chromparser 0.1.0__tar.gz

chromparser-0.1.0/LICENSE

@@ -0,0 +1,51 @@
+MIT License
+
+Copyright (c) 2025-2026 Sebastian Rejman
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+--------------------------------------------------------------------------------
+Third-party notice
+
+The Agilent .ch decoders in src/chromparser/vendors/agilent/ch.py are adapted
+from ImportAgilent.m in chemplexity/chromatography
+(https://github.com/chemplexity/chromatography), which is distributed under the
+following license:
+
+The MIT License (MIT)
+
+Copyright (c) 2014 James Dillon
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

chromparser-0.1.0/PKG-INFO

@@ -0,0 +1,162 @@
+Metadata-Version: 2.4
+Name: chromparser
+Version: 0.1.0
+Summary: Read chromatography raw files (Chromeleon, Thermo, Agilent, Shimadzu) into one data model and convert them to HDF5.
+Keywords: chromatography,GC,GC-MS,HPLC,Chromeleon,Agilent,Shimadzu,Thermo,hdf5
+Author: Sebastian Rejman
+Author-email: Sebastian Rejman <s.rejman@uu.nl>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Dist: numpy>=1.22
+Requires-Dist: h5py>=3.0
+Requires-Dist: olefile>=0.46
+Requires-Python: >=3.10
+Project-URL: homepage, https://github.com/MyonicS/chromparser
+Project-URL: documentation, https://myonics.github.io/chromparser/
+Project-URL: repository, https://github.com/MyonicS/chromparser
+Project-URL: issues, https://github.com/MyonicS/chromparser/issues
+Project-URL: changelog, https://github.com/MyonicS/chromparser/blob/main/CHANGELOG.md
+Description-Content-Type: text/markdown
+
+# chromparser
+
+[![License: MIT](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10%2B-blue.svg)](pyproject.toml)
+[![Tests](https://github.com/MyonicS/chromparser/actions/workflows/tests.yml/badge.svg)](https://github.com/MyonicS/chromparser/actions/workflows/tests.yml)
+[![Docs](https://github.com/MyonicS/chromparser/actions/workflows/docs.yml/badge.svg)](https://myonics.github.io/chromparser/)
+[![Status: beta](https://img.shields.io/badge/status-beta-yellow.svg)](CHANGELOG.md)
+[![Code style: ruff](https://img.shields.io/badge/code%20style-ruff-261230.svg)](https://github.com/astral-sh/ruff)
+
+chromparser reads chromatography raw files (Chromeleon, Thermo, Agilent,
+Shimadzu, ANDI netCDF) into one Python data model, and converts them to a
+single HDF5 layout or to ANDI netCDF. Pure Python on numpy, h5py and olefile;
+MIT licensed; every format is clean-room and documented.
+
+## Supported formats
+
+| Vendor | Files | Reader | Format id |
+| --- | --- | --- | --- |
+| Thermo Chromeleon 7 | `.cmbx` archives (signals and embedded MS) | `read_cmbx` | `chromeleon-cmbx` |
+| | raw signal files (`SignHdr`, from a data vault) | `read_chromeleon_raw` | `chromeleon-raw` |
+| | text exports (`.txt`), 7.2 and 7.3, any locale | `read_chromeleon_txt` | `chromeleon-txt` |
+| Thermo | `.raw` MS files (v66, centroid, single quad), e.g. extracted from `.cmbx` | `read_thermo_raw` | `thermo-raw` |
+| Agilent | `.ch` (versions 8, 81, 179, 181) | `read_agilent_ch` | `agilent-ch` |
+| | `.D` folders | `read_agilent_d` | `agilent-d` |
+| | OpenLab `.dx` archives | `read_agilent_dx` | `agilent-dx` |
+| Shimadzu GCMSsolution | `.qgd` (GC-MS, centroids) | `read_qgd` | `shimadzu-qgd` |
+| | `.gcd` (GC/FID) | `read_gcd` | `shimadzu-gcd` |
+| ANDI (netCDF) | ANDI-MS `.cdf` (GC-MS, centroids) | `read_andi_ms` | `andi-ms` |
+| | ANDI chromatography / AIA `.cdf` (one signal) | `read_andi_chrom` | `andi-chrom` |
+
+The format is detected from the content (magic bytes, OLE2 storages, zip
+members, netCDF variables, folder contents), never from the extension.
+Everything chromparser reads can also be written as ANDI files
+(`write_andi`), which AMDIS, NIST MS Search, MZmine, OpenChrom, MS-DIAL and
+XCMS read; ANDI loses metadata, HDF5 keeps everything
+([`docs/formats/andi.md`](docs/formats/andi.md)).
+
+> Chromeleon and Thermo are trademarks of Thermo Fisher Scientific, Agilent
+> and OpenLab of Agilent Technologies, Shimadzu and GCMSsolution of Shimadzu
+> Corporation. This project is not affiliated with or endorsed by them. The
+> formats were reverse engineered for interoperability; see `docs/formats/`.
+
+## Installation
+
+```bash
+pip install chromparser          # or: uv add chromparser
+```
+
+Python 3.10 or newer.
+
+## Usage
+
+### Command line
+
+```bash
+chromparser info run.cmbx sample.qgd data.D           # injections, channels, MS runs
+chromparser convert run.cmbx                           # writes run.h5 (layout v3)
+chromparser convert *.qgd --overwrite
+chromparser convert 152612018.raw --signal-unit pA     # unit is not in raw files
+chromparser convert old.h5                             # cmbx-reader v1/v2 -> old.v3.h5
+chromparser convert run.cmbx --to andi -o out/         # one ANDI .cdf per signal / MS run
+chromparser extract-ms run.cmbx -d out/                # the embedded Thermo .raw files
+```
+
+`chromparser convert --no-ms` skips the MS data of `.cmbx` archives.
+
+### Python
+
+```python
+import chromparser
+
+for injection in chromparser.read("run.cmbx"):  # always a list
+    print(injection.name, injection.inject_time, injection.metadata)
+    for channel, signal in injection.signals.items():
+        signal.time, signal.values, signal.unit  # minutes, as stored
+    for name, ms in injection.ms.items():
+        mz, intensity = ms.spectrum(ms.scan_number[0])
+        eic = ms.xic(57.0, tolerance=0.5)  # one value per scan
+
+injection = chromparser.read_one("FID1A.ch")  # files with one injection
+chromparser.sniff("mystery.dat")  # e.g. "shimadzu-qgd"
+chromparser.convert("sample.qgd", "sample.h5")
+injections = chromparser.read_hdf5("sample.h5")  # == chromparser.read("sample.qgd")
+chromparser.write_andi(injections, "out/")  # out/sample_MS.cdf, for AMDIS etc.
+```
+
+### Data model
+
+See [`docs/model.md`](docs/model.md) for the data model and the reader
+contract, and [`docs/hdf5.md`](docs/hdf5.md) for the HDF5 layout. In short:
+
+* `Signal`: `time` (min, float64), `values` (dtype as stored), `unit`,
+  `acquisition_start` (UTC), `sampling_interval` (s), `metadata`.
+* `MSData`: per scan `scan_number`, `retention_time` (min), `tic`, optional
+  `base_peak_*`, `filters`, `ms_level`; per peak `mz`, `intensity` (dtypes as
+  stored: float32 for Thermo, float64 m/z and uint32 intensity for Shimadzu)
+  and optional `flags` (bit 0 = saturated), CSR-indexed by `peak_offset`.
+* `inject_time` is local time: timezone-aware when the file has the offset,
+  naive when it stores only the wall time (Agilent `.ch`, Chromeleon 7.2
+  text exports).
+* Unsupported variants raise `UnsupportedVariant` saying what was found;
+  readers never return partial data silently. Recoverable oddities are
+  warnings, recorded in `metadata["warnings"]`.
+
+## Scope and limitations
+
+* Files and data types not in the table above are probably not supported
+  yet. chromparser then raises an error saying what it found; it does not
+  return partial data.
+* Agilent `.ch` versions 8, 81 and 181 are implemented from the documented
+  encodings but have not been checked against real files yet; please share
+  a sample if you have one.
+* Spectra are kept as centroids; binning to nominal m/z is left to the user
+  (`np.rint(ms.mz)`).
+
+If a file fails to read, please open an issue; a sample file helps a lot.
+
+## Development
+
+```bash
+uv sync                    # environment with the dev tools
+uv run pytest              # runs without local data
+uv run ruff check . && uv run ruff format --check .
+uv sync --group docs && uv run mkdocs serve   # the documentation site
+```
+
+Large local files make more tests run; see [`tests/README.md`](tests/README.md).
+Contributor notes are in [`AGENTS.md`](AGENTS.md).
+
+## License
+
+MIT. The Agilent `.ch` decoders are adapted from chemplexity/chromatography
+(MIT, Copyright (c) 2014 James Dillon); see [`LICENSE`](LICENSE).

chromparser-0.1.0/README.md

@@ -0,0 +1,133 @@
+# chromparser
+
+[![License: MIT](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10%2B-blue.svg)](pyproject.toml)
+[![Tests](https://github.com/MyonicS/chromparser/actions/workflows/tests.yml/badge.svg)](https://github.com/MyonicS/chromparser/actions/workflows/tests.yml)
+[![Docs](https://github.com/MyonicS/chromparser/actions/workflows/docs.yml/badge.svg)](https://myonics.github.io/chromparser/)
+[![Status: beta](https://img.shields.io/badge/status-beta-yellow.svg)](CHANGELOG.md)
+[![Code style: ruff](https://img.shields.io/badge/code%20style-ruff-261230.svg)](https://github.com/astral-sh/ruff)
+
+chromparser reads chromatography raw files (Chromeleon, Thermo, Agilent,
+Shimadzu, ANDI netCDF) into one Python data model, and converts them to a
+single HDF5 layout or to ANDI netCDF. Pure Python on numpy, h5py and olefile;
+MIT licensed; every format is clean-room and documented.
+
+## Supported formats
+
+| Vendor | Files | Reader | Format id |
+| --- | --- | --- | --- |
+| Thermo Chromeleon 7 | `.cmbx` archives (signals and embedded MS) | `read_cmbx` | `chromeleon-cmbx` |
+| | raw signal files (`SignHdr`, from a data vault) | `read_chromeleon_raw` | `chromeleon-raw` |
+| | text exports (`.txt`), 7.2 and 7.3, any locale | `read_chromeleon_txt` | `chromeleon-txt` |
+| Thermo | `.raw` MS files (v66, centroid, single quad), e.g. extracted from `.cmbx` | `read_thermo_raw` | `thermo-raw` |
+| Agilent | `.ch` (versions 8, 81, 179, 181) | `read_agilent_ch` | `agilent-ch` |
+| | `.D` folders | `read_agilent_d` | `agilent-d` |
+| | OpenLab `.dx` archives | `read_agilent_dx` | `agilent-dx` |
+| Shimadzu GCMSsolution | `.qgd` (GC-MS, centroids) | `read_qgd` | `shimadzu-qgd` |
+| | `.gcd` (GC/FID) | `read_gcd` | `shimadzu-gcd` |
+| ANDI (netCDF) | ANDI-MS `.cdf` (GC-MS, centroids) | `read_andi_ms` | `andi-ms` |
+| | ANDI chromatography / AIA `.cdf` (one signal) | `read_andi_chrom` | `andi-chrom` |
+
+The format is detected from the content (magic bytes, OLE2 storages, zip
+members, netCDF variables, folder contents), never from the extension.
+Everything chromparser reads can also be written as ANDI files
+(`write_andi`), which AMDIS, NIST MS Search, MZmine, OpenChrom, MS-DIAL and
+XCMS read; ANDI loses metadata, HDF5 keeps everything
+([`docs/formats/andi.md`](docs/formats/andi.md)).
+
+> Chromeleon and Thermo are trademarks of Thermo Fisher Scientific, Agilent
+> and OpenLab of Agilent Technologies, Shimadzu and GCMSsolution of Shimadzu
+> Corporation. This project is not affiliated with or endorsed by them. The
+> formats were reverse engineered for interoperability; see `docs/formats/`.
+
+## Installation
+
+```bash
+pip install chromparser          # or: uv add chromparser
+```
+
+Python 3.10 or newer.
+
+## Usage
+
+### Command line
+
+```bash
+chromparser info run.cmbx sample.qgd data.D           # injections, channels, MS runs
+chromparser convert run.cmbx                           # writes run.h5 (layout v3)
+chromparser convert *.qgd --overwrite
+chromparser convert 152612018.raw --signal-unit pA     # unit is not in raw files
+chromparser convert old.h5                             # cmbx-reader v1/v2 -> old.v3.h5
+chromparser convert run.cmbx --to andi -o out/         # one ANDI .cdf per signal / MS run
+chromparser extract-ms run.cmbx -d out/                # the embedded Thermo .raw files
+```
+
+`chromparser convert --no-ms` skips the MS data of `.cmbx` archives.
+
+### Python
+
+```python
+import chromparser
+
+for injection in chromparser.read("run.cmbx"):  # always a list
+    print(injection.name, injection.inject_time, injection.metadata)
+    for channel, signal in injection.signals.items():
+        signal.time, signal.values, signal.unit  # minutes, as stored
+    for name, ms in injection.ms.items():
+        mz, intensity = ms.spectrum(ms.scan_number[0])
+        eic = ms.xic(57.0, tolerance=0.5)  # one value per scan
+
+injection = chromparser.read_one("FID1A.ch")  # files with one injection
+chromparser.sniff("mystery.dat")  # e.g. "shimadzu-qgd"
+chromparser.convert("sample.qgd", "sample.h5")
+injections = chromparser.read_hdf5("sample.h5")  # == chromparser.read("sample.qgd")
+chromparser.write_andi(injections, "out/")  # out/sample_MS.cdf, for AMDIS etc.
+```
+
+### Data model
+
+See [`docs/model.md`](docs/model.md) for the data model and the reader
+contract, and [`docs/hdf5.md`](docs/hdf5.md) for the HDF5 layout. In short:
+
+* `Signal`: `time` (min, float64), `values` (dtype as stored), `unit`,
+  `acquisition_start` (UTC), `sampling_interval` (s), `metadata`.
+* `MSData`: per scan `scan_number`, `retention_time` (min), `tic`, optional
+  `base_peak_*`, `filters`, `ms_level`; per peak `mz`, `intensity` (dtypes as
+  stored: float32 for Thermo, float64 m/z and uint32 intensity for Shimadzu)
+  and optional `flags` (bit 0 = saturated), CSR-indexed by `peak_offset`.
+* `inject_time` is local time: timezone-aware when the file has the offset,
+  naive when it stores only the wall time (Agilent `.ch`, Chromeleon 7.2
+  text exports).
+* Unsupported variants raise `UnsupportedVariant` saying what was found;
+  readers never return partial data silently. Recoverable oddities are
+  warnings, recorded in `metadata["warnings"]`.
+
+## Scope and limitations
+
+* Files and data types not in the table above are probably not supported
+  yet. chromparser then raises an error saying what it found; it does not
+  return partial data.
+* Agilent `.ch` versions 8, 81 and 181 are implemented from the documented
+  encodings but have not been checked against real files yet; please share
+  a sample if you have one.
+* Spectra are kept as centroids; binning to nominal m/z is left to the user
+  (`np.rint(ms.mz)`).
+
+If a file fails to read, please open an issue; a sample file helps a lot.
+
+## Development
+
+```bash
+uv sync                    # environment with the dev tools
+uv run pytest              # runs without local data
+uv run ruff check . && uv run ruff format --check .
+uv sync --group docs && uv run mkdocs serve   # the documentation site
+```
+
+Large local files make more tests run; see [`tests/README.md`](tests/README.md).
+Contributor notes are in [`AGENTS.md`](AGENTS.md).
+
+## License
+
+MIT. The Agilent `.ch` decoders are adapted from chemplexity/chromatography
+(MIT, Copyright (c) 2014 James Dillon); see [`LICENSE`](LICENSE).

chromparser-0.1.0/pyproject.toml

@@ -0,0 +1,113 @@
+[project]
+name = "chromparser"
+version = "0.1.0"
+description = "Read chromatography raw files (Chromeleon, Thermo, Agilent, Shimadzu) into one data model and convert them to HDF5."
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+keywords = [
+    "chromatography",
+    "GC",
+    "GC-MS",
+    "HPLC",
+    "Chromeleon",
+    "Agilent",
+    "Shimadzu",
+    "Thermo",
+    "hdf5",
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering :: Chemistry",
+]
+requires-python = ">=3.10"
+dependencies = [
+    "numpy>=1.22",
+    "h5py>=3.0",
+    "olefile>=0.46",
+]
+
+[[project.authors]]
+name = "Sebastian Rejman"
+email = "s.rejman@uu.nl"
+
+[project.scripts]
+chromparser = "chromparser.cli:main"
+
+[project.urls]
+homepage = "https://github.com/MyonicS/chromparser"
+documentation = "https://myonics.github.io/chromparser/"
+repository = "https://github.com/MyonicS/chromparser"
+issues = "https://github.com/MyonicS/chromparser/issues"
+changelog = "https://github.com/MyonicS/chromparser/blob/main/CHANGELOG.md"
+
+[dependency-groups]
+dev = [
+    "pytest>=8.0",
+    "ruff>=0.6",
+    "scipy>=1.15.3",
+]
+docs = [
+    "matplotlib>=3.10.9",
+    "mkdocs-jupyter>=0.26.3",
+    "mkdocs-material>=9.7.7",
+]
+
+[build-system]
+requires = ["uv_build>=0.10.9,<0.11.0"]
+build-backend = "uv_build"
+
+[tool.pytest.ini_options]
+addopts = ["--import-mode=importlib"]
+testpaths = ["tests"]
+pythonpath = ["tests"]
+
+[tool.ruff]
+line-length = 88
+target-version = "py310"
+src = [
+    "src",
+    "tests",
+]
+
+[tool.ruff.lint]
+select = [
+    "B",
+    "D",
+    "E",
+    "F",
+    "I",
+    "NPY",
+    "PT",
+    "RUF",
+    "SIM",
+    "UP",
+    "W",
+]
+ignore = [
+    "E501",
+    "D105",
+    "D107",
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**" = ["D"]
+"tools/**" = ["D"]
+"docs/**/*.ipynb" = [
+    "D",
+    "I002",
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.ruff.lint.isort]
+known-first-party = ["chromparser"]
+required-imports = ["from __future__ import annotations"]

chromparser-0.1.0/pyproject.toml.orig

@@ -0,0 +1,84 @@
+[project]
+name = "chromparser"
+version = "0.1.0"
+description = "Read chromatography raw files (Chromeleon, Thermo, Agilent, Shimadzu) into one data model and convert them to HDF5."
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+authors = [{ name = "Sebastian Rejman", email = "s.rejman@uu.nl" }]
+keywords = [
+    "chromatography",
+    "GC",
+    "GC-MS",
+    "HPLC",
+    "Chromeleon",
+    "Agilent",
+    "Shimadzu",
+    "Thermo",
+    "hdf5",
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering :: Chemistry",
+]
+requires-python = ">=3.10"
+dependencies = ["numpy>=1.22", "h5py>=3.0", "olefile>=0.46"]
+
+[project.scripts]
+chromparser = "chromparser.cli:main"
+
+[project.urls]
+homepage = "https://github.com/MyonicS/chromparser"
+documentation = "https://myonics.github.io/chromparser/"
+repository = "https://github.com/MyonicS/chromparser"
+issues = "https://github.com/MyonicS/chromparser/issues"
+changelog = "https://github.com/MyonicS/chromparser/blob/main/CHANGELOG.md"
+
+[dependency-groups]
+dev = [
+    "pytest>=8.0",
+    "ruff>=0.6",
+    "scipy>=1.15.3",
+]
+docs = [
+    "matplotlib>=3.10.9",
+    "mkdocs-jupyter>=0.26.3",
+    "mkdocs-material>=9.7.7",
+]
+
+[build-system]
+requires = ["uv_build>=0.10.9,<0.11.0"]
+build-backend = "uv_build"
+
+[tool.pytest.ini_options]
+addopts = ["--import-mode=importlib"]
+testpaths = ["tests"]
+pythonpath = ["tests"]
+
+[tool.ruff]
+line-length = 88
+target-version = "py310"
+src = ["src", "tests"]
+
+[tool.ruff.lint]
+select = ["B", "D", "E", "F", "I", "NPY", "PT", "RUF", "SIM", "UP", "W"]
+ignore = ["E501", "D105", "D107"]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**" = ["D"]
+"tools/**" = ["D"]
+"docs/**/*.ipynb" = ["D", "I002"]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.ruff.lint.isort]
+known-first-party = ["chromparser"]
+required-imports = ["from __future__ import annotations"]