel=6.13.0=py39hef51801_0
  - ipython=8.3.0=py39hf3d152e_0
  - ipython_genutils=0.2.0=py_1
  - ipyvtklink=0.2.2=pyhd8ed1ab_0
  - ipywidgets=7.7.0=pyhd8ed1ab_0
  - isort=5.10.1=pyhd8ed1ab_0
  - jbig=2.1=h7f98852_2003
  - jedi=0.18.1=py39hf3d152e_1
  - jinja2=3.1.2=pyhd8ed1ab_0
  - jpeg=9e=h166bdaf_1
  - jsoncpp=1.9.5=h4bd325d_1
  - jsonschema=4.5.1=pyhd8ed1ab_0
  - jupyter=1.0.0=py39hf3d152e_7
  - jupyter_client=7.3.1=pyhd8ed1ab_0
  - jupyter_console=6.4.3=pyhd8ed1ab_0
  - jupyter_core=4.9.2=py39hf3d152e_0
  - jupyterlab_pygments=0.2.2=pyhd8ed1ab_0
  - jupyterlab_widgets=1.1.0=pyhd8ed1ab_0
  - keyutils=1.6.1=h166bdaf_0
  - kiwisolver=1.4.2=py39hf939315_1
  - krb5=1.19.3=h08a2579_0
  - lame=3.100=h7f98852_1001
  - lazy-object-proxy=1.7.1=py39hb9d737c_1
  - lcms2=2.12=hddcbb42_0
  - ld_impl_linux-64=2.36.1=hea4e1c9_2
  - lerc=3.0=h9c3ff4c_0
  - libblas=3.9.0=14_linux64_openblas
  - libbrotlicommon=1.0.9=h166bdaf_7
  - libbrotlidec=1.0.9=h166bdaf_7
  - libbrotlienc=1.0.9=h166bdaf_7
  - libcblas=3.9.0=14_linux64_openblas
  - libcbor=0.9.0=h9c3ff4c_0
  - libclang=13.0.1=default_hc23dcda_0
  - libcurl=7.83.0=h2283fc2_0
  - libdeflate=1.10=h7f98852_0
  - libdrm=2.4.109=h7f98852_0
  - libedit=3.1.20191231=he28a2e2_2
  - libev=4.33=h516909a_1
  - libevent=2.1.10=h28343ad_4
  - libffi=3.4.2=h7f98852_5
  - libfido2=1.11.0=he49606f_0
  - libgcc-ng=12.1.0=h8d9b700_16
  - libgfortran-ng=11.2.0=h69a702a_16
  - libgfortran5=11.2.0=h5c6108e_16
  - libglib=2.70.2=h174f98d_4
  - libglu=9.0.0=he1b5a44_1001
  - libgomp=12.1.0=h8d9b700_16
  - libiconv=1.16=h516909a_0
  - liblapack=3.9.0=14_linux64_openblas
  - libllvm13=13.0.1=hf817b99_2
  - libnetcdf=4.8.1=mpi_openmpi_he7012b2_2
  - libnghttp2=1.47.0=he49606f_0
  - libnsl=2.0.0=h7f98852_0
  - libogg=1.3.4=h7f98852_1
  - libopenblas=0.3.20=pthreads_h78a6416_0
  - libopus=1.3.1=h7f98852_1
  - libpciaccess=0.16=h516909a_0
  - libpng=1.6.37=h21135ba_2
  - libpq=14.2=h676c864_0
  - libsodium=1.0.18=h36c2ea0_1
  - libssh2=1.10.0=ha35d2d1_2
  - libstdcxx-ng=12.1.0=ha89aaad_16
  - libtheora=1.1.1=h7f98852_1005
  - libtiff=4.3.0=h542a066_3
  - libudev1=249=h7f98852_1
  - libuuid=2.32.1=h7f98852_1000
  - libva=2.14.0=h7f98852_0
  - libvorbis=1.3.7=h9c3ff4c_0
  - libvpx=1.11.0=h9c3ff4c_3
  - libwebp=1.2.2=h3452ae3_0
  - libwebp-base=1.2.2=h7f98852_1
  - libxcb=1.13=h7f98852_1004
  - libxkbcommon=1.0.3=he3ba5ed_0
  - libxml2=2.9.12=h885dcf4_1
  - libzip=1.8.0=h1c5bbd1_1
  - libzlib=1.2.11=h166bdaf_1014
  - loguru=0.6.0=py39hf3d152e_1
  - lz4-c=1.9.3=h9c3ff4c_1
  - markupsafe=2.1.1=py39hb9d737c_1
  - matplotlib=3.5.2=py39hf3d152e_0
  - matplotlib-base=3.5.2=py39h700656a_0
  - matplotlib-inline=0.1.3=pyhd8ed1ab_0
  - mccabe=0.6.1=py_1
  - mistune=0.8.4=py39h3811e60_1005
  - mpi=1.0=openmpi
  - mpi4py=3.1.3=py39h5418507_1
  - munkres=1.1.4=pyh9f0ad1d_0
  - mysql-common=8.0.29=h26416b9_0
  - mysql-libs=8.0.29=hbc51c84_0
  - nbclient=0.6.2=pyhd8ed1ab_0
  - nbconvert=6.5.0=pyhd8ed1ab_0
  - nbconvert-core=6.5.0=pyhd8ed1ab_0
  - nbconvert-pandoc=6.5.0=pyhd8ed1ab_0
  - nbformat=5.4.0=pyhd8ed1ab_0
  - nccl=2.12.10.1=h0800d71_0
  - ncurses=6.3=h27087fc_1
  - nest-asyncio=1.5.5=pyhd8ed1ab_0
  - netcdf4=1.5.8=mpi_openmpi_py39h957639f_1
  - nettle=3.6=he412f7d_0
  - notebook=6.4.11=pyha770c72_0
  - nspr=4.32=h9c3ff4c_1
  - nss=3.77=h2350873_0
  - numpy=1.23.0=py39hba7629e_0
  - openh264=2.1.1=h780b84a_0
  - openjpeg=2.4.0=hb52868f_1
  - openmpi=4.1.3=h846660c_103
  - openssh=9.0p1=h67c24c5_0
  - openssl=3.0.5=h166bdaf_0
  - orjson=3.6.8=py39hb9d737c_0
  - packaging=21.3=pyhd8ed1ab_0
  - pandoc=2.18=ha770c72_0
  - pandocfilters=1.5.0=pyhd8ed1ab_0
  - parso=0.8.3=pyhd8ed1ab_0
  - pcre=8.45=h9c3ff4c_0
  - pexpect=4.8.0=pyh9f0ad1d_2
  - pickleshare=0.7.5=py_1003
  - pillow=9.1.0=py39hae2aec6_2
  - pip=22.0.4=pyhd8ed1ab_0
  - platformdirs=2.5.1=pyhd8ed1ab_0
  - pluggy=1.0.0=py39hf3d152e_3
  - proj=9.0.0=h93bde94_1
  - prometheus_client=0.14.1=pyhd8ed1ab_0
  - prompt-toolkit=3.0.29=pyha770c72_0
  - prompt_toolkit=3.0.29=hd8ed1ab_0
  - psutil=5.9.0=py39hb9d737c_1
  - pthread-stubs=0.4=h36c2ea0_1001
  - ptyprocess=0.7.0=pyhd3deb0d_0
  - pugixml=1.11.4=h9c3ff4c_0
  - pure_eval=0.2.2=pyhd8ed1ab_0
  - py=1.11.0=pyh6c4a22f_0
  - pycodestyle=2.8.0=pyhd8ed1ab_0
  - pycparser=2.21=pyhd8ed1ab_0
  - pydantic=1.9.0=py39hb9d737c_1
  - pyflakes=2.4.0=pyhd8ed1ab_0
  - pygments=2.12.0=pyhd8ed1ab_0
  - pylint=2.13.8=pyhd8ed1ab_0
  - pyparsing=3.0.8=pyhd8ed1ab_0
  - pyqt=5.12.3=py39hf3d152e_8
  - pyqt-impl=5.12.3=py39hde8b62d_8
  - pyqt5-sip=4.19.18=py39he80948d_8
  - pyqtchart=5.12=py39h0fcd23e_8
  - pyqtwebengine=5.12.1=py39h0fcd23e_8
  - pyrsistent=0.18.1=py39hb9d737c_1
  - pytest=7.1.2=py39hf3d152e_0
  - python=3.9.12=h2660328_1_cpython
  - python-dateutil=2.8.2=pyhd8ed1ab_0
  - python-fastjsonschema=2.15.3=pyhd8ed1ab_0
  - python_abi=3.9=2_cp39
  - pyvista=0.34.0=pyhd8ed1ab_0
  - pyyaml=6.0=py39hb9d737c_4
  - pyzmq=22.3.0=py39headdf64_2
  - qt=5.12.9=h1304e3e_6
  - qtconsole=5.3.0=pyhd8ed1ab_0
  - qtconsole-base=5.3.0=pyhd8ed1ab_0
  - qtpy=2.1.0=pyhd8ed1ab_0
  - readline=8.1=h46c0cb4_0
  - scipy=1.8.0=py39hee8e79c_1
  - scooby=0.5.12=pyhd8ed1ab_0
  - send2trash=1.8.0=pyhd8ed1ab_0
  - setuptools=62.1.0=py39hf3d152e_0
  - six=1.16.0=pyh6c4a22f_0
  - soupsieve=2.3.1=pyhd8ed1ab_0
  - sqlite=3.38.5=h4ff8645_0
  - stack_data=0.2.0=pyhd8ed1ab_0
  - svt-av1=0.9.1=h27087fc_0
  - tbb=2021.5.0=h924138e_1
  - tbb-devel=2021.5.0=h924138e_1
  - terminado=0.13.3=py39hf3d152e_1
  - tinycss2=1.1.1=pyhd8ed1ab_0
  - tk=8.6.12=h27826a3_0
  - tomli=2.0.1=pyhd8ed1ab_0
  - tornado=6.1=py39hb9d737c_3
  - traitlets=5.1.1=pyhd8ed1ab_0
  - typing-extensions=4.2.0=hd8ed1ab_1
  - typing_extensions=4.2.0=pyha770c72_1
  - tzdata=2022a=h191b570_0
  - ucx=1.12.1=h7a399c7_1
  - unicodedata2=14.0.0=py39hb9d737c_1
  - utfcpp=3.2.1=ha770c72_0
  - vtk=9.1.0=qt_py39hd359688_207
  - wcwidth=0.2.5=pyh9f0ad1d_2
  - webencodings=0.5.1=py_1
  - wheel=0.37.1=pyhd8ed1ab_0
  - widgetsnbextension=3.6.0=py39hf3d152e_0
  - wrapt=1.14.1=py39hb9d737c_0
  - x264=1!161.3030=h7f98852_1
  - x265=3.5=h924138e_3
  - xorg-fixesproto=5.0=h7f98852_1002
  - xorg-kbproto=1.0.7=h7f98852_1002
  - xorg-libice=1.0.10=h7f98852_0
  - xorg-libsm=1.2.3=hd9c2040_1000
  - xorg-libx11=1.7.2=h7f98852_0
  - xorg-libxau=1.0.9=h7f98852_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xorg-libxext=1.3.4=h7f98852_1
  - xorg-libxfixes=5.0.3=h7f98852_1004
  - xorg-libxt=1.2.1=h7f98852_2
  - xorg-xextproto=7.3.0=h7f98852_1002
  - xorg-xproto=7.0.31=h7f98852_1007
  - xz=5.2.5=h516909a_1
  - yaml=0.2.5=h7f98852_2
  - zeromq=4.3.4=h9c3ff4c_1
  - zipp=3.8.0=pyhd8ed1ab_0
  - zlib=1.2.11=h166bdaf_1014
  - zstd=1.5.2=ha95c52a_0