Merge pull request #16 from SironaMedical/AIE-2957-add-flake8

AIE-2957 add flake8 checking

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+    ignore = E203, E266, E501, W503, B028, D100, D101, D102, D103, D104
+    max-line-length = 120

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 ---
 repos:
   - repo: https://github.com/psf/black
-    rev: 22.8.0
+    rev: 23.9.1
     hooks:
       - id: black
         language_version: python3
@@ -11,3 +11,15 @@ repos:
     hooks:
       - id: isort
         args: [ --profile, black ]
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.1.0
+    hooks:
+      - id: flake8
+        language: python
+        additional_dependencies: [flake8-bugbear, flake8-comprehensions, flake8-print, flake8-docstrings]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: end-of-file-fixer

data/i2b2_anno/110-01.txt

@@ -48,7 +48,3 @@ DD: **/**/**
 DT: **/**/**
 DV: **/**/**
           Approved but not reviewed by Attending Provider         
-
-
-
-

data/i2b2_anno/110-02.txt

@@ -66,8 +66,3 @@ P:   Follow up with Dr. ***** in 3 months.
 
 
 GPP/******/*******
-
-
-
-
-

data/i2b2_anno/110-03.txt

@@ -100,7 +100,3 @@ GI prophylaxis: Zantac
 
 _______________________
 **** ****, MD, EHMS pager *****
-
-
-
-

data/i2b2_anno/110-04.txt

@@ -176,6 +176,3 @@ Plan
 ______________________________
 
 **** * *********, M.D.
-
-
-

data/i2b2_anno/111-01.txt

@@ -66,8 +66,3 @@ ___________________________________                    *****/*****
 Dictated by:  ******* ******, M.D.    **** 
 
           Not reviewed by Attending Physician         
-
-
-
-
-

data/i2b2_notes/110-01.txt

@@ -48,7 +48,3 @@ DD: 04/07/69
 DT: 04/15/69
 DV: 04/07/69
           Approved but not reviewed by Attending Provider         
-
-
-
-

data/i2b2_notes/110-02.txt

@@ -66,8 +66,3 @@ Gilbert P. Perez, M.D.
 
 
 GPP/church/olinger
-
-
-
-
-

data/i2b2_notes/110-03.txt

@@ -100,7 +100,3 @@ GI prophylaxis: Zantac
 
 _______________________
 Mike Ivan, MD, EHMS pager 84710
-
-
-
-

data/i2b2_notes/110-04.txt

@@ -176,6 +176,3 @@ Plan
 ______________________________
 
 Owen M Gallagher, M.D.
-
-
-

data/i2b2_notes/111-01.txt

@@ -66,8 +66,3 @@ FILBERT BRIGHT, M.D.    FB59                     D:07/20/83
 Dictated by:  FILBERT BRIGHT, M.D.    FB59 
 
           Not reviewed by Attending Physician         
-
-
-
-
-

data/i2b2_xml/110-01.xml

@@ -65,4 +65,4 @@ DV: 04/07/69
 <DATE TYPE="DATE" comment="" end="1729" id="P7" start="1721" text="04/15/69" />
 <DATE TYPE="DATE" comment="" end="1742" id="P8" start="1734" text="04/07/69" />
 </TAGS>
-</deIdi2b2>
+</deIdi2b2>

data/i2b2_xml/110-02.xml

@@ -83,4 +83,4 @@ GPP/church/olinger
 <NAME TYPE="DOCTOR" comment="" end="1320" id="P6" start="1314" text="church" />
 <NAME TYPE="DOCTOR" comment="" end="1328" id="P7" start="1321" text="olinger" />
 </TAGS>
-</deIdi2b2>
+</deIdi2b2>

data/i2b2_xml/110-03.xml

@@ -119,4 +119,4 @@ Mike Ivan, MD, EHMS pager 84710
 <NAME TYPE="DOCTOR" comment="" end="3592" id="P10" start="3583" text="Mike Ivan" />
 <CONTACT TYPE="PHONE" comment="" end="3614" id="P12" start="3609" text="84710" />
 </TAGS>
-</deIdi2b2>
+</deIdi2b2>

data/i2b2_xml/110-04.xml

@@ -192,4 +192,4 @@ Owen M Gallagher, M.D.
 <NAME TYPE="DOCTOR" comment="" end="3877" id="P8" start="3872" text="Perez" />
 <NAME TYPE="DOCTOR" comment="" end="4080" id="P9" start="4064" text="Owen M Gallagher" />
 </TAGS>
-</deIdi2b2>
+</deIdi2b2>

data/i2b2_xml/111-01.xml

@@ -89,4 +89,4 @@ Dictated by:  FILBERT BRIGHT, M.D.    FB59
 <NAME TYPE="DOCTOR" comment="" end="1773" id="P12" start="1759" text="FILBERT BRIGHT" />
 <NAME TYPE="USERNAME" comment="" end="1787" id="P13" start="1783" text="FB59" />
 </TAGS>
-</deIdi2b2>
+</deIdi2b2>

data/phi/fn.txt

@@ -1,4 +1,4 @@
 [
     "SILVER",
     "church"
-]
+]

data/phi/fp.txt

@@ -30,4 +30,4 @@
     "Will",
     "Will",
     "Will"
-]
+]

data/phi/summary.json

@@ -74,4 +74,4 @@
             "num_false_negatives": 0
         }
     }
-}
+}

data/phi_notes_i2b2.json

@@ -392,4 +392,4 @@
             }
         ]
     }
-}
+}

philter_lite/__init__.py

@@ -1,3 +1,4 @@
+"""The philter_lite package."""
 from importlib import metadata
 
 from philter_lite.coordinate_map import CoordinateMap
@@ -8,6 +9,16 @@
 from .asterisk import transform_text_asterisk
 from .i2b2 import transform_text_i2b2
 
+__all__ = [
+    "CoordinateMap",
+    "Filter",
+    "filter_from_dict",
+    "load_filters",
+    "detect_phi",
+    "transform_text_asterisk",
+    "transform_text_i2b2",
+]
+
 _DISTRIBUTION_METADATA = metadata.metadata("philter_lite")
 
 __author__ = _DISTRIBUTION_METADATA["Author"]

philter_lite/asterisk.py

@@ -1,7 +1,8 @@
-from .coordinate_map import CoordinateMap, PUNCTUATION_MATCHER
+from .coordinate_map import PUNCTUATION_MATCHER, CoordinateMap
 
 
 def save_to_asterisk(contents, output_file):
+    """Write some data to a text file, using utf-8 encoding."""
     with open(output_file, "w", encoding="utf-8", errors="surrogateescape") as f:
         f.write(contents)
 
@@ -11,7 +12,6 @@ def transform_text_asterisk(txt, include_map: CoordinateMap):
     # read the text by character, any non-punc non-overlaps will be replaced
     contents = []
     for i in range(len(txt)):
-
         if i < last_marker:
             continue
 

philter_lite/configs/philter_delta.toml

@@ -2245,4 +2245,3 @@ context = "left_or_right"
 context_filter = "all"
 notes = ""
 keyword = "regex_context.initials"
-