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base repository: MouseLand/cellpose
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base: v0.1.0.1
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head repository: MouseLand/cellpose
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compare: master
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Showing with 9,447 additions and 4,990 deletions.
  1. +90 −0 .github/workflows/test_and_deploy.yml
  2. +0 −73 .travis.yml
  3. +94 −38 README.md
  4. +241 −156 cellpose/__main__.py
  5. 0 cellpose/contrib/__init__.py
  6. +260 −0 cellpose/contrib/distributed_segmentation.py
  7. +931 −0 cellpose/core.py
  8. +420 −109 cellpose/dynamics.py
  9. +0 −1,348 cellpose/gui.py
  10. +1,759 −0 cellpose/gui/gui.py
  11. +203 −85 cellpose/{ → gui}/guiparts.py
  12. +513 −0 cellpose/gui/io.py
  13. +122 −0 cellpose/gui/menus.py
  14. +256 −449 cellpose/io.py
  15. +0 −95 cellpose/menus.py
  16. +61 −19 cellpose/metrics.py
  17. +612 −1,136 cellpose/models.py
  18. +89 −44 cellpose/plot.py
  19. +0 −200 cellpose/resnet_style.py
  20. +233 −0 cellpose/resnet_torch.py
  21. +25 −17 cellpose/test_mkl.py
  22. +309 −182 cellpose/transforms.py
  23. +110 −48 cellpose/utils.py
  24. +25 −19 {tests → }/conftest.py
  25. +115 −40 docs/command.rst
  26. +50 −32 docs/gui.rst
  27. +11 −3 docs/index.rst
  28. +26 −5 docs/inputs.rst
  29. +25 −71 docs/installation.rst
  30. +110 −0 docs/models.rst
  31. +3 −3 docs/notebook.rst
  32. +11 −11 docs/outputs.rst
  33. +65 −30 docs/settings.rst
  34. +59 −12 docs/train.rst
  35. +11 −7 environment.yml
  36. +17 −17 imagej_roi_converter.py
  37. +719 −0 notebooks/Cellpose_cell_segmentation_2D_prediction_only.ipynb
  38. +61 −88 notebooks/run_cellpose.ipynb
  39. +899 −618 notebooks/run_cellpose_GPU.ipynb
  40. +527 −0 paper/train_maskrcnn.py
  41. +37 −19 setup.py
  42. +192 −0 tests/contrib/test_distributed_segmentation.py
  43. +22 −5 tests/test_import.py
  44. +22 −7 tests/test_output.py
  45. +33 −0 tests/test_shape.py
  46. +38 −4 tests/test_train.py
  47. +7 −0 tests/test_transforms.py
  48. +34 −0 tox.ini
90 changes: 90 additions & 0 deletions .github/workflows/test_and_deploy.yml
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# This workflows will upload a Python Package using Twine when a release is created
# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries

name: tests

on:
push:
branches:
- master
tags:
- "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
pull_request:
branches:
- master
workflow_dispatch:

jobs:
test:
name: ${{ matrix.platform }} py${{ matrix.python-version }}
runs-on: ${{ matrix.platform }}
strategy:
matrix:
platform: [ubuntu-latest, windows-latest, macos-latest]
python-version: [3.8]

steps:
- uses: actions/checkout@v2

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}

# these libraries, along with pytest-xvfb (added in the `deps` in tox.ini),
# enable testing on Qt on linux
- name: Install Linux libraries
if: runner.os == 'Linux'
run: |
sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 \
libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 \
libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0 pkg-config libhdf5-103 libhdf5-dev
# strategy borrowed from vispy for installing opengl libs on windows
- name: Install Windows OpenGL
if: runner.os == 'Windows'
run: |
git clone --depth 1 https://www.github.com/pyvista/gl-ci-helpers.git
powershell gl-ci-helpers/appveyor/install_opengl.ps1
# note: if you need dependencies from conda, considering using
# setup-miniconda: https://github.com/conda-incubator/setup-miniconda
# and
# tox-conda: https://github.com/tox-dev/tox-conda
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install dask dask_image scikit-learn
pip install wheel setuptools tox tox-gh-actions
# this runs the platform-specific tests declared in tox.ini
- name: Test with tox
run: tox
env:
PLATFORM: ${{ matrix.platform }}

- name: Coverage
uses: codecov/codecov-action@v1

deploy:
# this will run when you have tagged a commit, starting with "v*"
# and requires that you have put your twine API key in your
# github secrets (see readme for details)
needs: [test]
runs-on: ubuntu-latest
if: contains(github.ref, 'tags')
steps:
- uses: actions/checkout@v2
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install -U setuptools setuptools_scm wheel twine
- name: Build and publish
env:
TWINE_USERNAME: __token__
TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
run: |
git tag
python setup.py sdist bdist_wheel
twine upload dist/*
73 changes: 0 additions & 73 deletions .travis.yml

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