fixing bad mappings

.gitignore

@@ -1 +1,2 @@
 .venv
+/**/*.pyc

.vscode/launch.json

@@ -8,7 +8,7 @@
             "name": "Rings",
             "type": "debugpy",
             "request": "launch",
-            "program": "${workspaceFolder}/__init__.py",
+            "module": "fledermaus_formatter",
             "args": ["-i", "data/ringe_short.xlsx", "-o", "ringe_short_out.xlsx", "-t", "ring"],
             "console": "integratedTerminal"
         },
@@ -16,7 +16,7 @@
             "name": "Countings",
             "type": "debugpy",
             "request": "launch",
-            "program": "${workspaceFolder}/__init__.py",
+            "module": "fledermaus_formatter",
             "args": ["-i", "data/zählungen_short.xlsx", "-o", "zählungen_short_out.xlsx", "-t", "counting"],
             "console": "integratedTerminal"
         }

fledermaus_formatter/__main__.py

@@ -0,0 +1,4 @@
+from fledermaus_formatter.main import main
+
+if __name__ == "__main__":
+    main()

fledermaus_formatter/instructions/mappings.py

@@ -38,7 +38,7 @@ SPICIES = {
         "P.pip.",
         "P.pip",
         "PPIP",
-        "P.p."
+        "P.p.",
         "ppip",
         "Pipistrellus pipistrellus",
     ],
@@ -180,7 +180,7 @@ SPICIES = {
         "unbekannt",
         "unb.",
         "Unbestimmt",
-        "Mspecbech"
+        "Mspecbech",
     ],
     "Malc": [
         "M.alc.",
@@ -256,7 +256,7 @@ SPICIES = {
         "MMYO",
         "mmyo",
         "Myotis Myotis",
-        "Mspec.bech"
+        "Mspec.bech",
         "M.m.",
         "M.m",
         "MM",
@@ -310,18 +310,18 @@ CATCHED_BY = [
 AGE = {
     "j": [
         "j",
-        "juv"
+        "juv",
     ],
     "sub": [
         "sub",
         "subad",
-        "sub ad"
+        "sub ad",
         "sub adult",
-        "sub-adult"
+        "sub-adult",
     ],
     "a": [
         "a",
-        "ad"
+        "ad",
     ]
 }
 
@@ -329,15 +329,15 @@ REPRODUCTION = {
     "p": [
         "plak",
         "pl",
-        "p"
+        "p",
     ],
     "g": [
-        "g"
+        "g",
     ],
     "z": [
         "lak",
         "l",
-        "z"
+        "z",
     ]
 }
 

fledermaus_formatter/instructions/ring_formater.py

@@ -24,12 +24,10 @@ COL_INSTRUCTIONS = {
     {
         "command": "FIND_AND_REPLACE",
         "map": REPRODUCTION,
-        "reqire_full_match": True
     },
     {
         "command": "FIND_AND_REPLACE",
         "map": AGE,
-        "reqire_full_match": True
     },
     {
         "command": "REGEX_MOVE_TO_COL",
@@ -58,7 +56,8 @@ COL_INSTRUCTIONS = {
     },
     ("Art",): {
         "command": "FIND_AND_REPLACE",
-        "map": SPICIES
+        "map": SPICIES,
+        "reqire_full_match": True
     },
     ("Ort",): {
         "command": "REGEX_MOVE_TO_COL",

fledermaus_formatter/main.py

@@ -1,10 +1,10 @@
 import argparse
 import os
-from logger import logger 
+from fledermaus_formatter.logger import logger 
 
-from table_handler.serializer import TableSerializer
-import instructions.countings_formater as countings_formater
-import instructions.ring_formater as ring_formater
+from fledermaus_formatter.table_handler.serializer import TableSerializer
+import fledermaus_formatter.instructions.countings_formater as countings_formater
+import fledermaus_formatter.instructions.ring_formater as ring_formater
 
 from concurrent.futures import ProcessPoolExecutor, as_completed
 
@@ -97,7 +97,3 @@ def main():
         parser.error("You must provide either input/output files or input-dir/output-dir")
 
     logger.info("Done")
-
-
-if __name__ == "__main__":
-    main()

fledermaus_formatter/table_handler/commands/find_and_replace.py

@@ -9,11 +9,11 @@ class FindAndReplace:
     def execute_on_cell(self, entry) -> str:
         res = deepcopy(entry.value)
 
-        for species, alternatives in self.map.items():
-            for old_version in alternatives:
-                if self.require_full_match and old_version == res:
+        for correct_name, bad_names in self.map.items():
+            for bad_name in bad_names:
+                if self.require_full_match and bad_name == res:
                     # Todo remove random leading/trailing spaces before if
-                    res = species
+                    res = correct_name
                 elif not self.require_full_match:
-                    res = res.replace(old_version, species)
+                    res = res.replace(bad_name, correct_name)
         return res

fledermaus_formatter/table_handler/serializer.py

@@ -3,7 +3,7 @@ from openpyxl import Workbook, load_workbook
 from dataclasses import dataclass
 from pprint import pprint as print
 
-import instructions.mappings as mappings
+import fledermaus_formatter.instructions.mappings as mappings
 
 from .commands.find_and_replace import FindAndReplace
 from .commands.regex_edit_col import RegexEditCol
@@ -11,7 +11,7 @@ from .commands.regex_move_to_col import RegexMoveToCol
 from .commands.copy import Copy
 from .commands.regex_group_valuebased_choose import RegexGroupValuebasedChoose
 from .commands.row_color_to_value import RowColorToCalue
-from logger import logger
+from fledermaus_formatter.logger import logger
 
 from .conditions.regex_cell import RegexCellCondition
 

run.sh

@@ -2,25 +2,6 @@
 
 SCRIPT_DIR="$HOME/.config/fledermaus-formatter"
 
-to_absolute_args() {
-  local result=()
-
-  for arg in "$@"; do
-    if [ -e "$arg" ] || [ -d "$arg" ] || [ -f "$arg" ]; then
-      result+=("$(realpath "$arg")")
-    else
-      result+=("$arg")
-    fi
-  done
-
-  printf '%s\n' "${result[@]}"
-}
-
-ABS_ARGS=()
-while IFS= read -r line; do
-  ABS_ARGS+=("$line")
-done < <(to_absolute_args "$@")
-
-cd $SCRIPT_DIR
 source $SCRIPT_DIR/.venv/bin/activate
-$SCRIPT_DIR/.venv/bin/python3 __init__.py "${ABS_ARGS[@]}"
+export PYTHONPATH=$SCRIPT_DIR:$PYTHONPATH
+$SCRIPT_DIR/.venv/bin/python3 -m fledermaus_formatter "${ABS_ARGS[@]}"