Fix comma formatting

.github/workflows/publish.yml

@@ -11,15 +11,15 @@ jobs:
       - name: Set PATH
         run: echo "${HOME}/.local/bin" >> $GITHUB_PATH
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: "3.8"
 
       - name: Install dependencies
         run: |
-          curl -sSL https://install.python-poetry.org | python - --version 1.2.2
+          curl -sSL https://install.python-poetry.org | python - --version 1.8.1
           poetry install
 
       - name: Run tests

.github/workflows/test.yml

@@ -13,14 +13,14 @@ jobs:
       - name: Set PATH
         run: echo "${HOME}/.local/bin" >> $GITHUB_PATH
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Cache pip
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('poetry.lock') }}-${ GITHUB_REF }
@@ -30,7 +30,7 @@ jobs:
 
       - name: Install dependencies
         run: |
-          curl -sSL https://install.python-poetry.org | python - --version 1.2.2
+          curl -sSL https://install.python-poetry.org | python - --version 1.8.1
           poetry install
 
       - name: Run tests
@@ -48,14 +48,14 @@ jobs:
         python-version: [3.8]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Cache pip
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('docs/source/requirements.txt') }}-${ GITHUB_REF }

docs/source/conf.py

@@ -12,21 +12,23 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../..'))
+
+sys.path.insert(0, os.path.abspath("../.."))
 sys.setrecursionlimit(1500)
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'kmm'
-copyright = '2020, Aiwizo'
-author = 'Richard Löwenström, Felix Abrahamsson'
+project = "kmm"
+copyright = "2020, Aiwizo"
+author = "Richard Löwenström, Felix Abrahamsson"
 
 # The full version, including alpha/beta/rc tags
 # release = '0.1.0'
 from pkg_resources import get_distribution, DistributionNotFound
+
 try:
-    release = get_distribution('kmm').version
+    release = get_distribution("kmm").version
 except DistributionNotFound:
     pass
 
@@ -37,23 +39,23 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'recommonmark',
-    'sphinx.ext.viewcode',
-    'sphinx_rtd_theme',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "recommonmark",
+    "sphinx.ext.viewcode",
+    "sphinx_rtd_theme",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # -- Options for HTML output -------------------------------------------------
 
@@ -68,4 +70,3 @@
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 # html_static_path = ['_static']
-

kmm/header/car_direction.py

@@ -7,11 +7,7 @@
 def car_direction(tree: ElementTree):
 
     root = tree.getroot()
-    start_tags = [
-        child.text
-        for child in root
-        if child.tag == "Start"
-    ]
+    start_tags = [child.text for child in root if child.tag == "Start"]
 
     if len(start_tags) != 1:
         raise ValueError(f"Expected 1 'Start' tag in header, found {len(start_tags)}")

kmm/header/position_sync.py

@@ -5,11 +5,7 @@
 def position_sync(tree: ElementTree):
 
     root = tree.getroot()
-    sync_tags = [
-        child.text
-        for child in root
-        if child.tag == "Sync"
-    ]
+    sync_tags = [child.text for child in root if child.tag == "Sync"]
 
     if len(sync_tags) == 0:
         raise ValueError("Did not find a Sync tag in header.")

kmm/positions/positions.py

@@ -18,6 +18,7 @@ class Config:
     def from_path(
         path: Path,
         raise_on_malformed_data: bool = True,
+        replace_commas: bool = True,
     ):
         """
         Loads positions from .kmm or .kmm2 file.
@@ -26,7 +27,9 @@ def from_path(
             dataframe = kmm.positions.read_kmm(path)
         elif path.suffix == ".kmm2":
             dataframe = kmm.positions.read_kmm2(
-                path, raise_on_malformed_data=raise_on_malformed_data
+                path,
+                raise_on_malformed_data=raise_on_malformed_data,
+                replace_commas=replace_commas,
             )
         else:
             raise ValueError(f"Unable to parse file type {path.suffix}")
@@ -40,14 +43,19 @@ def read_sync_adjust(
         header_path: Path,
         adjustment: kmm.PositionAdjustment = kmm.PositionAdjustment.WIRE_CAMERA,
         raise_on_malformed_data: bool = True,
+        replace_commas: bool = True,
     ):
         """
         Loads positions from .kmm or .kmm2 file + .hdr file, then performs
         frame index sync, position adjustment and geodetic coordinate transformation.
         """
         header = kmm.Header.from_path(header_path, raise_on_malformed_data)
         return (
-            Positions.from_path(kmm_path, raise_on_malformed_data)
+            Positions.from_path(
+                kmm_path,
+                raise_on_malformed_data=raise_on_malformed_data,
+                replace_commas=replace_commas,
+            )
             .sync_frame_index(header, adjustment, raise_on_malformed_data)
             .geodetic()
         )

kmm/positions/read_kmm.py

@@ -1,3 +1,4 @@
+from io import StringIO
 from pathlib import Path
 
 import numpy as np
@@ -6,12 +7,19 @@
 
 
 @validate_arguments
-def read_kmm(path: Path):
+def read_kmm(path: Path, replace_commas: bool = True):
     try:
+        if replace_commas:
+            with open(path, "r", encoding="latin1") as f:
+                content = f.read()
+            content = content.replace(",", ".")
+            file_obj = StringIO(content)
+        else:
+            file_obj = path
         return pd.read_csv(
-            path,
+            file_obj,
             sep="\t",
-            encoding="latin1",
+            encoding="latin1" if not replace_commas else None,
             names=[
                 "centimeter",
                 "track_section",

kmm/positions/read_kmm2.py

@@ -1,4 +1,5 @@
 import re
+from io import StringIO
 from pathlib import Path
 
 import numpy as np
@@ -46,7 +47,9 @@
 
 
 @validate_arguments
-def read_kmm2(path: Path, raise_on_malformed_data: bool = True):
+def read_kmm2(
+    path: Path, raise_on_malformed_data: bool = True, replace_commas: bool = True
+):
     skiprows = [
         index
         for index, line in enumerate(path.read_text(encoding="latin1").splitlines())
@@ -58,13 +61,22 @@ def read_kmm2(path: Path, raise_on_malformed_data: bool = True):
             skiprows = [0] + skiprows
         elif raise_on_malformed_data and not line.startswith("POS"):
             raise ValueError("Malformed data, first line is not POS or VER")
+
     try:
+        if replace_commas:
+            with open(path, "r", encoding="latin1") as f:
+                content = f.read()
+            content = content.replace(",", ".")
+            file_obj = StringIO(content)
+        else:
+            file_obj = path
+
         try:
             df = pd.read_csv(
-                path,
+                file_obj,
                 skiprows=skiprows,
                 delimiter="\t",
-                encoding="latin1",
+                encoding="latin1" if not replace_commas else None,
                 low_memory=False,
                 header=None,
             )