Merge branch 'master' into add-pyndantic-config

# Conflicts:
#	setup.py

.devcontainer/onCreateCommand.sh

@@ -6,4 +6,4 @@ pip install wheel
 pip install openvino-dev==2023.0.1 # [OPTIONAL] to generate optimized models for inference
 pip install mlcube_docker          # [OPTIONAL] to deploy GaNDLF models as MLCube-compliant Docker containers
 pip install medmnist==2.1.0
-pip install torch==2.3.1 torchvision==0.18.1 torchaudio==2.3.1 --index-url https://download.pytorch.org/whl/cpu
+pip install torch==2.5.0 torchvision==0.20.0 torchaudio==2.5.0 --index-url https://download.pytorch.org/whl/cpu

.devcontainer/postCreateCommand.sh

@@ -6,7 +6,7 @@
 # if runnning on a GPU machine, install the GPU version of pytorch
 if command -v nvidia-smi &> /dev/null
 then
-	pip install torch==2.3.1 torchvision==0.18.1 torchaudio==2.3.1 --index-url https://download.pytorch.org/whl/cu121
+	pip install torch==2.5.0 torchvision==0.20.0 torchaudio==2.5.0 --index-url https://download.pytorch.org/whl/cu121
 fi
 
 pip install -e .

.github/workflows/dependencies/action.yml

@@ -100,5 +100,5 @@ runs:
           python -m pip install --upgrade pip==24.0
           python -m pip install wheel
           python -m pip install openvino-dev==2023.0.1 mlcube_docker
-          pip install torch==2.3.1 torchvision==0.18.1 torchaudio==2.3.1 --index-url https://download.pytorch.org/whl/cpu
+          pip install torch==2.5.0 torchvision==0.20.0 torchaudio==2.5.0 --index-url https://download.pytorch.org/whl/cpu
           pip install -e .

.github/workflows/spellchecker.yml

@@ -0,0 +1,186 @@
+name: Check Spelling
+
+# Comment management is handled through a secondary job, for details see:
+# https://github.com/check-spelling/check-spelling/wiki/Feature%3A-Restricted-Permissions
+#
+# `jobs.comment-push` runs when a push is made to a repository and the `jobs.spelling` job needs to make a comment
+#   (in odd cases, it might actually run just to collapse a comment, but that's fairly rare)
+#   it needs `contents: write` in order to add a comment.
+#
+# `jobs.comment-pr` runs when a pull_request is made to a repository and the `jobs.spelling` job needs to make a comment
+#   or collapse a comment (in the case where it had previously made a comment and now no longer needs to show a comment)
+#   it needs `pull-requests: write` in order to manipulate those comments.
+
+# Updating pull request branches is managed via comment handling.
+# For details, see: https://github.com/check-spelling/check-spelling/wiki/Feature:-Update-expect-list
+#
+# These elements work together to make it happen:
+#
+# `on.issue_comment`
+#   This event listens to comments by users asking to update the metadata.
+#
+# `jobs.update`
+#   This job runs in response to an issue_comment and will push a new commit
+#   to update the spelling metadata.
+#
+# `with.experimental_apply_changes_via_bot`
+#   Tells the action to support and generate messages that enable it
+#   to make a commit to update the spelling metadata.
+#
+# `with.ssh_key`
+#   In order to trigger workflows when the commit is made, you can provide a
+#   secret (typically, a write-enabled github deploy key).
+#
+#   For background, see: https://github.com/check-spelling/check-spelling/wiki/Feature:-Update-with-deploy-key
+
+# Sarif reporting
+#
+# Access to Sarif reports is generally restricted (by GitHub) to members of the repository.
+#
+# Requires enabling `security-events: write`
+# and configuring the action with `use_sarif: 1`
+#
+#   For information on the feature, see: https://github.com/check-spelling/check-spelling/wiki/Feature:-Sarif-output
+
+# Minimal workflow structure:
+#
+# on:
+#   push:
+#     ...
+#   pull_request_target:
+#     ...
+# jobs:
+#   # you only want the spelling job, all others should be omitted
+#   spelling:
+#     # remove `security-events: write` and `use_sarif: 1`
+#     # remove `experimental_apply_changes_via_bot: 1`
+#     ... otherwise adjust the `with:` as you wish
+
+on:
+  push:
+    branches:
+    - "**"
+    tags-ignore:
+    - "**"
+  pull_request_target:
+    branches:
+    - "**"
+    types:
+    - 'opened'
+    - 'reopened'
+    - 'synchronize'
+  issue_comment:
+    types:
+    - 'created'
+
+jobs:
+  spelling:
+    name: Check Spelling
+    permissions:
+      contents: read
+      pull-requests: read
+      actions: read
+      security-events: write
+    outputs:
+      followup: ${{ steps.spelling.outputs.followup }}
+    runs-on: ubuntu-latest
+    if: ${{ contains(github.event_name, 'pull_request') || github.event_name == 'push' }}
+    concurrency:
+      group: spelling-${{ github.event.pull_request.number || github.ref }}
+      # note: If you use only_check_changed_files, you do not want cancel-in-progress
+      cancel-in-progress: true
+    steps:
+    - name: check-spelling
+      id: spelling
+      uses: check-spelling/check-spelling@main
+      with:
+        config: .spelling
+        checkout: true
+        check_file_names: 1
+        spell_check_this: check-spelling/spell-check-this@prerelease
+        post_comment: 0
+        use_magic_file: 1
+        report-timing: 1
+        warnings: bad-regex,binary-file,deprecated-feature,large-file,limited-references,no-newline-at-eof,noisy-file,non-alpha-in-dictionary,token-is-substring,unexpected-line-ending,whitespace-in-dictionary,minified-file,unsupported-configuration,no-files-to-check
+        experimental_apply_changes_via_bot: 1
+        use_sarif: ${{ (!github.event.pull_request || (github.event.pull_request.head.repo.full_name == github.repository)) && 1 }}
+        extra_dictionary_limit: 20
+        extra_dictionaries:
+          cspell:software-terms/dict/softwareTerms.txt
+          cspell:python/src/python/python-lib.txt
+          cspell:python/src/python/python.txt
+          cspell:python/src/common/extra.txt
+          cspell:php/dict/php.txt
+          cspell:r/src/r.txt
+          cspell:aws/aws.txt
+          cspell:django/dict/django.txt
+          cspell:filetypes/filetypes.txt
+          cspell:node/dict/node.txt
+          cspell:golang/dict/go.txt
+          cspell:fullstack/dict/fullstack.txt
+          cspell:java/src/java.txt
+          cspell:k8s/dict/k8s.txt
+          cspell:css/dict/css.txt
+          cspell:npm/dict/npm.txt
+          cspell:latex/dict/latex.txt
+          cspell:latex/samples/sample-words.txt
+          cspell:html-symbol-entities/entities.txt
+          cspell:html/dict/html.txt
+          cspell:cpp/src/ecosystem.txt
+          cspell:mnemonics/src/mnemonics.txt
+
+  comment-push:
+    name: Report (Push)
+    # If your workflow isn't running on push, you can remove this job
+    runs-on: ubuntu-latest
+    needs: spelling
+    permissions:
+      contents: write
+    if: (success() || failure()) && needs.spelling.outputs.followup && github.event_name == 'push'
+    steps:
+    - name: comment
+      uses: check-spelling/check-spelling@main
+      with:
+        checkout: true
+        spell_check_this: check-spelling/spell-check-this@prerelease
+        task: ${{ needs.spelling.outputs.followup }}
+
+  comment-pr:
+    name: Report (PR)
+    # If you workflow isn't running on pull_request*, you can remove this job
+    runs-on: ubuntu-latest
+    needs: spelling
+    permissions:
+      contents: read
+      pull-requests: write
+    if: (success() || failure()) && needs.spelling.outputs.followup && contains(github.event_name, 'pull_request')
+    steps:
+    - name: comment
+      uses: check-spelling/check-spelling@main
+      with:
+        checkout: true
+        spell_check_this: check-spelling/spell-check-this@prerelease
+        task: ${{ needs.spelling.outputs.followup }}
+        experimental_apply_changes_via_bot: 1
+
+  update:
+    name: Update PR
+    permissions:
+      contents: write
+      pull-requests: write
+      actions: read
+    runs-on: ubuntu-latest
+    if: ${{
+        github.event_name == 'issue_comment' &&
+        github.event.issue.pull_request &&
+        contains(github.event.comment.body, '@check-spelling-bot apply')}}
+    concurrency:
+      group: spelling-update-${{ github.event.issue.number }}
+      cancel-in-progress: false
+    steps:
+    - name: apply spelling updates
+      uses: check-spelling/check-spelling@main
+      with:
+        experimental_apply_changes_via_bot: 1
+        checkout: true
+        ssh_key: "${{ secrets.CHECK_SPELLING }}"

.gitignore

@@ -25,6 +25,7 @@ testing/config_segmentation_temp.yaml
 testing/failures.log
 coverage.xml
 mlcube/workspace/*
+!.spelling/.spelling/expect.txt
 !mlcube/workspace/config.yml
 !mlcube/workspace/channelIDs.yml
 tutorials/classification_medmnist_notebook/dataset/pathmnist