Merge branch 'main' into pr/50

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ default_language_version:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: "v4.3.0"
+    rev: "v4.5.0"
     hooks:
       # General
       - id: check-added-large-files
@@ -35,7 +35,7 @@ repos:
       - id: check-hooks-apply
       - id: check-useless-excludes
   - repo: https://github.com/codespell-project/codespell
-    rev: "v2.2.2"
+    rev: "v2.2.6"
     hooks:
       - id: codespell
         args:
@@ -48,18 +48,18 @@ repos:
             '\Whttps?://\S*',
           ]
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v3.0.0-alpha.4"
+    rev: "v4.0.0-alpha.4"
     hooks:
       - id: prettier
         args: [--config, .meta/prettierrc.yml]
   - repo: https://github.com/adrienverge/yamllint
-    rev: "v1.28.0"
+    rev: "v1.33.0"
     hooks:
       - id: yamllint
         args: [-c, .meta/yamllint.yaml]
   # Shell
   - repo: https://github.com/shellcheck-py/shellcheck-py
-    rev: "v0.8.0.4"
+    rev: "v0.9.0.6"
     hooks:
       - id: shellcheck
   # Python
@@ -68,44 +68,44 @@ repos:
   #   hooks:
   #     - id: setup-cfg-fmt
   - repo: https://github.com/pre-commit/pygrep-hooks
-    rev: "v1.9.0"
+    rev: "v1.10.0"
     hooks:
       - id: python-check-blanket-noqa
       - id: python-check-mock-methods
       - id: python-use-type-annotations
       - id: python-no-log-warn
-  - repo: https://github.com/asottile/reorder_python_imports
-    rev: "v3.9.0"
+  - repo: https://github.com/asottile/reorder-python-imports
+    rev: "v3.12.0"
     hooks:
       - id: reorder-python-imports
         args: [--py36-plus]
   - repo: https://github.com/asottile/add-trailing-comma
-    rev: "v2.3.0"
+    rev: "v3.1.0"
     hooks:
       - id: add-trailing-comma
         args: [--py36-plus]
   - repo: https://github.com/asottile/pyupgrade
-    rev: "v3.2.0"
+    rev: "v3.15.0"
     hooks:
       - id: pyupgrade
         args: [--py36-plus]
   - repo: https://github.com/asottile/yesqa
-    rev: "v1.4.0"
+    rev: "v1.5.0"
     hooks:
       - id: yesqa
         additional_dependencies: [pep8-naming]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v0.982"
+    rev: "v1.7.1"
     hooks:
       - id: mypy
         args: [--config-file, .meta/mypy.ini]
   - repo: https://github.com/psf/black
-    rev: "22.10.0"
+    rev: "23.11.0"
     hooks:
       - id: black
         language_version: python38
   - repo: https://github.com/PyCQA/flake8
-    rev: "5.0.4"
+    rev: "6.1.0"
     hooks:
       - id: flake8
         additional_dependencies:

create_archive.py

@@ -48,7 +48,6 @@
 
 
 def _log_disk_usage(input_files: Tuple[Path]) -> None:
-
     escaped_root = str(PACS_ROOT).replace("/", r"\/")
     cmd = (
         rf"sed 's/^/{escaped_root}\//g' {' '.join((str(x) for x in input_files))} "
@@ -72,7 +71,6 @@ def _log_disk_usage(input_files: Tuple[Path]) -> None:
 
 
 def main() -> int:
-
     logging.info(f"Starting on {os.uname()[1]}")
 
     parser = argparse.ArgumentParser()

queries/extractAllSeriesRange.js

@@ -2,27 +2,27 @@
 // date. Usage: mongo --eval \"const date='201501'\" <script-name>.js"
 
 if (typeof date === "undefined") {
-  print("date must be passed to the script")
-  quit()
+  print("date must be passed to the script");
+  quit();
 }
 
-const CONN = new Mongo()
-CONN.getDB("admin").auth("...", "...")
+const CONN = new Mongo();
+CONN.getDB("admin").auth("...", "...");
 
-print("PatientID,DirectoryPath,Modality,ImagesInSeries")
+print("PatientID,DirectoryPath,Modality,ImagesInSeries");
 
-const DB_NAME = "dicom"
+const DB_NAME = "dicom";
 CONN.getDB(DB_NAME)
   .getCollection("series")
   .find({
     StudyDate: new RegExp("^" + date),
   })
   .forEach(function (doc) {
     // TODO(rkm 2020-10-27) Need to escape commas in some PatientIDs
-    s = ""
-    s += doc["PatientID"] + ","
-    s += doc["header"]["DirectoryPath"] + ","
-    s += doc["Modality"] + ","
-    s += doc["header"]["ImagesInSeries"]
-    print(s)
-  })
+    s = "";
+    s += doc["PatientID"] + ",";
+    s += doc["header"]["DirectoryPath"] + ",";
+    s += doc["Modality"] + ",";
+    s += doc["header"]["ImagesInSeries"];
+    print(s);
+  });

queries/processCounts.py

@@ -29,7 +29,6 @@ def process_csv(csv_path: Path) -> Counter[str]:
 
 
 def main() -> int:
-
     totals: Counter[str] = Counter()
     for f in sorted(glob.glob("results/proj_name_*.csv")):
         totals += Counter(process_csv(Path(f)))