Set up ruff and fix trivial rules (#165)

* Add `ruff.toml` * Remove isort and flake8 from pre-commit * Add ruff to pre-commit * Remove isort and flake8 from `setup.cfg` * Set target version to 3.10 for ruff * Automatically fix ruff linter * Add `mypy` and `ruff` as dev dependencies * Run `ruff check .` on codebase * Ruff ignore `ANN001` (missing type function arguments) * Ignore more ruff rules * Run `ruff check --unsafe-fixes .` * Remove commented out code * Fix TODO comment * Add file-specific ignore rules for ruff * Add GH issue links to TODOs * Fix ruff `B905`: add `strict=True` in `zip()` * Fix ruff `TRY200`: use `raise from` * Fix ruff `PTH123`: `open()` -> `Path.open()` * Fix ruff `PLR2004`: use of magic values * Fix ruff `PTH` rules * Fix ruff `S` rules * Remove unused ruff ignore comments * Add more rules to the ruff ignore list * Fix ruff rule PT * Fix single quotes * Fix Ruff rules PL * Fix ruff rule TRY * Fix ruff rule RET * Fix ruff rule FBT001 and whitespace * Fix ruff rule B * Fix ruff rule DTZ007 * Add missing imports * Set `orthanc` plugins as `namespace-packages` * Fix ruff rules remaining (not ignored) * ignore rules in ruff.toml * Fix ruff ignore comment * Fix ruff rules in orthanc-raw - add docstrings * Fix (some) ruff rules in orthanc-anon - add docstrings * `pixl_core`: fix ruff rule D100 Add docstrings to public modules * `pixl_core`: fix ruff rule D103 Add missing docstrings to public functions * `pixl_core`: fix ruff rule D101 * `pixl_core`: ignore ruff rule ARG001 Need further testing to check whether these arguments can be removed * `pixl_core`: fix ruff rule G004 * `pixl_core`: fix test checking datetime Fixing ruff rule DTZ007 in e96307b caused this test to fail because the timestamp didn't include the timezone. Also requires `import datetime` to access the `timezone` attribute * `cli`: fix ruff rule D100 (module docstrings) * `cli`: fix ruff rule D103 * `cli`: fix remaining ruff D10* rules * `cli`: fix failing tests after previous ruff issue fixes - `yaml.safe_load()` does not have a `Loader` argument - `import datetime` to get access to `timezone` - `datetime` -> `datetime.datetime` because of the previous * `cli`: fix ruff rule S101, replace `assert` with exceptions * `cli`: replace `print()` with `logger.info()` * `cli`: fix ruff rule S113, set request timeouts * `pixl_ehr`: ignore D1** ruff rules for tests * `pixl_ehr`: formatting * Ignore ruff rule S608 See #154 * Fix remaining ruff rules in orthanc-anon - add docstrings Azure Token * Fix ruff ignore comment PLW0602 * Fix ruff rules for orthanc-raw adding docstrings * Fix (some) ruff rules in orthanc-anon - add docstrings * Fix remaining ruff rules in orthanc-anon - add docstrings Azure Token * Fix ruff rule G004 in pixl_pacs * Fix datetime import error * Fix ruff rule RUF006 in pixl_pacs * Fix ruff rule RUF006 in pixl_ehr * Fix datetime import error * Fix ruff rules in pixl_ehr _processing * Ignore ruff rule PLW2901 see #157 * Fix ruff rule missing docstrings for pixl_pacs * `hasher`: fix expected error message * `hasher`: use `@pytest.mark` to define `dummy_key` fixture * Formatting * `hasher`: ignore `D1` rules for tests * `hasher`: ignore ruff rule T201 (print statements) * Fix ruff rule G004 for pixl_ehr * `hasher`: replace logging `f`-string * `hasher`: fix ruff rule D100, public module docstrings * `hasher`: ignore rule D103 for `endpoints` functions Docstrings feel like overkill for these functions * pre-commit applied locally * Fix ruff setup Specifying the `config=ruff.toml` ignores subdirectory `ruff.toml` files * More `ruff` autofixes * Ruff pixl_ehr docstrings * Fix `Path` API calls * Fix unspported left operand error * Fix `RuntimeError` message * Fix `fromisoformat()` call --------- Co-authored-by: ruaridhg <ruaridhg@users.noreply.github.com>
SAFEHR-data · Dec 4, 2023 · e0190a1 · e0190a1
1 parent 3f75c7b
commit e0190a1
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Showing 64 changed files with 763 additions and 456 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -13,24 +13,15 @@
 #  limitations under the License.
 ---
 repos:
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.6
     hooks:
-      - id: isort
-        name: isort (python)
-        args: ["--profile", "black", "--settings-path", "setup.cfg"]
-
-  - repo: https://github.com/ambv/black
-    rev: 23.9.1
-    hooks:
-      - id: black
-
-  - repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
-    hooks:
-    - id: flake8
-      args: ["--config", "setup.cfg"]
-      exclude: "tests|orthanc"
+      - id: ruff
+        args:
+          - --fix
+      - id: ruff-format
+        args:
+          - --config=ruff.toml
 
   - repo: local
     hooks:

diff --git a/cli/pyproject.toml b/cli/pyproject.toml
@@ -22,6 +22,11 @@ dependencies = [
 test = [
     "pytest==7.4.*"
 ]
+dev = [
+    "mypy",
+    "pre-commit",
+    "ruff",
+]
 
 [project.scripts]
 pixl = "pixl_cli.main:cli"

diff --git a/cli/src/pixl_cli/__init__.py b/cli/src/pixl_cli/__init__.py
@@ -11,6 +11,8 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
+"""PIXL command line interface"""
+
 from pixl_cli.main import cli
 
 __all__ = ["cli"]
diff --git a/cli/src/pixl_cli/_utils.py b/cli/src/pixl_cli/_utils.py
@@ -11,13 +11,12 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
-import os
 from pathlib import Path
 
 
 def clear_file(filepath: Path) -> None:
     """Clear the contents of a file"""
-    open(filepath, "w").close()
+    Path.open(filepath, "w").close()
 
 
 def string_is_non_empty(string: str) -> bool:
@@ -28,4 +27,4 @@ def string_is_non_empty(string: str) -> bool:
 def remove_file_if_it_exists(filepath: Path) -> None:
     """If a file exists remove it"""
     if filepath.exists():
-        os.remove(filepath)
+        Path.unlink(filepath)