2024-10-09T18:23:05,111 Created temporary directory: /tmp/pip-build-tracker-7mur0xe_ 2024-10-09T18:23:05,112 Initialized build tracking at /tmp/pip-build-tracker-7mur0xe_ 2024-10-09T18:23:05,113 Created build tracker: /tmp/pip-build-tracker-7mur0xe_ 2024-10-09T18:23:05,113 Entered build tracker: /tmp/pip-build-tracker-7mur0xe_ 2024-10-09T18:23:05,114 Created temporary directory: /tmp/pip-wheel-csal_s22 2024-10-09T18:23:05,118 Created temporary directory: /tmp/pip-ephem-wheel-cache-fg1gg_f0 2024-10-09T18:23:05,161 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-10-09T18:23:05,163 2 location(s) to search for versions of yeastvision: 2024-10-09T18:23:05,163 * https://pypi.org/simple/yeastvision/ 2024-10-09T18:23:05,163 * https://www.piwheels.org/simple/yeastvision/ 2024-10-09T18:23:05,164 Fetching project page and analyzing links: https://pypi.org/simple/yeastvision/ 2024-10-09T18:23:05,165 Getting page https://pypi.org/simple/yeastvision/ 2024-10-09T18:23:05,167 Found index url https://pypi.org/simple/ 2024-10-09T18:23:05,311 Fetched page https://pypi.org/simple/yeastvision/ as application/vnd.pypi.simple.v1+json 2024-10-09T18:23:05,321 Found link https://files.pythonhosted.org/packages/57/fb/3f0380699167021c57d3f08f387933fdf31a5e2922a848d753a39c3e9933/yeastvision-0.1.0.tar.gz (from https://pypi.org/simple/yeastvision/), version: 0.1.0 2024-10-09T18:23:05,322 Found link https://files.pythonhosted.org/packages/36/23/51ac3e708b7382b04b7d4add7be445fe3f793c34e3470b7cfb2ac2db9d3f/yeastvision-0.1.1.tar.gz (from https://pypi.org/simple/yeastvision/), version: 0.1.1 2024-10-09T18:23:05,323 Found link https://files.pythonhosted.org/packages/bc/56/f550202c9fc393d433781be22a0cb859ebd1490eac03b783b697df6e0961/yeastvision-0.1.3.tar.gz (from https://pypi.org/simple/yeastvision/), version: 0.1.3 2024-10-09T18:23:05,323 Found link https://files.pythonhosted.org/packages/bb/09/cc986488f0766309d6875010dff625708dccd4a8bd6648b459d54db7ba92/yeastvision-0.1.4.tar.gz (from https://pypi.org/simple/yeastvision/), version: 0.1.4 2024-10-09T18:23:05,324 Found link https://files.pythonhosted.org/packages/76/46/93e34eb58d789fddbdbb6a2bea2b721c232d10958a951e029891a8c578d9/yeastvision-0.1.5.tar.gz (from https://pypi.org/simple/yeastvision/), version: 0.1.5 2024-10-09T18:23:05,325 Found link https://files.pythonhosted.org/packages/56/c5/e3deb66d5c38c90beaa8ea8feae7871a0699d8dd3c5005999a395adad234/yeastvision-0.1.6.tar.gz (from https://pypi.org/simple/yeastvision/), version: 0.1.6 2024-10-09T18:23:05,326 Found link https://files.pythonhosted.org/packages/02/54/03ef7feb5a069c9ec29c9cc8bd7d30900248c1f02a425ca240a5698b718e/yeastvision-0.1.7.tar.gz (from https://pypi.org/simple/yeastvision/), version: 0.1.7 2024-10-09T18:23:05,327 Found link 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https://files.pythonhosted.org/packages/5f/6c/fd8a241605a51988f3cfa835c07805092e5b48cd185b5e5e2b6ee7dcb62c/yeastvision-0.1.61.tar.gz (from https://pypi.org/simple/yeastvision/), version: 0.1.61 2024-10-09T18:23:05,355 Found link https://files.pythonhosted.org/packages/bd/c0/5b0facb24ea41fd753a21a1949e1db234066a2b97ba46c8a7e904ce14ebc/yeastvision-0.1.62.tar.gz (from https://pypi.org/simple/yeastvision/), version: 0.1.62 2024-10-09T18:23:05,355 Found link https://files.pythonhosted.org/packages/17/d8/b37798b096a7f8043b55a95abae4b8138416456d2d34e935a38443c8d8d8/yeastvision-0.1.63.tar.gz (from https://pypi.org/simple/yeastvision/), version: 0.1.63 2024-10-09T18:23:05,356 Found link https://files.pythonhosted.org/packages/a1/b7/17819e36fe4ddae8b8bc5b0d01a46e9fb6c04413a4bb7f9328806079d82a/yeastvision-0.1.64.tar.gz (from https://pypi.org/simple/yeastvision/), version: 0.1.64 2024-10-09T18:23:05,357 Found link 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(from https://www.piwheels.org/simple/yeastvision/) 2024-10-09T18:23:05,539 Skipping link: No binaries permitted for yeastvision: https://www.piwheels.org/simple/yeastvision/yeastvision-0.1.54-py3-none-any.whl#sha256=e669abd0b152726a97f940fdd13ad579198327161997ede9214595a28fabb3fc (from https://www.piwheels.org/simple/yeastvision/) 2024-10-09T18:23:05,539 Skipping link: No binaries permitted for yeastvision: https://www.piwheels.org/simple/yeastvision/yeastvision-0.1.53-py3-none-any.whl#sha256=7d6f93e21c3e723d5628939c4a168bf5f85e9ce17216835c60dc4550483eb38b (from https://www.piwheels.org/simple/yeastvision/) 2024-10-09T18:23:05,540 Skipping link: No binaries permitted for yeastvision: https://www.piwheels.org/simple/yeastvision/yeastvision-0.1.52-py3-none-any.whl#sha256=8114cab8745d8c3c35466c4482220ffe0415df0d50fb1bfdf80757cf310d2530 (from https://www.piwheels.org/simple/yeastvision/) 2024-10-09T18:23:05,540 Skipping link: No binaries permitted for yeastvision: 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2024-10-09T18:23:06,060 Added yeastvision==0.1.62 from https://files.pythonhosted.org/packages/bd/c0/5b0facb24ea41fd753a21a1949e1db234066a2b97ba46c8a7e904ce14ebc/yeastvision-0.1.62.tar.gz to build tracker '/tmp/pip-build-tracker-7mur0xe_' 2024-10-09T18:23:06,061 Running setup.py (path:/tmp/pip-wheel-csal_s22/yeastvision_033d061177c24212b319d11912d9cf80/setup.py) egg_info for package yeastvision 2024-10-09T18:23:06,062 Created temporary directory: /tmp/pip-pip-egg-info-cvn2_t3l 2024-10-09T18:23:06,063 Preparing metadata (setup.py): started 2024-10-09T18:23:06,064 Running command python setup.py egg_info 2024-10-09T18:23:06,550 # Yeastvision 2024-10-09T18:23:06,551 2024-10-09T18:23:06,552 ### A GUI-based framework for deep-learning enabled segmentation, tracking, time-series analysis of the full Saccharomyces cerevisiae lifecycle 2024-10-09T18:23:06,554 #### Read the paper [Deep learning-driven imaging of cell division and cell growth across an entire eukaryotic life cycle](https://www.biorxiv.org/content/10.1101/2024.04.25.591211v1) 2024-10-09T18:23:06,555 ##### Developed at the [Miranda Laboratory](https://cals.ncsu.edu/plant-and-microbial-biology/people/oargell/) at NCSU 2024-10-09T18:23:06,556 [![PyPI version](https://badge.fury.io/py/yeastvision.svg)](https://badge.fury.io/py/yeastvision) 2024-10-09T18:23:06,556 [![Downloads](https://pepy.tech/badge/yeastvision)](https://pepy.tech/project/yeastvision) 2024-10-09T18:23:06,558 [![Downloads](https://pepy.tech/badge/yeastvision/month)](https://pepy.tech/project/yeastvision) 2024-10-09T18:23:06,558 [![Python version](https://img.shields.io/pypi/pyversions/yeastvision)](https://pypistats.org/packages/yeastvision) 2024-10-09T18:23:06,559 [![License: GPL v3](https://img.shields.io/github/license/berkyalcinkaya/yeastvision)](https://github.com/berkyalcinkaya/yeastvision/blob/main/LICENSE) 2024-10-09T18:23:06,560 [![Contributors](https://img.shields.io/github/contributors-anon/berkyalcinkaya/yeastvision)](https://github.com/berkyalcinkaya/yeastvision/graphs/contributors) 2024-10-09T18:23:06,560 [![repo size](https://img.shields.io/github/repo-size/berkyalcinkaya/yeastvision)](https://github.com/berkyalcinkaya/yeastvision/) 2024-10-09T18:23:06,560 [![GitHub stars](https://img.shields.io/github/stars/berkyalcinkaya/yeastvision?style=social)](https://github.com/berkyalcinkaya/yeastvision/) 2024-10-09T18:23:06,561 [![GitHub forks](https://img.shields.io/github/forks/berkyalcinkaya/yeastvision?style=social)](https://github.com/berkyalcinkaya/yeastvision/) 2024-10-09T18:23:06,562 ## The interface: segment, track, and analyze 2024-10-09T18:23:06,563 2024-10-09T18:23:06,564 ## Key Features 2024-10-09T18:23:06,565 - *FIEST Tracking Algorithm*: Enhance time-series resolution up to 16x using a generative video interpolation model[[1]](#1), used to enhance cell-tracking and lineage reconstruction 2024-10-09T18:23:06,566 - Load, analyze, and segment multiple experiments containing numerous phase/flourescent channels 2024-10-09T18:23:06,566 - Segment cytoplasm, vacuoles, buds, mating, and sporulating yeast cells 2024-10-09T18:23:06,567 - Extract and plot time-series data in the GUI 2024-10-09T18:23:06,567


2024-10-09T18:23:06,567 # Installation 2024-10-09T18:23:06,569 ## Local installation (< 2 minutes) 2024-10-09T18:23:06,570 ### System requirements 2024-10-09T18:23:06,571 This package supports Linux, Windows and Mac OS (versions later than Yosemite). GPU support is available for NVIDIA GPU's. A GPU is recommended, but not required, to run `yeastvision` 2024-10-09T18:23:06,572 ### Instructions 2024-10-09T18:23:06,573 `yeastvision` is ready to go for cpu-usage as soon as it downloaded. GPU-usage requires some additional steps after download. To download: 2024-10-09T18:23:06,574 1. Install an [Anaconda](https://www.anaconda.com/products/distribution) distribution of Python. Note you might need to use an anaconda prompt if you did not add anaconda to the path. 2024-10-09T18:23:06,575 2. Open an anaconda prompt/command prompt 2024-10-09T18:23:06,575 3. If you have an older `yeastvision` environment you should remove it with `conda env remove -n yeastvision` before creating a new one. 2024-10-09T18:23:06,576 4. Create a new environment with `conda create --name yeastvision python=3.10.0`. 2024-10-09T18:23:06,577 5. Activate this new environment by running `conda activate yeastvision` 2024-10-09T18:23:06,577 6. To download our package plus all dependencies, run `python -m pip install yeastvision` on Windows and `python3 -m pip install yeastvision` on Linux, Ubuntu, and Mac OS. 2024-10-09T18:23:06,579 You should upgrade the [yeastvision package](https://pypi.org/project/yeastvision/) periodically as it is still in development. To do so, run the following in the environment: 2024-10-09T18:23:06,580 ~~~sh 2024-10-09T18:23:06,580 python -m pip install yeastvision --upgrade 2024-10-09T18:23:06,581 ~~~ 2024-10-09T18:23:06,582 for Windows or 2024-10-09T18:23:06,582 ~~~sh 2024-10-09T18:23:06,583 python3 -m pip install yeastvision --upgrade 2024-10-09T18:23:06,583 ~~~ 2024-10-09T18:23:06,584 See [Troubleshooting: Common Problems](##troubleshooting:-common-problems) for potential install errors. 2024-10-09T18:23:06,586 ### Using yeastvision with Nvidia GPU: PyTorch Configurations 2024-10-09T18:23:06,587 To use your NVIDIA GPU with python, you will first need to install a [NVIDIA driver](https://www.nvidia.com/Download/index.aspx?lang=en-us) for 2024-10-09T18:23:06,587 your GPU. Once downloaded, ensure that your 2024-10-09T18:23:06,588 GPU is detected by running `nvidia-smi` in the terminal. 2024-10-09T18:23:06,590 `yeastvision` relies on `pytorch` for implementation of the deep-learning models, which we will need to configure for gpu usage. Ensure your yeastvision conda environment is active for the following commands. 2024-10-09T18:23:06,591 First, we need to remove the CPU version of torch and torchvision: 2024-10-09T18:23:06,591 ~~~ 2024-10-09T18:23:06,591 pip uninstall torch; pip uninstall torchvision 2024-10-09T18:23:06,592 ~~~ 2024-10-09T18:23:06,593 Now install `torch` and `torchvision` for CUDA version 11.3. Ensure that your nvidia drivers are up to date for version 11.3 by running `nvidia-smi` and check that a version 11.3 or greater is displayed in the top right corner of the output table. 2024-10-09T18:23:06,593 ~~~ 2024-10-09T18:23:06,594 conda install pytorch==1.12.0 torchvision==0.13.0 cudatoolkit=11.3 -c pytorch 2024-10-09T18:23:06,594 ~~~~ 2024-10-09T18:23:06,595 After install you can check `conda list` for `pytorch`, and its version info should have `cuXX.X`, not `cpu`. 2024-10-09T18:23:06,596 #### Common Install Issues: 2024-10-09T18:23:06,596 1. `ModuleNotFoundError: No module named 'chardet'`\ 2024-10-09T18:23:06,597 2. `lib/python3.10/site-packages/torch/lib/libtorch_cpu.so: undefined symbol: iJIT_NotifyEvent` 2024-10-09T18:23:06,598 These are addressed below in [Troubleshooting: Common Problems](##troubleshooting:-common-problems) 2024-10-09T18:23:06,599 # Running yeastvision 2024-10-09T18:23:06,600 ## Quickstart 2024-10-09T18:23:06,600 Activate the correct conda environment. In the command prompt, run either 2024-10-09T18:23:06,601 - `yeastvision -test` to open the GUI with our sample 10-frame movie. 2024-10-09T18:23:06,601 - `yeastvision` to open a blank GUI window. Drag and drop directory containing 2D-image files into the GUI to begin segmenting, labeling, or processing 2024-10-09T18:23:06,602 Yeastvision accepts directories of image files, loaded through drag-and-drop or the file menu. Each file in the directory should contain only a single 2D image, named with a standard image file extension. 2024-10-09T18:23:06,603 **Note:** As you segment, interpolate, or process images, GUI-generated labels and images are stored in the loaded directory as `.npz` files. Deleting these files results in loss of the data. 2024-10-09T18:23:06,605 **Yeastvision expects directories to contain only files with valid image extensions or `.npz` files created in previous yeastvision sessions.** 2024-10-09T18:23:06,606 **Important:** Ensure that all images in the same channel have the same dimensions. 2024-10-09T18:23:06,607 ## To load directories containing additional image channels and pre-generated masks, name your files properly: 2024-10-09T18:23:06,608 For experiments containing multiple channels and pre-generated labels, our GUI loading capabilities make it easy to: 2024-10-09T18:23:06,608 - Track pre-generated labels (a nucleus label, for example) 2024-10-09T18:23:06,609 - extract and plot fluorescence intensities 2024-10-09T18:23:06,609 - interpolate additional fluorescence channels. 2024-10-09T18:23:06,610 __When additional channels/masks are present in the directory, files should be named accordingly to their channel and mask type__: 2024-10-09T18:23:06,611 1. Each data type in the directory should have a standard id that directly precedes the file extension (ex: *_phase.tif, _channel2.png, _mask1.tif*) 2024-10-09T18:23:06,612 3. Any image that acts as a label should have `_mask` in the id (ex: *_mask_nucleus.tif, _mask_cytoplasm.jpg*). 2024-10-09T18:23:06,612 4. Ensure that each id has the same number of time points: Having 5 phase images but only 4 fluorescence images will raise an error. 2024-10-09T18:23:06,613 Here is an example of a directory with two time points, two channels, and two pre-generated labels, sorted by name: 2024-10-09T18:23:06,615 *im001_channel1.tif, im001_channel2.tif,
2024-10-09T18:23:06,615 im001_mask1.tif, im001_mask2.tif,
2024-10-09T18:23:06,616 im002_channel1.tif, im002_channel2.tif,
2024-10-09T18:23:06,616 im002_mask1.tif, im002_mask2.tif*
2024-10-09T18:23:06,619 # GUI Features 2024-10-09T18:23:06,620 ## Segmentation 2024-10-09T18:23:06,620 Yeastvision contains models to accurately segment yeast in all stages of their lifecycle. Simply choose one of the following models from the model dropdown and click run. 2024-10-09T18:23:06,621 **Pixel flow-based models** 2024-10-09T18:23:06,622 | Model | Segments | 2024-10-09T18:23:06,622 | ------ | -------- | 2024-10-09T18:23:06,623 | proSeg | proliferating cells (general cytoplasm segmentation) | 2024-10-09T18:23:06,623 | spoSeg | sporulating cells | 2024-10-09T18:23:06,624 | matSeg | mating cells | 2024-10-09T18:23:06,624 | budSeg | bud-necks | 2024-10-09T18:23:06,625 2024-10-09T18:23:06,625 Yeastvision contains models and tracking algorithms to analyze all stages of the yeast lifecycle 2024-10-09T18:23:06,626 ## Model Retraining 2024-10-09T18:23:06,627 1. Ensure that training data is loaded into the current experiment 2024-10-09T18:23:06,627 2. Select the model to be retrained from the mainscreen model dropdown 2024-10-09T18:23:06,628 3. Click Menu->Models->Retrain 2024-10-09T18:23:06,628 4. Ensure training data is correct and choose model suffix (default is date-time) 2024-10-09T18:23:06,629 5. Select hyperparameters (default should work for most use cases) 2024-10-09T18:23:06,629 6. Train the model, using terminal to gauge progress. 2024-10-09T18:23:06,630 7. The custom model will auto-run on the next available image in the training set, if there is not a mask already on this image. 2024-10-09T18:23:06,630 8. If you are happy with the new model, go to Menu->Models->Load Custom Models, and the model will be added to the model dropdown. Otherwise, retrain with new data 2024-10-09T18:23:06,632 #### Retraining Tips 2024-10-09T18:23:06,632 - Even though it possible to retrain using only CPU, training takes very long without a GPU 2024-10-09T18:23:06,633 - When you are initially producing a training set, leave some blank masks towards the end of the movie so that the training procedure has room to auto-run 2024-10-09T18:23:06,633 - The path to the new weights will be printed on the terminal. 2024-10-09T18:23:06,634 - Ensure that the fullname of the retrained model is present in the weights filename upon trying to load it via the models menu. This ensures that GUI can associate the weights with the correct model architecture 2024-10-09T18:23:06,635 ## Timeseries analysis: interpolation, tracking, and plotting 2024-10-09T18:23:06,636 1) Optional: Interpolate images to increase resolution, generating intermediate frames that improve tracking accuracy 2024-10-09T18:23:06,636 2) Segment and track the interpolated frame. Tracking automatically generates a cell data table that includes various morphological and image properties of each cell over each frame in the movie. 2024-10-09T18:23:06,637 3) Optional: reconstruct proliferating cell lineages 2024-10-09T18:23:06,638 4) Remove interpolated frames from the mask, so that only frames present in the original movie exist in the final tracked movie 2024-10-09T18:23:06,638 5) Produce some initial plots of the data using the 'show plot window' button. This will allow you to view single cell and population averages over time. 2024-10-09T18:23:06,639 ## Keyboard Shortcuts 2024-10-09T18:23:06,640 | Command | Function | 2024-10-09T18:23:06,641 | ----------- | ----------| 2024-10-09T18:23:06,642 | up/down | scroll through channnels| 2024-10-09T18:23:06,642 | cntrl + up/down| Scroll through labels | 2024-10-09T18:23:06,643 | right/left arrows | scroll through timeseries | 2024-10-09T18:23:06,644 | cntrl + right/left | scroll through timeseries by 3 | 2024-10-09T18:23:06,644 | O | outline Drawing | 2024-10-09T18:23:06,645 | B | brush Drawing | 2024-10-09T18:23:06,645 | E | eraser | 2024-10-09T18:23:06,646 | .| increment brush size | 2024-10-09T18:23:06,646 | , | decrecement brush size 2024-10-09T18:23:06,647 | Delete/Backspace | Delete Selected Cell | 2024-10-09T18:23:06,647 | c | show current label contours | 2024-10-09T18:23:06,648 | f | toggle probability (if present) | 2024-10-09T18:23:06,648 | space bar | toggle mask display | 2024-10-09T18:23:06,648 | p | show plot window | 2024-10-09T18:23:06,649 ## Troubleshooting: Common Problems 2024-10-09T18:23:06,650 | Problem | Solution | 2024-10-09T18:23:06,651 | ----------- | ----------- | 2024-10-09T18:23:06,651 |`lib/python3.10/site-packages/torch/lib/libtorch_cpu.so: undefined symbol: iJIT_NotifyEvent`| Install the latest version of torch and torchvision for your system into your yeastvision Conda env. Instructions [here](https://pytorch.org/get-started/locally/).| 2024-10-09T18:23:06,652 | `ModuleNotFoundError: No module named 'chardet'` | run `pip install chardet` | 2024-10-09T18:23:06,652 | Cannot scroll through images/masks on the display | Click on the display to bring focus back to this widget| 2024-10-09T18:23:06,652 | Loaded images without masks but cannot draw | An existing label must be present to draw: Add a blank label with File -> Add Blank Label | 2024-10-09T18:23:06,653 ## References 2024-10-09T18:23:06,654 [1] 2024-10-09T18:23:06,654 Huang, Z., Zhang, T., Heng, W., Shi, B., & Zhou, S. (2022). Real-time intermediate flow estimation for video frame interpolation. In Proceedings of the European Conference on Computer Vision (ECCV). 2024-10-09T18:23:06,655 Warning: 'classifiers' should be a list, got type 'tuple' 2024-10-09T18:23:07,188 running egg_info 2024-10-09T18:23:07,189 creating /tmp/pip-pip-egg-info-cvn2_t3l/yeastvision.egg-info 2024-10-09T18:23:07,216 writing /tmp/pip-pip-egg-info-cvn2_t3l/yeastvision.egg-info/PKG-INFO 2024-10-09T18:23:07,220 writing dependency_links to /tmp/pip-pip-egg-info-cvn2_t3l/yeastvision.egg-info/dependency_links.txt 2024-10-09T18:23:07,222 writing entry points to /tmp/pip-pip-egg-info-cvn2_t3l/yeastvision.egg-info/entry_points.txt 2024-10-09T18:23:07,224 writing requirements to /tmp/pip-pip-egg-info-cvn2_t3l/yeastvision.egg-info/requires.txt 2024-10-09T18:23:07,225 writing top-level names to /tmp/pip-pip-egg-info-cvn2_t3l/yeastvision.egg-info/top_level.txt 2024-10-09T18:23:07,226 writing manifest file '/tmp/pip-pip-egg-info-cvn2_t3l/yeastvision.egg-info/SOURCES.txt' 2024-10-09T18:23:07,338 reading manifest file '/tmp/pip-pip-egg-info-cvn2_t3l/yeastvision.egg-info/SOURCES.txt' 2024-10-09T18:23:07,340 reading manifest template 'MANIFEST.in' 2024-10-09T18:23:07,342 adding license file 'LICENSE' 2024-10-09T18:23:07,346 writing manifest file '/tmp/pip-pip-egg-info-cvn2_t3l/yeastvision.egg-info/SOURCES.txt' 2024-10-09T18:23:07,457 Preparing metadata (setup.py): finished with status 'done' 2024-10-09T18:23:07,462 Source in /tmp/pip-wheel-csal_s22/yeastvision_033d061177c24212b319d11912d9cf80 has version 0.1.62, which satisfies requirement yeastvision==0.1.62 from https://files.pythonhosted.org/packages/bd/c0/5b0facb24ea41fd753a21a1949e1db234066a2b97ba46c8a7e904ce14ebc/yeastvision-0.1.62.tar.gz 2024-10-09T18:23:07,463 Removed yeastvision==0.1.62 from https://files.pythonhosted.org/packages/bd/c0/5b0facb24ea41fd753a21a1949e1db234066a2b97ba46c8a7e904ce14ebc/yeastvision-0.1.62.tar.gz from build tracker '/tmp/pip-build-tracker-7mur0xe_' 2024-10-09T18:23:07,472 Created temporary directory: /tmp/pip-unpack-k9_y30l7 2024-10-09T18:23:07,473 Created temporary directory: /tmp/pip-unpack-l4blnl_6 2024-10-09T18:23:07,474 Building wheels for collected packages: yeastvision 2024-10-09T18:23:07,478 Created temporary directory: /tmp/pip-wheel-8seuev1b 2024-10-09T18:23:07,478 Building wheel for yeastvision (setup.py): started 2024-10-09T18:23:07,480 Destination directory: /tmp/pip-wheel-8seuev1b 2024-10-09T18:23:07,480 Running command python setup.py bdist_wheel 2024-10-09T18:23:07,964 # Yeastvision 2024-10-09T18:23:07,965 2024-10-09T18:23:07,966 ### A GUI-based framework for deep-learning enabled segmentation, tracking, time-series analysis of the full Saccharomyces cerevisiae lifecycle 2024-10-09T18:23:07,967 #### Read the paper [Deep learning-driven imaging of cell division and cell growth across an entire eukaryotic life cycle](https://www.biorxiv.org/content/10.1101/2024.04.25.591211v1) 2024-10-09T18:23:07,968 ##### Developed at the [Miranda Laboratory](https://cals.ncsu.edu/plant-and-microbial-biology/people/oargell/) at NCSU 2024-10-09T18:23:07,969 [![PyPI version](https://badge.fury.io/py/yeastvision.svg)](https://badge.fury.io/py/yeastvision) 2024-10-09T18:23:07,969 [![Downloads](https://pepy.tech/badge/yeastvision)](https://pepy.tech/project/yeastvision) 2024-10-09T18:23:07,970 [![Downloads](https://pepy.tech/badge/yeastvision/month)](https://pepy.tech/project/yeastvision) 2024-10-09T18:23:07,970 [![Python version](https://img.shields.io/pypi/pyversions/yeastvision)](https://pypistats.org/packages/yeastvision) 2024-10-09T18:23:07,971 [![License: GPL v3](https://img.shields.io/github/license/berkyalcinkaya/yeastvision)](https://github.com/berkyalcinkaya/yeastvision/blob/main/LICENSE) 2024-10-09T18:23:07,971 [![Contributors](https://img.shields.io/github/contributors-anon/berkyalcinkaya/yeastvision)](https://github.com/berkyalcinkaya/yeastvision/graphs/contributors) 2024-10-09T18:23:07,971 [![repo size](https://img.shields.io/github/repo-size/berkyalcinkaya/yeastvision)](https://github.com/berkyalcinkaya/yeastvision/) 2024-10-09T18:23:07,972 [![GitHub stars](https://img.shields.io/github/stars/berkyalcinkaya/yeastvision?style=social)](https://github.com/berkyalcinkaya/yeastvision/) 2024-10-09T18:23:07,973 [![GitHub forks](https://img.shields.io/github/forks/berkyalcinkaya/yeastvision?style=social)](https://github.com/berkyalcinkaya/yeastvision/) 2024-10-09T18:23:07,974 ## The interface: segment, track, and analyze 2024-10-09T18:23:07,975 2024-10-09T18:23:07,977 ## Key Features 2024-10-09T18:23:07,978 - *FIEST Tracking Algorithm*: Enhance time-series resolution up to 16x using a generative video interpolation model[[1]](#1), used to enhance cell-tracking and lineage reconstruction 2024-10-09T18:23:07,978 - Load, analyze, and segment multiple experiments containing numerous phase/flourescent channels 2024-10-09T18:23:07,979 - Segment cytoplasm, vacuoles, buds, mating, and sporulating yeast cells 2024-10-09T18:23:07,980 - Extract and plot time-series data in the GUI 2024-10-09T18:23:07,980


2024-10-09T18:23:07,981 # Installation 2024-10-09T18:23:07,982 ## Local installation (< 2 minutes) 2024-10-09T18:23:07,983 ### System requirements 2024-10-09T18:23:07,984 This package supports Linux, Windows and Mac OS (versions later than Yosemite). GPU support is available for NVIDIA GPU's. A GPU is recommended, but not required, to run `yeastvision` 2024-10-09T18:23:07,985 ### Instructions 2024-10-09T18:23:07,986 `yeastvision` is ready to go for cpu-usage as soon as it downloaded. GPU-usage requires some additional steps after download. To download: 2024-10-09T18:23:07,987 1. Install an [Anaconda](https://www.anaconda.com/products/distribution) distribution of Python. Note you might need to use an anaconda prompt if you did not add anaconda to the path. 2024-10-09T18:23:07,988 2. Open an anaconda prompt/command prompt 2024-10-09T18:23:07,989 3. If you have an older `yeastvision` environment you should remove it with `conda env remove -n yeastvision` before creating a new one. 2024-10-09T18:23:07,989 4. Create a new environment with `conda create --name yeastvision python=3.10.0`. 2024-10-09T18:23:07,990 5. Activate this new environment by running `conda activate yeastvision` 2024-10-09T18:23:07,990 6. To download our package plus all dependencies, run `python -m pip install yeastvision` on Windows and `python3 -m pip install yeastvision` on Linux, Ubuntu, and Mac OS. 2024-10-09T18:23:07,992 You should upgrade the [yeastvision package](https://pypi.org/project/yeastvision/) periodically as it is still in development. To do so, run the following in the environment: 2024-10-09T18:23:07,992 ~~~sh 2024-10-09T18:23:07,993 python -m pip install yeastvision --upgrade 2024-10-09T18:23:07,994 ~~~ 2024-10-09T18:23:07,994 for Windows or 2024-10-09T18:23:07,994 ~~~sh 2024-10-09T18:23:07,995 python3 -m pip install yeastvision --upgrade 2024-10-09T18:23:07,995 ~~~ 2024-10-09T18:23:07,996 See [Troubleshooting: Common Problems](##troubleshooting:-common-problems) for potential install errors. 2024-10-09T18:23:07,997 ### Using yeastvision with Nvidia GPU: PyTorch Configurations 2024-10-09T18:23:07,998 To use your NVIDIA GPU with python, you will first need to install a [NVIDIA driver](https://www.nvidia.com/Download/index.aspx?lang=en-us) for 2024-10-09T18:23:07,999 your GPU. Once downloaded, ensure that your 2024-10-09T18:23:07,999 GPU is detected by running `nvidia-smi` in the terminal. 2024-10-09T18:23:08,000 `yeastvision` relies on `pytorch` for implementation of the deep-learning models, which we will need to configure for gpu usage. Ensure your yeastvision conda environment is active for the following commands. 2024-10-09T18:23:08,001 First, we need to remove the CPU version of torch and torchvision: 2024-10-09T18:23:08,002 ~~~ 2024-10-09T18:23:08,002 pip uninstall torch; pip uninstall torchvision 2024-10-09T18:23:08,003 ~~~ 2024-10-09T18:23:08,004 Now install `torch` and `torchvision` for CUDA version 11.3. Ensure that your nvidia drivers are up to date for version 11.3 by running `nvidia-smi` and check that a version 11.3 or greater is displayed in the top right corner of the output table. 2024-10-09T18:23:08,004 ~~~ 2024-10-09T18:23:08,005 conda install pytorch==1.12.0 torchvision==0.13.0 cudatoolkit=11.3 -c pytorch 2024-10-09T18:23:08,006 ~~~~ 2024-10-09T18:23:08,007 After install you can check `conda list` for `pytorch`, and its version info should have `cuXX.X`, not `cpu`. 2024-10-09T18:23:08,008 #### Common Install Issues: 2024-10-09T18:23:08,008 1. `ModuleNotFoundError: No module named 'chardet'`\ 2024-10-09T18:23:08,009 2. `lib/python3.10/site-packages/torch/lib/libtorch_cpu.so: undefined symbol: iJIT_NotifyEvent` 2024-10-09T18:23:08,010 These are addressed below in [Troubleshooting: Common Problems](##troubleshooting:-common-problems) 2024-10-09T18:23:08,011 # Running yeastvision 2024-10-09T18:23:08,013 ## Quickstart 2024-10-09T18:23:08,013 Activate the correct conda environment. In the command prompt, run either 2024-10-09T18:23:08,014 - `yeastvision -test` to open the GUI with our sample 10-frame movie. 2024-10-09T18:23:08,014 - `yeastvision` to open a blank GUI window. Drag and drop directory containing 2D-image files into the GUI to begin segmenting, labeling, or processing 2024-10-09T18:23:08,015 Yeastvision accepts directories of image files, loaded through drag-and-drop or the file menu. Each file in the directory should contain only a single 2D image, named with a standard image file extension. 2024-10-09T18:23:08,016 **Note:** As you segment, interpolate, or process images, GUI-generated labels and images are stored in the loaded directory as `.npz` files. Deleting these files results in loss of the data. 2024-10-09T18:23:08,018 **Yeastvision expects directories to contain only files with valid image extensions or `.npz` files created in previous yeastvision sessions.** 2024-10-09T18:23:08,019 **Important:** Ensure that all images in the same channel have the same dimensions. 2024-10-09T18:23:08,020 ## To load directories containing additional image channels and pre-generated masks, name your files properly: 2024-10-09T18:23:08,021 For experiments containing multiple channels and pre-generated labels, our GUI loading capabilities make it easy to: 2024-10-09T18:23:08,022 - Track pre-generated labels (a nucleus label, for example) 2024-10-09T18:23:08,022 - extract and plot fluorescence intensities 2024-10-09T18:23:08,022 - interpolate additional fluorescence channels. 2024-10-09T18:23:08,023 __When additional channels/masks are present in the directory, files should be named accordingly to their channel and mask type__: 2024-10-09T18:23:08,024 1. Each data type in the directory should have a standard id that directly precedes the file extension (ex: *_phase.tif, _channel2.png, _mask1.tif*) 2024-10-09T18:23:08,024 3. Any image that acts as a label should have `_mask` in the id (ex: *_mask_nucleus.tif, _mask_cytoplasm.jpg*). 2024-10-09T18:23:08,025 4. Ensure that each id has the same number of time points: Having 5 phase images but only 4 fluorescence images will raise an error. 2024-10-09T18:23:08,025 Here is an example of a directory with two time points, two channels, and two pre-generated labels, sorted by name: 2024-10-09T18:23:08,026 *im001_channel1.tif, im001_channel2.tif,
2024-10-09T18:23:08,027 im001_mask1.tif, im001_mask2.tif,
2024-10-09T18:23:08,027 im002_channel1.tif, im002_channel2.tif,
2024-10-09T18:23:08,028 im002_mask1.tif, im002_mask2.tif*
2024-10-09T18:23:08,030 # GUI Features 2024-10-09T18:23:08,031 ## Segmentation 2024-10-09T18:23:08,032 Yeastvision contains models to accurately segment yeast in all stages of their lifecycle. Simply choose one of the following models from the model dropdown and click run. 2024-10-09T18:23:08,033 **Pixel flow-based models** 2024-10-09T18:23:08,034 | Model | Segments | 2024-10-09T18:23:08,034 | ------ | -------- | 2024-10-09T18:23:08,035 | proSeg | proliferating cells (general cytoplasm segmentation) | 2024-10-09T18:23:08,035 | spoSeg | sporulating cells | 2024-10-09T18:23:08,036 | matSeg | mating cells | 2024-10-09T18:23:08,036 | budSeg | bud-necks | 2024-10-09T18:23:08,038 2024-10-09T18:23:08,038 Yeastvision contains models and tracking algorithms to analyze all stages of the yeast lifecycle 2024-10-09T18:23:08,039 ## Model Retraining 2024-10-09T18:23:08,040 1. Ensure that training data is loaded into the current experiment 2024-10-09T18:23:08,040 2. Select the model to be retrained from the mainscreen model dropdown 2024-10-09T18:23:08,041 3. Click Menu->Models->Retrain 2024-10-09T18:23:08,042 4. Ensure training data is correct and choose model suffix (default is date-time) 2024-10-09T18:23:08,042 5. Select hyperparameters (default should work for most use cases) 2024-10-09T18:23:08,043 6. Train the model, using terminal to gauge progress. 2024-10-09T18:23:08,043 7. The custom model will auto-run on the next available image in the training set, if there is not a mask already on this image. 2024-10-09T18:23:08,044 8. If you are happy with the new model, go to Menu->Models->Load Custom Models, and the model will be added to the model dropdown. Otherwise, retrain with new data 2024-10-09T18:23:08,045 #### Retraining Tips 2024-10-09T18:23:08,046 - Even though it possible to retrain using only CPU, training takes very long without a GPU 2024-10-09T18:23:08,046 - When you are initially producing a training set, leave some blank masks towards the end of the movie so that the training procedure has room to auto-run 2024-10-09T18:23:08,047 - The path to the new weights will be printed on the terminal. 2024-10-09T18:23:08,047 - Ensure that the fullname of the retrained model is present in the weights filename upon trying to load it via the models menu. This ensures that GUI can associate the weights with the correct model architecture 2024-10-09T18:23:08,049 ## Timeseries analysis: interpolation, tracking, and plotting 2024-10-09T18:23:08,050 1) Optional: Interpolate images to increase resolution, generating intermediate frames that improve tracking accuracy 2024-10-09T18:23:08,050 2) Segment and track the interpolated frame. Tracking automatically generates a cell data table that includes various morphological and image properties of each cell over each frame in the movie. 2024-10-09T18:23:08,050 3) Optional: reconstruct proliferating cell lineages 2024-10-09T18:23:08,051 4) Remove interpolated frames from the mask, so that only frames present in the original movie exist in the final tracked movie 2024-10-09T18:23:08,051 5) Produce some initial plots of the data using the 'show plot window' button. This will allow you to view single cell and population averages over time. 2024-10-09T18:23:08,052 ## Keyboard Shortcuts 2024-10-09T18:23:08,053 | Command | Function | 2024-10-09T18:23:08,054 | ----------- | ----------| 2024-10-09T18:23:08,054 | up/down | scroll through channnels| 2024-10-09T18:23:08,055 | cntrl + up/down| Scroll through labels | 2024-10-09T18:23:08,055 | right/left arrows | scroll through timeseries | 2024-10-09T18:23:08,056 | cntrl + right/left | scroll through timeseries by 3 | 2024-10-09T18:23:08,056 | O | outline Drawing | 2024-10-09T18:23:08,056 | B | brush Drawing | 2024-10-09T18:23:08,057 | E | eraser | 2024-10-09T18:23:08,057 | .| increment brush size | 2024-10-09T18:23:08,058 | , | decrecement brush size 2024-10-09T18:23:08,058 | Delete/Backspace | Delete Selected Cell | 2024-10-09T18:23:08,059 | c | show current label contours | 2024-10-09T18:23:08,059 | f | toggle probability (if present) | 2024-10-09T18:23:08,060 | space bar | toggle mask display | 2024-10-09T18:23:08,061 | p | show plot window | 2024-10-09T18:23:08,062 ## Troubleshooting: Common Problems 2024-10-09T18:23:08,063 | Problem | Solution | 2024-10-09T18:23:08,064 | ----------- | ----------- | 2024-10-09T18:23:08,064 |`lib/python3.10/site-packages/torch/lib/libtorch_cpu.so: undefined symbol: iJIT_NotifyEvent`| Install the latest version of torch and torchvision for your system into your yeastvision Conda env. Instructions [here](https://pytorch.org/get-started/locally/).| 2024-10-09T18:23:08,065 | `ModuleNotFoundError: No module named 'chardet'` | run `pip install chardet` | 2024-10-09T18:23:08,065 | Cannot scroll through images/masks on the display | Click on the display to bring focus back to this widget| 2024-10-09T18:23:08,066 | Loaded images without masks but cannot draw | An existing label must be present to draw: Add a blank label with File -> Add Blank Label | 2024-10-09T18:23:08,067 ## References 2024-10-09T18:23:08,068 [1] 2024-10-09T18:23:08,068 Huang, Z., Zhang, T., Heng, W., Shi, B., & Zhou, S. (2022). Real-time intermediate flow estimation for video frame interpolation. In Proceedings of the European Conference on Computer Vision (ECCV). 2024-10-09T18:23:08,069 Warning: 'classifiers' should be a list, got type 'tuple' 2024-10-09T18:23:08,554 running bdist_wheel 2024-10-09T18:23:08,685 running build 2024-10-09T18:23:08,686 running build_py 2024-10-09T18:23:08,719 creating build/lib/yeastvision 2024-10-09T18:23:08,721 copying yeastvision/__main__.py -> build/lib/yeastvision 2024-10-09T18:23:08,726 copying yeastvision/install.py -> build/lib/yeastvision 2024-10-09T18:23:08,728 copying yeastvision/__init__.py -> build/lib/yeastvision 2024-10-09T18:23:08,729 copying yeastvision/utils.py -> build/lib/yeastvision 2024-10-09T18:23:08,732 creating build/lib/yeastvision/data 2024-10-09T18:23:08,734 copying yeastvision/data/ims.py -> build/lib/yeastvision/data 2024-10-09T18:23:08,737 copying yeastvision/data/__init__.py -> build/lib/yeastvision/data 2024-10-09T18:23:08,739 copying yeastvision/data/utils.py -> build/lib/yeastvision/data 2024-10-09T18:23:08,742 creating build/lib/yeastvision/plot 2024-10-09T18:23:08,743 copying yeastvision/plot/types.py -> build/lib/yeastvision/plot 2024-10-09T18:23:08,746 copying yeastvision/plot/cell_table.py -> build/lib/yeastvision/plot 2024-10-09T18:23:08,748 copying yeastvision/plot/plot.py -> build/lib/yeastvision/plot 2024-10-09T18:23:08,751 copying yeastvision/plot/__init__.py -> build/lib/yeastvision/plot 2024-10-09T18:23:08,753 copying yeastvision/plot/utils.py -> build/lib/yeastvision/plot 2024-10-09T18:23:08,755 creating build/lib/yeastvision/track 2024-10-09T18:23:08,757 copying yeastvision/track/mat.py -> build/lib/yeastvision/track 2024-10-09T18:23:08,760 copying yeastvision/track/data.py -> build/lib/yeastvision/track 2024-10-09T18:23:08,762 copying yeastvision/track/cell.py -> build/lib/yeastvision/track 2024-10-09T18:23:08,765 copying yeastvision/track/hungarian_track.py -> build/lib/yeastvision/track 2024-10-09T18:23:08,768 copying yeastvision/track/__init__.py -> build/lib/yeastvision/track 2024-10-09T18:23:08,770 copying yeastvision/track/lineage.py -> build/lib/yeastvision/track 2024-10-09T18:23:08,772 copying yeastvision/track/track.py -> build/lib/yeastvision/track 2024-10-09T18:23:08,775 copying yeastvision/track/utils.py -> build/lib/yeastvision/track 2024-10-09T18:23:08,777 creating build/lib/yeastvision/track/fiest 2024-10-09T18:23:08,779 copying yeastvision/track/fiest/mating.py -> build/lib/yeastvision/track/fiest 2024-10-09T18:23:08,781 copying yeastvision/track/fiest/correction.py -> build/lib/yeastvision/track/fiest 2024-10-09T18:23:08,784 copying yeastvision/track/fiest/tetrads.py -> build/lib/yeastvision/track/fiest 2024-10-09T18:23:08,786 copying yeastvision/track/fiest/__init__.py -> build/lib/yeastvision/track/fiest 2024-10-09T18:23:08,788 copying yeastvision/track/fiest/track.py -> build/lib/yeastvision/track/fiest 2024-10-09T18:23:08,791 copying yeastvision/track/fiest/utils.py -> build/lib/yeastvision/track/fiest 2024-10-09T18:23:08,794 copying yeastvision/track/fiest/FL.py -> build/lib/yeastvision/track/fiest 2024-10-09T18:23:08,797 copying yeastvision/track/fiest/full_lifecycle_utils.py -> build/lib/yeastvision/track/fiest 2024-10-09T18:23:08,800 creating build/lib/yeastvision/models 2024-10-09T18:23:08,801 copying yeastvision/models/cp.py -> build/lib/yeastvision/models 2024-10-09T18:23:08,804 copying yeastvision/models/__init__.py -> build/lib/yeastvision/models 2024-10-09T18:23:08,806 copying yeastvision/models/utils.py -> build/lib/yeastvision/models 2024-10-09T18:23:08,808 copying yeastvision/models/model.py -> build/lib/yeastvision/models 2024-10-09T18:23:08,811 creating build/lib/yeastvision/ims 2024-10-09T18:23:08,812 copying yeastvision/ims/interpolate.py -> build/lib/yeastvision/ims 2024-10-09T18:23:08,815 copying yeastvision/ims/__init__.py -> build/lib/yeastvision/ims 2024-10-09T18:23:08,817 copying yeastvision/ims/im_funcs.py -> build/lib/yeastvision/ims 2024-10-09T18:23:08,819 creating build/lib/yeastvision/ims/rife_model 2024-10-09T18:23:08,821 copying yeastvision/ims/rife_model/IFNet_m.py -> build/lib/yeastvision/ims/rife_model 2024-10-09T18:23:08,824 copying yeastvision/ims/rife_model/laplacian.py -> build/lib/yeastvision/ims/rife_model 2024-10-09T18:23:08,826 copying yeastvision/ims/rife_model/refine.py -> build/lib/yeastvision/ims/rife_model 2024-10-09T18:23:08,828 copying yeastvision/ims/rife_model/warplayer.py -> build/lib/yeastvision/ims/rife_model 2024-10-09T18:23:08,830 copying yeastvision/ims/rife_model/IFNet_2R.py -> build/lib/yeastvision/ims/rife_model 2024-10-09T18:23:08,832 copying yeastvision/ims/rife_model/__init__.py -> build/lib/yeastvision/ims/rife_model 2024-10-09T18:23:08,834 copying yeastvision/ims/rife_model/IFNet.py -> build/lib/yeastvision/ims/rife_model 2024-10-09T18:23:08,836 copying yeastvision/ims/rife_model/RIFE.py -> build/lib/yeastvision/ims/rife_model 2024-10-09T18:23:08,838 copying yeastvision/ims/rife_model/loss.py -> build/lib/yeastvision/ims/rife_model 2024-10-09T18:23:08,841 copying yeastvision/ims/rife_model/refine_2R.py -> build/lib/yeastvision/ims/rife_model 2024-10-09T18:23:08,844 creating build/lib/yeastvision/docs 2024-10-09T18:23:08,845 copying yeastvision/docs/__init__.py -> build/lib/yeastvision/docs 2024-10-09T18:23:08,847 creating build/lib/yeastvision/docs/figs 2024-10-09T18:23:08,849 copying yeastvision/docs/figs/__init__.py -> build/lib/yeastvision/docs/figs 2024-10-09T18:23:08,851 creating build/lib/yeastvision/ims/rife_model/pytorch_msssim 2024-10-09T18:23:08,852 copying yeastvision/ims/rife_model/pytorch_msssim/__init__.py -> build/lib/yeastvision/ims/rife_model/pytorch_msssim 2024-10-09T18:23:08,856 creating build/lib/yeastvision/parts 2024-10-09T18:23:08,857 copying yeastvision/parts/fiest_wizard.py -> build/lib/yeastvision/parts 2024-10-09T18:23:08,860 copying yeastvision/parts/workers.py -> build/lib/yeastvision/parts 2024-10-09T18:23:08,862 copying yeastvision/parts/canvas.py -> build/lib/yeastvision/parts 2024-10-09T18:23:08,864 copying yeastvision/parts/fiest_full_lifecycle_wizard.py -> build/lib/yeastvision/parts 2024-10-09T18:23:08,866 copying yeastvision/parts/guiparts.py -> build/lib/yeastvision/parts 2024-10-09T18:23:08,869 copying yeastvision/parts/__init__.py -> build/lib/yeastvision/parts 2024-10-09T18:23:08,871 copying yeastvision/parts/utils.py -> build/lib/yeastvision/parts 2024-10-09T18:23:08,873 copying yeastvision/parts/wizard_utils.py -> build/lib/yeastvision/parts 2024-10-09T18:23:08,875 copying yeastvision/parts/menu.py -> build/lib/yeastvision/parts 2024-10-09T18:23:08,878 copying yeastvision/parts/dialogs.py -> build/lib/yeastvision/parts 2024-10-09T18:23:08,881 creating build/lib/yeastvision/flou 2024-10-09T18:23:08,883 copying yeastvision/flou/__init__.py -> build/lib/yeastvision/flou 2024-10-09T18:23:08,885 copying yeastvision/flou/blob_detect.py -> build/lib/yeastvision/flou 2024-10-09T18:23:08,887 copying yeastvision/flou/utils.py -> build/lib/yeastvision/flou 2024-10-09T18:23:08,889 creating build/lib/yeastvision/disk 2024-10-09T18:23:08,891 copying yeastvision/disk/__init__.py -> build/lib/yeastvision/disk 2024-10-09T18:23:08,892 copying yeastvision/disk/io.py -> build/lib/yeastvision/disk 2024-10-09T18:23:08,895 copying yeastvision/disk/reader.py -> build/lib/yeastvision/disk 2024-10-09T18:23:08,898 creating build/lib/yeastvision/models/proSeg 2024-10-09T18:23:08,899 copying yeastvision/models/proSeg/__init__.py -> build/lib/yeastvision/models/proSeg 2024-10-09T18:23:08,901 copying yeastvision/models/proSeg/model.py -> build/lib/yeastvision/models/proSeg 2024-10-09T18:23:08,905 creating build/lib/yeastvision/models/budSeg 2024-10-09T18:23:08,906 copying yeastvision/models/budSeg/__init__.py -> build/lib/yeastvision/models/budSeg 2024-10-09T18:23:08,908 copying yeastvision/models/budSeg/model.py -> build/lib/yeastvision/models/budSeg 2024-10-09T18:23:08,912 creating build/lib/yeastvision/models/matSeg 2024-10-09T18:23:08,914 copying yeastvision/models/matSeg/__init__.py -> build/lib/yeastvision/models/matSeg 2024-10-09T18:23:08,916 copying yeastvision/models/matSeg/model.py -> build/lib/yeastvision/models/matSeg 2024-10-09T18:23:08,918 creating build/lib/yeastvision/models/spoSeg 2024-10-09T18:23:08,920 copying yeastvision/models/spoSeg/__init__.py -> build/lib/yeastvision/models/spoSeg 2024-10-09T18:23:08,922 copying yeastvision/models/spoSeg/model.py -> build/lib/yeastvision/models/spoSeg 2024-10-09T18:23:08,925 creating build/lib/yeastvision/models/flouSeg 2024-10-09T18:23:08,926 copying yeastvision/models/flouSeg/__init__.py -> build/lib/yeastvision/models/flouSeg 2024-10-09T18:23:08,928 copying yeastvision/models/flouSeg/model.py -> build/lib/yeastvision/models/flouSeg 2024-10-09T18:23:08,930 running egg_info 2024-10-09T18:23:08,959 writing yeastvision.egg-info/PKG-INFO 2024-10-09T18:23:08,964 writing dependency_links to yeastvision.egg-info/dependency_links.txt 2024-10-09T18:23:08,966 writing entry points to yeastvision.egg-info/entry_points.txt 2024-10-09T18:23:08,967 writing requirements to yeastvision.egg-info/requires.txt 2024-10-09T18:23:08,969 writing top-level names to yeastvision.egg-info/top_level.txt 2024-10-09T18:23:09,016 reading manifest file 'yeastvision.egg-info/SOURCES.txt' 2024-10-09T18:23:09,025 reading manifest template 'MANIFEST.in' 2024-10-09T18:23:09,026 adding license file 'LICENSE' 2024-10-09T18:23:09,033 writing manifest file 'yeastvision.egg-info/SOURCES.txt' 2024-10-09T18:23:09,044 copying yeastvision/models/model_types.json -> build/lib/yeastvision/models 2024-10-09T18:23:09,080 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-10-09T18:23:09,081 !! 2024-10-09T18:23:09,082 ******************************************************************************** 2024-10-09T18:23:09,083 Please avoid running ``setup.py`` directly. 2024-10-09T18:23:09,083 Instead, use pypa/build, pypa/installer or other 2024-10-09T18:23:09,083 standards-based tools. 2024-10-09T18:23:09,084 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-10-09T18:23:09,085 ******************************************************************************** 2024-10-09T18:23:09,086 !! 2024-10-09T18:23:09,086 self.initialize_options() 2024-10-09T18:23:09,111 installing to build/bdist.linux-armv7l/wheel 2024-10-09T18:23:09,112 running install 2024-10-09T18:23:09,137 running install_lib 2024-10-09T18:23:09,164 creating build/bdist.linux-armv7l/wheel 2024-10-09T18:23:09,167 creating build/bdist.linux-armv7l/wheel/yeastvision 2024-10-09T18:23:09,169 creating build/bdist.linux-armv7l/wheel/yeastvision/track 2024-10-09T18:23:09,171 copying build/lib/yeastvision/track/mat.py -> build/bdist.linux-armv7l/wheel/./yeastvision/track 2024-10-09T18:23:09,174 creating build/bdist.linux-armv7l/wheel/yeastvision/track/fiest 2024-10-09T18:23:09,176 copying build/lib/yeastvision/track/fiest/mating.py -> build/bdist.linux-armv7l/wheel/./yeastvision/track/fiest 2024-10-09T18:23:09,178 copying build/lib/yeastvision/track/fiest/correction.py -> build/bdist.linux-armv7l/wheel/./yeastvision/track/fiest 2024-10-09T18:23:09,182 copying build/lib/yeastvision/track/fiest/tetrads.py -> build/bdist.linux-armv7l/wheel/./yeastvision/track/fiest 2024-10-09T18:23:09,184 copying build/lib/yeastvision/track/fiest/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision/track/fiest 2024-10-09T18:23:09,186 copying build/lib/yeastvision/track/fiest/track.py -> build/bdist.linux-armv7l/wheel/./yeastvision/track/fiest 2024-10-09T18:23:09,189 copying build/lib/yeastvision/track/fiest/utils.py -> build/bdist.linux-armv7l/wheel/./yeastvision/track/fiest 2024-10-09T18:23:09,191 copying build/lib/yeastvision/track/fiest/FL.py -> build/bdist.linux-armv7l/wheel/./yeastvision/track/fiest 2024-10-09T18:23:09,194 copying build/lib/yeastvision/track/fiest/full_lifecycle_utils.py -> build/bdist.linux-armv7l/wheel/./yeastvision/track/fiest 2024-10-09T18:23:09,198 copying build/lib/yeastvision/track/data.py -> build/bdist.linux-armv7l/wheel/./yeastvision/track 2024-10-09T18:23:09,200 copying build/lib/yeastvision/track/cell.py -> build/bdist.linux-armv7l/wheel/./yeastvision/track 2024-10-09T18:23:09,203 copying build/lib/yeastvision/track/hungarian_track.py -> build/bdist.linux-armv7l/wheel/./yeastvision/track 2024-10-09T18:23:09,206 copying build/lib/yeastvision/track/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision/track 2024-10-09T18:23:09,207 copying build/lib/yeastvision/track/lineage.py -> build/bdist.linux-armv7l/wheel/./yeastvision/track 2024-10-09T18:23:09,210 copying build/lib/yeastvision/track/track.py -> build/bdist.linux-armv7l/wheel/./yeastvision/track 2024-10-09T18:23:09,213 copying build/lib/yeastvision/track/utils.py -> build/bdist.linux-armv7l/wheel/./yeastvision/track 2024-10-09T18:23:09,216 creating build/bdist.linux-armv7l/wheel/yeastvision/models 2024-10-09T18:23:09,218 creating build/bdist.linux-armv7l/wheel/yeastvision/models/flouSeg 2024-10-09T18:23:09,220 copying build/lib/yeastvision/models/flouSeg/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision/models/flouSeg 2024-10-09T18:23:09,222 copying build/lib/yeastvision/models/flouSeg/model.py -> build/bdist.linux-armv7l/wheel/./yeastvision/models/flouSeg 2024-10-09T18:23:09,224 copying build/lib/yeastvision/models/cp.py -> build/bdist.linux-armv7l/wheel/./yeastvision/models 2024-10-09T18:23:09,227 creating build/bdist.linux-armv7l/wheel/yeastvision/models/proSeg 2024-10-09T18:23:09,228 copying build/lib/yeastvision/models/proSeg/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision/models/proSeg 2024-10-09T18:23:09,231 copying build/lib/yeastvision/models/proSeg/model.py -> build/bdist.linux-armv7l/wheel/./yeastvision/models/proSeg 2024-10-09T18:23:09,233 copying build/lib/yeastvision/models/model_types.json -> build/bdist.linux-armv7l/wheel/./yeastvision/models 2024-10-09T18:23:09,236 creating build/bdist.linux-armv7l/wheel/yeastvision/models/matSeg 2024-10-09T18:23:09,237 copying build/lib/yeastvision/models/matSeg/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision/models/matSeg 2024-10-09T18:23:09,239 copying build/lib/yeastvision/models/matSeg/model.py -> build/bdist.linux-armv7l/wheel/./yeastvision/models/matSeg 2024-10-09T18:23:09,241 copying build/lib/yeastvision/models/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision/models 2024-10-09T18:23:09,244 creating build/bdist.linux-armv7l/wheel/yeastvision/models/budSeg 2024-10-09T18:23:09,245 copying build/lib/yeastvision/models/budSeg/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision/models/budSeg 2024-10-09T18:23:09,247 copying build/lib/yeastvision/models/budSeg/model.py -> build/bdist.linux-armv7l/wheel/./yeastvision/models/budSeg 2024-10-09T18:23:09,250 creating build/bdist.linux-armv7l/wheel/yeastvision/models/spoSeg 2024-10-09T18:23:09,251 copying build/lib/yeastvision/models/spoSeg/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision/models/spoSeg 2024-10-09T18:23:09,253 copying build/lib/yeastvision/models/spoSeg/model.py -> build/bdist.linux-armv7l/wheel/./yeastvision/models/spoSeg 2024-10-09T18:23:09,255 copying build/lib/yeastvision/models/utils.py -> build/bdist.linux-armv7l/wheel/./yeastvision/models 2024-10-09T18:23:09,258 copying build/lib/yeastvision/models/model.py -> build/bdist.linux-armv7l/wheel/./yeastvision/models 2024-10-09T18:23:09,260 copying build/lib/yeastvision/__main__.py -> build/bdist.linux-armv7l/wheel/./yeastvision 2024-10-09T18:23:09,265 creating build/bdist.linux-armv7l/wheel/yeastvision/disk 2024-10-09T18:23:09,267 copying build/lib/yeastvision/disk/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision/disk 2024-10-09T18:23:09,268 copying build/lib/yeastvision/disk/io.py -> build/bdist.linux-armv7l/wheel/./yeastvision/disk 2024-10-09T18:23:09,271 copying build/lib/yeastvision/disk/reader.py -> build/bdist.linux-armv7l/wheel/./yeastvision/disk 2024-10-09T18:23:09,273 copying build/lib/yeastvision/install.py -> build/bdist.linux-armv7l/wheel/./yeastvision 2024-10-09T18:23:09,276 creating build/bdist.linux-armv7l/wheel/yeastvision/parts 2024-10-09T18:23:09,278 copying build/lib/yeastvision/parts/fiest_wizard.py -> build/bdist.linux-armv7l/wheel/./yeastvision/parts 2024-10-09T18:23:09,281 copying build/lib/yeastvision/parts/workers.py -> build/bdist.linux-armv7l/wheel/./yeastvision/parts 2024-10-09T18:23:09,283 copying build/lib/yeastvision/parts/canvas.py -> build/bdist.linux-armv7l/wheel/./yeastvision/parts 2024-10-09T18:23:09,286 copying build/lib/yeastvision/parts/fiest_full_lifecycle_wizard.py -> build/bdist.linux-armv7l/wheel/./yeastvision/parts 2024-10-09T18:23:09,288 copying build/lib/yeastvision/parts/guiparts.py -> build/bdist.linux-armv7l/wheel/./yeastvision/parts 2024-10-09T18:23:09,291 copying build/lib/yeastvision/parts/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision/parts 2024-10-09T18:23:09,293 copying build/lib/yeastvision/parts/utils.py -> build/bdist.linux-armv7l/wheel/./yeastvision/parts 2024-10-09T18:23:09,294 copying build/lib/yeastvision/parts/wizard_utils.py -> build/bdist.linux-armv7l/wheel/./yeastvision/parts 2024-10-09T18:23:09,297 copying build/lib/yeastvision/parts/menu.py -> build/bdist.linux-armv7l/wheel/./yeastvision/parts 2024-10-09T18:23:09,299 copying build/lib/yeastvision/parts/dialogs.py -> build/bdist.linux-armv7l/wheel/./yeastvision/parts 2024-10-09T18:23:09,302 copying build/lib/yeastvision/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision 2024-10-09T18:23:09,304 creating build/bdist.linux-armv7l/wheel/yeastvision/docs 2024-10-09T18:23:09,305 creating build/bdist.linux-armv7l/wheel/yeastvision/docs/figs 2024-10-09T18:23:09,306 copying build/lib/yeastvision/docs/figs/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision/docs/figs 2024-10-09T18:23:09,308 copying build/lib/yeastvision/docs/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision/docs 2024-10-09T18:23:09,310 creating build/bdist.linux-armv7l/wheel/yeastvision/data 2024-10-09T18:23:09,311 copying build/lib/yeastvision/data/ims.py -> build/bdist.linux-armv7l/wheel/./yeastvision/data 2024-10-09T18:23:09,314 copying build/lib/yeastvision/data/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision/data 2024-10-09T18:23:09,315 copying build/lib/yeastvision/data/utils.py -> build/bdist.linux-armv7l/wheel/./yeastvision/data 2024-10-09T18:23:09,318 creating build/bdist.linux-armv7l/wheel/yeastvision/plot 2024-10-09T18:23:09,319 copying build/lib/yeastvision/plot/types.py -> build/bdist.linux-armv7l/wheel/./yeastvision/plot 2024-10-09T18:23:09,321 copying build/lib/yeastvision/plot/cell_table.py -> build/bdist.linux-armv7l/wheel/./yeastvision/plot 2024-10-09T18:23:09,323 copying build/lib/yeastvision/plot/plot.py -> build/bdist.linux-armv7l/wheel/./yeastvision/plot 2024-10-09T18:23:09,325 copying build/lib/yeastvision/plot/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision/plot 2024-10-09T18:23:09,327 copying build/lib/yeastvision/plot/utils.py -> build/bdist.linux-armv7l/wheel/./yeastvision/plot 2024-10-09T18:23:09,329 creating build/bdist.linux-armv7l/wheel/yeastvision/flou 2024-10-09T18:23:09,330 copying build/lib/yeastvision/flou/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision/flou 2024-10-09T18:23:09,332 copying build/lib/yeastvision/flou/blob_detect.py -> build/bdist.linux-armv7l/wheel/./yeastvision/flou 2024-10-09T18:23:09,333 copying build/lib/yeastvision/flou/utils.py -> build/bdist.linux-armv7l/wheel/./yeastvision/flou 2024-10-09T18:23:09,335 copying build/lib/yeastvision/utils.py -> build/bdist.linux-armv7l/wheel/./yeastvision 2024-10-09T18:23:09,338 creating build/bdist.linux-armv7l/wheel/yeastvision/ims 2024-10-09T18:23:09,340 creating build/bdist.linux-armv7l/wheel/yeastvision/ims/rife_model 2024-10-09T18:23:09,341 copying build/lib/yeastvision/ims/rife_model/IFNet_m.py -> build/bdist.linux-armv7l/wheel/./yeastvision/ims/rife_model 2024-10-09T18:23:09,343 copying build/lib/yeastvision/ims/rife_model/laplacian.py -> build/bdist.linux-armv7l/wheel/./yeastvision/ims/rife_model 2024-10-09T18:23:09,345 copying build/lib/yeastvision/ims/rife_model/refine.py -> build/bdist.linux-armv7l/wheel/./yeastvision/ims/rife_model 2024-10-09T18:23:09,347 copying build/lib/yeastvision/ims/rife_model/warplayer.py -> build/bdist.linux-armv7l/wheel/./yeastvision/ims/rife_model 2024-10-09T18:23:09,350 creating build/bdist.linux-armv7l/wheel/yeastvision/ims/rife_model/pytorch_msssim 2024-10-09T18:23:09,351 copying build/lib/yeastvision/ims/rife_model/pytorch_msssim/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision/ims/rife_model/pytorch_msssim 2024-10-09T18:23:09,353 copying build/lib/yeastvision/ims/rife_model/IFNet_2R.py -> build/bdist.linux-armv7l/wheel/./yeastvision/ims/rife_model 2024-10-09T18:23:09,355 copying build/lib/yeastvision/ims/rife_model/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision/ims/rife_model 2024-10-09T18:23:09,357 copying build/lib/yeastvision/ims/rife_model/IFNet.py -> build/bdist.linux-armv7l/wheel/./yeastvision/ims/rife_model 2024-10-09T18:23:09,360 copying build/lib/yeastvision/ims/rife_model/RIFE.py -> build/bdist.linux-armv7l/wheel/./yeastvision/ims/rife_model 2024-10-09T18:23:09,361 copying build/lib/yeastvision/ims/rife_model/loss.py -> build/bdist.linux-armv7l/wheel/./yeastvision/ims/rife_model 2024-10-09T18:23:09,363 copying build/lib/yeastvision/ims/rife_model/refine_2R.py -> build/bdist.linux-armv7l/wheel/./yeastvision/ims/rife_model 2024-10-09T18:23:09,365 copying build/lib/yeastvision/ims/interpolate.py -> build/bdist.linux-armv7l/wheel/./yeastvision/ims 2024-10-09T18:23:09,367 copying build/lib/yeastvision/ims/__init__.py -> build/bdist.linux-armv7l/wheel/./yeastvision/ims 2024-10-09T18:23:09,369 copying build/lib/yeastvision/ims/im_funcs.py -> build/bdist.linux-armv7l/wheel/./yeastvision/ims 2024-10-09T18:23:09,370 running install_egg_info 2024-10-09T18:23:09,403 Copying yeastvision.egg-info to build/bdist.linux-armv7l/wheel/./yeastvision-0.1.62-py3.11.egg-info 2024-10-09T18:23:09,415 running install_scripts 2024-10-09T18:23:09,435 creating build/bdist.linux-armv7l/wheel/yeastvision-0.1.62.dist-info/WHEEL 2024-10-09T18:23:09,437 creating '/tmp/pip-wheel-8seuev1b/yeastvision-0.1.62-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-10-09T18:23:09,439 adding 'yeastvision/__init__.py' 2024-10-09T18:23:09,455 adding 'yeastvision/__main__.py' 2024-10-09T18:23:09,458 adding 'yeastvision/install.py' 2024-10-09T18:23:09,460 adding 'yeastvision/utils.py' 2024-10-09T18:23:09,462 adding 'yeastvision/data/__init__.py' 2024-10-09T18:23:09,465 adding 'yeastvision/data/ims.py' 2024-10-09T18:23:09,466 adding 'yeastvision/data/utils.py' 2024-10-09T18:23:09,468 adding 'yeastvision/disk/__init__.py' 2024-10-09T18:23:09,470 adding 'yeastvision/disk/io.py' 2024-10-09T18:23:09,472 adding 'yeastvision/disk/reader.py' 2024-10-09T18:23:09,473 adding 'yeastvision/docs/__init__.py' 2024-10-09T18:23:09,475 adding 'yeastvision/docs/figs/__init__.py' 2024-10-09T18:23:09,476 adding 'yeastvision/flou/__init__.py' 2024-10-09T18:23:09,478 adding 'yeastvision/flou/blob_detect.py' 2024-10-09T18:23:09,479 adding 'yeastvision/flou/utils.py' 2024-10-09T18:23:09,480 adding 'yeastvision/ims/__init__.py' 2024-10-09T18:23:09,482 adding 'yeastvision/ims/im_funcs.py' 2024-10-09T18:23:09,484 adding 'yeastvision/ims/interpolate.py' 2024-10-09T18:23:09,486 adding 'yeastvision/ims/rife_model/IFNet.py' 2024-10-09T18:23:09,487 adding 'yeastvision/ims/rife_model/IFNet_2R.py' 2024-10-09T18:23:09,489 adding 'yeastvision/ims/rife_model/IFNet_m.py' 2024-10-09T18:23:09,490 adding 'yeastvision/ims/rife_model/RIFE.py' 2024-10-09T18:23:09,491 adding 'yeastvision/ims/rife_model/__init__.py' 2024-10-09T18:23:09,493 adding 'yeastvision/ims/rife_model/laplacian.py' 2024-10-09T18:23:09,494 adding 'yeastvision/ims/rife_model/loss.py' 2024-10-09T18:23:09,495 adding 'yeastvision/ims/rife_model/refine.py' 2024-10-09T18:23:09,497 adding 'yeastvision/ims/rife_model/refine_2R.py' 2024-10-09T18:23:09,498 adding 'yeastvision/ims/rife_model/warplayer.py' 2024-10-09T18:23:09,500 adding 'yeastvision/ims/rife_model/pytorch_msssim/__init__.py' 2024-10-09T18:23:09,502 adding 'yeastvision/models/__init__.py' 2024-10-09T18:23:09,504 adding 'yeastvision/models/cp.py' 2024-10-09T18:23:09,505 adding 'yeastvision/models/model.py' 2024-10-09T18:23:09,506 adding 'yeastvision/models/model_types.json' 2024-10-09T18:23:09,508 adding 'yeastvision/models/utils.py' 2024-10-09T18:23:09,510 adding 'yeastvision/models/budSeg/__init__.py' 2024-10-09T18:23:09,511 adding 'yeastvision/models/budSeg/model.py' 2024-10-09T18:23:09,512 adding 'yeastvision/models/flouSeg/__init__.py' 2024-10-09T18:23:09,514 adding 'yeastvision/models/flouSeg/model.py' 2024-10-09T18:23:09,515 adding 'yeastvision/models/matSeg/__init__.py' 2024-10-09T18:23:09,516 adding 'yeastvision/models/matSeg/model.py' 2024-10-09T18:23:09,518 adding 'yeastvision/models/proSeg/__init__.py' 2024-10-09T18:23:09,520 adding 'yeastvision/models/proSeg/model.py' 2024-10-09T18:23:09,521 adding 'yeastvision/models/spoSeg/__init__.py' 2024-10-09T18:23:09,522 adding 'yeastvision/models/spoSeg/model.py' 2024-10-09T18:23:09,524 adding 'yeastvision/parts/__init__.py' 2024-10-09T18:23:09,526 adding 'yeastvision/parts/canvas.py' 2024-10-09T18:23:09,531 adding 'yeastvision/parts/dialogs.py' 2024-10-09T18:23:09,533 adding 'yeastvision/parts/fiest_full_lifecycle_wizard.py' 2024-10-09T18:23:09,534 adding 'yeastvision/parts/fiest_wizard.py' 2024-10-09T18:23:09,537 adding 'yeastvision/parts/guiparts.py' 2024-10-09T18:23:09,539 adding 'yeastvision/parts/menu.py' 2024-10-09T18:23:09,540 adding 'yeastvision/parts/utils.py' 2024-10-09T18:23:09,541 adding 'yeastvision/parts/wizard_utils.py' 2024-10-09T18:23:09,542 adding 'yeastvision/parts/workers.py' 2024-10-09T18:23:09,544 adding 'yeastvision/plot/__init__.py' 2024-10-09T18:23:09,545 adding 'yeastvision/plot/cell_table.py' 2024-10-09T18:23:09,548 adding 'yeastvision/plot/plot.py' 2024-10-09T18:23:09,550 adding 'yeastvision/plot/types.py' 2024-10-09T18:23:09,551 adding 'yeastvision/plot/utils.py' 2024-10-09T18:23:09,552 adding 'yeastvision/track/__init__.py' 2024-10-09T18:23:09,555 adding 'yeastvision/track/cell.py' 2024-10-09T18:23:09,556 adding 'yeastvision/track/data.py' 2024-10-09T18:23:09,558 adding 'yeastvision/track/hungarian_track.py' 2024-10-09T18:23:09,560 adding 'yeastvision/track/lineage.py' 2024-10-09T18:23:09,563 adding 'yeastvision/track/mat.py' 2024-10-09T18:23:09,564 adding 'yeastvision/track/track.py' 2024-10-09T18:23:09,566 adding 'yeastvision/track/utils.py' 2024-10-09T18:23:09,572 adding 'yeastvision/track/fiest/FL.py' 2024-10-09T18:23:09,574 adding 'yeastvision/track/fiest/__init__.py' 2024-10-09T18:23:09,576 adding 'yeastvision/track/fiest/correction.py' 2024-10-09T18:23:09,578 adding 'yeastvision/track/fiest/full_lifecycle_utils.py' 2024-10-09T18:23:09,580 adding 'yeastvision/track/fiest/mating.py' 2024-10-09T18:23:09,581 adding 'yeastvision/track/fiest/tetrads.py' 2024-10-09T18:23:09,584 adding 'yeastvision/track/fiest/track.py' 2024-10-09T18:23:09,586 adding 'yeastvision/track/fiest/utils.py' 2024-10-09T18:23:09,588 adding 'yeastvision-0.1.62.dist-info/LICENSE' 2024-10-09T18:23:09,590 adding 'yeastvision-0.1.62.dist-info/METADATA' 2024-10-09T18:23:09,591 adding 'yeastvision-0.1.62.dist-info/WHEEL' 2024-10-09T18:23:09,592 adding 'yeastvision-0.1.62.dist-info/entry_points.txt' 2024-10-09T18:23:09,593 adding 'yeastvision-0.1.62.dist-info/top_level.txt' 2024-10-09T18:23:09,594 adding 'yeastvision-0.1.62.dist-info/RECORD' 2024-10-09T18:23:09,598 removing build/bdist.linux-armv7l/wheel 2024-10-09T18:23:09,735 Building wheel for yeastvision (setup.py): finished with status 'done' 2024-10-09T18:23:09,739 Created wheel for yeastvision: filename=yeastvision-0.1.62-py3-none-any.whl size=175225 sha256=d58a49f232e1c7b221f9dc908966241f3f5c65be0a565a88590237f6a1208040 2024-10-09T18:23:09,740 Stored in directory: /tmp/pip-ephem-wheel-cache-fg1gg_f0/wheels/68/03/bd/4b8d8b6338d853de5e48fad5c69119db11dfc3509644b43db1 2024-10-09T18:23:09,754 Successfully built yeastvision 2024-10-09T18:23:09,762 Removed build tracker: '/tmp/pip-build-tracker-7mur0xe_'