From e6cae1ced23f32feb2f42943d15b7dd49481c794 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Dec 2024 16:26:08 +0000 Subject: [PATCH 1/2] Bump codecov/codecov-action from 4 to 5 (#8245) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5.
Release notes

Sourced from codecov/codecov-action's releases.

v5.0.0

v5 Release

v5 of the Codecov GitHub Action will use the Codecov Wrapper to encapsulate the CLI. This will help ensure that the Action gets updates quicker.

Migration Guide

The v5 release also coincides with the opt-out feature for tokens for public repositories. In the Global Upload Token section of the settings page of an organization in codecov.io, you can set the ability for Codecov to receive a coverage reports from any source. This will allow contributors or other members of a repository to upload without needing access to the Codecov token. For more details see how to upload without a token.

[!WARNING]
The following arguments have been changed

  • file (this has been deprecated in favor of files)
  • plugin (this has been deprecated in favor of plugins)

The following arguments have been added:

You can see their usage in the action.yml file.

What's Changed

... (truncated)

Changelog

Sourced from codecov/codecov-action's changelog.

v5 Release

v5 of the Codecov GitHub Action will use the Codecov Wrapper to encapsulate the CLI. This will help ensure that the Action gets updates quicker.

Migration Guide

The v5 release also coincides with the opt-out feature for tokens for public repositories. In the Global Upload Token section of the settings page of an organization in codecov.io, you can set the ability for Codecov to receive a coverage reports from any source. This will allow contributors or other members of a repository to upload without needing access to the Codecov token. For more details see how to upload without a token.

[!WARNING] The following arguments have been changed

  • file (this has been deprecated in favor of files)
  • plugin (this has been deprecated in favor of plugins)

The following arguments have been added:

You can see their usage in the action.yml file.

What's Changed

... (truncated)

Commits

[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=codecov/codecov-action&package-manager=github_actions&previous-version=4&new-version=5)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) ---
Dependabot commands and options
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/cron.yml | 6 +++--- .github/workflows/pythonapp-gpu.yml | 2 +- .github/workflows/setupapp.yml | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml index 516e2d4743..e13848f8fc 100644 --- a/.github/workflows/cron.yml +++ b/.github/workflows/cron.yml @@ -75,7 +75,7 @@ jobs: if pgrep python; then pkill python; fi shell: bash - name: Upload coverage - uses: codecov/codecov-action@v4 + uses: codecov/codecov-action@v5 with: fail_ci_if_error: false files: ./coverage.xml @@ -123,7 +123,7 @@ jobs: if pgrep python; then pkill python; fi shell: bash - name: Upload coverage - uses: codecov/codecov-action@v4 + uses: codecov/codecov-action@v5 with: fail_ci_if_error: false files: ./coverage.xml @@ -228,7 +228,7 @@ jobs: if pgrep python; then pkill python; fi shell: bash - name: Upload coverage - uses: codecov/codecov-action@v4 + uses: codecov/codecov-action@v5 with: fail_ci_if_error: false files: ./coverage.xml diff --git a/.github/workflows/pythonapp-gpu.yml b/.github/workflows/pythonapp-gpu.yml index 70c3153076..d8623c8087 100644 --- a/.github/workflows/pythonapp-gpu.yml +++ b/.github/workflows/pythonapp-gpu.yml @@ -137,6 +137,6 @@ jobs: shell: bash - name: Upload coverage if: ${{ github.head_ref != 'dev' && github.event.pull_request.merged != true }} - uses: codecov/codecov-action@v4 + uses: codecov/codecov-action@v5 with: files: ./coverage.xml diff --git a/.github/workflows/setupapp.yml b/.github/workflows/setupapp.yml index 7e01f55cd9..d9ce9976b8 100644 --- a/.github/workflows/setupapp.yml +++ b/.github/workflows/setupapp.yml @@ -72,7 +72,7 @@ jobs: if pgrep python; then pkill python; fi shell: bash - name: Upload coverage - uses: codecov/codecov-action@v4 + uses: codecov/codecov-action@v5 with: fail_ci_if_error: false files: ./coverage.xml @@ -119,7 +119,7 @@ jobs: BUILD_MONAI=1 ./runtests.sh --build --quick --min coverage xml --ignore-errors - name: Upload coverage - uses: codecov/codecov-action@v4 + uses: codecov/codecov-action@v5 with: fail_ci_if_error: false files: ./coverage.xml From fe3ed448aba53f09d185f0decb95ca8debbff756 Mon Sep 17 00:00:00 2001 From: Vladislav Tumko <56307628+vectorvp@users.noreply.github.com> Date: Mon, 2 Dec 2024 10:37:51 +0400 Subject: [PATCH 2/2] docs: update brats classes description (#8246) Resolves #8225. ### Description Updated brats18 classes description. ### Types of changes - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [x] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Vladislav Tumko <56307628+vectorvp@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> --- monai/transforms/utility/array.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/monai/transforms/utility/array.py b/monai/transforms/utility/array.py index 84422a9ee5..2963c8a2f8 100644 --- a/monai/transforms/utility/array.py +++ b/monai/transforms/utility/array.py @@ -1054,12 +1054,11 @@ def __call__( class ConvertToMultiChannelBasedOnBratsClasses(Transform): """ - Convert labels to multi channels based on brats18 classes: - label 1 is the necrotic and non-enhancing tumor core - label 2 is the peritumoral edema - label 4 is the GD-enhancing tumor - The possible classes are TC (Tumor core), WT (Whole tumor) - and ET (Enhancing tumor). + Convert labels to multi channels based on `brats18 `_ classes, + which include TC (Tumor core), WT (Whole tumor) and ET (Enhancing tumor): + label 1 is the necrotic and non-enhancing tumor core, which should be counted under TC and WT subregion, + label 2 is the peritumoral edema, which is counted only under WT subregion, + label 4 is the GD-enhancing tumor, which should be counted under ET, TC, WT subregions. """ backend = [TransformBackends.TORCH, TransformBackends.NUMPY]