From 80dc6c5e9c6f6a788f26d0c69772fa8fdca23740 Mon Sep 17 00:00:00 2001 From: FelixAbrahamsson Date: Wed, 25 Jun 2025 09:48:52 +0200 Subject: [PATCH 1/3] improve: handle comma formatted kmms by default --- kmm/positions/positions.py | 6 ++++-- kmm/positions/read_kmm.py | 14 +++++++++++--- kmm/positions/read_kmm2.py | 16 +++++++++++++--- 3 files changed, 28 insertions(+), 8 deletions(-) diff --git a/kmm/positions/positions.py b/kmm/positions/positions.py index f212602..615f958 100644 --- a/kmm/positions/positions.py +++ b/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 +27,7 @@ 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}") @@ -40,6 +41,7 @@ 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 @@ -47,7 +49,7 @@ def read_sync_adjust( """ 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() ) diff --git a/kmm/positions/read_kmm.py b/kmm/positions/read_kmm.py index 3a437e6..586963d 100644 --- a/kmm/positions/read_kmm.py +++ b/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", diff --git a/kmm/positions/read_kmm2.py b/kmm/positions/read_kmm2.py index d2023cf..75d055d 100644 --- a/kmm/positions/read_kmm2.py +++ b/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 +47,7 @@ @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 +59,22 @@ 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, ) From 015ce27339ec29783654a9dac9f764bc0a1467e3 Mon Sep 17 00:00:00 2001 From: FelixAbrahamsson Date: Wed, 25 Jun 2025 09:50:12 +0200 Subject: [PATCH 2/3] improve: black formatting --- docs/source/conf.py | 27 +- kmm/header/car_direction.py | 6 +- kmm/header/position_sync.py | 6 +- kmm/positions/positions.py | 14 +- kmm/positions/read_kmm.py | 2 +- kmm/positions/read_kmm2.py | 8 +- poetry.lock | 1225 +++++++++++++++++++---------------- pyproject.toml | 1 + setup.py | 2 +- 9 files changed, 699 insertions(+), 592 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 6cbdc80..e8b473e 100644 --- a/docs/source/conf.py +++ b/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 @@ -37,15 +39,15 @@ # 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. @@ -53,7 +55,7 @@ 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'] - diff --git a/kmm/header/car_direction.py b/kmm/header/car_direction.py index 97fbbae..7e3898e 100644 --- a/kmm/header/car_direction.py +++ b/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)}") diff --git a/kmm/header/position_sync.py b/kmm/header/position_sync.py index 539631f..dd51c62 100644 --- a/kmm/header/position_sync.py +++ b/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.") diff --git a/kmm/positions/positions.py b/kmm/positions/positions.py index 615f958..a16d5c1 100644 --- a/kmm/positions/positions.py +++ b/kmm/positions/positions.py @@ -18,7 +18,7 @@ class Config: def from_path( path: Path, raise_on_malformed_data: bool = True, - replace_commas: bool=True, + replace_commas: bool = True, ): """ Loads positions from .kmm or .kmm2 file. @@ -27,7 +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, replace_commas=replace_commas + path, + raise_on_malformed_data=raise_on_malformed_data, + replace_commas=replace_commas, ) else: raise ValueError(f"Unable to parse file type {path.suffix}") @@ -41,7 +43,7 @@ def read_sync_adjust( header_path: Path, adjustment: kmm.PositionAdjustment = kmm.PositionAdjustment.WIRE_CAMERA, raise_on_malformed_data: bool = True, - replace_commas: bool=True, + replace_commas: bool = True, ): """ Loads positions from .kmm or .kmm2 file + .hdr file, then performs @@ -49,7 +51,11 @@ def read_sync_adjust( """ header = kmm.Header.from_path(header_path, raise_on_malformed_data) return ( - Positions.from_path(kmm_path, raise_on_malformed_data=raise_on_malformed_data, replace_commas=replace_commas) + 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() ) diff --git a/kmm/positions/read_kmm.py b/kmm/positions/read_kmm.py index 586963d..3666227 100644 --- a/kmm/positions/read_kmm.py +++ b/kmm/positions/read_kmm.py @@ -7,7 +7,7 @@ @validate_arguments -def read_kmm(path: Path, replace_commas: bool=True): +def read_kmm(path: Path, replace_commas: bool = True): try: if replace_commas: with open(path, "r", encoding="latin1") as f: diff --git a/kmm/positions/read_kmm2.py b/kmm/positions/read_kmm2.py index 75d055d..fe8bf14 100644 --- a/kmm/positions/read_kmm2.py +++ b/kmm/positions/read_kmm2.py @@ -47,7 +47,9 @@ @validate_arguments -def read_kmm2(path: Path, raise_on_malformed_data: bool = True, replace_commas: 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()) @@ -59,7 +61,7 @@ def read_kmm2(path: Path, raise_on_malformed_data: bool = True, replace_commas: 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: @@ -68,7 +70,7 @@ def read_kmm2(path: Path, raise_on_malformed_data: bool = True, replace_commas: file_obj = StringIO(content) else: file_obj = path - + try: df = pd.read_csv( file_obj, diff --git a/poetry.lock b/poetry.lock index d129911..5a58aa4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.1 and should not be changed by hand. 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"zipp" -version = "3.20.0" +version = "3.20.2" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.20.0-py3-none-any.whl", hash = "sha256:58da6168be89f0be59beb194da1250516fdaa062ccebd30127ac65d30045e10d"}, - {file = "zipp-3.20.0.tar.gz", hash = "sha256:0145e43d89664cfe1a2e533adc75adafed82fe2da404b4bbb6b026c0157bdb31"}, + {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"}, + {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"}, ] [package.extras] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.8,<3.11" -content-hash = "3f641527fdfe5b85bf7cad5facef73d876e885c20ee65d86de1e02b926ef0268" +content-hash = "b9cb34642274dbe964f2738f7635777c1a8a9089cf5555bf4988126dda4b2541" diff --git a/pyproject.toml b/pyproject.toml index d25062a..5f7e3f6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,6 +21,7 @@ sphinx-rtd-theme = "^0.5.2" recommonmark = "^0.7.1" ipykernel = "^6.29.3" ipywidgets = "^8.1.2" +black = "^22.0.1" [build-system] requires = ["poetry-core>=1.0.0"] diff --git a/setup.py b/setup.py index 028b859..404eed9 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ setup( - setup_requires=['pbr', 'setuptools_scm'], + setup_requires=["pbr", "setuptools_scm"], pbr=True, use_scm_version=True, ) From a7223542634ca2a99f91cfe07d102ecf8e0c5fda Mon Sep 17 00:00:00 2001 From: FelixAbrahamsson Date: Wed, 25 Jun 2025 09:51:03 +0200 Subject: [PATCH 3/3] fix: workflows --- .github/workflows/publish.yml | 6 +++--- .github/workflows/test.yml | 14 +++++++------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index b8a013b..2d0f955 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -11,15 +11,15 @@ jobs: - name: Set PATH run: echo "${HOME}/.local/bin" >> $GITHUB_PATH - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v4 with: python-version: "3.8" - name: Install dependencies run: | - curl -sSL https://install.python-poetry.org | python - --version 1.2.2 + curl -sSL https://install.python-poetry.org | python - --version 1.8.1 poetry install - name: Run tests diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index d2dd8e0..10253b1 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -13,14 +13,14 @@ jobs: - name: Set PATH run: echo "${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 }