2023-04-11T18:54:03,270 Created temporary directory: /tmp/pip-ephem-wheel-cache-mh8b93el 2023-04-11T18:54:03,273 Created temporary directory: /tmp/pip-build-tracker-ob5hzbyb 2023-04-11T18:54:03,273 Initialized build tracking at /tmp/pip-build-tracker-ob5hzbyb 2023-04-11T18:54:03,274 Created build tracker: /tmp/pip-build-tracker-ob5hzbyb 2023-04-11T18:54:03,274 Entered build tracker: /tmp/pip-build-tracker-ob5hzbyb 2023-04-11T18:54:03,274 Created temporary directory: /tmp/pip-wheel-qv2j3fj_ 2023-04-11T18:54:03,279 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2023-04-11T18:54:03,282 Created temporary directory: /tmp/pip-ephem-wheel-cache-10963y8j 2023-04-11T18:54:03,306 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-04-11T18:54:03,310 2 location(s) to search for versions of napari-cellseg3d: 2023-04-11T18:54:03,310 * https://pypi.org/simple/napari-cellseg3d/ 2023-04-11T18:54:03,310 * https://www.piwheels.org/simple/napari-cellseg3d/ 2023-04-11T18:54:03,310 Fetching project page and analyzing links: https://pypi.org/simple/napari-cellseg3d/ 2023-04-11T18:54:03,311 Getting page https://pypi.org/simple/napari-cellseg3d/ 2023-04-11T18:54:03,312 Found index url https://pypi.org/simple 2023-04-11T18:54:03,382 Fetched page https://pypi.org/simple/napari-cellseg3d/ as application/vnd.pypi.simple.v1+json 2023-04-11T18:54:03,389 Found link https://files.pythonhosted.org/packages/01/ad/e4f1b6334f2914f379a2187ec66e8a6c6d2bfad4221dfff63df73c5046b7/napari-cellseg3d-0.0.1rc1.tar.gz (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8), version: 0.0.1rc1 2023-04-11T18:54:03,389 Skipping link: No binaries permitted for napari-cellseg3d: https://files.pythonhosted.org/packages/25/50/5822c94d27d8a3f61b8e319c6a4630819c588e5656de71a627daf097c78d/napari_cellseg3d-0.0.1rc1-py3-none-any.whl (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,390 Found link https://files.pythonhosted.org/packages/45/f1/78a9e82d12efe2beee81d21b67ab2b77020a7048a063a2a4a1dc87797e5c/napari-cellseg3d-0.0.1rc2.tar.gz (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8), version: 0.0.1rc2 2023-04-11T18:54:03,391 Skipping link: No binaries permitted for napari-cellseg3d: https://files.pythonhosted.org/packages/86/c3/f7aa4ab0afd600ca63025dd4032384fbb7e9abfd69da73180856e293e34b/napari_cellseg3d-0.0.1rc2-py3-none-any.whl (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,391 Found link https://files.pythonhosted.org/packages/4b/40/8f071eafa7d4cbcf44fc80e2c7445438be8af6c03087bc49b68c06496430/napari-cellseg3d-0.0.1rc3.tar.gz (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8), version: 0.0.1rc3 2023-04-11T18:54:03,392 Skipping link: No binaries permitted for napari-cellseg3d: https://files.pythonhosted.org/packages/92/34/b6dc31630d2364f52003b23f7f23cf22b82eb1f92bfb0b6206be870571a3/napari_cellseg3d-0.0.1rc3-py3-none-any.whl (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,393 Found link https://files.pythonhosted.org/packages/be/01/5d9d9efb7c921fd6a3fd94191a28344bcef29d77fed2e6b7f72a3da5a841/napari-cellseg3d-0.0.1rc4.tar.gz (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8), version: 0.0.1rc4 2023-04-11T18:54:03,393 Skipping link: No binaries permitted for napari-cellseg3d: https://files.pythonhosted.org/packages/41/79/fbd4d21bf72eadc64ac05395fb718ba5714942ff4e8f107047adcec2616c/napari_cellseg3d-0.0.1rc4-py3-none-any.whl (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,394 Found link https://files.pythonhosted.org/packages/b5/73/ddd2fe7d703214674056ee5da61f9f41b999c3dfeb5e16d63e7563eb565d/napari-cellseg3d-0.0.2rc1.tar.gz (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8), version: 0.0.2rc1 2023-04-11T18:54:03,394 Skipping link: No binaries permitted for napari-cellseg3d: https://files.pythonhosted.org/packages/eb/10/d7ce6fc27bbaa890a6f8829628ebe6f83a170e17f4561bb87647493f3a15/napari_cellseg3d-0.0.2rc1-py3-none-any.whl (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,395 Skipping link: No binaries permitted for napari-cellseg3d: https://files.pythonhosted.org/packages/3b/7a/e53935927324e73a2e4028c2ba757455bfe40ceb7955d6a189ab1caa4ad4/napari_cellseg3d-0.0.2rc2-py3-none-any.whl (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,395 Found link https://files.pythonhosted.org/packages/30/19/60416eda7dd66096efaba80c705c69766043cdaaf5cca46ec02c3286e74a/napari_cellseg3d-0.0.2rc2.tar.gz (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8), version: 0.0.2rc2 2023-04-11T18:54:03,396 Skipping link: No binaries permitted for napari-cellseg3d: https://files.pythonhosted.org/packages/f8/4d/e10e0667405d6435ab06ac5082a362a058bbaa08cc00f9bec31a0bf0ba33/napari_cellseg3d-0.0.2rc3-py3-none-any.whl (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,397 Found link https://files.pythonhosted.org/packages/7e/76/65b3c390eb3ff612fcc089d18a5d57a939cf0025565004c1b6dc8df34d6a/napari_cellseg3d-0.0.2rc3.tar.gz (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8), version: 0.0.2rc3 2023-04-11T18:54:03,397 Skipping link: No binaries permitted for napari-cellseg3d: https://files.pythonhosted.org/packages/e4/c6/7ed38ccc32595ee36bef54a985c19453f9ffdbae0caac82b96c1d862424b/napari_cellseg3d-0.0.2rc4-py3-none-any.whl (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,398 Found link https://files.pythonhosted.org/packages/e5/8a/ed3a4858f90f2b68301ec9e9a7846bd2588410476b18d325d503968a9ecd/napari_cellseg3d-0.0.2rc4.tar.gz (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8), version: 0.0.2rc4 2023-04-11T18:54:03,398 Skipping link: No binaries permitted for napari-cellseg3d: https://files.pythonhosted.org/packages/3f/b4/fec2ab4909c4501ea74fb5ef7afe87d3a6c2eafbacb47de904aa2bba9350/napari_cellseg3d-0.0.2rc5-py3-none-any.whl (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,399 Found link https://files.pythonhosted.org/packages/8b/2f/976cfc3224fe3ca8c62dbb08b6666aff83c737f4f16c795b017f3f1fac78/napari_cellseg3d-0.0.2rc5.tar.gz (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8), version: 0.0.2rc5 2023-04-11T18:54:03,399 Skipping link: No binaries permitted for napari-cellseg3d: https://files.pythonhosted.org/packages/a5/55/a5768034e57e92ebdfa1a04c3f928e7ae14db4fe338e97cabcd58d3e8132/napari_cellseg3d-0.0.2rc6-py3-none-any.whl (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,400 Found link https://files.pythonhosted.org/packages/cb/98/2484712583687a2928e49fb3aaa517fc1e2144b5dd8d9d2dc0310a09c80f/napari_cellseg3d-0.0.2rc6.tar.gz (from https://pypi.org/simple/napari-cellseg3d/) (requires-python:>=3.8), version: 0.0.2rc6 2023-04-11T18:54:03,401 Fetching project page and analyzing links: https://www.piwheels.org/simple/napari-cellseg3d/ 2023-04-11T18:54:03,401 Getting page https://www.piwheels.org/simple/napari-cellseg3d/ 2023-04-11T18:54:03,402 Found index url https://www.piwheels.org/simple 2023-04-11T18:54:03,574 Fetched page https://www.piwheels.org/simple/napari-cellseg3d/ as text/html 2023-04-11T18:54:03,577 Skipping link: No binaries permitted for napari-cellseg3d: https://www.piwheels.org/simple/napari-cellseg3d/napari_cellseg3d-0.0.2rc5-py3-none-any.whl#sha256=08aab4882fd35065fe259a0028b80b2d47f178658512e3b204fd66e452033fd2 (from https://www.piwheels.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,578 Skipping link: No binaries permitted for napari-cellseg3d: https://www.piwheels.org/simple/napari-cellseg3d/napari_cellseg3d-0.0.2rc4-py3-none-any.whl#sha256=862043c814ed52de61479e59a56a14a27d07047c4bbb0739e101858783d2af64 (from https://www.piwheels.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,578 Skipping link: No binaries permitted for napari-cellseg3d: https://www.piwheels.org/simple/napari-cellseg3d/napari_cellseg3d-0.0.2rc3-py3-none-any.whl#sha256=56a0d9e706cf1681700da1e3fdd402c988881ab30e33292b6facd5c7b7682a3c (from https://www.piwheels.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,578 Skipping link: No binaries permitted for napari-cellseg3d: https://www.piwheels.org/simple/napari-cellseg3d/napari_cellseg3d-0.0.2rc2-py3-none-any.whl#sha256=69ce7febcdb3e5ea5f68d1382e44c4e77b75ca533be15d9cb9f5f11d91b1960e (from https://www.piwheels.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,578 Skipping link: No binaries permitted for napari-cellseg3d: https://www.piwheels.org/simple/napari-cellseg3d/napari_cellseg3d-0.0.2rc1-py3-none-any.whl#sha256=940c1a2c58838488e7fae27f0fe32c5ff4bb06cddbc6b284e4051b5a674a8658 (from https://www.piwheels.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,579 Skipping link: No binaries permitted for napari-cellseg3d: https://www.piwheels.org/simple/napari-cellseg3d/napari_cellseg3d-0.0.1rc4-py3-none-any.whl#sha256=6fb1ed496a06bb896bf3b295df2548d9db3ede855766c5eedee2cfbe822c31cc (from https://www.piwheels.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,579 Skipping link: No binaries permitted for napari-cellseg3d: https://www.piwheels.org/simple/napari-cellseg3d/napari_cellseg3d-0.0.1rc3-py3-none-any.whl#sha256=cb8a3283ecd77eda4f8fcec0398663205c103b40216b59147e3472d11856cb26 (from https://www.piwheels.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,579 Skipping link: No binaries permitted for napari-cellseg3d: https://www.piwheels.org/simple/napari-cellseg3d/napari_cellseg3d-0.0.1rc2-py3-none-any.whl#sha256=cf939e7d8417e4e9d0fa7d503df12ef60b67a98100dd7cdcffdf3f23b7dd600b (from https://www.piwheels.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,579 Skipping link: No binaries permitted for napari-cellseg3d: https://www.piwheels.org/simple/napari-cellseg3d/napari_cellseg3d-0.0.1rc1-py3-none-any.whl#sha256=c2c972a8ba77aef04eccda2f247a5aecf702b0d9f575e51e346cd62dbb0376e0 (from https://www.piwheels.org/simple/napari-cellseg3d/) (requires-python:>=3.8) 2023-04-11T18:54:03,579 Skipping link: not a file: https://www.piwheels.org/simple/napari-cellseg3d/ 2023-04-11T18:54:03,580 Skipping link: not a file: https://pypi.org/simple/napari-cellseg3d/ 2023-04-11T18:54:03,599 Given no hashes to check 1 links for project 'napari-cellseg3d': discarding no candidates 2023-04-11T18:54:03,615 Collecting napari-cellseg3d==0.0.2rc6 2023-04-11T18:54:03,618 Created temporary directory: /tmp/pip-unpack-981wsr45 2023-04-11T18:54:03,767 Downloading napari_cellseg3d-0.0.2rc6.tar.gz (591 kB) 2023-04-11T18:54:04,007 Added napari-cellseg3d==0.0.2rc6 from https://files.pythonhosted.org/packages/cb/98/2484712583687a2928e49fb3aaa517fc1e2144b5dd8d9d2dc0310a09c80f/napari_cellseg3d-0.0.2rc6.tar.gz to build tracker '/tmp/pip-build-tracker-ob5hzbyb' 2023-04-11T18:54:04,015 Created temporary directory: /tmp/pip-build-env-n1lb4xhh 2023-04-11T18:54:04,026 Installing build dependencies: started 2023-04-11T18:54:04,027 Running command pip subprocess to install build dependencies 2023-04-11T18:54:05,309 Using pip 23.0.1 from /home/piwheels/.local/lib/python3.9/site-packages/pip (python 3.9) 2023-04-11T18:54:05,943 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2023-04-11T18:54:05,970 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-04-11T18:54:07,649 Collecting setuptools 2023-04-11T18:54:07,760 Using cached https://www.piwheels.org/simple/setuptools/setuptools-67.6.1-py3-none-any.whl (1.1 MB) 2023-04-11T18:54:08,032 Collecting wheel 2023-04-11T18:54:08,056 Using cached https://www.piwheels.org/simple/wheel/wheel-0.40.0-py3-none-any.whl (64 kB) 2023-04-11T18:54:10,368 Installing collected packages: wheel, setuptools 2023-04-11T18:54:10,611 Creating /tmp/pip-build-env-n1lb4xhh/overlay/bin 2023-04-11T18:54:10,614 changing mode of /tmp/pip-build-env-n1lb4xhh/overlay/bin/wheel to 755 2023-04-11T18:54:12,895 Successfully installed setuptools-67.6.1 wheel-0.40.0 2023-04-11T18:54:13,394 Installing build dependencies: finished with status 'done' 2023-04-11T18:54:13,400 Getting requirements to build wheel: started 2023-04-11T18:54:13,401 Running command Getting requirements to build wheel 2023-04-11T18:54:13,941 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/dist.py:788: UserWarning: Usage of dash-separated 'napari-cellseg3d' will not be supported in future versions. Please use the underscore name 'napari_cellseg3d' instead 2023-04-11T18:54:13,942 warnings.warn( 2023-04-11T18:54:14,052 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/pyprojecttoml.py:108: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. 2023-04-11T18:54:14,052 warnings.warn(msg, _BetaConfiguration) 2023-04-11T18:54:14,079 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'description' defined outside of `pyproject.toml` would be ignored. 2023-04-11T18:54:14,079 !! 2023-04-11T18:54:14,080 ########################################################################## 2023-04-11T18:54:14,080 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-04-11T18:54:14,080 ########################################################################## 2023-04-11T18:54:14,080 The following seems to be defined outside of `pyproject.toml`: 2023-04-11T18:54:14,081 `description = 'plugin for cell segmentation'` 2023-04-11T18:54:14,081 According to the spec (see the link below), however, setuptools CANNOT 2023-04-11T18:54:14,081 consider this value unless 'description' is listed as `dynamic`. 2023-04-11T18:54:14,081 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-04-11T18:54:14,081 For the time being, `setuptools` will still consider the given value (as a 2023-04-11T18:54:14,082 **transitional** measure), but please note that future releases of setuptools will 2023-04-11T18:54:14,082 follow strictly the standard. 2023-04-11T18:54:14,082 To prevent this warning, you can list 'description' under `dynamic` or alternatively 2023-04-11T18:54:14,082 remove the `[project]` table from your file and rely entirely on other means of 2023-04-11T18:54:14,082 configuration. 2023-04-11T18:54:14,083 !! 2023-04-11T18:54:14,083 warnings.warn(msg, _WouldIgnoreField) 2023-04-11T18:54:14,083 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'readme' defined outside of `pyproject.toml` would be ignored. 2023-04-11T18:54:14,083 !! 2023-04-11T18:54:14,084 ########################################################################## 2023-04-11T18:54:14,084 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-04-11T18:54:14,084 ########################################################################## 2023-04-11T18:54:14,084 The following seems to be defined outside of `pyproject.toml`: 2023-04-11T18:54:14,085 `readme = '# napari-cellseg3D: a napari plug-in for direct 3D cell segmentation with deep learning\n\n\ncellseg3d logo\n\nCode style: black\n[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/AdaptiveMotorControlLab/CellSeg3d/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-cellseg3d.svg?color=green)](https://pypi.org/project/napari-cellseg3d)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-cellseg-annotator.svg?color=green)](https://python.org)\n[![codecov](https://codecov.io/gh/AdaptiveMotorControlLab/CellSeg3d/branch/main/graph/badge.svg?token=hzUcn3XN8F)](https://codecov.io/gh/AdaptiveMotorControlLab/CellSeg3d)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-cellseg3d)](https://www.napari-hub.org/plugins/napari-cellseg3d)\n\n\nA napari plugin for 3D cell segmentation: training, inference, and data review. In particular, this project was developed for analysis of mesoSPIM-acquired (cleared tissue + lightsheet) datasets.\n\n----------------------------------\n\n## News\n\n**June 2022: This is an alpha version, please expect bugs and issues, and help us make the code better by reporting them as an issue!**\n\n\n\n## Installation\n\nNote : we recommend using conda to create a new environment for the plugin.\n\n conda create --name python=3.8 napari-cellseg3d\n conda activate napari-cellseg3d\n\nYou can install `napari-cellseg3d` via [pip]: \n\n pip install napari-cellseg3d\n\nOR directly via [napari-hub]:\n\n- Install napari from pip with `pip install "napari[all]"`,\nthen from the “Plugins” menu within the napari application, select “Install/Uninstall Package(s)...”\n- Copy `napari-cellseg3d` and paste it where it says “Install by name/url…”\n- Click “Install”\n\n## Documentation\n\nAvailable at https://AdaptiveMotorControlLab.github.io/CellSeg3d\n\nYou can also generate docs by running ``make html`` in the docs folder.\n\n## Usage\n\nTo use the plugin, please run:\n```\nnapari\n```\nThen go into Plugins > napari-cellseg3d, and choose which tool to use.\n\n- **Review**: This module allows you to review your labels, from predictions or manual labeling, and correct them if needed. It then saves the status of each file in a csv, for easier monitoring.\n- **Inference**: This module allows you to use pre-trained segmentation algorithms on volumes to automatically label cells and compute statistics.\n- **Train**: This module allows you to train segmentation algorithms from labeled volumes.\n- **Utilities**: This module allows you to perform several actions like cropping your volumes and labels dynamically, by selecting a fixed size volume and moving it around the image; computing prediction scores from ground truth and predicition labels; or converting labels from instance to segmentation and the opposite.\n\n\n## Requirements\n**Python >= 3.8 required**\n\nRequires **pytorch** and **MONAI**.\nFor PyTorch, please see [PyTorch\'s website for installation instructions].\nA CUDA-capable GPU is not needed but very strongly recommended, especially for training.\nIf you get errors from MONAI regarding missing readers, please see [MONAI\'s optional dependencies] page for instructions on getting the readers required by your images.\n\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed description.\n\n\n## Testing\n\nTo run tests locally:\n\n- Locally : run ``pytest`` in the plugin folder\n- Locally with coverage : In the plugin folder, run ``coverage run --source=napari_cellseg3d -m pytest`` then ``coverage xml`` to generate a .xml coverage file.\n- With tox : run ``tox`` in the plugin folder (will simulate tests with several python and OS configs, requires substantial storage space)\n\n## Contributing\n\nContributions are very welcome.\n\nPlease ensure the coverage at least stays the same before you submit a pull request.\n\nFor local installation from Github cloning, please run:\n\n```\npip install -e .\n```\n\n## License\n\nDistributed under the terms of the [MIT] license.\n\n"napari-cellseg3d" is free and open source software.\n\n[napari-hub]: https://www.napari-hub.org/plugins/napari-cellseg3d\n\n[file an issue]: https://github.com/AdaptiveMotorControlLab/CellSeg3d/issues\n[napari]: https://github.com/napari/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n\n[PyTorch\'s website for installation instructions]: https://pytorch.org/get-started/locally/\n[MONAI\'s optional dependencies]: https://docs.monai.io/en/stable/installation.html#installing-the-recommended-dependencies\n\n## Acknowledgements\n\nThis plugin was developed by Cyril Achard, Maxime Vidal, Mackenzie Mathis. This work was funded, in part, from the Wyss Center to the [Mathis Laboratory of Adaptive Motor Control](https://www.mackenziemathislab.org/).\n\n\n## Plugin base\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]\'s [cookiecutter-napari-plugin] template.\n\n\n'` 2023-04-11T18:54:14,086 According to the spec (see the link below), however, setuptools CANNOT 2023-04-11T18:54:14,086 consider this value unless 'readme' is listed as `dynamic`. 2023-04-11T18:54:14,086 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-04-11T18:54:14,086 For the time being, `setuptools` will still consider the given value (as a 2023-04-11T18:54:14,086 **transitional** measure), but please note that future releases of setuptools will 2023-04-11T18:54:14,087 follow strictly the standard. 2023-04-11T18:54:14,087 To prevent this warning, you can list 'readme' under `dynamic` or alternatively 2023-04-11T18:54:14,087 remove the `[project]` table from your file and rely entirely on other means of 2023-04-11T18:54:14,087 configuration. 2023-04-11T18:54:14,088 !! 2023-04-11T18:54:14,088 warnings.warn(msg, _WouldIgnoreField) 2023-04-11T18:54:14,088 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'license' defined outside of `pyproject.toml` would be ignored. 2023-04-11T18:54:14,088 !! 2023-04-11T18:54:14,089 ########################################################################## 2023-04-11T18:54:14,089 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-04-11T18:54:14,089 ########################################################################## 2023-04-11T18:54:14,089 The following seems to be defined outside of `pyproject.toml`: 2023-04-11T18:54:14,089 `license = 'MIT'` 2023-04-11T18:54:14,090 According to the spec (see the link below), however, setuptools CANNOT 2023-04-11T18:54:14,090 consider this value unless 'license' is listed as `dynamic`. 2023-04-11T18:54:14,090 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-04-11T18:54:14,091 For the time being, `setuptools` will still consider the given value (as a 2023-04-11T18:54:14,091 **transitional** measure), but please note that future releases of setuptools will 2023-04-11T18:54:14,091 follow strictly the standard. 2023-04-11T18:54:14,091 To prevent this warning, you can list 'license' under `dynamic` or alternatively 2023-04-11T18:54:14,091 remove the `[project]` table from your file and rely entirely on other means of 2023-04-11T18:54:14,091 configuration. 2023-04-11T18:54:14,092 !! 2023-04-11T18:54:14,092 warnings.warn(msg, _WouldIgnoreField) 2023-04-11T18:54:14,092 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'classifiers' defined outside of `pyproject.toml` would be ignored. 2023-04-11T18:54:14,092 !! 2023-04-11T18:54:14,093 ########################################################################## 2023-04-11T18:54:14,093 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-04-11T18:54:14,094 ########################################################################## 2023-04-11T18:54:14,094 The following seems to be defined outside of `pyproject.toml`: 2023-04-11T18:54:14,094 `classifiers = ['Development Status :: 2 - Pre-Alpha', 'Intended Audience :: Science/Research', 'Framework :: napari', 'Topic :: Software Development :: Testing', 'Programming Language :: Python', 'Programming Language :: Python :: 3', 'Programming Language :: Python :: 3.8', 'Programming Language :: Python :: 3.9', 'Programming Language :: Python :: 3.10', 'Operating System :: OS Independent', 'License :: OSI Approved :: MIT License', 'Topic :: Scientific/Engineering :: Artificial Intelligence', 'Topic :: Scientific/Engineering :: Image Processing', 'Topic :: Scientific/Engineering :: Visualization']` 2023-04-11T18:54:14,094 According to the spec (see the link below), however, setuptools CANNOT 2023-04-11T18:54:14,095 consider this value unless 'classifiers' is listed as `dynamic`. 2023-04-11T18:54:14,095 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-04-11T18:54:14,095 For the time being, `setuptools` will still consider the given value (as a 2023-04-11T18:54:14,095 **transitional** measure), but please note that future releases of setuptools will 2023-04-11T18:54:14,095 follow strictly the standard. 2023-04-11T18:54:14,096 To prevent this warning, you can list 'classifiers' under `dynamic` or alternatively 2023-04-11T18:54:14,096 remove the `[project]` table from your file and rely entirely on other means of 2023-04-11T18:54:14,096 configuration. 2023-04-11T18:54:14,096 !! 2023-04-11T18:54:14,097 warnings.warn(msg, _WouldIgnoreField) 2023-04-11T18:54:14,097 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'urls' defined outside of `pyproject.toml` would be ignored. 2023-04-11T18:54:14,097 !! 2023-04-11T18:54:14,097 ########################################################################## 2023-04-11T18:54:14,097 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-04-11T18:54:14,098 ########################################################################## 2023-04-11T18:54:14,098 The following seems to be defined outside of `pyproject.toml`: 2023-04-11T18:54:14,098 `urls = {'Bug Tracker': 'https://github.com/AdaptiveMotorControlLab/CellSeg3d/issues', 'Documentation': 'https://adaptivemotorcontrollab.github.io/cellseg3d-docs/res/welcome.html', 'Source Code': 'https://github.com/AdaptiveMotorControlLab/CellSeg3d'}` 2023-04-11T18:54:14,099 According to the spec (see the link below), however, setuptools CANNOT 2023-04-11T18:54:14,099 consider this value unless 'urls' is listed as `dynamic`. 2023-04-11T18:54:14,099 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-04-11T18:54:14,099 For the time being, `setuptools` will still consider the given value (as a 2023-04-11T18:54:14,099 **transitional** measure), but please note that future releases of setuptools will 2023-04-11T18:54:14,100 follow strictly the standard. 2023-04-11T18:54:14,100 To prevent this warning, you can list 'urls' under `dynamic` or alternatively 2023-04-11T18:54:14,100 remove the `[project]` table from your file and rely entirely on other means of 2023-04-11T18:54:14,100 configuration. 2023-04-11T18:54:14,100 !! 2023-04-11T18:54:14,101 warnings.warn(msg, _WouldIgnoreField) 2023-04-11T18:54:14,101 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'entry-points' defined outside of `pyproject.toml` would be ignored. 2023-04-11T18:54:14,101 !! 2023-04-11T18:54:14,101 ########################################################################## 2023-04-11T18:54:14,101 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-04-11T18:54:14,101 ########################################################################## 2023-04-11T18:54:14,102 The following seems to be defined outside of `pyproject.toml`: 2023-04-11T18:54:14,102 `entry-points = {'napari.manifest': ['napari-cellseg3d = napari_cellseg3d:napari.yaml']}` 2023-04-11T18:54:14,102 According to the spec (see the link below), however, setuptools CANNOT 2023-04-11T18:54:14,102 consider this value unless 'entry-points' is listed as `dynamic`. 2023-04-11T18:54:14,103 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-04-11T18:54:14,103 For the time being, `setuptools` will still consider the given value (as a 2023-04-11T18:54:14,103 **transitional** measure), but please note that future releases of setuptools will 2023-04-11T18:54:14,103 follow strictly the standard. 2023-04-11T18:54:14,103 To prevent this warning, you can list 'entry-points' under `dynamic` or alternatively 2023-04-11T18:54:14,104 remove the `[project]` table from your file and rely entirely on other means of 2023-04-11T18:54:14,104 configuration. 2023-04-11T18:54:14,104 !! 2023-04-11T18:54:14,104 warnings.warn(msg, _WouldIgnoreField) 2023-04-11T18:54:14,105 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:203: UserWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2023-04-11T18:54:14,105 warnings.warn(msg) 2023-04-11T18:54:14,409 running egg_info 2023-04-11T18:54:14,414 writing napari_cellseg3d.egg-info/PKG-INFO 2023-04-11T18:54:14,417 writing dependency_links to napari_cellseg3d.egg-info/dependency_links.txt 2023-04-11T18:54:14,419 writing entry points to napari_cellseg3d.egg-info/entry_points.txt 2023-04-11T18:54:14,433 writing requirements to napari_cellseg3d.egg-info/requires.txt 2023-04-11T18:54:14,435 writing top-level names to napari_cellseg3d.egg-info/top_level.txt 2023-04-11T18:54:14,470 reading manifest file 'napari_cellseg3d.egg-info/SOURCES.txt' 2023-04-11T18:54:14,474 reading manifest template 'MANIFEST.in' 2023-04-11T18:54:14,475 warning: no files found matching 'napari.yaml' 2023-04-11T18:54:14,476 warning: no files found matching '*.png' under directory 'res' 2023-04-11T18:54:14,476 warning: no files found matching '*.json' under directory 'code_models' 2023-04-11T18:54:14,477 warning: no previously-included files matching '__pycache__' found under directory '*' 2023-04-11T18:54:14,478 warning: no previously-included files matching '*.py[co]' found under directory '*' 2023-04-11T18:54:14,478 adding license file 'LICENSE' 2023-04-11T18:54:14,484 writing manifest file 'napari_cellseg3d.egg-info/SOURCES.txt' 2023-04-11T18:54:14,585 Getting requirements to build wheel: finished with status 'done' 2023-04-11T18:54:14,594 Created temporary directory: /tmp/pip-modern-metadata-eh6bjfst 2023-04-11T18:54:14,597 Preparing metadata (pyproject.toml): started 2023-04-11T18:54:14,598 Running command Preparing metadata (pyproject.toml) 2023-04-11T18:54:15,143 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/dist.py:788: UserWarning: Usage of dash-separated 'napari-cellseg3d' will not be supported in future versions. Please use the underscore name 'napari_cellseg3d' instead 2023-04-11T18:54:15,144 warnings.warn( 2023-04-11T18:54:15,173 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/pyprojecttoml.py:108: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. 2023-04-11T18:54:15,173 warnings.warn(msg, _BetaConfiguration) 2023-04-11T18:54:15,200 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'description' defined outside of `pyproject.toml` would be ignored. 2023-04-11T18:54:15,201 !! 2023-04-11T18:54:15,201 ########################################################################## 2023-04-11T18:54:15,201 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-04-11T18:54:15,201 ########################################################################## 2023-04-11T18:54:15,202 The following seems to be defined outside of `pyproject.toml`: 2023-04-11T18:54:15,202 `description = 'plugin for cell segmentation'` 2023-04-11T18:54:15,202 According to the spec (see the link below), however, setuptools CANNOT 2023-04-11T18:54:15,202 consider this value unless 'description' is listed as `dynamic`. 2023-04-11T18:54:15,203 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-04-11T18:54:15,203 For the time being, `setuptools` will still consider the given value (as a 2023-04-11T18:54:15,203 **transitional** measure), but please note that future releases of setuptools will 2023-04-11T18:54:15,203 follow strictly the standard. 2023-04-11T18:54:15,203 To prevent this warning, you can list 'description' under `dynamic` or alternatively 2023-04-11T18:54:15,203 remove the `[project]` table from your file and rely entirely on other means of 2023-04-11T18:54:15,204 configuration. 2023-04-11T18:54:15,204 !! 2023-04-11T18:54:15,204 warnings.warn(msg, _WouldIgnoreField) 2023-04-11T18:54:15,205 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'readme' defined outside of `pyproject.toml` would be ignored. 2023-04-11T18:54:15,205 !! 2023-04-11T18:54:15,205 ########################################################################## 2023-04-11T18:54:15,205 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-04-11T18:54:15,205 ########################################################################## 2023-04-11T18:54:15,206 The following seems to be defined outside of `pyproject.toml`: 2023-04-11T18:54:15,206 `readme = '# napari-cellseg3D: a napari plug-in for direct 3D cell segmentation with deep learning\n\n\ncellseg3d logo\n\nCode style: black\n[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/AdaptiveMotorControlLab/CellSeg3d/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-cellseg3d.svg?color=green)](https://pypi.org/project/napari-cellseg3d)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-cellseg-annotator.svg?color=green)](https://python.org)\n[![codecov](https://codecov.io/gh/AdaptiveMotorControlLab/CellSeg3d/branch/main/graph/badge.svg?token=hzUcn3XN8F)](https://codecov.io/gh/AdaptiveMotorControlLab/CellSeg3d)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-cellseg3d)](https://www.napari-hub.org/plugins/napari-cellseg3d)\n\n\nA napari plugin for 3D cell segmentation: training, inference, and data review. In particular, this project was developed for analysis of mesoSPIM-acquired (cleared tissue + lightsheet) datasets.\n\n----------------------------------\n\n## News\n\n**June 2022: This is an alpha version, please expect bugs and issues, and help us make the code better by reporting them as an issue!**\n\n\n\n## Installation\n\nNote : we recommend using conda to create a new environment for the plugin.\n\n conda create --name python=3.8 napari-cellseg3d\n conda activate napari-cellseg3d\n\nYou can install `napari-cellseg3d` via [pip]: \n\n pip install napari-cellseg3d\n\nOR directly via [napari-hub]:\n\n- Install napari from pip with `pip install "napari[all]"`,\nthen from the “Plugins” menu within the napari application, select “Install/Uninstall Package(s)...”\n- Copy `napari-cellseg3d` and paste it where it says “Install by name/url…”\n- Click “Install”\n\n## Documentation\n\nAvailable at https://AdaptiveMotorControlLab.github.io/CellSeg3d\n\nYou can also generate docs by running ``make html`` in the docs folder.\n\n## Usage\n\nTo use the plugin, please run:\n```\nnapari\n```\nThen go into Plugins > napari-cellseg3d, and choose which tool to use.\n\n- **Review**: This module allows you to review your labels, from predictions or manual labeling, and correct them if needed. It then saves the status of each file in a csv, for easier monitoring.\n- **Inference**: This module allows you to use pre-trained segmentation algorithms on volumes to automatically label cells and compute statistics.\n- **Train**: This module allows you to train segmentation algorithms from labeled volumes.\n- **Utilities**: This module allows you to perform several actions like cropping your volumes and labels dynamically, by selecting a fixed size volume and moving it around the image; computing prediction scores from ground truth and predicition labels; or converting labels from instance to segmentation and the opposite.\n\n\n## Requirements\n**Python >= 3.8 required**\n\nRequires **pytorch** and **MONAI**.\nFor PyTorch, please see [PyTorch\'s website for installation instructions].\nA CUDA-capable GPU is not needed but very strongly recommended, especially for training.\nIf you get errors from MONAI regarding missing readers, please see [MONAI\'s optional dependencies] page for instructions on getting the readers required by your images.\n\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed description.\n\n\n## Testing\n\nTo run tests locally:\n\n- Locally : run ``pytest`` in the plugin folder\n- Locally with coverage : In the plugin folder, run ``coverage run --source=napari_cellseg3d -m pytest`` then ``coverage xml`` to generate a .xml coverage file.\n- With tox : run ``tox`` in the plugin folder (will simulate tests with several python and OS configs, requires substantial storage space)\n\n## Contributing\n\nContributions are very welcome.\n\nPlease ensure the coverage at least stays the same before you submit a pull request.\n\nFor local installation from Github cloning, please run:\n\n```\npip install -e .\n```\n\n## License\n\nDistributed under the terms of the [MIT] license.\n\n"napari-cellseg3d" is free and open source software.\n\n[napari-hub]: https://www.napari-hub.org/plugins/napari-cellseg3d\n\n[file an issue]: https://github.com/AdaptiveMotorControlLab/CellSeg3d/issues\n[napari]: https://github.com/napari/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n\n[PyTorch\'s website for installation instructions]: https://pytorch.org/get-started/locally/\n[MONAI\'s optional dependencies]: https://docs.monai.io/en/stable/installation.html#installing-the-recommended-dependencies\n\n## Acknowledgements\n\nThis plugin was developed by Cyril Achard, Maxime Vidal, Mackenzie Mathis. This work was funded, in part, from the Wyss Center to the [Mathis Laboratory of Adaptive Motor Control](https://www.mackenziemathislab.org/).\n\n\n## Plugin base\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]\'s [cookiecutter-napari-plugin] template.\n\n\n'` 2023-04-11T18:54:15,206 According to the spec (see the link below), however, setuptools CANNOT 2023-04-11T18:54:15,207 consider this value unless 'readme' is listed as `dynamic`. 2023-04-11T18:54:15,207 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-04-11T18:54:15,207 For the time being, `setuptools` will still consider the given value (as a 2023-04-11T18:54:15,207 **transitional** measure), but please note that future releases of setuptools will 2023-04-11T18:54:15,207 follow strictly the standard. 2023-04-11T18:54:15,208 To prevent this warning, you can list 'readme' under `dynamic` or alternatively 2023-04-11T18:54:15,208 remove the `[project]` table from your file and rely entirely on other means of 2023-04-11T18:54:15,208 configuration. 2023-04-11T18:54:15,208 !! 2023-04-11T18:54:15,209 warnings.warn(msg, _WouldIgnoreField) 2023-04-11T18:54:15,209 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'license' defined outside of `pyproject.toml` would be ignored. 2023-04-11T18:54:15,209 !! 2023-04-11T18:54:15,209 ########################################################################## 2023-04-11T18:54:15,210 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-04-11T18:54:15,210 ########################################################################## 2023-04-11T18:54:15,210 The following seems to be defined outside of `pyproject.toml`: 2023-04-11T18:54:15,210 `license = 'MIT'` 2023-04-11T18:54:15,210 According to the spec (see the link below), however, setuptools CANNOT 2023-04-11T18:54:15,211 consider this value unless 'license' is listed as `dynamic`. 2023-04-11T18:54:15,211 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-04-11T18:54:15,211 For the time being, `setuptools` will still consider the given value (as a 2023-04-11T18:54:15,211 **transitional** measure), but please note that future releases of setuptools will 2023-04-11T18:54:15,211 follow strictly the standard. 2023-04-11T18:54:15,212 To prevent this warning, you can list 'license' under `dynamic` or alternatively 2023-04-11T18:54:15,212 remove the `[project]` table from your file and rely entirely on other means of 2023-04-11T18:54:15,212 configuration. 2023-04-11T18:54:15,212 !! 2023-04-11T18:54:15,213 warnings.warn(msg, _WouldIgnoreField) 2023-04-11T18:54:15,213 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'classifiers' defined outside of `pyproject.toml` would be ignored. 2023-04-11T18:54:15,213 !! 2023-04-11T18:54:15,213 ########################################################################## 2023-04-11T18:54:15,214 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-04-11T18:54:15,214 ########################################################################## 2023-04-11T18:54:15,214 The following seems to be defined outside of `pyproject.toml`: 2023-04-11T18:54:15,214 `classifiers = ['Development Status :: 2 - Pre-Alpha', 'Intended Audience :: Science/Research', 'Framework :: napari', 'Topic :: Software Development :: Testing', 'Programming Language :: Python', 'Programming Language :: Python :: 3', 'Programming Language :: Python :: 3.8', 'Programming Language :: Python :: 3.9', 'Programming Language :: Python :: 3.10', 'Operating System :: OS Independent', 'License :: OSI Approved :: MIT License', 'Topic :: Scientific/Engineering :: Artificial Intelligence', 'Topic :: Scientific/Engineering :: Image Processing', 'Topic :: Scientific/Engineering :: Visualization']` 2023-04-11T18:54:15,215 According to the spec (see the link below), however, setuptools CANNOT 2023-04-11T18:54:15,215 consider this value unless 'classifiers' is listed as `dynamic`. 2023-04-11T18:54:15,215 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-04-11T18:54:15,215 For the time being, `setuptools` will still consider the given value (as a 2023-04-11T18:54:15,215 **transitional** measure), but please note that future releases of setuptools will 2023-04-11T18:54:15,216 follow strictly the standard. 2023-04-11T18:54:15,216 To prevent this warning, you can list 'classifiers' under `dynamic` or alternatively 2023-04-11T18:54:15,216 remove the `[project]` table from your file and rely entirely on other means of 2023-04-11T18:54:15,216 configuration. 2023-04-11T18:54:15,217 !! 2023-04-11T18:54:15,217 warnings.warn(msg, _WouldIgnoreField) 2023-04-11T18:54:15,217 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'urls' defined outside of `pyproject.toml` would be ignored. 2023-04-11T18:54:15,217 !! 2023-04-11T18:54:15,217 ########################################################################## 2023-04-11T18:54:15,218 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-04-11T18:54:15,218 ########################################################################## 2023-04-11T18:54:15,218 The following seems to be defined outside of `pyproject.toml`: 2023-04-11T18:54:15,218 `urls = {'Bug Tracker': 'https://github.com/AdaptiveMotorControlLab/CellSeg3d/issues', 'Documentation': 'https://adaptivemotorcontrollab.github.io/cellseg3d-docs/res/welcome.html', 'Source Code': 'https://github.com/AdaptiveMotorControlLab/CellSeg3d'}` 2023-04-11T18:54:15,218 According to the spec (see the link below), however, setuptools CANNOT 2023-04-11T18:54:15,219 consider this value unless 'urls' is listed as `dynamic`. 2023-04-11T18:54:15,219 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-04-11T18:54:15,219 For the time being, `setuptools` will still consider the given value (as a 2023-04-11T18:54:15,219 **transitional** measure), but please note that future releases of setuptools will 2023-04-11T18:54:15,219 follow strictly the standard. 2023-04-11T18:54:15,220 To prevent this warning, you can list 'urls' under `dynamic` or alternatively 2023-04-11T18:54:15,220 remove the `[project]` table from your file and rely entirely on other means of 2023-04-11T18:54:15,220 configuration. 2023-04-11T18:54:15,220 !! 2023-04-11T18:54:15,221 warnings.warn(msg, _WouldIgnoreField) 2023-04-11T18:54:15,221 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'entry-points' defined outside of `pyproject.toml` would be ignored. 2023-04-11T18:54:15,221 !! 2023-04-11T18:54:15,221 ########################################################################## 2023-04-11T18:54:15,221 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-04-11T18:54:15,222 ########################################################################## 2023-04-11T18:54:15,222 The following seems to be defined outside of `pyproject.toml`: 2023-04-11T18:54:15,222 `entry-points = {'napari.manifest': ['napari-cellseg3d = napari_cellseg3d:napari.yaml']}` 2023-04-11T18:54:15,223 According to the spec (see the link below), however, setuptools CANNOT 2023-04-11T18:54:15,223 consider this value unless 'entry-points' is listed as `dynamic`. 2023-04-11T18:54:15,223 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-04-11T18:54:15,224 For the time being, `setuptools` will still consider the given value (as a 2023-04-11T18:54:15,224 **transitional** measure), but please note that future releases of setuptools will 2023-04-11T18:54:15,224 follow strictly the standard. 2023-04-11T18:54:15,224 To prevent this warning, you can list 'entry-points' under `dynamic` or alternatively 2023-04-11T18:54:15,224 remove the `[project]` table from your file and rely entirely on other means of 2023-04-11T18:54:15,225 configuration. 2023-04-11T18:54:15,225 !! 2023-04-11T18:54:15,225 warnings.warn(msg, _WouldIgnoreField) 2023-04-11T18:54:15,225 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:203: UserWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2023-04-11T18:54:15,225 warnings.warn(msg) 2023-04-11T18:54:15,511 running dist_info 2023-04-11T18:54:15,517 creating /tmp/pip-modern-metadata-eh6bjfst/napari_cellseg3d.egg-info 2023-04-11T18:54:15,521 writing /tmp/pip-modern-metadata-eh6bjfst/napari_cellseg3d.egg-info/PKG-INFO 2023-04-11T18:54:15,524 writing dependency_links to /tmp/pip-modern-metadata-eh6bjfst/napari_cellseg3d.egg-info/dependency_links.txt 2023-04-11T18:54:15,526 writing entry points to /tmp/pip-modern-metadata-eh6bjfst/napari_cellseg3d.egg-info/entry_points.txt 2023-04-11T18:54:15,528 writing requirements to /tmp/pip-modern-metadata-eh6bjfst/napari_cellseg3d.egg-info/requires.txt 2023-04-11T18:54:15,529 writing top-level names to /tmp/pip-modern-metadata-eh6bjfst/napari_cellseg3d.egg-info/top_level.txt 2023-04-11T18:54:15,531 writing manifest file '/tmp/pip-modern-metadata-eh6bjfst/napari_cellseg3d.egg-info/SOURCES.txt' 2023-04-11T18:54:15,560 reading manifest file '/tmp/pip-modern-metadata-eh6bjfst/napari_cellseg3d.egg-info/SOURCES.txt' 2023-04-11T18:54:15,562 reading manifest template 'MANIFEST.in' 2023-04-11T18:54:15,563 warning: no files found matching 'napari.yaml' 2023-04-11T18:54:15,563 warning: no files found matching '*.png' under directory 'res' 2023-04-11T18:54:15,564 warning: no files found matching '*.json' under directory 'code_models' 2023-04-11T18:54:15,565 warning: no previously-included files matching '__pycache__' found under directory '*' 2023-04-11T18:54:15,566 warning: no previously-included files matching '*.py[co]' found under directory '*' 2023-04-11T18:54:15,566 adding license file 'LICENSE' 2023-04-11T18:54:15,570 writing manifest file '/tmp/pip-modern-metadata-eh6bjfst/napari_cellseg3d.egg-info/SOURCES.txt' 2023-04-11T18:54:15,571 creating '/tmp/pip-modern-metadata-eh6bjfst/napari_cellseg3d-0.0.2rc6.dist-info' 2023-04-11T18:54:15,718 Preparing metadata (pyproject.toml): finished with status 'done' 2023-04-11T18:54:15,726 Source in /tmp/pip-wheel-qv2j3fj_/napari-cellseg3d_61c26985a55849e4aa40706129d5938c has version 0.0.2rc6, which satisfies requirement napari-cellseg3d==0.0.2rc6 from https://files.pythonhosted.org/packages/cb/98/2484712583687a2928e49fb3aaa517fc1e2144b5dd8d9d2dc0310a09c80f/napari_cellseg3d-0.0.2rc6.tar.gz 2023-04-11T18:54:15,727 Removed napari-cellseg3d==0.0.2rc6 from https://files.pythonhosted.org/packages/cb/98/2484712583687a2928e49fb3aaa517fc1e2144b5dd8d9d2dc0310a09c80f/napari_cellseg3d-0.0.2rc6.tar.gz from build tracker '/tmp/pip-build-tracker-ob5hzbyb' 2023-04-11T18:54:15,735 Created temporary directory: /tmp/pip-unpack-4h8awqtw 2023-04-11T18:54:15,735 Building wheels for collected packages: napari-cellseg3d 2023-04-11T18:54:15,740 Created temporary directory: /tmp/pip-wheel-mr4croth 2023-04-11T18:54:15,740 Destination directory: /tmp/pip-wheel-mr4croth 2023-04-11T18:54:15,743 Building wheel for napari-cellseg3d (pyproject.toml): started 2023-04-11T18:54:15,744 Running command Building wheel for napari-cellseg3d (pyproject.toml) 2023-04-11T18:54:16,261 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/dist.py:788: UserWarning: Usage of dash-separated 'napari-cellseg3d' will not be supported in future versions. Please use the underscore name 'napari_cellseg3d' instead 2023-04-11T18:54:16,262 warnings.warn( 2023-04-11T18:54:16,290 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/pyprojecttoml.py:108: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. 2023-04-11T18:54:16,290 warnings.warn(msg, _BetaConfiguration) 2023-04-11T18:54:16,317 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'description' defined outside of `pyproject.toml` would be ignored. 2023-04-11T18:54:16,317 !! 2023-04-11T18:54:16,317 ########################################################################## 2023-04-11T18:54:16,317 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-04-11T18:54:16,318 ########################################################################## 2023-04-11T18:54:16,318 The following seems to be defined outside of `pyproject.toml`: 2023-04-11T18:54:16,318 `description = 'plugin for cell segmentation'` 2023-04-11T18:54:16,319 According to the spec (see the link below), however, setuptools CANNOT 2023-04-11T18:54:16,319 consider this value unless 'description' is listed as `dynamic`. 2023-04-11T18:54:16,319 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-04-11T18:54:16,319 For the time being, `setuptools` will still consider the given value (as a 2023-04-11T18:54:16,319 **transitional** measure), but please note that future releases of setuptools will 2023-04-11T18:54:16,319 follow strictly the standard. 2023-04-11T18:54:16,320 To prevent this warning, you can list 'description' under `dynamic` or alternatively 2023-04-11T18:54:16,320 remove the `[project]` table from your file and rely entirely on other means of 2023-04-11T18:54:16,320 configuration. 2023-04-11T18:54:16,320 !! 2023-04-11T18:54:16,321 warnings.warn(msg, _WouldIgnoreField) 2023-04-11T18:54:16,321 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'readme' defined outside of `pyproject.toml` would be ignored. 2023-04-11T18:54:16,321 !! 2023-04-11T18:54:16,321 ########################################################################## 2023-04-11T18:54:16,321 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-04-11T18:54:16,322 ########################################################################## 2023-04-11T18:54:16,322 The following seems to be defined outside of `pyproject.toml`: 2023-04-11T18:54:16,322 `readme = '# napari-cellseg3D: a napari plug-in for direct 3D cell segmentation with deep learning\n\n\ncellseg3d logo\n\nCode style: black\n[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/AdaptiveMotorControlLab/CellSeg3d/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-cellseg3d.svg?color=green)](https://pypi.org/project/napari-cellseg3d)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-cellseg-annotator.svg?color=green)](https://python.org)\n[![codecov](https://codecov.io/gh/AdaptiveMotorControlLab/CellSeg3d/branch/main/graph/badge.svg?token=hzUcn3XN8F)](https://codecov.io/gh/AdaptiveMotorControlLab/CellSeg3d)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-cellseg3d)](https://www.napari-hub.org/plugins/napari-cellseg3d)\n\n\nA napari plugin for 3D cell segmentation: training, inference, and data review. In particular, this project was developed for analysis of mesoSPIM-acquired (cleared tissue + lightsheet) datasets.\n\n----------------------------------\n\n## News\n\n**June 2022: This is an alpha version, please expect bugs and issues, and help us make the code better by reporting them as an issue!**\n\n\n\n## Installation\n\nNote : we recommend using conda to create a new environment for the plugin.\n\n conda create --name python=3.8 napari-cellseg3d\n conda activate napari-cellseg3d\n\nYou can install `napari-cellseg3d` via [pip]: \n\n pip install napari-cellseg3d\n\nOR directly via [napari-hub]:\n\n- Install napari from pip with `pip install "napari[all]"`,\nthen from the “Plugins” menu within the napari application, select “Install/Uninstall Package(s)...”\n- Copy `napari-cellseg3d` and paste it where it says “Install by name/url…”\n- Click “Install”\n\n## Documentation\n\nAvailable at https://AdaptiveMotorControlLab.github.io/CellSeg3d\n\nYou can also generate docs by running ``make html`` in the docs folder.\n\n## Usage\n\nTo use the plugin, please run:\n```\nnapari\n```\nThen go into Plugins > napari-cellseg3d, and choose which tool to use.\n\n- **Review**: This module allows you to review your labels, from predictions or manual labeling, and correct them if needed. It then saves the status of each file in a csv, for easier monitoring.\n- **Inference**: This module allows you to use pre-trained segmentation algorithms on volumes to automatically label cells and compute statistics.\n- **Train**: This module allows you to train segmentation algorithms from labeled volumes.\n- **Utilities**: This module allows you to perform several actions like cropping your volumes and labels dynamically, by selecting a fixed size volume and moving it around the image; computing prediction scores from ground truth and predicition labels; or converting labels from instance to segmentation and the opposite.\n\n\n## Requirements\n**Python >= 3.8 required**\n\nRequires **pytorch** and **MONAI**.\nFor PyTorch, please see [PyTorch\'s website for installation instructions].\nA CUDA-capable GPU is not needed but very strongly recommended, especially for training.\nIf you get errors from MONAI regarding missing readers, please see [MONAI\'s optional dependencies] page for instructions on getting the readers required by your images.\n\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed description.\n\n\n## Testing\n\nTo run tests locally:\n\n- Locally : run ``pytest`` in the plugin folder\n- Locally with coverage : In the plugin folder, run ``coverage run --source=napari_cellseg3d -m pytest`` then ``coverage xml`` to generate a .xml coverage file.\n- With tox : run ``tox`` in the plugin folder (will simulate tests with several python and OS configs, requires substantial storage space)\n\n## Contributing\n\nContributions are very welcome.\n\nPlease ensure the coverage at least stays the same before you submit a pull request.\n\nFor local installation from Github cloning, please run:\n\n```\npip install -e .\n```\n\n## License\n\nDistributed under the terms of the [MIT] license.\n\n"napari-cellseg3d" is free and open source software.\n\n[napari-hub]: https://www.napari-hub.org/plugins/napari-cellseg3d\n\n[file an issue]: https://github.com/AdaptiveMotorControlLab/CellSeg3d/issues\n[napari]: https://github.com/napari/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n\n[PyTorch\'s website for installation instructions]: https://pytorch.org/get-started/locally/\n[MONAI\'s optional dependencies]: https://docs.monai.io/en/stable/installation.html#installing-the-recommended-dependencies\n\n## Acknowledgements\n\nThis plugin was developed by Cyril Achard, Maxime Vidal, Mackenzie Mathis. This work was funded, in part, from the Wyss Center to the [Mathis Laboratory of Adaptive Motor Control](https://www.mackenziemathislab.org/).\n\n\n## Plugin base\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]\'s [cookiecutter-napari-plugin] template.\n\n\n'` 2023-04-11T18:54:16,323 According to the spec (see the link below), however, setuptools CANNOT 2023-04-11T18:54:16,323 consider this value unless 'readme' is listed as `dynamic`. 2023-04-11T18:54:16,323 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-04-11T18:54:16,323 For the time being, `setuptools` will still consider the given value (as a 2023-04-11T18:54:16,323 **transitional** measure), but please note that future releases of setuptools will 2023-04-11T18:54:16,324 follow strictly the standard. 2023-04-11T18:54:16,324 To prevent this warning, you can list 'readme' under `dynamic` or alternatively 2023-04-11T18:54:16,324 remove the `[project]` table from your file and rely entirely on other means of 2023-04-11T18:54:16,324 configuration. 2023-04-11T18:54:16,325 !! 2023-04-11T18:54:16,325 warnings.warn(msg, _WouldIgnoreField) 2023-04-11T18:54:16,325 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'license' defined outside of `pyproject.toml` would be ignored. 2023-04-11T18:54:16,325 !! 2023-04-11T18:54:16,326 ########################################################################## 2023-04-11T18:54:16,326 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-04-11T18:54:16,326 ########################################################################## 2023-04-11T18:54:16,326 The following seems to be defined outside of `pyproject.toml`: 2023-04-11T18:54:16,326 `license = 'MIT'` 2023-04-11T18:54:16,327 According to the spec (see the link below), however, setuptools CANNOT 2023-04-11T18:54:16,327 consider this value unless 'license' is listed as `dynamic`. 2023-04-11T18:54:16,327 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-04-11T18:54:16,327 For the time being, `setuptools` will still consider the given value (as a 2023-04-11T18:54:16,328 **transitional** measure), but please note that future releases of setuptools will 2023-04-11T18:54:16,328 follow strictly the standard. 2023-04-11T18:54:16,328 To prevent this warning, you can list 'license' under `dynamic` or alternatively 2023-04-11T18:54:16,328 remove the `[project]` table from your file and rely entirely on other means of 2023-04-11T18:54:16,328 configuration. 2023-04-11T18:54:16,329 !! 2023-04-11T18:54:16,329 warnings.warn(msg, _WouldIgnoreField) 2023-04-11T18:54:16,329 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'classifiers' defined outside of `pyproject.toml` would be ignored. 2023-04-11T18:54:16,329 !! 2023-04-11T18:54:16,330 ########################################################################## 2023-04-11T18:54:16,330 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-04-11T18:54:16,330 ########################################################################## 2023-04-11T18:54:16,330 The following seems to be defined outside of `pyproject.toml`: 2023-04-11T18:54:16,330 `classifiers = ['Development Status :: 2 - Pre-Alpha', 'Intended Audience :: Science/Research', 'Framework :: napari', 'Topic :: Software Development :: Testing', 'Programming Language :: Python', 'Programming Language :: Python :: 3', 'Programming Language :: Python :: 3.8', 'Programming Language :: Python :: 3.9', 'Programming Language :: Python :: 3.10', 'Operating System :: OS Independent', 'License :: OSI Approved :: MIT License', 'Topic :: Scientific/Engineering :: Artificial Intelligence', 'Topic :: Scientific/Engineering :: Image Processing', 'Topic :: Scientific/Engineering :: Visualization']` 2023-04-11T18:54:16,331 According to the spec (see the link below), however, setuptools CANNOT 2023-04-11T18:54:16,331 consider this value unless 'classifiers' is listed as `dynamic`. 2023-04-11T18:54:16,331 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-04-11T18:54:16,331 For the time being, `setuptools` will still consider the given value (as a 2023-04-11T18:54:16,332 **transitional** measure), but please note that future releases of setuptools will 2023-04-11T18:54:16,332 follow strictly the standard. 2023-04-11T18:54:16,332 To prevent this warning, you can list 'classifiers' under `dynamic` or alternatively 2023-04-11T18:54:16,332 remove the `[project]` table from your file and rely entirely on other means of 2023-04-11T18:54:16,332 configuration. 2023-04-11T18:54:16,333 !! 2023-04-11T18:54:16,333 warnings.warn(msg, _WouldIgnoreField) 2023-04-11T18:54:16,333 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'urls' defined outside of `pyproject.toml` would be ignored. 2023-04-11T18:54:16,333 !! 2023-04-11T18:54:16,333 ########################################################################## 2023-04-11T18:54:16,334 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-04-11T18:54:16,334 ########################################################################## 2023-04-11T18:54:16,334 The following seems to be defined outside of `pyproject.toml`: 2023-04-11T18:54:16,334 `urls = {'Bug Tracker': 'https://github.com/AdaptiveMotorControlLab/CellSeg3d/issues', 'Documentation': 'https://adaptivemotorcontrollab.github.io/cellseg3d-docs/res/welcome.html', 'Source Code': 'https://github.com/AdaptiveMotorControlLab/CellSeg3d'}` 2023-04-11T18:54:16,334 According to the spec (see the link below), however, setuptools CANNOT 2023-04-11T18:54:16,335 consider this value unless 'urls' is listed as `dynamic`. 2023-04-11T18:54:16,335 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-04-11T18:54:16,335 For the time being, `setuptools` will still consider the given value (as a 2023-04-11T18:54:16,335 **transitional** measure), but please note that future releases of setuptools will 2023-04-11T18:54:16,335 follow strictly the standard. 2023-04-11T18:54:16,336 To prevent this warning, you can list 'urls' under `dynamic` or alternatively 2023-04-11T18:54:16,336 remove the `[project]` table from your file and rely entirely on other means of 2023-04-11T18:54:16,336 configuration. 2023-04-11T18:54:16,336 !! 2023-04-11T18:54:16,337 warnings.warn(msg, _WouldIgnoreField) 2023-04-11T18:54:16,337 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'entry-points' defined outside of `pyproject.toml` would be ignored. 2023-04-11T18:54:16,337 !! 2023-04-11T18:54:16,338 ########################################################################## 2023-04-11T18:54:16,338 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-04-11T18:54:16,338 ########################################################################## 2023-04-11T18:54:16,339 The following seems to be defined outside of `pyproject.toml`: 2023-04-11T18:54:16,339 `entry-points = {'napari.manifest': ['napari-cellseg3d = napari_cellseg3d:napari.yaml']}` 2023-04-11T18:54:16,339 According to the spec (see the link below), however, setuptools CANNOT 2023-04-11T18:54:16,339 consider this value unless 'entry-points' is listed as `dynamic`. 2023-04-11T18:54:16,340 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-04-11T18:54:16,340 For the time being, `setuptools` will still consider the given value (as a 2023-04-11T18:54:16,340 **transitional** measure), but please note that future releases of setuptools will 2023-04-11T18:54:16,340 follow strictly the standard. 2023-04-11T18:54:16,340 To prevent this warning, you can list 'entry-points' under `dynamic` or alternatively 2023-04-11T18:54:16,340 remove the `[project]` table from your file and rely entirely on other means of 2023-04-11T18:54:16,341 configuration. 2023-04-11T18:54:16,341 !! 2023-04-11T18:54:16,341 warnings.warn(msg, _WouldIgnoreField) 2023-04-11T18:54:16,341 /tmp/pip-build-env-n1lb4xhh/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:203: UserWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2023-04-11T18:54:16,342 warnings.warn(msg) 2023-04-11T18:54:16,616 running bdist_wheel 2023-04-11T18:54:16,631 running build 2023-04-11T18:54:16,631 running build_py 2023-04-11T18:54:16,637 creating build 2023-04-11T18:54:16,637 creating build/lib 2023-04-11T18:54:16,638 creating build/lib/napari_cellseg3d 2023-04-11T18:54:16,640 copying ./napari_cellseg3d/plugins.py -> build/lib/napari_cellseg3d 2023-04-11T18:54:16,642 copying ./napari_cellseg3d/setup.py -> build/lib/napari_cellseg3d 2023-04-11T18:54:16,644 copying ./napari_cellseg3d/interface.py -> build/lib/napari_cellseg3d 2023-04-11T18:54:16,647 copying ./napari_cellseg3d/config.py -> build/lib/napari_cellseg3d 2023-04-11T18:54:16,650 copying ./napari_cellseg3d/utils.py -> build/lib/napari_cellseg3d 2023-04-11T18:54:16,653 copying ./napari_cellseg3d/__init__.py -> build/lib/napari_cellseg3d 2023-04-11T18:54:16,655 creating build/lib/docs 2023-04-11T18:54:16,656 copying ./docs/conf.py -> build/lib/docs 2023-04-11T18:54:16,659 creating build/lib/napari_cellseg3d/res 2023-04-11T18:54:16,660 copying ./napari_cellseg3d/res/__init__.py -> build/lib/napari_cellseg3d/res 2023-04-11T18:54:16,663 creating build/lib/napari_cellseg3d/_tests 2023-04-11T18:54:16,664 copying ./napari_cellseg3d/_tests/test_plugin_inference.py -> build/lib/napari_cellseg3d/_tests 2023-04-11T18:54:16,666 copying ./napari_cellseg3d/_tests/test_helper.py -> build/lib/napari_cellseg3d/_tests 2023-04-11T18:54:16,668 copying ./napari_cellseg3d/_tests/conftest.py -> build/lib/napari_cellseg3d/_tests 2023-04-11T18:54:16,670 copying ./napari_cellseg3d/_tests/test_utils.py -> build/lib/napari_cellseg3d/_tests 2023-04-11T18:54:16,672 copying ./napari_cellseg3d/_tests/test_model_framework.py -> build/lib/napari_cellseg3d/_tests 2023-04-11T18:54:16,674 copying ./napari_cellseg3d/_tests/test_review.py -> build/lib/napari_cellseg3d/_tests 2023-04-11T18:54:16,675 copying ./napari_cellseg3d/_tests/test_training.py -> build/lib/napari_cellseg3d/_tests 2023-04-11T18:54:16,677 copying ./napari_cellseg3d/_tests/test_weight_download.py -> build/lib/napari_cellseg3d/_tests 2023-04-11T18:54:16,679 copying ./napari_cellseg3d/_tests/test_dock_widget.py -> build/lib/napari_cellseg3d/_tests 2023-04-11T18:54:16,681 copying ./napari_cellseg3d/_tests/test_plugin_utils.py -> build/lib/napari_cellseg3d/_tests 2023-04-11T18:54:16,683 copying ./napari_cellseg3d/_tests/test_interface.py -> build/lib/napari_cellseg3d/_tests 2023-04-11T18:54:16,685 copying ./napari_cellseg3d/_tests/__init__.py -> build/lib/napari_cellseg3d/_tests 2023-04-11T18:54:16,686 copying ./napari_cellseg3d/_tests/fixtures.py -> build/lib/napari_cellseg3d/_tests 2023-04-11T18:54:16,689 creating build/lib/napari_cellseg3d/dev_scripts 2023-04-11T18:54:16,690 copying ./napari_cellseg3d/dev_scripts/thread_test.py -> build/lib/napari_cellseg3d/dev_scripts 2023-04-11T18:54:16,693 copying ./napari_cellseg3d/dev_scripts/view_sample.py -> build/lib/napari_cellseg3d/dev_scripts 2023-04-11T18:54:16,695 copying ./napari_cellseg3d/dev_scripts/view_brain.py -> build/lib/napari_cellseg3d/dev_scripts 2023-04-11T18:54:16,697 copying ./napari_cellseg3d/dev_scripts/convert.py -> build/lib/napari_cellseg3d/dev_scripts 2023-04-11T18:54:16,699 copying ./napari_cellseg3d/dev_scripts/drafts.py -> build/lib/napari_cellseg3d/dev_scripts 2023-04-11T18:54:16,700 copying ./napari_cellseg3d/dev_scripts/weight_conversion.py -> build/lib/napari_cellseg3d/dev_scripts 2023-04-11T18:54:16,703 copying ./napari_cellseg3d/dev_scripts/__init__.py -> build/lib/napari_cellseg3d/dev_scripts 2023-04-11T18:54:16,706 creating build/lib/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,707 copying ./napari_cellseg3d/code_plugins/plugin_model_inference.py -> build/lib/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,710 copying ./napari_cellseg3d/code_plugins/plugin_base.py -> build/lib/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,713 copying ./napari_cellseg3d/code_plugins/plugin_convert.py -> build/lib/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,716 copying ./napari_cellseg3d/code_plugins/plugin_review.py -> build/lib/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,719 copying ./napari_cellseg3d/code_plugins/plugin_metrics.py -> build/lib/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,722 copying ./napari_cellseg3d/code_plugins/plugin_crop.py -> build/lib/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,725 copying ./napari_cellseg3d/code_plugins/plugin_model_training.py -> build/lib/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,728 copying ./napari_cellseg3d/code_plugins/plugin_review_dock.py -> build/lib/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,731 copying ./napari_cellseg3d/code_plugins/plugin_utilities.py -> build/lib/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,733 copying ./napari_cellseg3d/code_plugins/__init__.py -> build/lib/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,734 copying ./napari_cellseg3d/code_plugins/plugin_helper.py -> build/lib/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,737 creating build/lib/napari_cellseg3d/code_models 2023-04-11T18:54:16,738 copying ./napari_cellseg3d/code_models/model_instance_seg.py -> build/lib/napari_cellseg3d/code_models 2023-04-11T18:54:16,741 copying ./napari_cellseg3d/code_models/model_framework.py -> build/lib/napari_cellseg3d/code_models 2023-04-11T18:54:16,743 copying ./napari_cellseg3d/code_models/model_workers.py -> build/lib/napari_cellseg3d/code_models 2023-04-11T18:54:16,746 copying ./napari_cellseg3d/code_models/__init__.py -> build/lib/napari_cellseg3d/code_models 2023-04-11T18:54:16,749 creating build/lib/napari_cellseg3d/code_models/models 2023-04-11T18:54:16,750 copying ./napari_cellseg3d/code_models/models/model_TRAILMAP.py -> build/lib/napari_cellseg3d/code_models/models 2023-04-11T18:54:16,752 copying ./napari_cellseg3d/code_models/models/model_SegResNet.py -> build/lib/napari_cellseg3d/code_models/models 2023-04-11T18:54:16,754 copying ./napari_cellseg3d/code_models/models/model_VNet.py -> build/lib/napari_cellseg3d/code_models/models 2023-04-11T18:54:16,756 copying ./napari_cellseg3d/code_models/models/model_TRAILMAP_MS.py -> build/lib/napari_cellseg3d/code_models/models 2023-04-11T18:54:16,758 copying ./napari_cellseg3d/code_models/models/model_test.py -> build/lib/napari_cellseg3d/code_models/models 2023-04-11T18:54:16,760 copying ./napari_cellseg3d/code_models/models/model_SwinUNetR.py -> build/lib/napari_cellseg3d/code_models/models 2023-04-11T18:54:16,761 copying ./napari_cellseg3d/code_models/models/__init__.py -> build/lib/napari_cellseg3d/code_models/models 2023-04-11T18:54:16,763 creating build/lib/napari_cellseg3d/code_models/models/pretrained 2023-04-11T18:54:16,764 copying ./napari_cellseg3d/code_models/models/pretrained/__init__.py -> build/lib/napari_cellseg3d/code_models/models/pretrained 2023-04-11T18:54:16,767 creating build/lib/napari_cellseg3d/code_models/models/unet 2023-04-11T18:54:16,768 copying ./napari_cellseg3d/code_models/models/unet/buildingblocks.py -> build/lib/napari_cellseg3d/code_models/models/unet 2023-04-11T18:54:16,771 copying ./napari_cellseg3d/code_models/models/unet/model.py -> build/lib/napari_cellseg3d/code_models/models/unet 2023-04-11T18:54:16,773 copying ./napari_cellseg3d/code_models/models/unet/__init__.py -> build/lib/napari_cellseg3d/code_models/models/unet 2023-04-11T18:54:16,775 running egg_info 2023-04-11T18:54:16,783 writing napari_cellseg3d.egg-info/PKG-INFO 2023-04-11T18:54:16,785 writing dependency_links to napari_cellseg3d.egg-info/dependency_links.txt 2023-04-11T18:54:16,787 writing entry points to napari_cellseg3d.egg-info/entry_points.txt 2023-04-11T18:54:16,788 writing requirements to napari_cellseg3d.egg-info/requires.txt 2023-04-11T18:54:16,790 writing top-level names to napari_cellseg3d.egg-info/top_level.txt 2023-04-11T18:54:16,812 reading manifest file 'napari_cellseg3d.egg-info/SOURCES.txt' 2023-04-11T18:54:16,815 reading manifest template 'MANIFEST.in' 2023-04-11T18:54:16,816 warning: no files found matching 'napari.yaml' 2023-04-11T18:54:16,817 warning: no files found matching '*.png' under directory 'res' 2023-04-11T18:54:16,817 warning: no files found matching '*.json' under directory 'code_models' 2023-04-11T18:54:16,818 warning: no previously-included files matching '__pycache__' found under directory '*' 2023-04-11T18:54:16,819 warning: no previously-included files matching '*.py[co]' found under directory '*' 2023-04-11T18:54:16,819 adding license file 'LICENSE' 2023-04-11T18:54:16,824 writing manifest file 'napari_cellseg3d.egg-info/SOURCES.txt' 2023-04-11T18:54:16,835 copying ./napari_cellseg3d/napari.yaml -> build/lib/napari_cellseg3d 2023-04-11T18:54:16,837 copying ./napari_cellseg3d/res/logo_alpha.png -> build/lib/napari_cellseg3d/res 2023-04-11T18:54:16,850 copying ./napari_cellseg3d/code_models/models/pretrained/pretrained_model_urls.json -> build/lib/napari_cellseg3d/code_models/models/pretrained 2023-04-11T18:54:16,852 creating build/lib/napari_cellseg3d/_tests/res 2023-04-11T18:54:16,853 copying ./napari_cellseg3d/_tests/res/test.png -> build/lib/napari_cellseg3d/_tests/res 2023-04-11T18:54:16,871 installing to build/bdist.linux-armv7l/wheel 2023-04-11T18:54:16,871 running install 2023-04-11T18:54:16,897 running install_lib 2023-04-11T18:54:16,902 creating build/bdist.linux-armv7l 2023-04-11T18:54:16,902 creating build/bdist.linux-armv7l/wheel 2023-04-11T18:54:16,904 creating build/bdist.linux-armv7l/wheel/napari_cellseg3d 2023-04-11T18:54:16,906 creating build/bdist.linux-armv7l/wheel/napari_cellseg3d/res 2023-04-11T18:54:16,907 copying build/lib/napari_cellseg3d/res/logo_alpha.png -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/res 2023-04-11T18:54:16,920 copying build/lib/napari_cellseg3d/res/__init__.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/res 2023-04-11T18:54:16,922 copying build/lib/napari_cellseg3d/plugins.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d 2023-04-11T18:54:16,924 creating build/bdist.linux-armv7l/wheel/napari_cellseg3d/_tests 2023-04-11T18:54:16,925 copying build/lib/napari_cellseg3d/_tests/test_plugin_inference.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/_tests 2023-04-11T18:54:16,928 copying build/lib/napari_cellseg3d/_tests/test_helper.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/_tests 2023-04-11T18:54:16,930 creating build/bdist.linux-armv7l/wheel/napari_cellseg3d/_tests/res 2023-04-11T18:54:16,931 copying build/lib/napari_cellseg3d/_tests/res/test.png -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/_tests/res 2023-04-11T18:54:16,933 copying build/lib/napari_cellseg3d/_tests/conftest.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/_tests 2023-04-11T18:54:16,935 copying build/lib/napari_cellseg3d/_tests/test_utils.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/_tests 2023-04-11T18:54:16,937 copying build/lib/napari_cellseg3d/_tests/test_model_framework.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/_tests 2023-04-11T18:54:16,939 copying build/lib/napari_cellseg3d/_tests/test_review.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/_tests 2023-04-11T18:54:16,941 copying build/lib/napari_cellseg3d/_tests/test_training.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/_tests 2023-04-11T18:54:16,943 copying build/lib/napari_cellseg3d/_tests/test_weight_download.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/_tests 2023-04-11T18:54:16,945 copying build/lib/napari_cellseg3d/_tests/test_dock_widget.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/_tests 2023-04-11T18:54:16,947 copying build/lib/napari_cellseg3d/_tests/test_plugin_utils.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/_tests 2023-04-11T18:54:16,949 copying build/lib/napari_cellseg3d/_tests/test_interface.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/_tests 2023-04-11T18:54:16,951 copying build/lib/napari_cellseg3d/_tests/__init__.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/_tests 2023-04-11T18:54:16,953 copying build/lib/napari_cellseg3d/_tests/fixtures.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/_tests 2023-04-11T18:54:16,955 copying build/lib/napari_cellseg3d/setup.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d 2023-04-11T18:54:16,957 creating build/bdist.linux-armv7l/wheel/napari_cellseg3d/dev_scripts 2023-04-11T18:54:16,958 copying build/lib/napari_cellseg3d/dev_scripts/thread_test.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/dev_scripts 2023-04-11T18:54:16,961 copying build/lib/napari_cellseg3d/dev_scripts/view_sample.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/dev_scripts 2023-04-11T18:54:16,963 copying build/lib/napari_cellseg3d/dev_scripts/view_brain.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/dev_scripts 2023-04-11T18:54:16,965 copying build/lib/napari_cellseg3d/dev_scripts/convert.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/dev_scripts 2023-04-11T18:54:16,967 copying build/lib/napari_cellseg3d/dev_scripts/drafts.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/dev_scripts 2023-04-11T18:54:16,969 copying build/lib/napari_cellseg3d/dev_scripts/weight_conversion.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/dev_scripts 2023-04-11T18:54:16,972 copying build/lib/napari_cellseg3d/dev_scripts/__init__.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/dev_scripts 2023-04-11T18:54:16,973 copying build/lib/napari_cellseg3d/interface.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d 2023-04-11T18:54:16,977 creating build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,978 copying build/lib/napari_cellseg3d/code_plugins/plugin_model_inference.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,981 copying build/lib/napari_cellseg3d/code_plugins/plugin_base.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,984 copying build/lib/napari_cellseg3d/code_plugins/plugin_convert.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,987 copying build/lib/napari_cellseg3d/code_plugins/plugin_review.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,990 copying build/lib/napari_cellseg3d/code_plugins/plugin_metrics.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,992 copying build/lib/napari_cellseg3d/code_plugins/plugin_crop.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,995 copying build/lib/napari_cellseg3d/code_plugins/plugin_model_training.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_plugins 2023-04-11T18:54:16,999 copying build/lib/napari_cellseg3d/code_plugins/plugin_review_dock.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_plugins 2023-04-11T18:54:17,001 copying build/lib/napari_cellseg3d/code_plugins/plugin_utilities.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_plugins 2023-04-11T18:54:17,004 copying build/lib/napari_cellseg3d/code_plugins/__init__.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_plugins 2023-04-11T18:54:17,005 copying build/lib/napari_cellseg3d/code_plugins/plugin_helper.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_plugins 2023-04-11T18:54:17,008 copying build/lib/napari_cellseg3d/config.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d 2023-04-11T18:54:17,010 copying build/lib/napari_cellseg3d/napari.yaml -> build/bdist.linux-armv7l/wheel/napari_cellseg3d 2023-04-11T18:54:17,012 copying build/lib/napari_cellseg3d/utils.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d 2023-04-11T18:54:17,016 creating build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models 2023-04-11T18:54:17,017 copying build/lib/napari_cellseg3d/code_models/model_instance_seg.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models 2023-04-11T18:54:17,019 copying build/lib/napari_cellseg3d/code_models/model_framework.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models 2023-04-11T18:54:17,022 copying build/lib/napari_cellseg3d/code_models/model_workers.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models 2023-04-11T18:54:17,026 creating build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models/models 2023-04-11T18:54:17,027 copying build/lib/napari_cellseg3d/code_models/models/model_TRAILMAP.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models/models 2023-04-11T18:54:17,030 creating build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models/models/pretrained 2023-04-11T18:54:17,031 copying build/lib/napari_cellseg3d/code_models/models/pretrained/pretrained_model_urls.json -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models/models/pretrained 2023-04-11T18:54:17,033 copying build/lib/napari_cellseg3d/code_models/models/pretrained/__init__.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models/models/pretrained 2023-04-11T18:54:17,034 copying build/lib/napari_cellseg3d/code_models/models/model_SegResNet.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models/models 2023-04-11T18:54:17,036 copying build/lib/napari_cellseg3d/code_models/models/model_VNet.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models/models 2023-04-11T18:54:17,038 copying build/lib/napari_cellseg3d/code_models/models/model_TRAILMAP_MS.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models/models 2023-04-11T18:54:17,041 creating build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models/models/unet 2023-04-11T18:54:17,041 copying build/lib/napari_cellseg3d/code_models/models/unet/buildingblocks.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models/models/unet 2023-04-11T18:54:17,044 copying build/lib/napari_cellseg3d/code_models/models/unet/model.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models/models/unet 2023-04-11T18:54:17,047 copying build/lib/napari_cellseg3d/code_models/models/unet/__init__.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models/models/unet 2023-04-11T18:54:17,048 copying build/lib/napari_cellseg3d/code_models/models/model_test.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models/models 2023-04-11T18:54:17,050 copying build/lib/napari_cellseg3d/code_models/models/model_SwinUNetR.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models/models 2023-04-11T18:54:17,053 copying build/lib/napari_cellseg3d/code_models/models/__init__.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models/models 2023-04-11T18:54:17,054 copying build/lib/napari_cellseg3d/code_models/__init__.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d/code_models 2023-04-11T18:54:17,056 copying build/lib/napari_cellseg3d/__init__.py -> build/bdist.linux-armv7l/wheel/napari_cellseg3d 2023-04-11T18:54:17,058 creating build/bdist.linux-armv7l/wheel/docs 2023-04-11T18:54:17,059 copying build/lib/docs/conf.py -> build/bdist.linux-armv7l/wheel/docs 2023-04-11T18:54:17,062 running install_egg_info 2023-04-11T18:54:17,066 Copying napari_cellseg3d.egg-info to build/bdist.linux-armv7l/wheel/napari_cellseg3d-0.0.2rc6-py3.9.egg-info 2023-04-11T18:54:17,079 running install_scripts 2023-04-11T18:54:17,107 creating build/bdist.linux-armv7l/wheel/napari_cellseg3d-0.0.2rc6.dist-info/WHEEL 2023-04-11T18:54:17,110 creating '/tmp/pip-wheel-mr4croth/.tmp-n7uybw4q/napari_cellseg3d-0.0.2rc6-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-04-11T18:54:17,113 adding 'docs/conf.py' 2023-04-11T18:54:17,115 adding 'napari_cellseg3d/__init__.py' 2023-04-11T18:54:17,117 adding 'napari_cellseg3d/config.py' 2023-04-11T18:54:17,123 adding 'napari_cellseg3d/interface.py' 2023-04-11T18:54:17,125 adding 'napari_cellseg3d/napari.yaml' 2023-04-11T18:54:17,126 adding 'napari_cellseg3d/plugins.py' 2023-04-11T18:54:17,127 adding 'napari_cellseg3d/setup.py' 2023-04-11T18:54:17,131 adding 'napari_cellseg3d/utils.py' 2023-04-11T18:54:17,133 adding 'napari_cellseg3d/_tests/__init__.py' 2023-04-11T18:54:17,134 adding 'napari_cellseg3d/_tests/conftest.py' 2023-04-11T18:54:17,135 adding 'napari_cellseg3d/_tests/fixtures.py' 2023-04-11T18:54:17,136 adding 'napari_cellseg3d/_tests/test_dock_widget.py' 2023-04-11T18:54:17,137 adding 'napari_cellseg3d/_tests/test_helper.py' 2023-04-11T18:54:17,139 adding 'napari_cellseg3d/_tests/test_interface.py' 2023-04-11T18:54:17,140 adding 'napari_cellseg3d/_tests/test_model_framework.py' 2023-04-11T18:54:17,141 adding 'napari_cellseg3d/_tests/test_plugin_inference.py' 2023-04-11T18:54:17,143 adding 'napari_cellseg3d/_tests/test_plugin_utils.py' 2023-04-11T18:54:17,144 adding 'napari_cellseg3d/_tests/test_review.py' 2023-04-11T18:54:17,145 adding 'napari_cellseg3d/_tests/test_training.py' 2023-04-11T18:54:17,146 adding 'napari_cellseg3d/_tests/test_utils.py' 2023-04-11T18:54:17,148 adding 'napari_cellseg3d/_tests/test_weight_download.py' 2023-04-11T18:54:17,150 adding 'napari_cellseg3d/_tests/res/test.png' 2023-04-11T18:54:17,152 adding 'napari_cellseg3d/code_models/__init__.py' 2023-04-11T18:54:17,154 adding 'napari_cellseg3d/code_models/model_framework.py' 2023-04-11T18:54:17,156 adding 'napari_cellseg3d/code_models/model_instance_seg.py' 2023-04-11T18:54:17,161 adding 'napari_cellseg3d/code_models/model_workers.py' 2023-04-11T18:54:17,164 adding 'napari_cellseg3d/code_models/models/__init__.py' 2023-04-11T18:54:17,165 adding 'napari_cellseg3d/code_models/models/model_SegResNet.py' 2023-04-11T18:54:17,167 adding 'napari_cellseg3d/code_models/models/model_SwinUNetR.py' 2023-04-11T18:54:17,168 adding 'napari_cellseg3d/code_models/models/model_TRAILMAP.py' 2023-04-11T18:54:17,169 adding 'napari_cellseg3d/code_models/models/model_TRAILMAP_MS.py' 2023-04-11T18:54:17,171 adding 'napari_cellseg3d/code_models/models/model_VNet.py' 2023-04-11T18:54:17,172 adding 'napari_cellseg3d/code_models/models/model_test.py' 2023-04-11T18:54:17,174 adding 'napari_cellseg3d/code_models/models/pretrained/__init__.py' 2023-04-11T18:54:17,176 adding 'napari_cellseg3d/code_models/models/pretrained/pretrained_model_urls.json' 2023-04-11T18:54:17,177 adding 'napari_cellseg3d/code_models/models/unet/__init__.py' 2023-04-11T18:54:17,180 adding 'napari_cellseg3d/code_models/models/unet/buildingblocks.py' 2023-04-11T18:54:17,182 adding 'napari_cellseg3d/code_models/models/unet/model.py' 2023-04-11T18:54:17,184 adding 'napari_cellseg3d/code_plugins/__init__.py' 2023-04-11T18:54:17,186 adding 'napari_cellseg3d/code_plugins/plugin_base.py' 2023-04-11T18:54:17,189 adding 'napari_cellseg3d/code_plugins/plugin_convert.py' 2023-04-11T18:54:17,192 adding 'napari_cellseg3d/code_plugins/plugin_crop.py' 2023-04-11T18:54:17,193 adding 'napari_cellseg3d/code_plugins/plugin_helper.py' 2023-04-11T18:54:17,195 adding 'napari_cellseg3d/code_plugins/plugin_metrics.py' 2023-04-11T18:54:17,199 adding 'napari_cellseg3d/code_plugins/plugin_model_inference.py' 2023-04-11T18:54:17,204 adding 'napari_cellseg3d/code_plugins/plugin_model_training.py' 2023-04-11T18:54:17,206 adding 'napari_cellseg3d/code_plugins/plugin_review.py' 2023-04-11T18:54:17,208 adding 'napari_cellseg3d/code_plugins/plugin_review_dock.py' 2023-04-11T18:54:17,210 adding 'napari_cellseg3d/code_plugins/plugin_utilities.py' 2023-04-11T18:54:17,212 adding 'napari_cellseg3d/dev_scripts/__init__.py' 2023-04-11T18:54:17,213 adding 'napari_cellseg3d/dev_scripts/convert.py' 2023-04-11T18:54:17,214 adding 'napari_cellseg3d/dev_scripts/drafts.py' 2023-04-11T18:54:17,216 adding 'napari_cellseg3d/dev_scripts/thread_test.py' 2023-04-11T18:54:17,217 adding 'napari_cellseg3d/dev_scripts/view_brain.py' 2023-04-11T18:54:17,218 adding 'napari_cellseg3d/dev_scripts/view_sample.py' 2023-04-11T18:54:17,220 adding 'napari_cellseg3d/dev_scripts/weight_conversion.py' 2023-04-11T18:54:17,222 adding 'napari_cellseg3d/res/__init__.py' 2023-04-11T18:54:17,281 adding 'napari_cellseg3d/res/logo_alpha.png' 2023-04-11T18:54:17,286 adding 'napari_cellseg3d-0.0.2rc6.dist-info/LICENSE' 2023-04-11T18:54:17,288 adding 'napari_cellseg3d-0.0.2rc6.dist-info/METADATA' 2023-04-11T18:54:17,289 adding 'napari_cellseg3d-0.0.2rc6.dist-info/WHEEL' 2023-04-11T18:54:17,290 adding 'napari_cellseg3d-0.0.2rc6.dist-info/entry_points.txt' 2023-04-11T18:54:17,291 adding 'napari_cellseg3d-0.0.2rc6.dist-info/top_level.txt' 2023-04-11T18:54:17,293 adding 'napari_cellseg3d-0.0.2rc6.dist-info/RECORD' 2023-04-11T18:54:17,303 removing build/bdist.linux-armv7l/wheel 2023-04-11T18:54:17,426 Building wheel for napari-cellseg3d (pyproject.toml): finished with status 'done' 2023-04-11T18:54:17,449 Created wheel for napari-cellseg3d: filename=napari_cellseg3d-0.0.2rc6-py3-none-any.whl size=605865 sha256=0c24e73d626d9705494b2e929d8d3e52df81b9d5ccac15406cd6d02277062979 2023-04-11T18:54:17,450 Stored in directory: /tmp/pip-ephem-wheel-cache-10963y8j/wheels/a9/83/32/9a316b251e45bbf13f9f9cb82b1bda6907b876c34c966cfb63 2023-04-11T18:54:17,465 Successfully built napari-cellseg3d 2023-04-11T18:54:17,491 Removed build tracker: '/tmp/pip-build-tracker-ob5hzbyb'