diff --git a/.github/workflows/EVENT_merge_to_master.yml b/.github/workflows/EVENT_merge_to_master.yml index a3215c494..d49415792 100644 --- a/.github/workflows/EVENT_merge_to_master.yml +++ b/.github/workflows/EVENT_merge_to_master.yml @@ -7,6 +7,9 @@ on: - master workflow_call: +permissions: + contents: read + concurrency: group: ${{ github.workflow }}-${{ github.ref }} cancel-in-progress: true @@ -24,7 +27,7 @@ jobs: warn_on_fail: needs: [run_tests, documentation] - if : ${{ failure() }} + if: ${{ failure() }} name: Slack message us on fail uses: ./.github/workflows/JOB_slack_message.yml secrets: inherit @@ -35,9 +38,12 @@ jobs: success: needs: [run_tests, documentation] - if : ${{ success() }} + if: ${{ success() }} name: Success runs-on: ubuntu-latest + permissions: + contents: write + statuses: write steps: - name: Harden Runner uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1 diff --git a/.github/workflows/EVENT_pull_request.yml b/.github/workflows/EVENT_pull_request.yml index 8e8944268..7c9f50e40 100644 --- a/.github/workflows/EVENT_pull_request.yml +++ b/.github/workflows/EVENT_pull_request.yml @@ -5,6 +5,8 @@ on: pull_request: types: [opened, synchronize, reopened] +permissions: + contents: read # Prevent running concurrently concurrency: @@ -16,6 +18,8 @@ jobs: get_changed_files: name: Get changed files uses: ./.github/workflows/JOB_get_changed_files.yml + permissions: + contents: read format: name: Check format of python @@ -23,6 +27,8 @@ jobs: uses: ./.github/workflows/JOB_format.yml with: files: ${{ needs.get_changed_files.outputs.python_changed_files }} + permissions: + contents: read lint: name: Lint python @@ -30,6 +36,8 @@ jobs: uses: ./.github/workflows/JOB_lint.yml with: files: ${{ needs.get_changed_files.outputs.python_changed_files }} + permissions: + contents: read # typecheck: # name: Analyse types in python @@ -37,8 +45,11 @@ jobs: # uses: ./.github/workflows/JOB_typecheck.yml # with: # files: ${{ needs.get_changed_files.outputs.python_changed_files }} + # permissions: + # contents: read run_tests: name: Run tests uses: ./.github/workflows/JOB_tests.yml - + permissions: + contents: read diff --git a/.github/workflows/EVENT_release.yml b/.github/workflows/EVENT_release.yml index a43ddc407..7341c249b 100644 --- a/.github/workflows/EVENT_release.yml +++ b/.github/workflows/EVENT_release.yml @@ -22,6 +22,9 @@ on: description: "Is the release a draft" required: false +permissions: + contents: read + env: release_id: ${{ inputs.release_id || github.event.release.id }} release_tag: ${{ inputs.release_tag || github.event.release.tag_name }} @@ -31,6 +34,8 @@ env: jobs: validate_tag: runs-on: ubuntu-latest + permissions: + contents: read steps: - name: Harden Runner uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1 @@ -70,6 +75,7 @@ jobs: runs-on: ubuntu-latest permissions: id-token: write + contents: write steps: - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7 with: @@ -98,6 +104,7 @@ jobs: runs-on: ubuntu-latest permissions: id-token: write + contents: write steps: - name: Harden Runner uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1 diff --git a/.github/workflows/EVENT_tag.yml b/.github/workflows/EVENT_tag.yml index 15a672f24..e0ac39292 100644 --- a/.github/workflows/EVENT_tag.yml +++ b/.github/workflows/EVENT_tag.yml @@ -21,6 +21,8 @@ jobs: create_release: name: Create Release runs-on: ubuntu-latest + permissions: + contents: write steps: - name: Harden Runner uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1 @@ -41,4 +43,3 @@ jobs: release_name: ${{ github.ref }} draft: true prerelease: false - diff --git a/.github/workflows/EVENT_update-linear-labels.yml b/.github/workflows/EVENT_update-linear-labels.yml index d221d10f8..a95b76b7f 100644 --- a/.github/workflows/EVENT_update-linear-labels.yml +++ b/.github/workflows/EVENT_update-linear-labels.yml @@ -1,5 +1,8 @@ name: "Update Linear Labels" +permissions: + contents: read + on: pull_request: branches: [master] @@ -10,6 +13,8 @@ jobs: if: github.ref_name != 'master' && !github.event.pull_request.head.repo.fork name: Update Linear runs-on: ubuntu-latest + permissions: + contents: write steps: - name: Harden Runner uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1 diff --git a/.github/workflows/JOB_check-master-can-release.yml b/.github/workflows/JOB_check-master-can-release.yml index d6c8f7120..aecc78304 100644 --- a/.github/workflows/JOB_check-master-can-release.yml +++ b/.github/workflows/JOB_check-master-can-release.yml @@ -4,9 +4,14 @@ run-name: check-master-can-release on: workflow_call: +permissions: + contents: read + jobs: check-master-can-release: runs-on: ubuntu-latest + permissions: + contents: read steps: - name: Harden Runner uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1 @@ -48,4 +53,3 @@ jobs: if (commits.length === 0) { throw new Error('No commits in master since last release'); } - diff --git a/.github/workflows/JOB_e2e.yml b/.github/workflows/JOB_e2e.yml index e6861bccc..9fc8d1705 100644 --- a/.github/workflows/JOB_e2e.yml +++ b/.github/workflows/JOB_e2e.yml @@ -1,5 +1,8 @@ name: E2E Tests +permissions: + contents: read + on: schedule: - cron: "0 8 * * mon-fri" @@ -18,6 +21,8 @@ on: jobs: e2e: name: End to End Testing + permissions: + contents: read strategy: fail-fast: false matrix: @@ -59,6 +64,8 @@ jobs: name: Slack Notifier Bot needs: e2e if: failure() && github.event_name == 'schedule' + permissions: + contents: read uses: ./.github/workflows/JOB_slack_message.yml with: message: | diff --git a/.github/workflows/JOB_lint.yml b/.github/workflows/JOB_lint.yml index 861e134c1..3aa556782 100644 --- a/.github/workflows/JOB_lint.yml +++ b/.github/workflows/JOB_lint.yml @@ -9,10 +9,15 @@ on: description: "Files to lint" required: true +permissions: + contents: read + jobs: lint: if: ${{ inputs.files != '' }} runs-on: ubuntu-latest + permissions: + contents: read steps: - name: Harden Runner uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1 @@ -33,4 +38,3 @@ jobs: - name: Ruff Lint shell: bash run: bash ${{ github.workspace }}/deploy/format_lint.sh lint ${{ inputs.files }} - diff --git a/.github/workflows/JOB_typecheck.yml b/.github/workflows/JOB_typecheck.yml index ba61f4e99..1ca9d2348 100644 --- a/.github/workflows/JOB_typecheck.yml +++ b/.github/workflows/JOB_typecheck.yml @@ -36,6 +36,5 @@ jobs: - name: MyPy typecheck shell: bash run: | - pip install pydantic + pip install pydantic==2.8.2 bash ${{ github.workspace }}/deploy/format_lint.sh typecheck ${{ inputs.files }} - diff --git a/darwin/exporter/formats/nifti.py b/darwin/exporter/formats/nifti.py index 447f83731..9a861e8dc 100644 --- a/darwin/exporter/formats/nifti.py +++ b/darwin/exporter/formats/nifti.py @@ -14,7 +14,7 @@ import nibabel as nib from nibabel.orientations import io_orientation, ornt_transform except ImportError: - import_fail_string = """ + import_fail_string = r""" You must install darwin-py with pip install darwin-py\[medical] in order to export using nifti format """ diff --git a/darwin/future/data_objects/dataset.py b/darwin/future/data_objects/dataset.py index 134a50f5a..aff98152f 100644 --- a/darwin/future/data_objects/dataset.py +++ b/darwin/future/data_objects/dataset.py @@ -1,6 +1,6 @@ from typing import List, Optional -from pydantic import PositiveInt, validator +from pydantic import PositiveInt, field_validator from darwin.future.data_objects.release import ReleaseList from darwin.future.data_objects.validators import parse_name @@ -30,7 +30,7 @@ class DatasetCore(DefaultDarwin): releases: Optional[ReleaseList] = None # Data Validation - _name_validator = validator("name", allow_reuse=True)(parse_name) + _name_validator = field_validator("name")(parse_name) DatasetList = List[DatasetCore] diff --git a/darwin/future/data_objects/release.py b/darwin/future/data_objects/release.py index c7e5063e7..2c4b3f68e 100644 --- a/darwin/future/data_objects/release.py +++ b/darwin/future/data_objects/release.py @@ -1,6 +1,6 @@ from typing import List -from pydantic import validator +from pydantic import field_validator from darwin.future.data_objects import validators as darwin_validators from darwin.future.pydantic_base import DefaultDarwin @@ -26,7 +26,7 @@ def __str__(self) -> str: return self.name # Data Validation - _name_validator = validator("name", allow_reuse=True)(darwin_validators.parse_name) + _name_validator = field_validator("name")(darwin_validators.parse_name) ReleaseList = List[ReleaseCore] diff --git a/darwin/future/data_objects/sorting.py b/darwin/future/data_objects/sorting.py index bfb7b9c3a..b7bd8edd4 100644 --- a/darwin/future/data_objects/sorting.py +++ b/darwin/future/data_objects/sorting.py @@ -1,6 +1,6 @@ from typing import Literal, Optional -from pydantic import BaseModel, Field, root_validator +from pydantic import BaseModel, Field, model_validator class SortingMethods(BaseModel): @@ -12,7 +12,7 @@ class SortingMethods(BaseModel): priority: Optional[Literal["asc", "desc"]] = Field(None) updated_at: Optional[Literal["asc", "desc"]] = Field(None) - @root_validator(pre=True) + @model_validator(mode="before") def check_at_least_one_field(cls, values): assert any(value is not None for value in values.values()) return values diff --git a/darwin/future/data_objects/team.py b/darwin/future/data_objects/team.py index e23d1ccce..9c54e0430 100644 --- a/darwin/future/data_objects/team.py +++ b/darwin/future/data_objects/team.py @@ -2,7 +2,7 @@ from typing import List, Optional -from pydantic import validator +from pydantic import field_validator from darwin.future.core.client import ClientCore from darwin.future.core.team.get_raw import get_team_raw @@ -56,7 +56,7 @@ class TeamCore(DefaultDarwin): default_role: TeamMemberRole = TeamMemberRole.USER # Data Validation - _slug_validator = validator("slug", allow_reuse=True)(parse_name) + _slug_validator = field_validator("slug")(parse_name) @staticmethod def from_client(client: ClientCore, team_slug: Optional[str] = None) -> TeamCore: diff --git a/darwin/importer/formats/nifti.py b/darwin/importer/formats/nifti.py index cf4e530d6..e871b2532 100644 --- a/darwin/importer/formats/nifti.py +++ b/darwin/importer/formats/nifti.py @@ -15,7 +15,7 @@ import nibabel as nib from scipy.ndimage import zoom except ImportError: - import_fail_string = """ + import_fail_string = r""" You must install darwin-py with pip install darwin-py\[medical] in order to import using nifti format """ diff --git a/deploy/_filter_files.py b/deploy/_filter_files.py index ae183fa44..23856c96d 100755 --- a/deploy/_filter_files.py +++ b/deploy/_filter_files.py @@ -11,11 +11,7 @@ def main(argv: List[str]) -> None: if file_extension.startswith("."): file_extension = file_extension[1:] - files_out = [ - file - for file in files_in - if file.endswith(f".{file_extension}") and "future" in file - ] + files_out = [file for file in files_in if file.endswith(f".{file_extension}")] print(" ".join(files_out)) diff --git a/poetry.lock b/poetry.lock index cf3b865cc..8f4b0b9a4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -19,17 +19,17 @@ typing-extensions = ">=4.9.0" [[package]] name = "albumentations" -version = "1.4.12" +version = "1.4.14" description = "An efficient library for image augmentation, providing extensive transformations to support machine learning and computer vision tasks." optional = true python-versions = ">=3.8" files = [ - {file = "albumentations-1.4.12-py3-none-any.whl", hash = "sha256:1da512fba0093e297fae387a0ecba0252054606680878bf71d5d5f63e88cde07"}, - {file = "albumentations-1.4.12.tar.gz", hash = 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