From 5b13c7942193b2d018157b20b76ef3425ec40cac Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 8 Jan 2024 10:58:04 +0100
Subject: [PATCH] Rebuilt dependency files
---
README.md | 6 +-
requirements.yml | 272 +++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 276 insertions(+), 2 deletions(-)
create mode 100644 requirements.yml
diff --git a/README.md b/README.md
index edfb4197..fddf05b7 100644
--- a/README.md
+++ b/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
diff --git a/requirements.yml b/requirements.yml
new file mode 100644
index 00000000..b1447ee9
--- /dev/null
+++ b/requirements.yml
@@ -0,0 +1,272 @@
+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
--
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