Rebuilt dependency files

README.md

@@ -5,13 +5,15 @@ model_server implement image analysis jobs for online use (e.g. in feedback micr
 
 1. Install Git:<br>https://git-scm.com/download/win
 2. Install Miniforge for environment management:<br>https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge-pypy3-Windows-x86_64.exe
-3. Under the Start menu, open Miniforge3 > Miniforge Prompt
+3. Under the Start menu, open `Miniforge3 > Miniforge Prompt`
 4. In the new terminal, run:<br>
    `cd %userprofile%`<br>
    `git clone https://almf-staff:KJmFvyPRbpzoVZDqfMzV@git.embl.de/rhodes/model_server.git`
 5. Open the newly created project root: `cd model_server`
 6. Create the environment: `mamba create -n model_server_env --override-channels -c pytorch -c ilastik-forge -c conda-forge ilastik`
-7. Activate the environment: `mamba activate model_server_env`
+7. In the same terminal, run: `mamba init`
+8. Now close and re-open the terminal: `Miniforge3 > Miniforge Prompt`
+9. Now activate the environment: `mamba activate model_server_env`
 
 # Examples
 

requirements.yml

+name: model_server_env
+channels:
+  - pytorch
+  - ilastik-forge
+  - conda-forge
+  - defaults
+dependencies:
+  - affogato=0.3.3
+  - annotated-types=0.5.0
+  - anyio=3.7.1
+  - aom=3.5.0
+  - appdirs=1.4.4
+  - 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
+  - brotli-python=1.0.9
+  - bzip2=1.0.8
+  - 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
+  - cfitsio=4.2.0
+  - charls=2.3.4
+  - charset-normalizer=3.2.0
+  - click=8.1.7
+  - colorama=0.4.6
+  - contourpy=1.1.0
+  - cycler=0.11.0
+  - czifile=2019.7.2
+  - dav1d=1.2.1
+  - dill=0.3.7
+  - dpct=1.2.post39
+  - et_xmlfile=1.1.0
+  - 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
+  - fribidi=1.0.10
+  - fs=2.4.16
+  - future=0.18.3
+  - getopt-win32=0.1
+  - gettext=0.21.1
+  - giflib=5.2.1
+  - 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
+  - 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
+  - jsonschema=4.19.0
+  - jsonschema-specifications=2023.7.1
+  - jxrlib=1.1
+  - 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
+  - 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=4.23.4
+  - libsqlite=3.43.0
+  - libssh2=1.11.0
+  - libtiff=4.4.0
+  - libuv=1.44.2
+  - libvorbis=1.3.7
+  - libwebp=1.3.1
+  - libwebp-base=1.3.1
+  - libxcb=1.13
+  - libxml2=2.11.5
+  - libzlib=1.2.13
+  - libzopfli=1.0.3
+  - llvmlite=0.40.1
+  - lz4-c=1.9.4
+  - 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
+  - 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
+  - mkl=2022.1.0
+  - mkl-devel=2022.1.0
+  - mkl-include=2022.1.0
+  - mrcfile=1.4.3
+  - msys2-conda-epoch=20160418
+  - munkres=1.1.4
+  - ndstructs=0.0.5dev0
+  - networkx=3.1
+  - 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
+  - pango=1.50.14
+  - pcre2=10.40
+  - pillow=9.2.0
+  - pip=23.2.1
+  - pixman=0.40.0
+  - pkgutil-resolve-name=1.3.10
+  - platformdirs=3.10.0
+  - ply=3.11
+  - 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=5.15.9
+  - pyqt5-sip=12.12.2
+  - pyqtgraph=0.13.3
+  - pysocks=1.7.1
+  - python=3.9.18
+  - python-dateutil=2.8.2
+  - 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
+  - pyyaml=6.0.1
+  - qimage2ndarray=1.8.3
+  - qt-main=5.15.8
+  - referencing=0.30.2
+  - requests=2.31.0
+  - 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
+  - scipy=1.11.2
+  - setuptools=68.1.2
+  - shellingham=1.5.3
+  - sip=6.7.11
+  - six=1.16.0
+  - 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
+  - toml=0.10.2
+  - tomli=2.0.1
+  - toolz=0.12.0
+  - torchvision=0.14.1
+  - tqdm=4.66.1
+  - typer=0.9.0
+  - typing-extensions=4.7.1
+  - typing_extensions=4.7.1
+  - tzdata=2023c
+  - 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
+  - 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
+  - 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
+  - zstd=1.5.5
+  - pip:
+      - build==1.0.3
+      - importlib-metadata==7.0.0
+      - pyproject-hooks==1.0.0