diff --git a/.gitignore b/.gitignore index e807c4516f427be4247ac50af7f654efdce509a2..e1a09c0e84c91d70be96bce960ed00c331aac2b9 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,2 @@ -.idea* +.idea *__pycache__* \ No newline at end of file diff --git a/environment.yml b/environment.yml index 11ef57e8b87b6b217f608a207ec9f9ecbd5d75c9..b113ed9ac82adc957388ee9774f097a244aeb23d 100644 --- a/environment.yml +++ b/environment.yml @@ -1,482 +1,269 @@ -name: base +name: model_server_env channels: + - pytorch + - ilastik-forge + - conda-forge - defaults dependencies: - - _anaconda_depends=2023.07 - - abseil-cpp=20211102.0 - - aiobotocore=2.4.2 - - aiofiles=22.1.0 - - aiohttp=3.8.3 - - aioitertools=0.7.1 - - aiosignal=1.2.0 - - aiosqlite=0.18.0 - - alabaster=0.7.12 - - anaconda-catalogs=0.2.0 - - anaconda-client=1.12.0 - - anaconda-navigator=2.4.2 - - anaconda-project=0.11.1 - - anyio=3.5.0 + - affogato=0.3.3 + - annotated-types=0.5.0 + - anyio=3.7.1 + - aom=3.5.0 - appdirs=1.4.4 - - argon2-cffi=21.3.0 - - argon2-cffi-bindings=21.2.0 - - arrow=1.2.3 - - arrow-cpp=11.0.0 - - astroid=2.14.2 - - astropy=5.1 - - asttokens=2.0.5 - - async-timeout=4.0.2 - - atomicwrites=1.4.0 - - attrs=22.1.0 - - automat=20.2.0 - - autopep8=1.6.0 - - aws-c-common=0.4.57 - - aws-c-event-stream=0.1.6 - - aws-checksums=0.1.9 - - aws-sdk-cpp=1.8.185 - - babel=2.11.0 - - backcall=0.2.0 - - backports=1.1 - - backports.functools_lru_cache=1.6.4 - - backports.tempfile=1.0 - - backports.weakref=1.0.post1 - - bcrypt=3.2.0 - - beautifulsoup4=4.12.2 - - binaryornot=0.4.4 - - black=23.3.0 - - blas=1.0 - - bleach=4.1.0 - - blosc=1.21.3 - - bokeh=3.2.1 - - boltons=23.0.0 - - boost-cpp=1.73.0 - - boto3=1.24.28 - - botocore=1.27.59 - - bottleneck=1.3.5 + - attrs=23.1.0 + - bioimageio.core=0.5.8 + - bioimageio.spec=0.4.9 + - blas=2.118 + - blas-devel=3.9.0 + - blosc=1.21.5 + - boost=1.74.0 + - boost-cpp=1.74.0 - brotli=1.0.9 - brotli-bin=1.0.9 - - brotlipy=0.7.0 + - brotli-python=1.0.9 - bzip2=1.0.8 - - c-ares=1.19.0 - - c-blosc2=2.8.0 - - ca-certificates=2023.05.30 + - c-blosc2=2.10.2 + - ca-certificates=2023.7.22 + - cached-property=1.5.2 + - cached_property=1.5.2 + - cachetools=5.3.1 + - cairo=1.16.0 - certifi=2023.7.22 - - cffi=1.15.1 - - cfitsio=3.470 - - chardet=4.0.0 - - charls=2.2.0 - - charset-normalizer=2.0.4 - - click=8.0.4 - - cloudpickle=2.2.1 - - clyent=1.2.2 + - cfitsio=4.2.0 + - charls=2.3.4 + - charset-normalizer=3.2.0 + - click=8.1.7 - colorama=0.4.6 - - colorcet=3.0.1 - - comm=0.1.2 - - conda=23.7.2 - - conda-build=3.26.0 - - conda-content-trust=0.1.1 - - conda-index=0.2.3 - - conda-libmamba-solver=23.5.0 - - conda-pack=0.6.0 - - conda-package-handling=2.2.0 - - conda-package-streaming=0.9.0 - - conda-repo-cli=1.0.41 - - conda-token=0.4.0 - - conda-verify=3.4.2 - - console_shortcut=0.1.1 - - constantly=15.1.0 - - contourpy=1.0.5 - - cookiecutter=1.7.3 - - cryptography=41.0.2 - - cssselect=1.1.0 - - curl=8.1.1 + - contourpy=1.1.0 - cycler=0.11.0 - - cytoolz=0.12.0 - - daal4py=2023.1.1 - - dal=2023.1.1 - - dask=2023.6.0 - - dask-core=2023.6.0 - - datashader=0.15.1 - - datashape=0.5.4 - - debugpy=1.6.7 - - decorator=5.1.1 - - defusedxml=0.7.1 - - diff-match-patch=20200713 - - dill=0.3.6 - - distributed=2023.6.0 - - docstring-to-markdown=0.11 - - docutils=0.18.1 - - entrypoints=0.4 + - czifile=2019.7.2 + - dav1d=1.2.1 + - dill=0.3.7 + - dpct=1.2.post39 - et_xmlfile=1.1.0 - - executing=0.8.3 - - filelock=3.9.0 - - flake8=6.0.0 - - flask=2.2.2 - - fmt=9.1.0 - - fonttools=4.25.0 + - exceptiongroup=1.1.3 + - expat=2.5.0 + - fastapi=0.101.1 + - fastfilters=0.2.4.post83 + - fftw=3.3.10 + - font-ttf-dejavu-sans-mono=2.37 + - font-ttf-inconsolata=3.000 + - font-ttf-source-code-pro=2.038 + - font-ttf-ubuntu=0.83 + - fontconfig=2.14.2 + - fonts-conda-ecosystem=1 + - fonts-conda-forge=1 + - fonttools=4.42.1 - freetype=2.12.1 - - frozenlist=1.3.3 - - fsspec=2023.3.0 + - fribidi=1.0.10 + - fs=2.4.16 - future=0.18.3 - - gensim=4.3.0 - - gflags=2.2.2 + - getopt-win32=0.1 + - gettext=0.21.1 - giflib=5.2.1 - - glib=2.69.1 - - glob2=0.7 - - glog=0.5.0 - - greenlet=2.0.1 - - gst-plugins-base=1.18.5 - - gstreamer=1.18.5 - - h5py=3.7.0 - - hdf5=1.10.6 - - heapdict=1.0.1 - - holoviews=1.17.0 - - hvplot=0.8.4 - - hyperlink=21.0.0 - - icc_rt=2022.1.0 - - icu=58.2 + - glib=2.78.0 + - glib-tools=2.78.0 + - glpk=5.0 + - graphite2=1.3.13 + - graphviz=8.1.0 + - greenlet=2.0.2 + - grpcio=1.41.1 + - gst-plugins-base=1.22.5 + - gstreamer=1.22.5 + - gts=0.7.6 + - h11=0.14.0 + - h5py=3.8.0 + - harfbuzz=6.0.0 + - hdf5=1.12.2 + - hytra=1.1.5 + - icu=70.1 - idna=3.4 - - imagecodecs=2021.8.26 - - imageio=2.26.0 - - imagesize=1.4.1 - - imbalanced-learn=0.10.1 - - importlib-metadata=6.0.0 - - importlib_metadata=6.0.0 - - incremental=21.3.0 - - inflection=0.5.1 - - iniconfig=1.1.1 - - intake=0.6.8 - - intel-openmp=2023.1.0 - - intervaltree=3.1.0 - - ipykernel=6.19.2 - - ipython=8.12.0 - - ipython_genutils=0.2.0 - - ipywidgets=8.0.4 - - isort=5.9.3 - - itemadapter=0.3.0 - - itemloaders=1.0.4 - - itsdangerous=2.0.1 - - jaraco.classes=3.2.1 - - jedi=0.18.1 - - jellyfish=0.9.0 - - jinja2=3.1.2 - - jinja2-time=0.2.0 - - jmespath=0.10.0 - - joblib=1.2.0 + - ilastik=1.4.1b6 + - ilastik-core=1.4.1b6 + - ilastik-feature-selection=0.2.0 + - ilastikrag=0.1.4 + - ilastiktools=0.2.post37 + - imagecodecs=2022.9.26 + - imagecodecs-lite=2019.12.3 + - imageio=2.31.1 + - imath=3.1.6 + - importlib-resources=6.0.1 + - importlib_resources=6.0.1 + - inferno=v0.4.2 + - intel-openmp=2023.2.0 + - joblib=1.3.2 - jpeg=9e - - jq=1.6 - - json5=0.9.6 - - jsonpatch=1.32 - - jsonpointer=2.1 - - jsonschema=4.17.3 - - jupyter=1.0.0 - - jupyter_client=7.4.9 - - jupyter_console=6.6.3 - - jupyter_core=5.3.0 - - jupyter_events=0.6.3 - - jupyter_server=1.23.4 - - jupyter_server_fileid=0.9.0 - - jupyter_server_ydoc=0.8.0 - - jupyter_ydoc=0.2.4 - - jupyterlab=3.6.3 - - jupyterlab_pygments=0.1.2 - - jupyterlab_server=2.22.0 - - jupyterlab_widgets=3.0.5 + - jsonschema=4.19.0 + - jsonschema-specifications=2023.7.1 - jxrlib=1.1 - - keyring=23.13.1 - - kiwisolver=1.4.4 - - krb5=1.19.4 - - lazy-object-proxy=1.6.0 - - lazy_loader=0.2 - - lcms2=2.12 - - lerc=3.0 - - libaec=1.0.4 - - libarchive=3.6.2 - - libboost=1.73.0 + - kiwisolver=1.4.5 + - krb5=1.20.1 + - lazy_loader=0.3 + - lcms2=2.14 + - lemon=1.3.1 + - lerc=4.0.0 + - libabseil=20230802.0 + - libaec=1.0.6 + - libavif=0.11.1 + - libblas=3.9.0 - libbrotlicommon=1.0.9 - libbrotlidec=1.0.9 - libbrotlienc=1.0.9 - - libclang=14.0.6 - - libclang13=14.0.6 - - libcurl=8.1.1 - - libdeflate=1.17 - - libevent=2.1.12 - - libffi=3.4.4 - - libiconv=1.16 - - liblief=0.12.3 - - libllvm14=14.0.6 - - libmamba=1.4.1 - - libmambapy=1.4.1 - - libogg=1.3.5 + - libcblas=3.9.0 + - libclang=15.0.7 + - libclang13=15.0.7 + - libcurl=8.1.2 + - libdeflate=1.14 + - libexpat=2.5.0 + - libffi=3.4.2 + - libgd=2.3.3 + - libglib=2.78.0 + - libhwloc=2.9.2 + - libiconv=1.17 + - liblapack=3.9.0 + - liblapacke=3.9.0 + - libogg=1.3.4 - libpng=1.6.39 - - libprotobuf=3.20.3 - - libsodium=1.0.18 - - libsolv=0.7.22 - - libspatialindex=1.9.3 - - libssh2=1.10.0 - - libthrift=0.15.0 - - libtiff=4.5.0 + - libprotobuf=4.23.4 + - libsqlite=3.43.0 + - libssh2=1.11.0 + - libtiff=4.4.0 + - libuv=1.44.2 - libvorbis=1.3.7 - - libwebp=1.2.4 - - libwebp-base=1.2.4 - - libxml2=2.10.3 - - libxslt=1.1.37 + - libwebp=1.3.1 + - libwebp-base=1.3.1 + - libxcb=1.13 + - libxml2=2.11.5 + - libzlib=1.2.13 - libzopfli=1.0.3 - - linkify-it-py=2.0.0 - - llvmlite=0.40.0 - - locket=1.0.0 - - lxml=4.9.2 - - lz4=4.3.2 + - llvmlite=0.40.1 - lz4-c=1.9.4 - - lzo=2.10 - - m2-msys2-runtime=2.5.0.17080.65c939c - - m2-patch=2.7.5 + - m2w64-gcc-libgfortran=5.3.0 + - m2w64-gcc-libs=5.3.0 + - m2w64-gcc-libs-core=5.3.0 + - m2w64-gmp=6.1.0 - m2w64-libwinpthread-git=5.0.0.4634.697f757 - - markdown=3.4.1 - - markdown-it-py=2.2.0 - - markupsafe=2.1.1 - - matplotlib=3.7.1 - - matplotlib-base=3.7.1 - - matplotlib-inline=0.1.6 - - mccabe=0.7.0 - - mdit-py-plugins=0.3.0 + - mamutexport=0.2.1.post6 + - marching_cubes=0.3.post9 + - markdown-it-py=3.0.0 + - marshmallow=3.20.1 + - marshmallow-jsonschema=0.13.0 + - marshmallow-union=0.1.15.post1 + - matplotlib-base=3.7.2 - mdurl=0.1.0 - - menuinst=1.4.19 - - mistune=0.8.4 - - mkl=2023.1.0 - - mkl-service=2.4.0 - - mkl_fft=1.3.6 - - mkl_random=1.2.2 - - more-itertools=8.12.0 - - mpmath=1.3.0 - - msgpack-python=1.0.3 + - mkl=2022.1.0 + - mkl-devel=2022.1.0 + - mkl-include=2022.1.0 + - mrcfile=1.4.3 - msys2-conda-epoch=20160418 - - multidict=6.0.2 - - multipledispatch=0.6.0 - munkres=1.1.4 - - mypy_extensions=0.4.3 - - navigator-updater=0.4.0 - - nbclassic=0.5.5 - - nbclient=0.5.13 - - nbconvert=6.5.4 - - nbformat=5.7.0 - - nest-asyncio=1.5.6 + - ndstructs=0.0.5dev0 - networkx=3.1 - - nltk=3.8.1 - - notebook=6.5.4 - - notebook-shim=0.2.2 - - numba=0.57.0 - - numexpr=2.8.4 - - numpy=1.24.3 - - numpy-base=1.24.3 - - numpydoc=1.5.0 - - openjpeg=2.4.0 - - openpyxl=3.0.10 - - openssl=1.1.1u - - orc=1.7.4 - - packaging=23.0 + - nifty=1.2.1 + - numba=0.57.1 + - numpy=1.22.4 + - openexr=3.1.5 + - openjpeg=2.5.0 + - openpyxl=3.1.2 + - openssl=3.1.2 + - packaging=23.1 - pandas=1.5.3 - - pandocfilters=1.5.0 - - panel=1.2.1 - - param=1.13.0 - - paramiko=2.8.1 - - parsel=1.6.0 - - parso=0.8.3 - - partd=1.2.0 - - pathlib=1.0.1 - - pathspec=0.10.3 - - patsy=0.5.3 - - pcre=8.45 - - pcre2=10.37 - - pep8=1.7.1 - - pexpect=4.8.0 - - pickleshare=0.7.5 - - pillow=9.4.0 + - pango=1.50.14 + - pcre2=10.40 + - pillow=9.2.0 - pip=23.2.1 - - pkginfo=1.9.6 - - platformdirs=2.5.2 - - plotly=5.9.0 - - pluggy=1.0.0 + - pixman=0.40.0 + - pkgutil-resolve-name=1.3.10 + - platformdirs=3.10.0 - ply=3.11 - - pooch=1.4.0 - - powershell_shortcut=0.0.1 - - poyo=0.5.0 - - prometheus_client=0.14.1 - - prompt-toolkit=3.0.36 - - prompt_toolkit=3.0.36 - - protego=0.1.16 - - psutil=5.9.0 - - ptyprocess=0.7.0 - - pure_eval=0.2.2 - - py-cpuinfo=8.0.0 - - py-lief=0.12.3 - - pyarrow=11.0.0 - - pyasn1=0.4.8 - - pyasn1-modules=0.2.8 - - pybind11-abi=4 - - pycodestyle=2.10.0 - - pycosat=0.6.4 - - pycparser=2.21 - - pyct=0.5.0 - - pycurl=7.45.2 - - pydispatcher=2.0.5 - - pydocstyle=6.3.0 - - pyerfa=2.0.0 - - pyflakes=3.0.1 - - pygments=2.15.1 - - pyjwt=2.4.0 - - pylint=2.16.2 - - pylint-venv=2.3.0 - - pyls-spyder=0.4.0 - - pynacl=1.5.0 - - pyodbc=4.0.34 - - pyopenssl=23.2.0 + - pooch=1.7.0 + - protobuf=4.23.4 + - psutil=5.9.5 + - pthread-stubs=0.4 + - pthreads-win32=2.9.1 + - pydantic=1.10.2 + - pydantic-core=2.6.3 + - pygments=2.16.1 + - pyopengl=3.1.6 - pyparsing=3.0.9 - - pyqt=5.15.7 - - pyqt5-sip=12.11.0 - - pyqtwebengine=5.15.7 - - pyrsistent=0.18.0 + - pyqt=5.15.9 + - pyqt5-sip=12.12.2 + - pyqtgraph=0.13.3 - pysocks=1.7.1 - - pytables=3.8.0 - - pytest=7.4.0 - - python=3.11.4 + - python=3.9.18 - python-dateutil=2.8.2 - - python-fastjsonschema=2.16.2 - - python-json-logger=2.0.7 - - python-libarchive-c=2.9 - - python-lmdb=1.4.1 - - python-lsp-black=1.2.1 - - python-lsp-jsonrpc=1.0.0 - - python-lsp-server=1.7.2 - - python-slugify=5.0.2 - - python-snappy=0.6.1 - - pytoolconfig=1.2.5 - - pytz=2022.7 - - pyviz_comms=2.3.0 + - python-elf=0.4.7 + - python-stdnum=1.19 + - python_abi=3.9 + - pytorch=1.13.1 + - pytorch-mutex=1.0 + - pytz=2023.3.post1 - pywavelets=1.4.1 - - pywin32=305 - - pywin32-ctypes=0.2.0 - - pywinpty=2.0.10 - - pyyaml=6.0 - - pyzmq=23.2.0 - - qdarkstyle=3.0.2 - - qstylizer=0.2.2 - - qt-main=5.15.2 - - qt-webengine=5.15.9 - - qtawesome=1.2.2 - - qtconsole=5.4.2 - - qtpy=2.2.0 - - qtwebkit=5.212 - - queuelib=1.5.0 - - re2=2022.04.01 - - regex=2022.7.9 - - reproc=14.2.4 - - reproc-cpp=14.2.4 + - pyyaml=6.0.1 + - qimage2ndarray=1.8.3 + - qt-main=5.15.8 + - referencing=0.30.2 - requests=2.31.0 - - requests-file=1.5.1 - - requests-toolbelt=1.0.0 - - rfc3339-validator=0.1.4 - - rfc3986-validator=0.1.1 - - rope=1.7.0 - - rtree=1.0.1 - - ruamel.yaml=0.17.21 - - ruamel_yaml=0.17.21 - - s3fs=2023.3.0 - - s3transfer=0.6.0 - - sacremoses=0.0.43 - - scikit-image=0.20.0 + - rich=13.5.1 + - rpds-py=0.10.2 + - ruamel.yaml=0.17.32 + - ruamel.yaml.clib=0.2.7 + - scikit-image=0.21.0 - scikit-learn=1.3.0 - - scikit-learn-intelex=2023.1.1 - - scipy=1.10.1 - - scrapy=2.8.0 - - seaborn=0.12.2 - - send2trash=1.8.0 - - service_identity=18.1.0 - - setuptools=68.0.0 - - sip=6.6.2 + - scipy=1.11.2 + - setuptools=68.1.2 + - shellingham=1.5.3 + - sip=6.7.11 - six=1.16.0 - - smart_open=5.2.1 - - snappy=1.1.9 - - sniffio=1.2.0 - - snowballstemmer=2.2.0 - - sortedcontainers=2.4.0 - - soupsieve=2.4 - - sphinx=5.0.2 - - sphinxcontrib-applehelp=1.0.2 - - sphinxcontrib-devhelp=1.0.2 - - sphinxcontrib-htmlhelp=2.0.0 - - sphinxcontrib-jsmath=1.0.1 - - sphinxcontrib-qthelp=1.0.3 - - sphinxcontrib-serializinghtml=1.1.5 - - spyder=5.4.3 - - spyder-kernels=2.4.3 - - sqlalchemy=1.4.39 - - sqlite=3.41.2 - - stack_data=0.2.0 - - statsmodels=0.14.0 - - sympy=1.11.1 - - tabulate=0.8.10 - - tbb=2021.8.0 - - tbb4py=2021.8.0 - - tblib=1.7.0 - - tenacity=8.2.2 - - terminado=0.17.1 - - text-unidecode=1.3 - - textdistance=4.2.1 - - threadpoolctl=2.2.0 - - three-merge=0.1.1 - - tifffile=2021.7.2 - - tinycss2=1.2.1 + - skan=0.11.0 + - snappy=1.1.10 + - sniffio=1.3.0 + - starlette=0.27.0 + - tbb=2021.10.0 + - tensorboardx=2.6.2.2 + - threadpoolctl=3.2.0 + - tifffile=2022.10.10 + - tiktorch=23.6.0 - tk=8.6.12 - - tldextract=3.2.0 - toml=0.10.2 - - tomlkit=0.11.1 + - tomli=2.0.1 - toolz=0.12.0 - - tornado=6.3.2 - - tqdm=4.65.0 - - traitlets=5.7.1 - - transformers=2.1.1 - - twisted=22.10.0 - - twisted-iocpsupport=1.0.2 + - torchvision=0.14.1 + - tqdm=4.66.1 + - typer=0.9.0 - typing-extensions=4.7.1 - typing_extensions=4.7.1 - tzdata=2023c - - uc-micro-py=1.0.1 - - ujson=5.4.0 - - unidecode=1.2.0 - - urllib3=1.26.16 - - utf8proc=2.6.1 - - vc=14.2 - - vs2015_runtime=14.27.29016 - - w3lib=1.21.0 - - watchdog=2.1.6 - - wcwidth=0.2.5 - - webencodings=0.5.1 - - websocket-client=0.58.0 - - werkzeug=2.2.3 - - whatthepatch=1.0.2 - - wheel=0.38.4 - - widgetsnbextension=4.0.5 + - ucrt=10.0.22621.0 + - unicodedata2=15.0.0 + - urllib3=2.0.4 + - uvicorn=0.23.2 + - vc=14.3 + - vc14_runtime=14.36.32532 + - vigra=1.11.1 + - volumina=1.3.10 + - vs2015_runtime=14.36.32532 + - wheel=0.41.2 - win_inet_pton=1.1.0 - - winpty=0.4.3 - - wrapt=1.14.1 - - xarray=2023.6.0 - - xlwings=0.29.1 - - xyzservices=2022.9.0 - - xz=5.4.2 - - y-py=0.5.9 + - xarray=2023.8.0 + - xorg-kbproto=1.0.7 + - xorg-libice=1.0.10 + - xorg-libsm=1.2.3 + - xorg-libx11=1.8.4 + - xorg-libxau=1.0.11 + - xorg-libxdmcp=1.1.3 + - xorg-libxext=1.3.4 + - xorg-libxpm=3.5.16 + - xorg-libxt=1.3.0 + - xorg-xextproto=7.3.0 + - xorg-xproto=7.0.31 + - xz=5.2.6 - yaml=0.2.5 - - yaml-cpp=0.7.0 - - yapf=0.31.0 - - yarl=1.8.1 - - ypy-websocket=0.8.2 - - zeromq=4.3.4 - - zfp=0.5.5 - - zict=2.2.0 - - zipp=3.11.0 + - yapsy=1.12.2 + - z5py=2.0.16 + - zfp=1.0.0 + - zipp=3.16.2 - zlib=1.2.13 - zlib-ng=2.0.7 - - zope=1.0 - - zope.interface=5.4.0 - - zstandard=0.19.0 - zstd=1.5.5 -prefix: C:\Users\rhodes\AppData\Local\anaconda3 +prefix: C:\Users\rhodes\AppData\Local\mambaforge\envs\model_server_env