Devops: Use recursive dependencies for pre-commit extra (#6368)

As of pip 21.2, it is possible to recursively reference extras in an
extra requirement. This allows us to complete the `pre-commit`
extra to install the other extras whose requirements are necessary
as they are imported during pre-commit hooks.

.github/workflows/ci-style.yml

@@ -16,18 +16,12 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-    - name: Install system dependencies
-      # note libkrb5-dev is required as a dependency for the gssapi pip install
-      run: |
-        sudo apt update
-        sudo apt install libkrb5-dev ruby ruby-dev
-
     - name: Install python dependencies
       uses: ./.github/actions/install-aiida-core
       with:
         python-version: '3.10'
         extras: '[pre-commit]'
-        from-requirements: 'true'
+        from-requirements: 'false'
 
     - name: Run pre-commit
       run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

pyproject.toml

@@ -210,6 +210,7 @@ notebook = [
   'notebook~=6.1,>=6.1.5'
 ]
 pre-commit = [
+  'aiida-core[atomic_tools,rest,tests,tui]',
   'mypy~=1.7.1',
   'packaging~=23.0',
   'pre-commit~=2.2',

src/aiida/storage/sqlite_zip/migrations/versions/main_0000a_replace_nulls.py

@@ -42,8 +42,8 @@ def upgrade():
     )
 
     # remove rows with null values, which may have previously resulted from deletion of a user or computer
-    op.execute(db_dbauthinfo.delete().where(db_dbauthinfo.c.aiidauser_id.is_(None)))  # type: ignore[arg-type]
-    op.execute(db_dbauthinfo.delete().where(db_dbauthinfo.c.dbcomputer_id.is_(None)))  # type: ignore[arg-type]
+    op.execute(db_dbauthinfo.delete().where(db_dbauthinfo.c.aiidauser_id.is_(None)))
+    op.execute(db_dbauthinfo.delete().where(db_dbauthinfo.c.dbcomputer_id.is_(None)))
 
     op.execute(db_dbauthinfo.update().where(db_dbauthinfo.c.enabled.is_(None)).values(enabled=True))
     op.execute(db_dbauthinfo.update().where(db_dbauthinfo.c.auth_params.is_(None)).values(auth_params={}))
@@ -60,8 +60,8 @@ def upgrade():
     )
 
     # remove rows with null values, which may have previously resulted from deletion of a node or user
-    op.execute(db_dbcomment.delete().where(db_dbcomment.c.dbnode_id.is_(None)))  # type: ignore[arg-type]
-    op.execute(db_dbcomment.delete().where(db_dbcomment.c.user_id.is_(None)))  # type: ignore[arg-type]
+    op.execute(db_dbcomment.delete().where(db_dbcomment.c.dbnode_id.is_(None)))
+    op.execute(db_dbcomment.delete().where(db_dbcomment.c.user_id.is_(None)))
 
     op.execute(db_dbcomment.update().where(db_dbcomment.c.content.is_(None)).values(content=''))
     op.execute(db_dbcomment.update().where(db_dbcomment.c.ctime.is_(None)).values(ctime=timezone.now()))