Dependency updates and RO-Crate 1.3 support

.github/dependabot.yml

@@ -4,3 +4,7 @@ updates:
     directory: "/"
     schedule:
       interval: "weekly"
+    groups:
+      weekly-batch:
+        patterns:
+          - "*"

.github/workflows/build-with-profiles.yml

@@ -43,8 +43,8 @@ jobs:
           # Add the five-safes profile (via EXTRA_PROFILES_PATH) and warm its
           # cache, using the shared Dockerfile's build args.
           build-args: |
-            FIVE_SAFES_PROFILE_VERSION=five-safes-0.7.4-beta
-            PROFILES_ARCHIVE_URL=https://github.com/eScienceLab/rocrate-validator/archive/refs/tags/five-safes-0.7.4-beta.tar.gz
+            FIVE_SAFES_PROFILE_VERSION=five-safes-0.8.0
+            PROFILES_ARCHIVE_URL=https://github.com/eScienceLab/rocrate-validator/archive/refs/tags/five-safes-0.8.0.tar.gz
             EXTRA_PROFILES_PATH=/app/extra-profiles
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}

.github/workflows/lint.yml

@@ -21,7 +21,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           # Keep in sync with requirements-dev.txt
-          pip install ruff==0.15.17
+          pip install ruff==0.16.8
 
       - name: Lint
         run: ruff check .

.github/workflows/test_docker.yml

@@ -21,7 +21,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           # Keep in sync with requirements-dev.txt
-          pip install pytest==9.1.0 requests==2.34.2 boto3==1.43.29
+          pip install pytest==9.1.1 requests==2.34.2 boto3==1.43.97
 
       - name: Run integration tests (brings up the compose stack)
         run: |

docker-compose.yml

@@ -7,7 +7,7 @@
 services:
   flask:
     platform: linux/x86_64
-    image: "ghcr.io/esciencelab/ro-crate-validation-service:0.1"
+    image: "ghcr.io/esciencelab/ro-crate-validation-service:latest"
     ports:
       - "5001:5000"
     environment:
@@ -28,7 +28,7 @@ services:
 
   celery_worker:
     platform: linux/x86_64
-    image: "ghcr.io/esciencelab/ro-crate-validation-service:0.1"
+    image: "ghcr.io/esciencelab/ro-crate-validation-service:latest"
     command: celery -A app.celery_worker.celery worker --loglevel=info -E
     environment:
       - CELERY_BROKER_URL=redis://redis:6379/0

pyproject.toml

@@ -14,14 +14,14 @@ authors = [{ name = "eScience Lab, The University of Manchester" }]
 # Direct runtime dependencies:
 dependencies = [
     "celery==5.6.3",
-    "boto3==1.43.29",
+    "boto3==1.43.97",
     "requests==2.34.2",
     "Flask==3.1.3",
     "Werkzeug==3.1.8",
-    "redis==8.0.1",
-    "python-dotenv==1.2.2",
-    "apiflask==3.1.0",
-    "roc-validator==0.11.2",
+    "redis==8.1.0",
+    "python-dotenv==1.2.3",
+    "apiflask==3.1.2",
+    "roc-validator==0.11.4",
 ]
 
 [project.optional-dependencies]

requirements-dev.txt

@@ -2,46 +2,46 @@
 # This file is autogenerated by pip-compile with Python 3.11
 # by the following command:
 #
-#    pip-compile --extra=dev --output-file=requirements-dev.txt pyproject.toml
+#    pip-compile --extra=dev --no-index --output-file=requirements-dev.txt
 #
 amqp==5.3.1
     # via kombu
-annotated-types==0.7.0
+annotated-types==0.8.0
     # via pydantic
-apiflask==3.1.0
+apiflask==3.1.2
     # via ro-crate-validation-service (pyproject.toml)
 apispec==6.10.0
     # via apiflask
 attrs==26.1.0
     # via
     #   cattrs
     #   requests-cache
-billiard==4.2.4
+billiard==4.3.0
     # via celery
 blinker==1.9.0
     # via flask
-boto3==1.43.29
+boto3==1.43.97
     # via
     #   moto
     #   ro-crate-validation-service (pyproject.toml)
-botocore==1.43.31
+botocore==1.43.97
     # via
     #   boto3
     #   moto
     #   s3transfer
-build==1.5.0
+build==1.6.1
     # via pip-tools
-cattrs==26.1.0
+cattrs==26.2.0
     # via requests-cache
 celery==5.6.3
     # via ro-crate-validation-service (pyproject.toml)
-certifi==2026.6.17
+certifi==2026.7.22
     # via requests
-cffi==2.1.0
+cffi==2.1.1
     # via cryptography
-charset-normalizer==3.4.7
+charset-normalizer==3.5.1
     # via requests
-click==8.4.1
+click==8.5.0
     # via
     #   celery
     #   click-didyoumean
@@ -55,11 +55,11 @@ click-didyoumean==0.3.1
     # via celery
 click-plugins==1.1.1.2
     # via celery
-click-repl==0.3.0
+click-repl==0.4.0
     # via celery
 colorlog==6.12.0
     # via roc-validator
-cryptography==50.0.0
+cryptography==50.0.1
     # via moto
 dnspython==2.8.0
     # via email-validator
@@ -79,12 +79,12 @@ flask-marshmallow==1.5.0
     # via apiflask
 html5rdf==1.2.1
     # via rdflib
-idna==3.15
+idna==3.20
     # via
     #   email-validator
     #   requests
     #   url-normalize
-importlib-metadata==9.0.0
+importlib-metadata==9.0.1
     # via pyshacl
 iniconfig==2.3.0
     # via pytest
@@ -107,18 +107,18 @@ markupsafe==3.0.3
     #   flask
     #   jinja2
     #   werkzeug
-marshmallow==4.3.0
+marshmallow==4.3.1
     # via
     #   apiflask
     #   flask-marshmallow
     #   webargs
 mdurl==0.1.2
     # via markdown-it-py
-moto[s3]==5.2.2
+moto[s3]==5.2.3
     # via ro-crate-validation-service (pyproject.toml)
-owlrl==7.1.4
+owlrl==7.6.2
     # via pyshacl
-packaging==26.2
+packaging==26.3
     # via
     #   apispec
     #   build
@@ -131,11 +131,11 @@ pfzy==0.3.4
     # via inquirerpy
 pip-tools==7.6.1
     # via ro-crate-validation-service (pyproject.toml)
-platformdirs==4.10.0
+platformdirs==4.11.10
     # via requests-cache
 pluggy==1.6.0
     # via pytest
-prettytable==3.17.0
+prettytable==3.18.0
     # via pyshacl
 prompt-toolkit==3.0.53
     # via
@@ -145,24 +145,24 @@ py-partiql-parser==0.6.3
     # via moto
 pycparser==3.0
     # via cffi
-pydantic[email]==2.13.4
+pydantic[email]==2.13.5
     # via apiflask
-pydantic-core==2.46.4
+pydantic-core==2.46.5
     # via pydantic
-pygments==2.20.0
+pygments==2.21.0
     # via
     #   enum-tools
     #   pytest
     #   rich
 pyparsing==3.3.2
     # via rdflib
-pyproject-hooks==1.2.0
+pyproject-hooks==1.3.3
     # via
     #   build
     #   pip-tools
-pyshacl==0.31.0
+pyshacl==0.40.1
     # via roc-validator
-pytest==9.1.0
+pytest==9.1.1
     # via
     #   pytest-mock
     #   ro-crate-validation-service (pyproject.toml)
@@ -172,7 +172,7 @@ python-dateutil==2.9.0.post0
     # via
     #   botocore
     #   celery
-python-dotenv==1.2.2
+python-dotenv==1.2.3
     # via ro-crate-validation-service (pyproject.toml)
 pyyaml==6.0.3
     # via
@@ -183,7 +183,7 @@ rdflib[html]==7.6.0
     #   owlrl
     #   pyshacl
     #   roc-validator
-redis==8.0.1
+redis==8.1.0
     # via ro-crate-validation-service (pyproject.toml)
 requests==2.34.2
     # via
@@ -194,40 +194,41 @@ requests==2.34.2
     #   roc-validator
 requests-cache==1.3.3
     # via roc-validator
-responses==0.26.2
+responses==0.26.3
     # via moto
 rich==13.9.4
     # via
     #   rich-click
     #   roc-validator
-rich-click==1.9.8
+rich-click==1.9.9
     # via roc-validator
-roc-validator==0.11.2
+roc-validator==0.11.4
     # via ro-crate-validation-service (pyproject.toml)
-ruff==0.15.17
+ruff==0.16.8
     # via ro-crate-validation-service (pyproject.toml)
-s3transfer==0.18.0
+s3transfer==0.19.2
     # via boto3
 six==1.17.0
     # via python-dateutil
 toml==0.10.2
     # via roc-validator
-typing-extensions==4.15.0
+typing-extensions==4.16.0
     # via
     #   cattrs
+    #   click-repl
     #   enum-tools
     #   pydantic
     #   pydantic-core
     #   typing-inspection
-typing-inspection==0.4.2
+typing-inspection==0.4.4
     # via pydantic
-tzdata==2026.2
+tzdata==2026.4
     # via kombu
-tzlocal==5.4.3
+tzlocal==5.4.4
     # via celery
 url-normalize==3.0.0
     # via requests-cache
-urllib3==2.7.0
+urllib3==2.8.0
     # via
     #   botocore
     #   requests
@@ -238,7 +239,7 @@ vine==5.1.0
     #   amqp
     #   celery
     #   kombu
-wcwidth==0.8.1
+wcwidth==0.8.4
     # via
     #   prettytable
     #   prompt-toolkit
@@ -249,7 +250,7 @@ werkzeug==3.1.8
     #   flask
     #   moto
     #   ro-crate-validation-service (pyproject.toml)
-wheel==0.47.0
+wheel==0.48.0
     # via pip-tools
 xmltodict==1.0.4
     # via moto