adding graph + tile stitching to trigger tests

.gitattributes

@@ -0,0 +1 @@
+tests/testdata/tilestitching_testdata/*.tif filter=lfs diff=lfs merge=lfs -text

.github/workflows/publish-to-pypi.yml

@@ -1,13 +1,14 @@
 name: Publish PathML distribution to PyPI and TestPyPI
 
 on:
+  workflow_dispatch:
   release:
     types: [published]
 
 jobs:
   build-n-publish:
     name: Build and publish PathML distribution to PyPI and TestPyPI
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@master
     - name: Set up Python 3.9

.github/workflows/tests-conda.yml

@@ -1,6 +1,7 @@
 name: Tests
 
-on: 
+on:
+  workflow_dispatch:
   pull_request:
     branches:
       - dev
@@ -17,60 +18,132 @@ jobs:
       max-parallel: 5
       matrix:
         python-version: [3.8, 3.9]
+    timeout-minutes: 60 # add a timeout
 
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-    # Test matrix by printing the current Python version
     - name: Display Python version
       run: python -c "import sys; print(sys.version)"
     - name: Install dependencies
       shell: bash -l {0}
       run: |
         sudo apt-get update
-        # install openslide
         sudo apt-get install openslide-tools
-        # install pandoc for making documentation
         sudo apt-get install pandoc
     - name: Setup Miniconda
-      # You may pin to the exact commit or the version.
-      # uses: conda-incubator/setup-miniconda@f4c00b0ec69bdc87b1ab4972613558dd9f4f36f3
-      uses: conda-incubator/[email protected]
+      uses: conda-incubator/setup-miniconda@v2
       with:
-        add_pip_as_python_dependency: false
-        environment-file: environment.yml
+        auto-activate-base: false
         activate-environment: pathml
+        environment-file: environment.yml
+        mamba-version: "*"
         python-version: ${{ matrix.python-version }}
+    - name: Debugging
+      run: |
+        echo "Printing the environment.yml file..."
+        cat environment.yml
+        echo "Checking the status of mamba..."
+        mamba --version
+        echo "Checking the available disk space..."
+        df -h
+    - name: Install dependencies with mamba
+      shell: bash -l {0}
+      run: mamba env update --file environment.yml --name pathml
     - name: Conda info
       shell: bash -l {0}
       run: |
         conda info
         conda list
-    - name: pip install pathml
-      shell: bash -l {0}
+
+    - name: Set default Temurin JDK 17
+      run: |
+        sudo update-java-alternatives --set temurin-17-jdk-amd64 || true
+        java -version
+
+    - name: Install PathML
+      shell: bash -l {0}      
       run: pip install -e .
+
+    - name: Install python-spams
+      shell: bash -l {0}      
+      run: pip install spams
+
     - name: disk usage
       shell: bash -l {0}
       run: |
         sudo df -h
         sudo du -h
-    - name: Test with pytest and generate coverage report
+
+    # - name: Check Coverage Command
+    #   run: |
+    #     which coverage
+    #     coverage --version
+
+    # - name: Test with pytest for tile_stitcher
+    #   run: |
+    #     java -version
+    #     python -m pytest tests/preprocessing_tests/test_tilestitcher.py
+
+    # - name: Test with pytest and generate coverage report
+    #   shell: bash -l {0}
+    #   run: |
+    #     coverage run -m pytest -m "not slow and not exclude"
+    #     coverage xml
+    # - name: Upload coverage to Codecov
+    #   uses: codecov/codecov-action@v2
+    #   with:
+    #     token: ${{ secrets.CODECOV_TOKEN }}
+    #     env_vars: OS,PYTHON
+    #     fail_ci_if_error: true
+    #     files: ./coverage.xml
+    #     name: codecov-umbrella
+    #     verbose: true
+
+    - name: Test other modules with pytest and generate coverage
+      shell: bash -l {0}
+      run: |
+        COVERAGE_FILE=.coverage_others coverage run -m pytest -m "not slow and not exclude"
+
+    - name: Test tile_stitcher with pytest and generate coverage
       shell: bash -l {0}
       run: |
-        coverage run -m pytest -m "not slow"
-        coverage xml
-    - name: Upload coverage to Codecov
+        COVERAGE_FILE=.coverage_tilestitcher coverage run -m pytest tests/preprocessing_tests/test_tilestitcher.py
+
+    - name: List Files in Directory
+      shell: bash -l {0}
+      run: |
+        ls -la
+
+    - name: Combine Coverage Data
+      shell: bash -l {0}
+      run: |
+        coverage combine .coverage_tilestitcher .coverage_others
+
+    - name: Generate Combined Coverage Report
+      shell: bash -l {0}
+      run: |
+        coverage xml -o combined_coverage.xml
+
+    # - name: Combine coverage data
+    #   shell: bash -l {0}
+    #   run: |
+    #     coverage combine coverage_tilestitcher.xml coverage_others.xml
+    #     coverage xml -o coverage_combined.xml
+
+    - name: Upload combined coverage to Codecov
       uses: codecov/codecov-action@v2
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         env_vars: OS,PYTHON
         fail_ci_if_error: true
-        files: ./coverage.xml
+        files: ./combined_coverage.xml
         name: codecov-umbrella
         verbose: true
+
     - name: Compile docs
       shell: bash -l {0}
       run: |

.gitignore

@@ -33,3 +33,6 @@ scratch.ipynb
 
 # dask
 dask-worker-space/
+
+# tile stitching files
+tools/*

.pre-commit-config.yaml

@@ -16,7 +16,7 @@ repos:
       - id: black
 
   - repo: https://github.com/timothycrosley/isort
-    rev: 5.10.1
+    rev: 5.11.5
     hooks:
       - id: isort
 

.readthedocs.yaml

@@ -5,13 +5,17 @@
 # Required
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+
 # Build documentation with Sphinx
 sphinx:
     configuration: docs/source/conf.py
     builder: html
     fail_on_warning: false
 
 python:
-   version: "3.8"
    install:
    - requirements: docs/readthedocs-requirements.txt

README.md

@@ -1,19 +1,27 @@
-<img src=https://raw.githubusercontent.com/Dana-Farber-AIOS/pathml/master/docs/source/_static/images/logo.png width="300"> 
-
-<img src=https://raw.githubusercontent.com/Dana-Farber-AIOS/pathml/master/docs/source/_static/images/overview.png width="750">
+🤖🔬 **PathML: Tools for computational pathology**
 
+[![Downloads](https://static.pepy.tech/badge/pathml)](https://pepy.tech/project/pathml)
 [![Documentation Status](https://readthedocs.org/projects/pathml/badge/?version=latest)](https://pathml.readthedocs.io/en/latest/?badge=latest)
+[![codecov](https://codecov.io/gh/Dana-Farber-AIOS/pathml/branch/master/graph/badge.svg?token=UHSQPTM28Y)](https://codecov.io/gh/Dana-Farber-AIOS/pathml)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![PyPI version](https://img.shields.io/pypi/v/pathml)](https://pypi.org/project/pathml/)
-[![Downloads](https://pepy.tech/badge/pathml)](https://pepy.tech/project/pathml)
-[![codecov](https://codecov.io/gh/Dana-Farber-AIOS/pathml/branch/master/graph/badge.svg?token=UHSQPTM28Y)](https://codecov.io/gh/Dana-Farber-AIOS/pathml)
+
+⭐ **PathML objective is to lower the barrier to entry to digital pathology**
+
+Imaging datasets in cancer research are growing exponentially in both quantity and information density. These massive datasets may enable derivation of insights for cancer research and clinical care, but only if researchers are equipped with the tools to leverage advanced computational analysis approaches such as machine learning and artificial intelligence. In this work, we highlight three themes to guide development of such computational tools: scalability, standardization, and ease of use. We then apply these principles to develop PathML, a general-purpose research toolkit for computational pathology. We describe the design of the PathML framework and demonstrate applications in diverse use cases. 
+
+🚀 **The fastest way to get started?**
+
+    docker pull pathml/pathml && docker run -it -p 8888:8888 pathml/pathml
 
 | Branch | Test status   |
 | ------ | ------------- |
 | master | ![tests](https://github.com/Dana-Farber-AIOS/pathml/actions/workflows/tests-conda.yml/badge.svg?branch=master) |
 | dev    | ![tests](https://github.com/Dana-Farber-AIOS/pathml/actions/workflows/tests-conda.yml/badge.svg?branch=dev) |
 
-An open-source toolkit for computational pathology and machine learning.
+<img src=https://raw.githubusercontent.com/Dana-Farber-AIOS/pathml/master/docs/source/_static/images/logo.png width="300"> 
+
+<img src=https://raw.githubusercontent.com/Dana-Farber-AIOS/pathml/master/docs/source/_static/images/overview.png width="750">
 
 **View [documentation](https://pathml.readthedocs.io/en/latest/)**
 
@@ -125,6 +133,24 @@ Note that these instructions assume that there are no other processes using port
 Please refer to the `Docker run` [documentation](https://docs.docker.com/engine/reference/run/) for further instructions
 on accessing the container, e.g. for mounting volumes to access files on a local machine from within the container.
 
+## Option 4: Google Colab
+
+To get PathML running in a Colab environment:
+
+````
+import os
+!pip install openslide-python
+!apt-get install openslide-tools
+!apt-get install openjdk-8-jdk-headless -qq > /dev/null
+os.environ["JAVA_HOME"] = "/usr/lib/jvm/java-8-openjdk-amd64"
+!update-alternatives --set java /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java
+!java -version
+!pip install pathml
+````
+
+*Thanks to all of our open-source collaborators for helping maintain these installation instructions!*  
+*Please open an issue for any bugs or other problems during installation process.*
+
 ## CUDA
 
 To use GPU acceleration for model training or other tasks, you must install CUDA. 
@@ -191,12 +217,36 @@ See [contributing](https://github.com/Dana-Farber-AIOS/pathml/blob/master/CONTRI
 
 # Citing
 
-If you use `PathML` in your work, please cite our paper:
+If you use `PathML` please cite:
+
+- [**J. Rosenthal et al., "Building tools for machine learning and artificial intelligence in cancer research: best practices and a case study with the PathML toolkit for computational pathology." Molecular Cancer Research, 2022.**](https://doi.org/10.1158/1541-7786.MCR-21-0665)
+
+So far, PathML was used in the following manuscripts: 
+
+- [J. Linares et al. **Molecular Cell** 2021](https://www.cell.com/molecular-cell/fulltext/S1097-2765(21)00729-2)
+- [A. Shmatko et al. **Nature Cancer** 2022](https://www.nature.com/articles/s43018-022-00436-4)
+- [J. Pocock et al. **Nature Communications Medicine** 2022](https://www.nature.com/articles/s43856-022-00186-5)
+- [S. Orsulic et al. **Frontiers in Oncology** 2022](https://www.frontiersin.org/articles/10.3389/fonc.2022.924945/full)
+- [D. Brundage et al. **arXiv** 2022](https://arxiv.org/abs/2203.13888)
+- [A. Marcolini et al. **SoftwareX** 2022](https://www.sciencedirect.com/science/article/pii/S2352711022001558)
+- [M. Rahman et al. **Bioengineering** 2022](https://www.mdpi.com/2306-5354/9/8/335)
+- [C. Lama et al. **bioRxiv** 2022](https://www.biorxiv.org/content/10.1101/2022.09.28.509751v1.full)
+- the list continues [**here 🔗 for 2023 and onwards**](https://scholar.google.com/scholar?oi=bibs&hl=en&cites=1157052756975292108)
+
+# Users
+
+<table style="border: 0px !important;"><tr><td>This is where in the world our most enthusiastic supporters are located:
+   <br/><br/>
+<img src="https://user-images.githubusercontent.com/25375373/208137141-e450aa86-8433-415a-9cc7-c4274139bdc2.png" width="500px">
+   </td><td>   
+and this is where they work:
+   <br/><br/>
+<img src="https://user-images.githubusercontent.com/25375373/208137644-f73c86d0-c5c7-4094-80d9-ea11e0edbdc5.png" width="400px">
+</td>                                                                                                                             
+</tr>
+</table>
 
-Rosenthal J, Carelli R, Omar M, Brundage D, Halbert E, Nyman J, Hari SN, Van Allen EM, Marchionni L, Umeton R, Loda M. 
-Building tools for machine learning and artificial intelligence in cancer research: best practices and a case study 
-with the PathML toolkit for computational pathology. *Molecular Cancer Research*, 2021. 
-DOI: [10.1158/1541-7786.MCR-21-0665](https://doi.org/10.1158/1541-7786.MCR-21-0665)
+Source: https://ossinsight.io/analyze/Dana-Farber-AIOS/pathml#people
 
 # License
 
@@ -209,6 +259,6 @@ Commercial license options are available also.
 
 Questions? Comments? Suggestions? Get in touch!
 
-[PathML@dfci.harvard.edu](mailto:PathML@dfci.harvard.edu)
+[pathml@dfci.harvard.edu](mailto:pathml@dfci.harvard.edu)
 
 <img src=https://raw.githubusercontent.com/Dana-Farber-AIOS/pathml/master/docs/source/_static/images/dfci_cornell_joint_logos.png width="750"> 

docs/readthedocs-requirements.txt

@@ -1,7 +1,7 @@
-sphinx==4.3.2
+sphinx==7.1.2
 nbsphinx==0.8.8
 nbsphinx-link==1.3.0
-sphinx-rtd-theme==1.0.0
-sphinx-autoapi==1.8.4
-ipython==7.31.1
+sphinx-rtd-theme==1.3.0
+sphinx-autoapi==3.0.0
+ipython==8.10.0
 sphinx-copybutton==0.4.0

environment.yml

@@ -1,33 +1,37 @@
 name: pathml
 
 channels:
-    - conda-forge
     - pytorch
+    - conda-forge
 
 dependencies:
     - pip==21.3.1
-    - python==3.8
-    - numpy==1.19.5
-    - scipy==1.7.3
-    - scikit-image==0.18.3
+    - numpy # orig = 1.19.5
+    - scipy # orig = 1.7.3
+    - scikit-image # orig 0.18.3
     - matplotlib==3.5.1
-    - python-spams==2.6.1
-    - openjdk==8.0.152
-    - pytorch==1.10.1
+    - openjdk<=18.0.0
+    - pytorch==1.13.1 # orig = 1.10.1
     - h5py==3.1.0
     - dask==2021.12.0
     - pydicom==2.2.2
-    - pytest==6.2.5
+    - pytest==7.4.0 # orig = 6.2.5
     - pre-commit==2.16.0
     - coverage==5.5
+    - networkx==3.1
     - pip:
         - python-bioformats==4.0.0
         - python-javabridge==4.0.0
-        - protobuf==3.20.1
-        - deepcell==0.11.0
+        - protobuf==3.20.3
+        - deepcell==0.12.7 # orig = 0.11.0
+        - onnx==1.14.0
+        - onnxruntime==1.15.1
         - opencv-contrib-python==4.5.3.56
-        - openslide-python==1.1.2
+        - openslide-python==1.2.0
         - scanpy==1.8.2
         - anndata==0.7.8
         - tqdm==4.62.3
         - loguru==0.5.3
+        - pandas==1.5.2 # orig no req
+        - torch-geometric==2.3.1
+        - jpype1