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Migrate from circleci to github actions
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‎.github/workflows/ci.yml‎

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name: CI
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on:
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push:
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branches:
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- main
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pull_request:
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branches:
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- main
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jobs:
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pre_commit_check:
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name: Pre-Commit Check
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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env:
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BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- uses: conda-incubator/setup-miniconda@v3
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with:
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auto-update-conda: true
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auto-activate-base: false
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activate-environment: tiktorch-server-env
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environment-file: environment.yml
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channel-priority: flexible
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miniforge-variant: Miniforge3
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- name: Run Pre-Commit
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run: |
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echo $BRANCH_NAME
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echo ${{ github.event.pull_request.base.ref }}
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echo ${{ github.event.pull_request.head.sha }}
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git fetch origin
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pre-commit run --from-ref origin/${{ github.event.pull_request.base.ref }} --to-ref ${{ github.event.pull_request.head.sha }}
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test-dev:
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- uses: conda-incubator/setup-miniconda@v3
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with:
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auto-update-conda: true
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auto-activate-base: false
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activate-environment: tiktorch-server-env
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environment-file: environment.yml
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channel-priority: flexible
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miniforge-variant: Miniforge3
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- name: conda diagnostics
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run: |
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conda info
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- name: install submodules
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run: |
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git submodule init
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git submodule update
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make install_submodules
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- name: Run tests
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run: |
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pytest -v -s --cov=tiktorch --cov-report=xml
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v4
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with:
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file: ./coverage.xml
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fail_ci_if_error: true
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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conda-noarch-build:
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runs-on: ubuntu-latest
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outputs:
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version: ${{ steps.version.outputs.version }}
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- uses: conda-incubator/setup-miniconda@v3
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with:
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auto-update-conda: true
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auto-activate-base: true
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channel-priority: flexible
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miniforge-variant: Miniforge3
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- name: install common conda dependencies
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run: mamba install -n base -c conda-forge conda-build setuptools_scm -y
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- name: Cache Conda Packages
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uses: actions/cache@v4
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with:
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path: |
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pkgs/noarch
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pkgs/channeldata.json
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key: ${{ github.sha }}-packages
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- id: version
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run: |
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vers=$( python setup.py --version )
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echo "version=${vers}" >> $GITHUB_OUTPUT
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- name: Linux Conda Build Test
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run: |
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mkdir -p ./pkgs/noarch
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conda build -c conda-forge conda-recipe --no-test --output-folder ./pkgs
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test-build-conda-packages:
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needs: [conda-noarch-build]
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strategy:
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fail-fast: false
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matrix:
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os: [macos-latest, windows-latest, ubuntu-latest]
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runs-on: ${{ matrix.os }}
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env:
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TIKTORCH_PACKAGE_NAME: tiktorch-${{ needs.conda-noarch-build.outputs.version }}-py_0.tar.bz2
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steps:
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# Use GNU tar instead of BSD tar on Windows
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- name: "Use GNU tar instead of BSD tar"
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if: matrix.os == 'windows-latest'
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shell: cmd
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run: echo C:\Program Files\Git\usr\bin>>"%GITHUB_PATH%"
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- name: Checkout code
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- uses: conda-incubator/setup-miniconda@v3
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with:
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auto-update-conda: true
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auto-activate-base: true
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channel-priority: flexible
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miniforge-variant: Miniforge3
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- name: install common conda dependencies
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run: mamba install -n base -c conda-forge conda-build setuptools_scm -y
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- name: Cache Conda Packages
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uses: actions/cache@v4
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with:
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path: |
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pkgs/noarch
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pkgs/channeldata.json
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key: ${{ github.sha }}-packages
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enableCrossOsArchive: true
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- name: Linux Test
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if: matrix.os == 'ubuntu-latest'
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shell: bash -l {0}
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run: |
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conda build --test --override-channels \
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-c ./pkgs -c pytorch -c ilastik-forge -c conda-forge \
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./pkgs/noarch/${TIKTORCH_PACKAGE_NAME}
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- name: macOS Test
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if: matrix.os == 'macos-latest'
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shell: bash -l {0}
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run: |
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conda build --test --override-channels \
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-c ./pkgs -c pytorch -c ilastik-forge -c conda-forge \
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./pkgs/noarch/${TIKTORCH_PACKAGE_NAME}
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- name: Windows Test
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if: matrix.os == 'windows-latest'
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# HACK: due to a bug in conda-build need to point to
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# libarchive explicitly.
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# https://github.com/conda/conda/issues/12563#issuecomment-1494264704
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env:
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LIBARCHIVE: C:\Miniconda\Library\bin\archive.dll
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shell: cmd /C CALL {0}
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run: |
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conda build --test --override-channels ^
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-c %CD%\pkgs -c pytorch -c ilastik-forge -c conda-forge ^
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.\pkgs\noarch\%TIKTORCH_PACKAGE_NAME%

‎Makefile‎

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remove_devenv:
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conda env remove --yes --name $(TIKTORCH_ENV_NAME)
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.PHONY: *

‎README.md‎

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[![CircleCI](https://circleci.com/gh/ilastik/tiktorch.svg?style=shield)](https://circleci.com/gh/ilastik/tiktorch)
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[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
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[![Conda](https://anaconda.org/ilastik-forge/tiktorch/badges/version.svg)](https://anaconda.org/ilastik-forge/tiktorch)
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[![codecov](https://codecov.io/gh/ilastik/tiktorch/branch/main/graph/badge.svg)](https://codecov.io/gh/ilastik/tiktorch)
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`tiktorch` is the neural network prediction server for [`ilastik`](https://ilastik.org).
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The server is used in the [Neural Network Workflow](https://www.ilastik.org/documentation/nn/nn).

‎conda-recipe/meta.yaml‎

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build:
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noarch: python
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number: 0
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script: python -m pip install --no-deps --ignore-installed .
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script:
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- python -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv
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entry_points:
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- tiktorch-server = tiktorch.server.base:main
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- {{ dep.lower() }}
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{% endfor %}
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run_constrained:
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- mkl <2024.1.0 # [linux] until pytorch is compatible with the current version
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- cudatoolkit >=10.2
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{% for dep in setup_py_data['extras_require']['server-pytorch'] %}
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- {{ dep.lower() }}
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{% endfor %}
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{% for dep in setup_py_data['extras_require']['server-tensorflow'] %}
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- {{ dep.lower() }}
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{% endfor %}
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about:
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home: https://github.com/ilastik/tiktorch
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{% for dep in setup_py_data['extras_require']['server-pytorch'] %}
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- {{ dep.lower() }}
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{% endfor %}
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{% for dep in setup_py_data['extras_require']['server-tensorflow'] %}
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- {{ dep.lower() }}
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{% endfor %}
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# this is still necessary, torchvision doesn't work properly with cpuonly mutex
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- torchvision=*=*cpu
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- cpuonly
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- pytest
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- pytest-grpc
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imports:
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# client
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- tiktorch
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# server
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- tiktorch.server.base
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- tiktorch.server.session
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source_files:
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- tests
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- tiktorch
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- pytest.ini
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commands:
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- pytest
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‎environment.yml‎

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- marshmallow=3.12.*
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- marshmallow-jsonschema
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- protobuf
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- pytest
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- pytest-grpc
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- pyyaml=5.3.*
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- requests
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- ruamel.yaml
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- scikit-learn
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- scipy
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- typing-extensions
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- xarray
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- setuptools
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- pip
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# pytorch
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# remove cpuonly, add cudatoolkit and cudnn for gpu support
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- pytorch=1.13.*
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- inferno=v0.4.*
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- pytorch=2.4.*
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# currently it's necessary to force the cpu version, remove
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# torchvision pin when going for gpu
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# - torchvision
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#- cpuonly
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- cpuonly
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# - cudatoolkit >=10.2
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# - cudnn
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# - tochvision
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- typer
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# dev stuff
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- pytest
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- pytest-cov
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- pytest-grpc
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- bump2version
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- mypy
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- pre_commit
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- pip
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- mkl <2024.1.0 # [linux] until pytorch is compatible with the current version
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‎pytest.ini‎

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[pytest]
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add_opts = -s --doctest-modules
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python_files = test_*.py
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addopts =
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-v
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-s
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--color=yes
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--doctest-modules
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--ignore=tests/data
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testpaths = tests
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#log_format = %(asctime)s.%(msecs)03d %(levelname)s %(message)s
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#log_date_format = %M:%S.%f

‎setup.py‎

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],
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extras_require={
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"server-pytorch": [
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"inferno",
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"pytorch>=1.6",
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"scikit-learn",
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],
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"server-tensorflow": [
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"tensorflow>=2.9",
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"scikit-learn",
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],
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]
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},
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entry_points={"console_scripts": ["tiktorch=tiktorch.server.base:main"]},
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# extras_require={"test": ["pytest"]},

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