feature/mx-1562 code maintenance (#82)

# PR Context - preparation for mx-1381 and to keep #69 smaller - already removing public-api module for mx-1562, not closing that ticket yet though # Changes - update cruft and dev dependencies - randomize test order by default # Removed - remove `mex.common.public_api` module and the correlating sinks - remove `PathWrapper.resolve` and `PathWrapper.raw` methods --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
robert-koch-institut · Feb 22, 2024 · 9ec130c · 9ec130c
1 parent 417250d
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diff --git a/.cruft.json b/.cruft.json
@@ -1,6 +1,6 @@
 {
   "checkout": null,
-  "commit": "d1a461de3c7ff099045b71a156ad667887c32368",
+  "commit": "6067fc53d1335a9bda900c5eff8dbf1c42bfe4ca",
   "context": {
     "cookiecutter": {
       "project_name": "common",

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,12 +3,12 @@ default_language_version:
   python: python3.11
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.2.0
+    rev: v0.2.1
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
   - repo: https://github.com/psf/black
-    rev: 24.1.1
+    rev: 24.2.0
     hooks:
       - id: black
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -20,6 +20,12 @@ repos:
         exclude: .cruft.json
       - id: check-yaml
         name: yaml
+      - id: end-of-file-fixer
+        name: eof
+      - id: trailing-whitespace
+        name: whitespaces
+      - id: fix-byte-order-marker
+        name: byte-order
   - repo: https://github.com/python-poetry/poetry
     rev: 1.7.1
     hooks:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,41 +19,42 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Security
 
-## [0.19.4] - 2024-02-15
-
-### Added
+## [0.20.0] - 2024-02-22
 
 ### Changes
 
-- update cruft and minor dependencies
-
-### Deprecated
+- update cruft and dev dependencies
+- randomize test order by default
 
 ### Removed
 
-- date-time format validation for mapping model generation
+- remove `mex.common.public_api` module and the correlating sinks
+- remove `PathWrapper.resolve` and `PathWrapper.raw` methods
 
 ### Fixed
 
-### Security
+- remove `pytest.mark` from fixture in `mex.common.testing.plugin`
 
-## [0.19.3] - 2024-02-06
+## [0.19.4] - 2024-02-15
 
-### Added
+### Changes
+
+- update cruft and minor dependencies
+
+### Removed
+
+- date-time format validation for mapping model generation
+
+## [0.19.3] - 2024-02-06
 
 ### Changes
 
 - update cruft to apply new workflow trigger config
 - update poetry and pre-commit dependencies
 
-### Deprecated
-
-### Removed
-
 ### Fixed
-- fix mex mapping model name
 
-### Security
+- fix mex mapping model name
 
 ## [0.19.2] - 2024-02-02
 
@@ -66,14 +67,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - `mex.bat test` uses random order and xdist plugins by default
 
-### Deprecated
-
-### Removed
-
-### Fixed
-
-### Security
-
 ## [0.19.1] - 2024-01-19
 
 ### Added
@@ -133,8 +126,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Deprecated
 
 - deprecate `MExModel.get_entity_type`, use `cls.__name__` instead
-- deprecate `mex.common.models.MODEL_CLASSES[_BY_ENTITY_TYPE]`, use the more precise lists or dicts like `EXTRACTED_MODEL_CLASSES_BY_NAME` instead
-
+- deprecate `mex.common.models.MODEL_CLASSES[_BY_ENTITY_TYPE]`,
+  use the more precise lists or dicts like `EXTRACTED_MODEL_CLASSES_BY_NAME` instead
 
 ## [0.17.1] - 2023-12-20
 

diff --git a/mex.bat b/mex.bat
@@ -32,10 +32,9 @@ echo linting all files
 pre-commit run --all-files
 if %errorlevel% neq 0 exit /b %errorlevel%
 
-@REM run the pytest test suite with unit and integration tests in random order
-@REM distributed across all available CPU cores
+@REM run pytest unit and integration tests distributed across available cores
 echo running all tests
-poetry run pytest --random-order-bucket=global --numprocesses=auto --dist=worksteal
+poetry run pytest --numprocesses=auto --dist=worksteal
 exit /b %errorlevel%
 
 

diff --git a/mex/common/exceptions.py b/mex/common/exceptions.py
@@ -5,7 +5,7 @@ def __str__(self) -> str:
         """Format this exception as a string for logging."""
         return (
             f"{self.__class__.__name__}: "
-            f"{(', '.join((str(arg) for arg in self.args)))} "
+            f"{(', '.join(str(arg) for arg in self.args))} "
         )
 
 

diff --git a/mex/common/ldap/README.md b/mex/common/ldap/README.md
@@ -1,31 +1,31 @@
-Helper extractor to extract data from Lightweight Directory Access Protocol (LDAP). 
+Helper extractor to extract data from Lightweight Directory Access Protocol (LDAP).
 
 Common use cases:
-- extract employee accounts  of your organization
+- extract employee accounts of your organization
 - extract functional accounts of your organization
 
-Possible queries are for example the account name, surname, given name, or email. 
+Possible queries are for example the account name, surname, given name, or email.
 
 # Configuration
 
-For configuring the ldap connection, set the settings parameter `ldap_url` 
-(see `mex.common.settings` for further info) to an LDAP url (see 
-[LDAP URL definition](https://datatracker.ietf.org/doc/html/rfc2255#section-3) for 
+For configuring the ldap connection, set the settings parameter `ldap_url`
+(see `mex.common.settings` for further info) to an LDAP url (see
+[LDAP URL definition](https://datatracker.ietf.org/doc/html/rfc2255#section-3) for
 further information).
 
 # Extracting data
 
-Use the `LDAPConnector` from the `ldap.connector` module to extract data. 
+Use the `LDAPConnector` from the `ldap.connector` module to extract data.
 
 # Transforming data
 
-The module `ldap.transform` contains functions for transforming LDAP data into MEx 
+The module `ldap.transform` contains functions for transforming LDAP data into MEx
 models.
 
-The `mex_person.stableTargetId` attribute can be used in any entity that requires a 
+The `mex_person.stableTargetId` attribute can be used in any entity that requires a
 `PersonID`.
 
 # Convenience Functions
 
-The module `ldap.extract` holds convenience functions, e.g. for build a mapping from 
+The module `ldap.extract` holds convenience functions, e.g. for build a mapping from
 query strings to `stableTargetId`s.
diff --git a/mex/common/ldap/connector.py b/mex/common/ldap/connector.py
@@ -74,7 +74,7 @@ def _fetch(
             if attributes := entry.get("attributes"):
                 yield model_cls.model_validate(attributes)
 
-    @cache
+    @cache  # noqa: B019
     def _paged_ldap_search(
         self, fields: tuple[str], search_filter: str, search_base: str
     ) -> list[dict[str, str]]:

diff --git a/mex/common/organigram/README.md b/mex/common/organigram/README.md
@@ -5,7 +5,7 @@ Common use cases:
 
 # Configuration
 
-The extractor reads data from a json file, whose path is set with the settings parameter 
+The extractor reads data from a json file, whose path is set with the settings parameter
 `organigram_path` (see `mex.common.settings` for further info).
 
 # Extracting data
@@ -16,15 +16,15 @@ The module `organigram.extract` contains functions for data extraction.
 
 The module `organigram.transform` contains functions for data transformation.
 
-Use the `stableTargetId` attribute of the transformed objects to set attributes 
+Use the `stableTargetId` attribute of the transformed objects to set attributes
 requiring an `OrganizationalUnitID`.
 
 # Convenience Functions
 
-The module `organigram.extract` holds convenience functions, e.g. for building a mapping 
+The module `organigram.extract` holds convenience functions, e.g. for building a mapping
 from email addresses or synonyms to `ExtractedOrganizationalUnit`.
 
 # json file format
 
-See example file in `assets/raw-data/organigram/organizational_units.json`. 
+See example file in `assets/raw-data/organigram/organizational_units.json`.
 For mandatory / optional attributes, see model in `mex/common/organigram/models.py`.
diff --git a/mex/common/organigram/extract.py b/mex/common/organigram/extract.py
@@ -19,7 +19,7 @@ def extract_organigram_units() -> Generator[OrganigramUnit, None, None]:
         Generator for organigram units
     """
     settings = BaseSettings.get()
-    with open(settings.organigram_path, "r") as fh:
+    with open(settings.organigram_path) as fh:
         for raw in json.load(fh):
             yield OrganigramUnit.model_validate(raw)
 

diff --git a/mex/common/primary_source/extract.py b/mex/common/primary_source/extract.py
@@ -17,6 +17,6 @@ def extract_seed_primary_sources() -> Generator[SeedPrimarySource, None, None]:
         Generator for seed primary sources
     """
     settings = BaseSettings.get()
-    with open(settings.primary_sources_path, "r") as fh:
+    with open(settings.primary_sources_path) as fh:
         for raw in json.load(fh):
             yield SeedPrimarySource.model_validate(raw)
diff --git a/mex/common/public_api/__init__.py b/mex/common/public_api/__init__.py