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Inference ONNX #367

Merged
merged 198 commits into from
Mar 20, 2024
Merged

Inference ONNX #367

merged 198 commits into from
Mar 20, 2024

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 12, 2023

  1. adding platforms for build and push

    @jamesgwen
    jamesgwen committed Jul 12, 2023
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Commits on Jul 14, 2023

  1. updating push action version and adding platforms for mac support

    @jamesgwen
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Commits on Jul 17, 2023

  1. changing openslide version in environ yml

    @jamesgwen
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  2. adding adjusted openslide dependency in yml

    @jamesgwen
    jamesgwen committed Jul 17, 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 11, 2023

  1. adding inference to init file

    @jamesgwen
    jamesgwen committed Aug 11, 2023
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  2. add inference classes and functions

    @jamesgwen
    jamesgwen committed Aug 11, 2023
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  3. add tests for inference

    @jamesgwen
    jamesgwen committed Aug 11, 2023
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  4. fixed import statements

    @jamesgwen
    jamesgwen committed Aug 11, 2023
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  5. fixing import statements in the init and the test inference

    @jamesgwen
    jamesgwen committed Aug 11, 2023
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  6. fixing init files

    @jamesgwen
    jamesgwen committed Aug 11, 2023
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  7. fixing comma in inference init

    @jamesgwen
    jamesgwen committed Aug 11, 2023
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  8. getting rid of unused packages

    @jamesgwen
    jamesgwen committed Aug 11, 2023
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  9. fixed files via black

    @jamesgwen
    jamesgwen committed Aug 11, 2023
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  10. fixed spacing and alpha order

    @jamesgwen
    jamesgwen committed Aug 11, 2023
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  11. added dependencies

    @jamesgwen
    jamesgwen committed Aug 11, 2023
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  12. re black the test inference file

    @jamesgwen
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Commits on Aug 14, 2023

  1. update protobuf version in envi yml

    @jamesgwen
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  2. changing numpy version

    @jamesgwen
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  3. adjusting deepcel version

    @jamesgwen
    jamesgwen committed Aug 14, 2023
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  4. deleted comment from yml file

    @jamesgwen
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  5. updating pytest version

    @jamesgwen
    jamesgwen committed Aug 14, 2023
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  6. setting pandas version

    @jamesgwen
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  7. adding test onnx and fixing path in test file

    @jamesgwen
    jamesgwen committed Aug 14, 2023
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  8. fixing remote test

    @jamesgwen
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  9. fixing path to onnx model in test data

    @jamesgwen
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Commits on Aug 15, 2023

  1. changing numpy to latest version

    @jamesgwen
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  2. adjusting numpy to 1.24.0

    @jamesgwen
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  3. switching to numpy 1.22.4

    @jamesgwen
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Commits on Aug 17, 2023

  1. Merge branch 'dev-onnx' into inference

    @jamesgwen
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  2. adding pandas

    @jamesgwen
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Commits on Aug 23, 2023

  1. Update README.md 

    updated the Download counter button
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Commits on Aug 29, 2023

  1. Merge pull request #366 from jamesgwen/inference 

    Merging Inference subpackage to dev.
    @sreekarreddydfci
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Commits on Sep 6, 2023

  1. adding repr tests

    @jamesgwen
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  2. fixing print statements in repr tests

    @jamesgwen
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Commits on Sep 7, 2023

  1. adding example notebook and fixing comments in inference file

    @jamesgwen
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  2. adding model w/ initializers, modified tests and notebook

    @jamesgwen
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  3. fixed test format

    @jamesgwen
    jamesgwen committed Sep 7, 2023
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  4. fixing name in card

    @jamesgwen
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Commits on Oct 17, 2023

  1. adding comment to adj openslide

    @jamesgwen
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Commits on Oct 18, 2023

  1. changing readthedocs recs

    @jamesgwen
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  2. chaning mamba to miniforge

    @jamesgwen
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  3. addjusting sphinx version

    @jamesgwen
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  4. changing sphinx-rtd-theme version

    @jamesgwen
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  5. adjusting sphynx

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Commits on Nov 1, 2023

  1. adding pytorch to onnx function

    @jamesgwen
    jamesgwen committed Nov 1, 2023
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  2. attempt to get pytorch class to load

    @jamesgwen
    jamesgwen committed Nov 1, 2023
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  3. deleting simple model module

    @jamesgwen
    jamesgwen committed Nov 1, 2023
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  4. adding new .pt file and new test

    @jamesgwen
    jamesgwen committed Nov 1, 2023
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  5. adding new tutorial

    @jamesgwen
    jamesgwen committed Nov 1, 2023
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Commits on Nov 6, 2023

  1. new example book

    @jamesgwen
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Commits on Nov 8, 2023

  1. further edits

    @jamesgwen
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Commits on Nov 11, 2023

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

    @VarunUllanat
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Commits on Nov 14, 2023

  1. Added tilestitcher code

    @sreekarreddydfci
    sreekarreddydfci committed Nov 14, 2023
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  2. Added testdata

    @sreekarreddydfci
    sreekarreddydfci committed Nov 14, 2023
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  3. Added notebook

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  4. Added testcases

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  5. Updates testcases and tutorial notebook 

    Added utils to setup qupath and updated testcases.
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  6. Updated markers to run testcases

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  7. Added description

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  8. Update tests-conda.yml 

    Added jdk 17 installation and exclude testcases with "exclude" marker.
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  9. Update tests-conda.yml 

    updated mamba
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  10. Update environment.yml 

    Added Jpype dependency
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  11. Update environment.yml 

    Added Jpype1
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  12. Update environment.yml 

    Updated openslide
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  13. Update tests-conda.yml 

    Added testcase execution for tile_stitcher, and combining coverage files from two test case runs.
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  14. Update environment.yml 

    Excluded openjdk 8 dependency, as we are setting up jdk 17.
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Commits on Nov 15, 2023

  1. Update tests-conda.yml 

    Added code to check and debug java versions.
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  2. Update utils.py 

    Updated qupath downlod path
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  3. Update tests-conda.yml 

    Changing priority of JVM to version 17
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  4. Update tests-conda.yml 

    Removed duplicate code
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  5. Fixed precommit hook errors

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  6. pull changes

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  7. fixed precommit hook errors, and updated qupath download url

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  8. Update tests-conda.yml

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  9. Update tests-conda.yml 

    Changing jdk priority to version 17
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  10. Update tests-conda.yml 

    Running test case on tilestitcher.py
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  11. Update tests-conda.yml 

    Combining coverage reports
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  12. Update tests-conda.yml 

    Debug coverage command
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  13. Update tests-conda.yml 

    Debug coverage pytest error
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  14. Update tests-conda.yml 

    added shell command to run coverage using pytest
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  15. Update tests-conda.yml 

    Modified coverage combine code
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  16. Update tests-conda.yml 

    debug coverage combining
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  17. Update tests-conda.yml 

    added extension to combine coverage files
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  18. Update tests-conda.yml 

    Modified coverage combine commands
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  19. Update readthedocs-requirements.txt 

    Updated sphinx and sphinx-autoapi to resolve error: https://stackoverflow.com/questions/77257145/sphinx-autoapi-error-module-object-has-no-attribute-doc-with-various-sphi
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  20. Update readthedocs-requirements.txt 

    Update dependencies to resolve error : https://stackoverflow.com/questions/77257145/sphinx-autoapi-error-module-object-has-no-attribute-doc-with-various-sphi
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  21. Added new tests for hactnet

    @VarunUllanat
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  22. Update precommit-hooks.yaml 

    added black- format checking
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  23. Added tests for graph preprocessing and dataset feature extraction" 

    l
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Commits on Nov 16, 2023

  1. Added new graph utils tests

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Commits on Nov 17, 2023

  1. bugfix in colab installation instructions in README.md

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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
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Commits on Nov 20, 2023

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

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Commits on Nov 22, 2023

  1. changing torch version

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  2. Merge pull request #378 from VarunUllanat/dev_graph 

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

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Commits on Nov 24, 2023

  1. Cleaned up files and added comments and docstrings

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Commits on Nov 29, 2023

  1. add test cases

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  2. reformatted pathml/datasets/datasets.py

    @VarunUllanat
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  3. removed torchvision dependency in environment.yml

    @VarunUllanat
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  4. Merge branch 'dev_graph' into dev_graph

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  5. Removed unused import in graph_tests

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  6. Merge branch 'dev_graph' of https://github.com/VarunUllanat/pathml in… 

    …to dev_graph

Updating local
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  7. Merge pull request #379 from VarunUllanat/dev_graph 

    Cleaned up code and added comments and exception handling
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    VarunUllanat authored Nov 29, 2023
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  8. Merge branch 'tilestitching-dev2' into dev-tilestitching

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  9. added tilestitching code

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  10. cleaned docs requirement file

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  11. Remove tools folder

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Commits on Nov 30, 2023

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

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

    Remove torchvision dependency in tests and added nn.Module input for …
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  3. Merge remote-tracking branch 'upstream/dev_graph' into dev-tilestitching

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  4. merged latest changes

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  5. merged latest changes

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  6. Update environment.yml 

    Added torchvision and spams
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  7. Update environment.yml

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  8. Update environment.yml

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  9. fixed typos in example notebook

    @jamesgwen
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Commits on Dec 1, 2023

  1. Make flake8 compliant

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  2. Merge pull request #381 from VarunUllanat/dev_graph 

    Make flake8 compliant and update tests
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  3. Updated environment.yml to include flexible numpy and scipy versions

    @VarunUllanat
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  4. Merge pull request #383 from VarunUllanat/dev_graph 

    Updated environment.yml to include flexible numpy and scipy versions
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  5. Added capabilities for all possible versions of skimage and flake8 co… 

    …mpliant
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  6. Merge pull request #385 from VarunUllanat/dev_graph 

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

  1. Changes spams installation in github workflows

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  2. Merge pull request #387 from VarunUllanat/dev_graph 

    Changes spams installation in github workflows
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  3. Updated skimage version for importing the graph module

    @VarunUllanat
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  4. Merge pull request #389 from VarunUllanat/dev_graph 

    Updated skimage version for importing the graph module
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  5. merging graphapi with tilestitching

    @sreekarreddydfci
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  6. Modified skimage graph import

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Commits on Dec 4, 2023

  1. Added tilestitching code

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  2. Update environment.yml 

    Added JPype1
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  3. Create testdata folder for tilestitching data

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  4. Add large .tif file with Git LFS

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  5. ≈Merge branch 'dev_graphAPI' of https://github.com/sreekarreddydfci/p… 

    …athml into dev_graphAPI
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  6. Remove readme file in tests

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  7. Update tests-conda.yml 

    Separately executed test cases for tilestitching functionality and other PathML modules.
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  8. Added exclude marker to run tests

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  9. Merge branch 'dev_graphAPI' of https://github.com/sreekarreddydfci/pa… 

    …thml into dev_graphAPI
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  10. Edited a testcase

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  11. Commented testcases

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  12. Merge pull request #391 from sreekarreddydfci/dev_graphAPI 

    Added tilestitching code
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Commits on Dec 5, 2023

  1. Pasted the code from graphAPI

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  2. Update environment.yml

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  3. Added testcases

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  4. Added test cases and environment file

    @sreekarreddydfci
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  5. Updated env

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  6. Updated env

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Commits on Dec 6, 2023

  1. Merge pull request #393 from sreekarreddydfci/dev-tilestitching 

    Dev tilestitching
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  2. Make flake8 compliant

    @VarunUllanat
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  3. Removed tile stiching generated files

    @VarunUllanat
    VarunUllanat committed Dec 6, 2023
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  4. Make flake8 compliant

    @VarunUllanat
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  5. Flake8 compliant

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    VarunUllanat committed Dec 6, 2023
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  6. Merge branch 'dev_graph' into dev-tilestitching

    @VarunUllanat
    VarunUllanat authored Dec 6, 2023
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  7. Merge pull request #394 from Dana-Farber-AIOS/dev-tilestitching 

    Dev tilestitching
    @VarunUllanat
    VarunUllanat authored Dec 6, 2023
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  8. Merge branch 'dev_graph' into dev-onnx

    @VarunUllanat
    VarunUllanat authored Dec 6, 2023
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