rsethi21 · rsethi21 · Apr 16, 2024 · Apr 16, 2024 · Apr 18, 2024 · Apr 18, 2024
diff --git a/.github/ISSUE_TEMPLATE/---bug-report.md b/.github/ISSUE_TEMPLATE/---bug-report.md
@@ -26,7 +26,7 @@ Steps to reproduce the behavior:
 
  - Slideflow Version (e.g., 1.0):
  - OS (e.g., Ubuntu):
- - How you installed PyTorch (`pip`, source):
+ - How you installed Slideflow (`pip`, source):
  - Python version:
  - CUDA/cuDNN version:
  - GPU models and configuration:

diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -20,6 +20,12 @@ jobs:
         python -m
         pip install -r requirements.txt
         --user
+    - name: Initialize submodule
+      run: >-
+        git submodule init
+    - name: Update submodule
+      run: >-
+        git submodule update --remote --recursive
     - name: Build a binary wheel
       run: >-
         python

diff --git a/.github/workflows/publish-to-test-pypi.yml b/.github/workflows/publish-to-test-pypi.yml
@@ -20,6 +20,12 @@ jobs:
         python -m
         pip install -r requirements.txt
         --user
+    - name: Initialize submodule
+      run: >-
+        git submodule init
+    - name: Update submodule
+      run: >-
+        git submodule update --remote --recursive
     - name: Build a binary wheel
       run: >-
         python

diff --git a/.gitignore b/.gitignore
@@ -1,8 +1,17 @@
 docs/build/*
 *.pyc
 *.egg-info
+*.ipynb_checkpoints
+*.pdf
+.vscode/*
 .neptune/*
 docs-source/build/*
+docs-source/pytorch_sphinx_theme/yarn.lock.backup
 build/*
 dist/*
-slideflow_test/*
+tutorials/*
+slideflow_test/*
+torch_test/*
+warn_report*.txt
+slideflow.log
+.DS_Store
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "slideflow/simclr/simclr"]
+	path = slideflow/simclr/simclr
+	url = https://github.com/jamesdolezal/simclr.git
diff --git a/LICENSE b/LICENSE
diff --git a/README.md b/README.md
diff --git a/datasets/breast_er/breast_er.json b/datasets/breast_er/breast_er.json
@@ -0,0 +1,4 @@
+{
+    "name": "TCGA_BRCA",
+    "annotations": "./breast_labels.csv"
+}
diff --git a/datasets/breast_er/breast_labels.csv b/datasets/breast_er/breast_labels.csv
diff --git a/datasets/gdc_manifest.tar.xz b/datasets/gdc_manifest.tar.xz
diff --git a/datasets/lung_adeno_squam/lung_adeno_squam.json b/datasets/lung_adeno_squam/lung_adeno_squam.json
@@ -0,0 +1,4 @@
+{
+    "name": "TCGA_LUNG",
+    "annotations": "./lung_labels.csv"
+}
diff --git a/datasets/lung_adeno_squam/lung_labels.csv b/datasets/lung_adeno_squam/lung_labels.csv
diff --git a/datasets/lung_adeno_squam/lung_labels_mini.csv b/datasets/lung_adeno_squam/lung_labels_mini.csv
@@ -0,0 +1,21 @@
+patient,subtype,site,slide
+TCGA-83-5908,adenocarcinoma,Site-28,TCGA-83-5908-01Z-00-DX1.381c8f82-61a0-4e9d-982d-1ad0af7bead9
+TCGA-62-A46V,adenocarcinoma,Site-124,TCGA-62-A46V-01Z-00-DX1.631E54D0-9E57-4932-B4EF-81820E56A95B
+TCGA-44-2655,adenocarcinoma,Site-29,TCGA-44-2655-01Z-00-DX1.ee255271-780c-461c-ab23-5cd3504b5e4a
+TCGA-05-4418,adenocarcinoma,Site-61,TCGA-05-4418-01Z-00-DX1.f3863ea5-564f-482f-9878-cc104cf69401
+TCGA-49-4487,adenocarcinoma,Site-69,TCGA-49-4487-01Z-00-DX1.3a3a0720-463c-430e-849b-e2f8991bdfa5
+TCGA-38-4631,adenocarcinoma,Site-130,TCGA-38-4631-01Z-00-DX1.5e0c873a-9c4c-4e0b-bf2e-e3cd8b760761
+TCGA-55-1594,adenocarcinoma,Site-67,TCGA-55-1594-01Z-00-DX1.bd90c500-7c0b-4c45-a3f7-2d9177384b1d
+TCGA-75-6207,adenocarcinoma,Site-93,TCGA-75-6207-01Z-00-DX1.837B7B0F-424C-423B-9045-A905E7C1C54C
+TCGA-MP-A4TD,adenocarcinoma,Site-180,TCGA-MP-A4TD-01Z-00-DX1.937DEBC9-F5D5-4682-AA9A-13D8226EE06C
+TCGA-78-7537,adenocarcinoma,Site-96,TCGA-78-7537-01Z-00-DX1.e5597e41-ebba-4d6f-8a1f-15cd81d8f026
+TCGA-21-A5DI,squamous,Site-40,TCGA-21-A5DI-01Z-00-DX1.E9123261-ADE7-468C-9E9A-334E131FFF97
+TCGA-43-5670,squamous,Site-29,TCGA-43-5670-01Z-00-DX1.1b5d262e-1f39-4f6f-883c-52101b57791f
+TCGA-18-3415,squamous,Site-97,TCGA-18-3415-01Z-00-DX1.8C62F2CD-4A2F-4D1E-A662-D7D5AFE557AB
+TCGA-43-2576,squamous,Site-29,TCGA-43-2576-01Z-00-DX1.779df209-95e1-4303-9c32-4083e8088d8e
+TCGA-33-4533,squamous,Site-69,TCGA-33-4533-01Z-00-DX1.ee36717d-0571-40b3-8ab5-5465d2cca920
+TCGA-NC-A5HT,squamous,Site-177,TCGA-NC-A5HT-01Z-00-DX1.9295B0E3-37FE-4914-AFB3-78B56C893B6D
+TCGA-56-8628,squamous,Site-67,TCGA-56-8628-01Z-00-DX1.AAC57164-E0F9-4DF0-87EA-5C50FB201895
+TCGA-63-A5MM,squamous,Site-93,TCGA-63-A5MM-01Z-00-DX1.F385687A-3741-4E73-87F1-D9B00B1B6186
+TCGA-21-1081,squamous,Site-40,TCGA-21-1081-01Z-00-DX1.fce8927a-2c5f-4a64-8414-da66424b3859
+TCGA-60-2707,squamous,Site-103,TCGA-60-2707-01Z-00-DX1.4aafd76b-eb0e-4ab9-a740-682c169a3c3d
diff --git a/datasets/thyroid_brs/thyroid_brs.json b/datasets/thyroid_brs/thyroid_brs.json
@@ -0,0 +1,4 @@
+{
+    "name": "TCGA_THCA",
+    "annotations": "./thyroid_labels.csv"
+}
diff --git a/datasets/thyroid_brs/thyroid_labels.csv b/datasets/thyroid_brs/thyroid_labels.csv
diff --git a/docs-source/pytorch_sphinx_theme/.circleci/config.yml b/docs-source/pytorch_sphinx_theme/.circleci/config.yml
@@ -0,0 +1,39 @@
+version: 2
+jobs:
+  build:
+    docker:
+      - image: circleci/node:7.10
+
+    working_directory: ~/repo
+
+    steps:
+      - add_ssh_keys:
+          fingerprints:
+            - "e0:f1:7b:8c:b1:4c:49:6f:b9:bd:af:84:6d:dd:93:cb"      
+      - checkout
+
+      - restore_cache:
+          keys:
+          - v1-dependencies-{{ checksum "package.json" }}
+          - v1-dependencies-
+
+      - run: yarn install
+
+      - save_cache:
+          paths:
+            - node_modules
+          key: v1-dependencies-{{ checksum "package.json" }}
+      - run: cp .circleci/mock.env.json .env.json
+      - run: grunt build
+      - run: git config credential.helper 'cache --timeout=120'
+      - run: git config user.email "ericnakagawa@gmail.com"
+      - run: git config user.name "CircleCI Bot"
+      - run: git add .
+      - run: git commit -m "Deploying theme build via CircleCI"
+      - run: git push -q git@github.com:pytorch/pytorch_sphinx_theme.git master
+
+workflows:
+  version: 2
+  commit-and-build:
+      jobs:
+        - build
diff --git a/docs-source/pytorch_sphinx_theme/.circleci/mock.env.json b/docs-source/pytorch_sphinx_theme/.circleci/mock.env.json
@@ -0,0 +1,4 @@
+{
+  "TUTORIALS_DIR": "../tutorials",
+  "DOCS_DIR": "../pytorch/docs/source"
+}
diff --git a/docs-source/pytorch_sphinx_theme/.gitattributes b/docs-source/pytorch_sphinx_theme/.gitattributes
@@ -0,0 +1,15 @@
+# Document global line endings settings
+# https://help.github.com/articles/dealing-with-line-endings/
+*       text eol=lf
+
+
+# Denote all files that are truly binary and should not be modified.
+*.ai    binary
+*.jpg   binary
+*.otf   binary
+*.png   binary
+*.eot   binary
+*.ttf   binary
+*.whl   binary
+*.woff  binary
+*.woff2 binary
diff --git a/docs-source/pytorch_sphinx_theme/.gitignore b/docs-source/pytorch_sphinx_theme/.gitignore
@@ -0,0 +1,12 @@
+*build/
+*.DS_Store
+*.map
+node_modules
+npm-debug.log
+yarn-error.log
+package-lock.json
+__pycache__
+.env.json
+dist/
+*.egg-info/
+scss/vendor/*
diff --git a/docs-source/pytorch_sphinx_theme/.nvmrc b/docs-source/pytorch_sphinx_theme/.nvmrc
@@ -0,0 +1 @@
+8.4.0
diff --git a/docs-source/pytorch_sphinx_theme/Gruntfile.js b/docs-source/pytorch_sphinx_theme/Gruntfile.js
@@ -39,8 +39,8 @@ module.exports = function(grunt) {
           {
               expand: true,
               flatten: true,
-              src: ['fonts/FreightSans/*'],
-              dest: 'pytorch_sphinx_theme/static/fonts/FreightSans',
+              src: ['fonts/IBMPlexSans/*'],
+              dest: 'pytorch_sphinx_theme/static/fonts/IBMPlexSans',
               filter: 'isFile'
           },
 

diff --git a/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-bold-italic.woff b/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-bold-italic.woff
diff --git a/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-bold-italic.woff2 b/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-bold-italic.woff2
diff --git a/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-bold.woff b/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-bold.woff
diff --git a/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-bold.woff2 b/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-bold.woff2
diff --git a/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-book-italic.woff b/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-book-italic.woff
diff --git a/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-book-italic.woff2 b/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-book-italic.woff2
diff --git a/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-book.woff b/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-book.woff
diff --git a/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-book.woff2 b/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-book.woff2
diff --git a/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-light-italic.woff b/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-light-italic.woff
diff --git a/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-light-italic.woff2 b/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-light-italic.woff2
diff --git a/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-light.woff b/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-light.woff
diff --git a/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-light.woff2 b/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-light.woff2
diff --git a/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-medium-italic.woff b/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-medium-italic.woff
diff --git a/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-medium-italic.woff2 b/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-medium-italic.woff2
diff --git a/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-medium.woff b/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-medium.woff
diff --git a/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-medium.woff2 b/docs-source/pytorch_sphinx_theme/fonts/FreightSans/freight-sans-medium.woff2
diff --git a/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-Bold.woff2 b/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-Bold.woff2
diff --git a/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-BoldItalic.woff2 b/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-BoldItalic.woff2
diff --git a/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-Italic.woff2 b/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-Italic.woff2
diff --git a/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-Light.woff2 b/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-Light.woff2
diff --git a/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-LightItalic.woff2 b/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-LightItalic.woff2
diff --git a/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-Medium.woff2 b/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-Medium.woff2
diff --git a/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-MediumItalic.woff2 b/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-MediumItalic.woff2
diff --git a/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-Regular.woff2 b/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-Regular.woff2
diff --git a/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-Thin.woff2 b/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-Thin.woff2
diff --git a/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-ThinItalic.woff2 b/docs-source/pytorch_sphinx_theme/fonts/IBMPlexSans/IBMPlexSans-ThinItalic.woff2
diff --git a/docs-source/pytorch_sphinx_theme/images/slideflow-banner.png b/docs-source/pytorch_sphinx_theme/images/slideflow-banner.png
diff --git a/docs-source/pytorch_sphinx_theme/pytorch_sphinx_theme/fonts.html b/docs-source/pytorch_sphinx_theme/pytorch_sphinx_theme/fonts.html
@@ -1,10 +1,10 @@
 <!-- Preload the theme fonts -->
 
-<link rel="preload" href="{{ pathto('_static/fonts/FreightSans/freight-sans-book.woff2', 1) }}" as="font" type="font/woff2" crossorigin="anonymous">
-<link rel="preload" href="{{ pathto('_static/fonts/FreightSans/freight-sans-medium.woff2', 1) }}" as="font" type="font/woff2" crossorigin="anonymous">
+<link rel="preload" href="{{ pathto('_static/fonts/IBMPlexSans/IBMPlexSans-Regular.ttf', 1) }}" as="font" type="font/woff2" crossorigin="anonymous">
+<link rel="preload" href="{{ pathto('_static/fonts/IBMPlexSans/IBMPlexSans-Medium.ttf', 1) }}" as="font" type="font/woff2" crossorigin="anonymous">
 <link rel="preload" href="{{ pathto('_static/fonts/IBMPlexMono/IBMPlexMono-Medium.woff2', 1) }}" as="font" type="font/woff2" crossorigin="anonymous">
-<link rel="preload" href="{{ pathto('_static/fonts/FreightSans/freight-sans-bold.woff2', 1) }}" as="font" type="font/woff2" crossorigin="anonymous">
-<link rel="preload" href="{{ pathto('_static/fonts/FreightSans/freight-sans-medium-italic.woff2', 1) }}" as="font" type="font/woff2" crossorigin="anonymous">
+<link rel="preload" href="{{ pathto('_static/fonts/IBMPlexSans/IBMPlexSans-Medium.ttf', 1) }}" as="font" type="font/woff2" crossorigin="anonymous">
+<link rel="preload" href="{{ pathto('_static/fonts/IBMPlexSans/IBMPlexSans-MediumItalic.ttf', 1) }}" as="font" type="font/woff2" crossorigin="anonymous">
 <link rel="preload" href="{{ pathto('_static/fonts/IBMPlexMono/IBMPlexMono-SemiBold.woff2', 1) }}" as="font" type="font/woff2" crossorigin="anonymous">
 
 <!-- Preload the katex fonts -->

diff --git a/docs-source/pytorch_sphinx_theme/pytorch_sphinx_theme/layout.html b/docs-source/pytorch_sphinx_theme/pytorch_sphinx_theme/layout.html
@@ -78,14 +78,7 @@
   {%- block extrahead %}
   <!-- Google Analytics -->
   {% if theme_analytics_id %}
-    <script async src="https://www.googletagmanager.com/gtag/js?id={{ theme_analytics_id }}"></script>
-    <script>
-      window.dataLayer = window.dataLayer || [];
-      function gtag(){dataLayer.push(arguments);}
-      gtag('js', new Date());
-
-      gtag('config', '{{ theme_analytics_id }}');
-    </script>
+    <script defer data-domain="slideflow.dev" src="https://plausible.io/js/script.js"></script>
   {% endif %}
   <!-- End Google Analytics -->
   {% endblock %}
@@ -95,15 +88,7 @@
 
   {% include "fonts.html" %}
   <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.15.2/css/all.css" integrity="sha384-vSIIfh2YWi9wW0r9iZe7RJPrKwp6bG+s9QZMoITbCckVJqGCCRhc+ccxNcdpHuYu" crossorigin="anonymous">
-  <!-- Global site tag (gtag.js) - Google Analytics -->
-  <script async src="https://www.googletagmanager.com/gtag/js?id=G-43E5QNVXH2"></script>
-  <script>
-    window.dataLayer = window.dataLayer || [];
-    function gtag(){dataLayer.push(arguments);}
-    gtag('js', new Date());
-
-    gtag('config', 'G-43E5QNVXH2');
-  </script>
+  <script defer data-domain="slideflow.dev" src="https://plausible.io/js/script.js"></script>
 </head>
 
 <div class="container-fluid header-holder tutorials-header" id="header-holder">
@@ -286,7 +271,7 @@
      {% endif %}
 
   {% endif %}
-
+  <script type="text/javascript" src="{{ pathto('_static/js/vendor/jquery-3.6.3.min.js', 1) }}"></script>
   <script type="text/javascript" src="{{ pathto('_static/js/vendor/popper.min.js', 1) }}"></script>
   <script type="text/javascript" src="{{ pathto('_static/js/vendor/bootstrap.min.js', 1) }}"></script>
   <script src="https://cdnjs.cloudflare.com/ajax/libs/list.js/1.5.0/list.min.js"></script>
@@ -338,7 +323,7 @@
   <!-- End Mobile Menu -->
 
   <script script type="text/javascript">
-    var collapsedSections = ['Source', 'Tutorials'];
+    var collapsedSections = [];
   </script>
 
   <script type="text/javascript" src="{{ pathto('_static/js/vendor/anchor.min.js', 1) }}"></script>

diff --git a/docs-source/pytorch_sphinx_theme/pytorch_sphinx_theme/static/css/theme.css b/docs-source/pytorch_sphinx_theme/pytorch_sphinx_theme/static/css/theme.css
diff --git a/docs-source/pytorch_sphinx_theme/pytorch_sphinx_theme/static/images/logo-icon.svg b/docs-source/pytorch_sphinx_theme/pytorch_sphinx_theme/static/images/logo-icon.svg
diff --git a/...h_sphinx_theme/pytorch_sphinx_theme/static/images/slideflow-logo-name-large.png b/...h_sphinx_theme/pytorch_sphinx_theme/static/images/slideflow-logo-name-large.png
diff --git a/docs-source/pytorch_sphinx_theme/pytorch_sphinx_theme/static/js/theme.js b/docs-source/pytorch_sphinx_theme/pytorch_sphinx_theme/static/js/theme.js
@@ -515,7 +515,6 @@ window.sideMenus = {
         "#pytorch-right-menu #pytorch-side-scroll-right \
          > ul > li > a.reference.internal"
       );
-
       for (var i = 0; i < titleLinks.length; i++) {
         var link = titleLinks[i];
 
@@ -534,7 +533,6 @@ window.sideMenus = {
       var menuLinks = document.querySelectorAll(
         "#pytorch-right-menu ul li ul li a.reference.internal"
       );
-
       for (var i = 0; i < menuLinks.length; i++) {
         if (
           menuLinks[i].nextElementSibling &&
@@ -633,16 +631,7 @@ window.sideMenus = {
   },
 
   handleLeftMenu: function () {
-    var windowHeight = utilities.windowHeight();
-    var topOfFooterRelativeToWindow = document.getElementById("docs-tutorials-resources").getBoundingClientRect().top;
-
-    if (topOfFooterRelativeToWindow >= windowHeight) {
-      document.getElementById("pytorch-left-menu").style.height = "100%";
-    } else {
-      var howManyPixelsOfTheFooterAreInTheWindow = windowHeight - topOfFooterRelativeToWindow;
-      var leftMenuDifference = howManyPixelsOfTheFooterAreInTheWindow;
-      document.getElementById("pytorch-left-menu").style.height = (windowHeight - leftMenuDifference) + "px";
-    }
+    document.getElementById("pytorch-left-menu").style.height = "100%";
   },
 
   handleRightMenu: function() {

diff --git a/docs-source/pytorch_sphinx_theme/pytorch_sphinx_theme/static/js/vendor/jquery-3.6.3.min.js b/docs-source/pytorch_sphinx_theme/pytorch_sphinx_theme/static/js/vendor/jquery-3.6.3.min.js