Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

Author: shaneahmed

.github/workflows/python-package.yml

@@ -30,7 +30,7 @@ jobs:
         sudo apt update
         sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-        python -m pip install ruff==0.6.5 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.7.4 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3
@@ -58,7 +58,7 @@ jobs:
     - name: Test with pytest
       run: |
         pytest --basetemp={envtmpdir} \
-           --cov=tiatoolbox --cov-report=term --cov-report=xml \
+           --cov=tiatoolbox --cov-report=term --cov-report=xml --cov-config=pyproject.toml \
            --capture=sys \
            --durations=10 --durations-min=1.0 \
            --maxfail=1

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 ci:
   autofix_prs: true
-  autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
-  autoupdate_schedule: 'weekly'
+  autoupdate_commit_msg: ':technologist: pre-commit autoupdate'
+  autoupdate_schedule: 'monthly'
 repos:
   - repo: local
     hooks:
@@ -11,7 +11,7 @@ repos:
         files: tests/.*\btest_\w*.py
         require_serial: true
         language: system
-        stages: [push]
+        stages: [pre-push]
       - id: notebook-markdown-format
         name: notebook markdown format
         entry: python pre-commit/notebook_markdown_format.py
@@ -23,15 +23,15 @@ repos:
         - mdformat-black
         - mdformat-myst
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.17
+    rev: 0.7.18
     hooks:
     - id: mdformat
       # Optionally add plugins
       additional_dependencies:
       - mdformat-gfm  # GitHub flavoured markdown
       - mdformat-black  # Black formatting for python verbatim blocks
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-ast               # Simply checks whether the files parse as valid Python.
       - id: fix-byte-order-marker   # Removes utf-8 byte order marker.
@@ -60,7 +60,7 @@ repos:
       - id: rst-inline-touching-normal # Detect mistake of inline code touching normal text in rst.
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.5
+    rev: v0.7.4
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

CITATION.cff

@@ -24,7 +24,7 @@ authors:
   orcid: "https://orcid.org/0000-0003-0969-2990"
 - family-names: "Bashir"
   given-names: "Raja Muhammad Saad"
-  orcid: "https://orcid.org/0000-0002-8984-696"
+  orcid: "https://orcid.org/0000-0002-8984-6963"
 - family-names: "Bilal"
   given-names: "Mohsin"
   orcid: "https://orcid.org/0000-0001-8632-2729"
@@ -74,7 +74,7 @@ preferred-citation:
     orcid: "https://orcid.org/0000-0003-0969-2990"
   - family-names: "Bashir"
     given-names: "Raja Muhammad Saad"
-    orcid: "https://orcid.org/0000-0002-8984-696"
+    orcid: "https://orcid.org/0000-0002-8984-6963"
   - family-names: "Bilal"
     given-names: "Mohsin"
     orcid: "https://orcid.org/0000-0001-8632-2729"