diff --git a/.copier-answers.yml b/.copier-answers.yml
index c8c7d0fbb4310a7336a1d80bed64b473ccfc36e0..2d83678d32e11366820aa281d4408857e34a0635 100644
--- a/.copier-answers.yml
+++ b/.copier-answers.yml
@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier
-_commit: v0.2.3
+_commit: v0.3.3
 _src_path: https://gitlab.softwareheritage.org/swh/devel/swh-py-template.git
 description: Software Heritage indexer
 distribution_name: swh-indexer
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4e2ed8379599b01439a61c7bc864ae760a50e51a..83621e1ba5b0f1c6bec76eb9c20784c143ed9812 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,18 +1,18 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: check-json
       - id: check-yaml
 
   - repo: https://github.com/python/black
-    rev: 24.8.0
+    rev: 25.1.0
     hooks:
       - id: black
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
+    rev: 6.0.0
     hooks:
       - id: isort
 
@@ -20,16 +20,16 @@ repos:
     rev: 7.1.1
     hooks:
       - id: flake8
-        additional_dependencies: [flake8-bugbear==24.4.26]
+        additional_dependencies: [flake8-bugbear==24.12.12, flake8-pyproject]
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         name: Check source code spelling
         args: [-L assertIn]
         exclude: ^(swh/indexer/data/)
-        stages: [commit]
+        stages: [pre-commit]
       - id: codespell
         name: Check commit message spelling
         stages: [commit-msg]
diff --git a/mypy.ini b/mypy.ini
deleted file mode 100644
index b08c3882b9c539a5a74a1653cbc7107a6fdb0817..0000000000000000000000000000000000000000
--- a/mypy.ini
+++ /dev/null
@@ -1,37 +0,0 @@
-[mypy]
-namespace_packages = True
-warn_unused_ignores = True
-explicit_package_bases = True
-# ^ Needed for mypy to detect py.typed from swh packages installed
-# in editable mode
-
-# 3rd party libraries without stubs (yet)
-[mypy-confluent_kafka.*]
-ignore_missing_imports = True
-
-[mypy-iso8601.*]
-ignore_missing_imports = True
-
-[mypy-magic.*]
-ignore_missing_imports = True
-
-[mypy-pkg_resources.*]
-ignore_missing_imports = True
-
-[mypy-psycopg2.*]
-ignore_missing_imports = True
-
-[mypy-pybtex.*]
-ignore_missing_imports = True
-
-[mypy-pyld.*]
-ignore_missing_imports = True
-
-[mypy-rdflib.*]
-ignore_missing_imports = True
-
-[mypy-xmltodict.*]
-ignore_missing_imports = True
-
-# [mypy-add_your_lib_here.*]
-# ignore_missing_imports = True
diff --git a/pyproject.toml b/pyproject.toml
index 74672064c613131ceb8cb7d0f82aab27387271a8..2e9bd3eb637459468768a8cc13a3329b647ef7cf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -59,3 +59,35 @@ ensure_newline_before_comments = true
 line_length = 88
 force_sort_within_sections = true
 known_first_party = ['swh']
+
+[tool.mypy]
+namespace_packages = true
+warn_unused_ignores = true
+explicit_package_bases = true
+# ^ Needed for mypy to detect py.typed from swh packages installed
+# in editable mode
+
+plugins = []
+
+# 3rd party libraries without stubs (yet)
+[[tool.mypy.overrides]]
+module = [
+    "pybtex.*",
+    "pyld.*",
+]
+ignore_missing_imports = true
+
+[tool.flake8]
+select = ["C", "E", "F", "W", "B950"]
+ignore = [
+    "E203", # whitespaces before ':' <https://github.com/psf/black/issues/315>
+    "E231", # missing whitespace after ','
+    "E501", # line too long, use B950 warning from flake8-bugbear instead
+    "W503" # line break before binary operator <https://github.com/psf/black/issues/52>
+]
+max-line-length = 88
+
+[tool.pytest.ini_options]
+norecursedirs = "build docs .*"
+asyncio_mode = "strict"
+consider_namespace_packages = true
diff --git a/pytest.ini b/pytest.ini
deleted file mode 100644
index fe398a0babf5a774f332240c7ce22d38f7330ba1..0000000000000000000000000000000000000000
--- a/pytest.ini
+++ /dev/null
@@ -1,4 +0,0 @@
-[pytest]
-norecursedirs = build docs .*
-asyncio_mode = strict
-consider_namespace_packages = true
diff --git a/requirements-test.txt b/requirements-test.txt
index 1372615ef55f6c59be1d4920fd16fb65d8544ba1..02475ed8bbc944191bb13c8ad20f2897d8e60cfa 100644
--- a/requirements-test.txt
+++ b/requirements-test.txt
@@ -6,4 +6,6 @@ swh.core[testing] >= 3.0.0
 swh.storage[testing] >= 2.0.0
 
 types-click
+types-confluent-kafka
 types-pyyaml
+types-xmltodict
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index adf9af3e48c7da13135e5dfb6505a1909bc26066..0000000000000000000000000000000000000000
--- a/setup.cfg
+++ /dev/null
@@ -1,8 +0,0 @@
-[flake8]
-# E203: whitespaces before ':' <https://github.com/psf/black/issues/315>
-# E231: missing whitespace after ','
-# E501: line too long, use B950 warning from flake8-bugbear instead
-# W503: line break before binary operator <https://github.com/psf/black/issues/52>
-select = C,E,F,W,B950
-ignore = E203,E231,E501,E704,W503
-max-line-length = 88
diff --git a/swh/indexer/metadata_dictionary/codemeta.py b/swh/indexer/metadata_dictionary/codemeta.py
index 86d0ae5038d1f578e2d0d25b273c86ed7579ed16..1210e4289d4a45fa02a9452a0b80c278959436f2 100644
--- a/swh/indexer/metadata_dictionary/codemeta.py
+++ b/swh/indexer/metadata_dictionary/codemeta.py
@@ -231,4 +231,4 @@ class JsonSwordCodemetaMapping(SwordCodemetaMapping):
             # Root tag was stripped by swh-deposit
             json_doc = {"entry": json_doc}
 
-            return super().translate(xmltodict.unparse(json_doc))
+            return super().translate(xmltodict.unparse(json_doc).encode())
diff --git a/tox.ini b/tox.ini
index 11aaae71cab3f43f75d7ceec899f02f0616f6ffe..deb03597b55404009bfeadf548522112a01c068a 100644
--- a/tox.ini
+++ b/tox.ini
@@ -24,7 +24,7 @@ commands =
 [testenv:black]
 skip_install = true
 deps =
-  black==24.8.0
+  black==25.1.0
 commands =
   {envpython} -m black --check swh
 
@@ -32,8 +32,10 @@ commands =
 skip_install = true
 deps =
   flake8==7.1.1
-  flake8-bugbear==24.4.26
+  flake8-bugbear==24.12.12
+  flake8-pyproject==1.2.3
   pycodestyle==2.12.1
+
 commands =
   {envpython} -m flake8
 
@@ -41,7 +43,7 @@ commands =
 extras =
   testing
 deps =
-  mypy==1.11.1
+  mypy==1.15.0
 commands =
   mypy swh