diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index fa558a692..e071e8da7 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -59,7 +59,7 @@ jobs: # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages steps: - name: Checkout repository - uses: actions/checkout@v6 + uses: actions/checkout@v7 # Add any setup steps before running the `github/codeql-action/init` action. # This includes steps like installing compilers or runtimes (`actions/setup-node` diff --git a/.github/workflows/cogstack-es_main.yml b/.github/workflows/cogstack-es_main.yml index f154b6cef..f9999ab63 100644 --- a/.github/workflows/cogstack-es_main.yml +++ b/.github/workflows/cogstack-es_main.yml @@ -26,7 +26,7 @@ jobs: max-parallel: 4 steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v6 with: @@ -51,7 +51,7 @@ jobs: max-parallel: 4 steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v6 with: @@ -72,7 +72,7 @@ jobs: needs: types-lint-tests steps: - name: Checkout main - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: fetch-depth: 0 # fetch all history fetch-tags: true # fetch tags explicitly diff --git a/.github/workflows/cogstack-es_release.yml b/.github/workflows/cogstack-es_release.yml index 0ef22974c..bc301043b 100644 --- a/.github/workflows/cogstack-es_release.yml +++ b/.github/workflows/cogstack-es_release.yml @@ -17,7 +17,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout main - uses: actions/checkout@v6 + uses: actions/checkout@v7 - name: Release Tag # If GITHUB_REF=refs/tags/cogstack-es/v0.1.2, this returns v0.1.2. Note it's including the "v" though it probably shouldnt diff --git a/.github/workflows/medcat-den_main.yml b/.github/workflows/medcat-den_main.yml index 7ba3f6bf0..cc53d343c 100644 --- a/.github/workflows/medcat-den_main.yml +++ b/.github/workflows/medcat-den_main.yml @@ -23,7 +23,7 @@ jobs: python-version: [ '3.10', '3.11', '3.12' ] max-parallel: 4 steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - name: Install uv for Python ${{ matrix.python-version }} uses: astral-sh/setup-uv@v7 with: @@ -50,7 +50,7 @@ jobs: needs: build steps: - name: Checkout main - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: fetch-depth: 0 # fetch all history fetch-tags: true # fetch tags explicitly diff --git a/.github/workflows/medcat-den_release.yml b/.github/workflows/medcat-den_release.yml index 2abcdc60a..d947aa65a 100644 --- a/.github/workflows/medcat-den_release.yml +++ b/.github/workflows/medcat-den_release.yml @@ -17,7 +17,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout main - uses: actions/checkout@v6 + uses: actions/checkout@v7 - name: Release Tag # If GITHUB_REF=refs/tags/medcat-den/v0.1.2, this returns v0.1.2. Note it's including the "v" though it probably shouldnt diff --git a/.github/workflows/medcat-deps-update.yml b/.github/workflows/medcat-deps-update.yml index c4adfadd5..6adfb9c65 100644 --- a/.github/workflows/medcat-deps-update.yml +++ b/.github/workflows/medcat-deps-update.yml @@ -15,7 +15,7 @@ jobs: steps: - name: Checkout repo - uses: actions/checkout@v6 + uses: actions/checkout@v7 - name: Extract version from tag id: version diff --git a/.github/workflows/medcat-embedding-linker_ci.yml b/.github/workflows/medcat-embedding-linker_ci.yml index 2d1027b69..2876d784b 100644 --- a/.github/workflows/medcat-embedding-linker_ci.yml +++ b/.github/workflows/medcat-embedding-linker_ci.yml @@ -25,7 +25,7 @@ jobs: python-version: [ '3.10', '3.11', '3.12' ] max-parallel: 4 steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - name: Install uv for Python ${{ matrix.python-version }} uses: astral-sh/setup-uv@v7 with: @@ -52,7 +52,7 @@ jobs: needs: build steps: - name: Checkout main - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: fetch-depth: 0 # fetch all history fetch-tags: true # fetch tags explicitly @@ -88,7 +88,7 @@ jobs: needs: build steps: - name: Checkout main - uses: actions/checkout@v6 + uses: actions/checkout@v7 - name: Install uv for Python 3.10 uses: astral-sh/setup-uv@v7 diff --git a/.github/workflows/medcat-gliner_ci.yml b/.github/workflows/medcat-gliner_ci.yml index 48c5f4f91..a091a8cac 100644 --- a/.github/workflows/medcat-gliner_ci.yml +++ b/.github/workflows/medcat-gliner_ci.yml @@ -31,7 +31,7 @@ jobs: max-parallel: 4 steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - name: Install uv for Python ${{ matrix.python-version }} uses: astral-sh/setup-uv@v7 @@ -63,7 +63,7 @@ jobs: needs: tests steps: - name: Checkout main - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: fetch-depth: 0 # fetch all history fetch-tags: true # fetch tags explicitly @@ -99,7 +99,7 @@ jobs: needs: tests steps: - name: Checkout main - uses: actions/checkout@v6 + uses: actions/checkout@v7 - name: Install uv for Python 3.10 uses: astral-sh/setup-uv@v7 diff --git a/.github/workflows/medcat-model-distributor_build.yml b/.github/workflows/medcat-model-distributor_build.yml index ee2ee017a..6d9248041 100644 --- a/.github/workflows/medcat-model-distributor_build.yml +++ b/.github/workflows/medcat-model-distributor_build.yml @@ -22,7 +22,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - name: 🧹 Free up disk space run: | @@ -61,7 +61,7 @@ jobs: needs: integration-test steps: - name: Checkout - uses: actions/checkout@v6 + uses: actions/checkout@v7 - name: Log in to Docker Hub uses: docker/login-action@v4 diff --git a/.github/workflows/medcat-scripts_main.yml b/.github/workflows/medcat-scripts_main.yml index d8f083e34..b7dd6b8e0 100644 --- a/.github/workflows/medcat-scripts_main.yml +++ b/.github/workflows/medcat-scripts_main.yml @@ -22,7 +22,7 @@ jobs: python-version: [ '3.10', '3.11', '3.12', '3.13' ] max-parallel: 4 steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - name: Install uv for Python ${{ matrix.python-version }} uses: astral-sh/setup-uv@v7 with: diff --git a/.github/workflows/medcat-service_docker.yml b/.github/workflows/medcat-service_docker.yml index 8eae5b82f..01937a206 100644 --- a/.github/workflows/medcat-service_docker.yml +++ b/.github/workflows/medcat-service_docker.yml @@ -22,7 +22,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout - uses: actions/checkout@v6 + uses: actions/checkout@v7 - name: 🧹 Free up disk space run: | diff --git a/.github/workflows/medcat-service_run-tests.yml b/.github/workflows/medcat-service_run-tests.yml index 936e56484..9cfb9fb26 100644 --- a/.github/workflows/medcat-service_run-tests.yml +++ b/.github/workflows/medcat-service_run-tests.yml @@ -18,11 +18,11 @@ jobs: runs-on: ubuntu-latest steps: - name: checkout repo - uses: actions/checkout@v6 + uses: actions/checkout@v7 - name: Cache MedMen Model id: cache-medmen - uses: actions/cache@v5 + uses: actions/cache@v6 with: path: models/medmen key: medmen-${{ hashFiles('medcat-service/scripts/download_medmen.sh') }} diff --git a/.github/workflows/medcat-trainer-v1_ci.yml b/.github/workflows/medcat-trainer-v1_ci.yml index b29ca5016..c16aed720 100644 --- a/.github/workflows/medcat-trainer-v1_ci.yml +++ b/.github/workflows/medcat-trainer-v1_ci.yml @@ -16,7 +16,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout main - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: ref: ${{ github.ref }} diff --git a/.github/workflows/medcat-trainer-v1_qa.yml b/.github/workflows/medcat-trainer-v1_qa.yml index ef937f81c..e95622034 100644 --- a/.github/workflows/medcat-trainer-v1_qa.yml +++ b/.github/workflows/medcat-trainer-v1_qa.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout main - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: ref: 'main' diff --git a/.github/workflows/medcat-trainer-v1_release.yml b/.github/workflows/medcat-trainer-v1_release.yml index 29659cfc2..0dbe2e4ea 100644 --- a/.github/workflows/medcat-trainer-v1_release.yml +++ b/.github/workflows/medcat-trainer-v1_release.yml @@ -15,7 +15,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout main - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: ref: "main" diff --git a/.github/workflows/medcat-trainer_ci.yml b/.github/workflows/medcat-trainer_ci.yml index b9ca71e02..30e1eb7bd 100644 --- a/.github/workflows/medcat-trainer_ci.yml +++ b/.github/workflows/medcat-trainer_ci.yml @@ -23,7 +23,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout main - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: ref: ${{ github.ref }} @@ -65,7 +65,7 @@ jobs: - name: Upload client coverage report if: always() - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@v7 with: name: client-coverage path: | @@ -107,7 +107,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout main - uses: actions/checkout@v6 + uses: actions/checkout@v7 - name: Set up Node.js uses: actions/setup-node@v6 @@ -140,7 +140,7 @@ jobs: - name: Upload frontend coverage report if: always() - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@v7 with: name: frontend-coverage path: medcat-trainer/webapp/frontend/coverage @@ -155,7 +155,7 @@ jobs: - local # tests against ../medcat-v2 steps: - name: Checkout main - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: ref: ${{ github.ref }} @@ -226,7 +226,7 @@ jobs: - name: Upload backend coverage report if: always() - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@v7 with: name: backend-coverage path: | @@ -245,7 +245,7 @@ jobs: image_version: ${{ steps.meta.outputs.version }} steps: - name: Checkout main - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: ref: ${{ github.ref }} diff --git a/.github/workflows/medcat-v1-tutorials_main.yml b/.github/workflows/medcat-v1-tutorials_main.yml index 25bf32479..b986c1d43 100644 --- a/.github/workflows/medcat-v1-tutorials_main.yml +++ b/.github/workflows/medcat-v1-tutorials_main.yml @@ -31,7 +31,7 @@ jobs: ] steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - name: Setup Python uses: actions/setup-python@v6 with: diff --git a/.github/workflows/medcat-v1_main.yml b/.github/workflows/medcat-v1_main.yml index 2cf6d22d1..6b74ad8d3 100644 --- a/.github/workflows/medcat-v1_main.yml +++ b/.github/workflows/medcat-v1_main.yml @@ -20,7 +20,7 @@ jobs: max-parallel: 4 steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v6 with: @@ -102,7 +102,7 @@ jobs: steps: - name: Checkout main - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: ref: 'main' fetch-depth: 0 diff --git a/.github/workflows/medcat-v1_production.yml b/.github/workflows/medcat-v1_production.yml index 91832b290..ebd6b15f1 100644 --- a/.github/workflows/medcat-v1_production.yml +++ b/.github/workflows/medcat-v1_production.yml @@ -24,7 +24,7 @@ jobs: steps: - name: Checkout production - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: ref: ${{ github.event.release.target_commitish }} fetch-depth: 0 diff --git a/.github/workflows/medcat-v2-lib-stability.yml b/.github/workflows/medcat-v2-lib-stability.yml index 024eefd9e..ec94198b4 100644 --- a/.github/workflows/medcat-v2-lib-stability.yml +++ b/.github/workflows/medcat-v2-lib-stability.yml @@ -18,7 +18,7 @@ jobs: warm_hf_cache: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - uses: astral-sh/setup-uv@v7 with: # start at lowest possible @@ -52,7 +52,7 @@ jobs: python-version: [ "3.10", "3.11", "3.12", "3.13"] steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - uses: actions/download-artifact@v8 with: name: hf-cache diff --git a/.github/workflows/medcat-v2-tutorials_main.yml b/.github/workflows/medcat-v2-tutorials_main.yml index c7fe8eb3c..c5d18b50e 100644 --- a/.github/workflows/medcat-v2-tutorials_main.yml +++ b/.github/workflows/medcat-v2-tutorials_main.yml @@ -17,7 +17,7 @@ jobs: basic-and-meta: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - name: Setup Python uses: actions/setup-python@v6 with: @@ -61,7 +61,7 @@ jobs: ] steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - name: Setup Python uses: actions/setup-python@v6 with: diff --git a/.github/workflows/medcat-v2_main.yml b/.github/workflows/medcat-v2_main.yml index 4efb4dbf4..a48888b16 100644 --- a/.github/workflows/medcat-v2_main.yml +++ b/.github/workflows/medcat-v2_main.yml @@ -14,14 +14,14 @@ jobs: test-resource-utils: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - name: Check test utils are in sync run: diff tests/resource_fetch.py ../medcat-den/tests/resource_fetch.py base-install-imports: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 # NOTE: using oldest supported python version - name: Install uv for Python 3.10 uses: astral-sh/setup-uv@v7 @@ -43,7 +43,7 @@ jobs: python-version: [ '3.10', '3.11', '3.12', '3.13' ] max-parallel: 5 steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - name: Install uv for Python ${{ matrix.python-version }} uses: astral-sh/setup-uv@v7 with: diff --git a/.github/workflows/medcat-v2_release.yml b/.github/workflows/medcat-v2_release.yml index 17e4a540a..ad9176058 100644 --- a/.github/workflows/medcat-v2_release.yml +++ b/.github/workflows/medcat-v2_release.yml @@ -24,7 +24,7 @@ jobs: version_only: ${{ steps.extract.outputs.version_only }} steps: - name: Checkout repository - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: fetch-depth: 0 @@ -85,7 +85,7 @@ jobs: python-version: ["3.10", "3.11", "3.12"] steps: - name: Checkout repository - uses: actions/checkout@v6 + uses: actions/checkout@v7 - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v6 diff --git a/.github/workflows/upload-test-models-to-release.yml b/.github/workflows/upload-test-models-to-release.yml index c362b8fb3..cd3c245ef 100644 --- a/.github/workflows/upload-test-models-to-release.yml +++ b/.github/workflows/upload-test-models-to-release.yml @@ -12,7 +12,7 @@ jobs: upload-test-models: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - name: Upload test models to release env: