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Updated skimage version for importing the graph module and trigger tests #390

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Updated skimage version for importing the graph module and trigger tests #390

wants to merge 72 commits into from

Commits on Dec 16, 2022

  1. add users and papers to README

    @Dana-Farber
    Dana-Farber authored Dec 16, 2022
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  2. Update README.md

    @Dana-Farber
    Dana-Farber authored Dec 16, 2022
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Commits on Feb 7, 2023

  1. Update README.md

    @Dana-Farber
    Dana-Farber authored Feb 7, 2023
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Commits on Feb 8, 2023

  1. Update README.md

    @Dana-Farber
    Dana-Farber authored Feb 8, 2023
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  2. Update README.md

    @Dana-Farber
    Dana-Farber authored Feb 8, 2023
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Commits on Feb 11, 2023

  1. Bump ipython from 7.31.1 to 8.10.0 in /docs 

    Bumps [ipython](https://github.com/ipython/ipython) from 7.31.1 to 8.10.0.
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](ipython/ipython@7.31.1...8.10.0)

---
updated-dependencies:
- dependency-name: ipython
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
    @dependabot
    dependabot[bot] authored Feb 11, 2023
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Commits on Apr 13, 2023

  1. Merge pull request #346 from Dana-Farber-AIOS/dependabot/pip/docs/ipy… 

    …thon-8.10.0

Bump ipython from 7.31.1 to 8.10.0 in /docs
    @jacob-rosenthal
    jacob-rosenthal authored Apr 13, 2023
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  2. Merge branch 'master' into v2.1.1

    @jacob-rosenthal
    jacob-rosenthal committed Apr 13, 2023
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Commits on Apr 19, 2023

  1. bump isort version for python 3.7 compatibility

    @jacob-rosenthal
    jacob-rosenthal committed Apr 19, 2023
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Commits on May 5, 2023

  1. Update README.md 

    Add instructions for Google colab
    @jacob-rosenthal
    jacob-rosenthal authored May 5, 2023
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Commits on May 9, 2023

  1. Update readthedocs-requirements.txt 

    Added urllib3
    @sreekarreddydfci
    sreekarreddydfci authored May 9, 2023
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  2. Update .readthedocs.yaml 

    Added new build, due to conflicts with urllib3 recent updates.
    @sreekarreddydfci
    sreekarreddydfci authored May 9, 2023
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  3. Update .readthedocs.yaml 

    Modified file
    @sreekarreddydfci
    sreekarreddydfci authored May 9, 2023
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  4. Update .readthedocs.yaml 

    added build
    @sreekarreddydfci
    sreekarreddydfci authored May 9, 2023
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  5. Update readthedocs-requirements.txt

    @sreekarreddydfci
    sreekarreddydfci authored May 9, 2023
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Commits on May 10, 2023

  1. Merge pull request #347 from Dana-Farber-AIOS/v2.1.1 

    v2.1.1
    @jacob-rosenthal
    jacob-rosenthal authored May 10, 2023
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Commits on May 11, 2023

  1. Merge pull request #348 from sreekarreddydfci/master 

    Fixed docs
    @jacob-rosenthal
    jacob-rosenthal authored May 11, 2023
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Commits on May 17, 2023

  1. Update _version.py 

    Update version
    @sreekarreddydfci
    sreekarreddydfci authored May 17, 2023
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Commits on May 18, 2023

  1. Update publish-to-pypi.yml 

    Updated Ubuntu OS
    @sreekarreddydfci
    sreekarreddydfci authored May 18, 2023
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Commits on May 22, 2023

  1. Update publish-to-pypi.yml 

    Changed ubuntu version to 22.04
    @sreekarreddydfci
    sreekarreddydfci authored May 22, 2023
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  2. Update publish-to-pypi.yml

    @sreekarreddydfci
    sreekarreddydfci authored May 22, 2023
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  3. Update publish-to-pypi.yml

    @sreekarreddydfci
    sreekarreddydfci authored May 22, 2023
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  4. Update publish-to-pypi.yml 

    Changed Ubuntu version
    @sreekarreddydfci
    sreekarreddydfci authored May 22, 2023
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  5. Update tests-conda.yml 

    Update GitHub Actions workflow to use mamba for dependency management
    @sreekarreddydfci
    sreekarreddydfci authored May 22, 2023
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  6. Update tests-conda.yml

    @sreekarreddydfci
    sreekarreddydfci authored May 22, 2023
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  7. Update tests-conda.yml 

    Excluding python=3.9 to resolve the following issue is github action runs:

 Could not solve for environment specs
  The following packages are incompatible
  ├─ python 3.8  is requested and can be installed;
  └─ python 3.9**  is uninstallable because it conflicts with any installable versions previously reported.
    @sreekarreddydfci
    sreekarreddydfci authored May 22, 2023
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  8. Update tests-conda.yml 

    Added python 3.9 to test the environment
    @sreekarreddydfci
    sreekarreddydfci authored May 22, 2023
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  9. Update environment.yml 

    Excluding python 3.8 as requirement
    @sreekarreddydfci
    sreekarreddydfci authored May 22, 2023
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Commits on May 23, 2023

  1. Merge pull request #351 from Dana-Farber-AIOS/sreekarreddydfci-patch-1 

    Update _version.py
    @jacob-rosenthal
    jacob-rosenthal authored May 23, 2023
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Commits on May 26, 2023

  1. Update environment.yml 

    Excluded python version as dependency
    @sreekarreddydfci
    sreekarreddydfci authored May 26, 2023
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  2. Update environment.yml 

    Exclude python-spams dependency
    @sreekarreddydfci
    sreekarreddydfci authored May 26, 2023
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  3. Update tests-conda.yml 

    Replaced conda with mamba
    @sreekarreddydfci
    sreekarreddydfci authored May 26, 2023
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  4. Update tests-conda.yml 

    Using setup-micromamba to setup environment, installing python-spams.
    @sreekarreddydfci
    sreekarreddydfci authored May 26, 2023
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  5. Update tests-conda.yml 

    Added micromamba to setup environment
    @sreekarreddydfci
    sreekarreddydfci authored May 26, 2023
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  6. Update tests-conda.yml 

    rollback to mamba, couldn't resolve openjdk 8 when using micromamba
    @sreekarreddydfci
    sreekarreddydfci authored May 26, 2023
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  7. Merge pull request #1 from sreekarreddydfci/sreekarreddydfci-patch-1 

    Update environment.yml and test-conda.yml
    @sreekarreddydfci
    sreekarreddydfci authored May 26, 2023
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Commits on May 30, 2023

  1. Remove commented out lines

    @jacob-rosenthal
    jacob-rosenthal authored May 30, 2023
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  2. Merge pull request #354 from sreekarreddydfci/master 

    Update Environment Configuration and Dependencies
    @jacob-rosenthal
    jacob-rosenthal authored May 30, 2023
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  3. Merge branch 'master' into sreekarreddydfci-patch-2

    @jacob-rosenthal
    jacob-rosenthal authored May 30, 2023
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  4. Merge pull request #352 from Dana-Farber-AIOS/sreekarreddydfci-patch-2 

    Update publish-to-pypi.yml
    @jacob-rosenthal
    jacob-rosenthal authored May 30, 2023
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  5. allow manual workflow triggering

    @jacob-rosenthal
    jacob-rosenthal committed May 30, 2023
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  6. Merge pull request #355 from Dana-Farber-AIOS/workflows-dispatch 

    allow manual workflow triggering
    @jacob-rosenthal
    jacob-rosenthal authored May 30, 2023
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Commits on Jul 26, 2023

  1. Update environment.yml (#361) 

    Update openslide-python to v1.2.0 to resolve 'ANTIALIAS' AttributeError

This commit upgrades openslide-python to version 1.2.0 to address an AttributeError related to the 'ANTIALIAS' attribute in the PIL.Image module. The issue was triggered due to the deprecation of 'ANTIALIAS' in Pillow v10.0.0.
    @sreekarreddydfci
    sreekarreddydfci authored Jul 26, 2023
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Commits on Aug 23, 2023

  1. Update README.md 

    updated the Download counter button
    @Dana-Farber
    Dana-Farber authored Aug 23, 2023
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Commits on Nov 11, 2023

  1. Added graph API and restructured pathml.ml.models

    @VarunUllanat
    VarunUllanat committed Nov 11, 2023
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Commits on Nov 15, 2023

  1. Added new tests for hactnet

    @VarunUllanat
    VarunUllanat committed Nov 15, 2023
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  2. Added tests for graph preprocessing and dataset feature extraction" 

    l
    @VarunUllanat
    VarunUllanat committed Nov 15, 2023
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Commits on Nov 16, 2023

  1. Added new graph utils tests

    @VarunUllanat
    VarunUllanat committed Nov 16, 2023
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Commits on Nov 17, 2023

  1. bugfix in colab installation instructions in README.md

    @Dana-Farber
    Dana-Farber authored Nov 17, 2023
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  2. Merge pull request #376 from Dana-Farber-AIOS/Dana-Farber-patch-1 

    bugfix in colab installation instructions in README.md
    @Dana-Farber
    Dana-Farber authored Nov 17, 2023
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Commits on Nov 20, 2023

  1. Update readthedocs-requirements.txt (#377)

    @sreekarreddydfci
    sreekarreddydfci authored Nov 20, 2023
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Commits on Nov 22, 2023

  1. Merge pull request #378 from VarunUllanat/dev_graph 

    Adding graph API codebase, tests and notebooks
    @VarunUllanat
    VarunUllanat authored Nov 22, 2023
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  2. Cleaned up code and fixed pre-commit errors

    @VarunUllanat
    VarunUllanat committed Nov 22, 2023
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Commits on Nov 24, 2023

  1. Cleaned up files and added comments and docstrings

    @VarunUllanat
    VarunUllanat committed Nov 24, 2023
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Commits on Nov 29, 2023

  1. reformatted pathml/datasets/datasets.py

    @VarunUllanat
    VarunUllanat committed Nov 29, 2023
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  2. removed torchvision dependency in environment.yml

    @VarunUllanat
    VarunUllanat committed Nov 29, 2023
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  3. Merge branch 'dev_graph' into dev_graph

    @VarunUllanat
    VarunUllanat authored Nov 29, 2023
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  4. Removed unused import in graph_tests

    @VarunUllanat
    VarunUllanat committed Nov 29, 2023
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  5. Merge branch 'dev_graph' of https://github.com/VarunUllanat/pathml in… 

    …to dev_graph

Updating local
    @VarunUllanat
    VarunUllanat committed Nov 29, 2023
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  6. Merge pull request #379 from VarunUllanat/dev_graph 

    Cleaned up code and added comments and exception handling
    @VarunUllanat
    VarunUllanat authored Nov 29, 2023
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Commits on Nov 30, 2023

  1. Remove torchvision dependency in tests and added nn.Module input for … 

    …DeepPatchFeatureExtractor
    @VarunUllanat
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  2. Merge pull request #380 from VarunUllanat/dev_graph 

    Remove torchvision dependency in tests and added nn.Module input for …
    @VarunUllanat
    VarunUllanat authored Nov 30, 2023
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Commits on Dec 1, 2023

  1. Make flake8 compliant

    @VarunUllanat
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  2. Merge pull request #381 from VarunUllanat/dev_graph 

    Make flake8 compliant and update tests
    @VarunUllanat
    VarunUllanat authored Dec 1, 2023
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  3. Updated environment.yml to include flexible numpy and scipy versions

    @VarunUllanat
    VarunUllanat committed Dec 1, 2023
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  4. Merge pull request #383 from VarunUllanat/dev_graph 

    Updated environment.yml to include flexible numpy and scipy versions
    @VarunUllanat
    VarunUllanat authored Dec 1, 2023
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  5. Added capabilities for all possible versions of skimage and flake8 co… 

    …mpliant
    @VarunUllanat
    VarunUllanat committed Dec 1, 2023
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  6. Merge pull request #385 from VarunUllanat/dev_graph 

    Added capabilities for all possible versions of skimage and flake8 co…
    @VarunUllanat
    VarunUllanat authored Dec 1, 2023
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Commits on Dec 2, 2023

  1. Changes spams installation in github workflows

    @VarunUllanat
    VarunUllanat committed Dec 2, 2023
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  2. Merge pull request #387 from VarunUllanat/dev_graph 

    Changes spams installation in github workflows
    @VarunUllanat
    VarunUllanat authored Dec 2, 2023
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  3. Updated skimage version for importing the graph module

    @VarunUllanat
    VarunUllanat committed Dec 2, 2023
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  4. Merge pull request #389 from VarunUllanat/dev_graph 

    Updated skimage version for importing the graph module
    @VarunUllanat
    VarunUllanat authored Dec 2, 2023
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