diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 2aa5127..1555f15 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -13,7 +13,6 @@ "extensions": [ "ms-python.black-formatter", "ms-python.python", - "ms-toolsai.jupyter", "streetsidesoftware.code-spell-checker", "tamasfe.even-better-toml" ], diff --git a/.github/CODE_OF_CONDUCT.md b/.github/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..b8e9dd3 --- /dev/null +++ b/.github/CODE_OF_CONDUCT.md @@ -0,0 +1,128 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, religion, or sexual identity +and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the + overall community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or + advances of any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email + address, without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official e-mail address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +a-taniguchi@mail.kitami-it.ac.jp. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series +of actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or +permanent ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within +the community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.0, available at +https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. + +Community Impact Guidelines were inspired by [Mozilla's code of conduct +enforcement ladder](https://github.com/mozilla/diversity). + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see the FAQ at +https://www.contributor-covenant.org/faq. Translations are available at +https://www.contributor-covenant.org/translations. diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml new file mode 100644 index 0000000..cc91fb9 --- /dev/null +++ b/.github/workflows/docs.yaml @@ -0,0 +1,25 @@ +name: Docs + +on: + release: + types: + - created + +jobs: + job: + name: Docs + runs-on: ubuntu-latest + container: ghcr.io/astral-sh/uv:python3.12-bookworm + env: + UV_PROJECT_ENVIRONMENT: /usr/local + permissions: + contents: write + steps: + - uses: actions/checkout@v4 + - run: uv sync --frozen + - run: docs/build + - uses: peaceiris/actions-gh-pages@v4 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: ./docs/_build + keep_files: true diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml index 3d90104..d5e76d1 100644 --- a/.github/workflows/tests.yaml +++ b/.github/workflows/tests.yaml @@ -29,3 +29,6 @@ jobs: - uses: actions/checkout@v4 - run: uv sync --frozen - run: black --check ${PYTHON_DIRS} + - run: pyright ${PYTHON_DIRS} + - run: pytest -v tests + - run: docs/build diff --git a/.gitignore b/.gitignore index b7faf40..1ee9271 100644 --- a/.gitignore +++ b/.gitignore @@ -69,6 +69,7 @@ instance/ .scrapy # Sphinx documentation +docs/_apidoc/ docs/_build/ # PyBuilder @@ -182,9 +183,9 @@ cython_debug/ .abstra/ # Visual Studio Code -# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore +# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore # that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore -# and can be added to the global gitignore or merged into this file. However, if you prefer, +# and can be added to the global gitignore or merged into this file. However, if you prefer, # you could uncomment the following to ignore the entire vscode folder # .vscode/ diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..a435084 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,27 @@ +# This CITATION.cff file was generated with cffinit. +# Visit https://bit.ly/cffinit to generate yours today! + +cff-version: 1.2.0 +title: sam45 +message: >- + If you use this software, please cite it using the + metadata from this file. +type: software +authors: + - given-names: Akio + family-names: Taniguchi + email: a-taniguchi@mail.kitami-it.ac.jp + affiliation: Kitami Institute of Technology + orcid: 'https://orcid.org/0000-0002-9695-6183' +repository-code: 'https://github.com/astropenguin/sam45' +url: 'https://astropenguin.github.io/sam45' +abstract: NRO/SAM45 log data reader +keywords: + - astronomy + - nro + - python + - radio-astronomy + - sam45 +license: MIT +version: 1.0.0rc1 +date-released: '2025-12-25' diff --git a/README.md b/README.md index b9ae5e8..7d427c2 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,41 @@ -# sam45 +# SAM45 + +[![Release](https://img.shields.io/pypi/v/sam45?label=Release&color=cornflowerblue&style=flat-square)](https://pypi.org/project/sam45/) +[![Python](https://img.shields.io/pypi/pyversions/sam45?label=Python&color=cornflowerblue&style=flat-square)](https://pypi.org/project/sam45/) +[![Downloads](https://img.shields.io/pypi/dm/sam45?label=Downloads&color=cornflowerblue&style=flat-square)](https://pepy.tech/project/sam45) +[![Tests](https://img.shields.io/github/actions/workflow/status/astropenguin/45m/tests.yaml?label=Tests&style=flat-square)](https://github.com/astropenguin/sam45/actions) + NRO/SAM45 log data reader + +## Installation + +```shell +pip install sam45 +``` + +## Usage + +The following functions will read a SAM45 log to extract each information as [a NumPy structured array](https://numpy.org/doc/stable/user/basics.rec.html). + +```python +import sam45 + +data_ctl = sam45.read.ctl("/path/to/log") +data_obs = sam45.read.obs("/path/to/log") +data_dat = sam45.read.dat("/path/to/log") +data_end = sam45.read.end("/path/to/log") +``` + +## Data types + +The data type of each information is defined as [a NumPy structured data type](https://numpy.org/doc/stable/reference/arrays.dtypes.html). +It complies with the definition as of December 5, 2025. + +```python +import sam45 + +dtype_ctl = sam45.dtypes.ctl +dtype_obs = sam45.dtypes.obs +dtype_dat = sam45.dtypes.dat +dtype_end = sam45.dtypes.end +``` diff --git a/docs/_static/switcher.json b/docs/_static/switcher.json new file mode 100644 index 0000000..e3a87e5 --- /dev/null +++ b/docs/_static/switcher.json @@ -0,0 +1,7 @@ +[ + { + "name": "1.0.0rc1 (latest)", + "version": "1.0.0rc1", + "url": "https://astropenguin.github.io/sam45/" + } +] diff --git a/docs/build b/docs/build new file mode 100755 index 0000000..96ccf61 --- /dev/null +++ b/docs/build @@ -0,0 +1,8 @@ +#!/bin/bash -eu + +export LANG=C.UTF-8 +export LC_ALL=C.UTF-8 + +sphinx-apidoc -efMT -d 2 -o docs/_apidoc sam45 +sphinx-build -a -b html docs docs/_build +sphinx-build -a -b html docs docs/_build/1.0.0rc1 diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 0000000..41c40ab --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,23 @@ +copyright = "2025 Akio Taniguchi" +extensions = [ + "myst_parser", + "sphinx.ext.autodoc", + "sphinx.ext.autosummary", + "sphinx.ext.napoleon", + "sphinx.ext.viewcode", +] +html_static_path = ["_static"] +html_theme = "pydata_sphinx_theme" +html_theme_options = { + "github_url": "https://github.com/astropenguin/sam45", + "logo": {"text": "SAM45"}, + "navbar_end": [ + "version-switcher", + "theme-switcher", + "navbar-icon-links", + ], + "switcher": { + "json_url": "https://astropenguin.github.io/sam45/_static/switcher.json", + "version_match": "1.0.0rc1", + }, +} diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..f522f68 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,11 @@ +```{include} ../README.md +``` + +```{toctree} +--- +hidden: +--- + +Home +Package guide <_apidoc/sam45> +``` diff --git a/pyproject.toml b/pyproject.toml index 65c39ef..e9ea9e3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,8 +1,15 @@ [project] name = "sam45" -version = "0.1.0" +version = "1.0.0rc1" description = "NRO/SAM45 log data reader" readme = "README.md" +keywords = [ + "astronomy", + "nro", + "python", + "radio-astronomy", + "sam45", +] requires-python = ">=3.10,<3.15" dependencies = [ "numpy>=2,<3", @@ -20,20 +27,30 @@ classifiers = [ [[project.authors]] name = "Akio Taniguchi" -email = "taniguchi.akio@gmail.com" +email = "a-taniguchi@mail.kitami-it.ac.jp" [project.license] file = "LICENSE" [project.urls] +homepage = "https://astropenguin.github.io/sam45" repository = "https://github.com/astropenguin/sam45" [dependency-groups] dev = [ "black>=25,<26", "ipython>=8,<10", + "myst-parser>=3,<5", + "pandas-stubs>=2,<3", + "pydata-sphinx-theme>=0.16,<1.0", + "pyright>=1,<2", + "pytest>=9,<10", + "sphinx>=8,<9", ] [build-system] requires = ["hatchling"] build-backend = "hatchling.build" + +[tool.pyright] +typeCheckingMode = "strict" diff --git a/sam45/__init__.py b/sam45/__init__.py index 39bb3af..969d651 100644 --- a/sam45/__init__.py +++ b/sam45/__init__.py @@ -1,5 +1,7 @@ -__all__ = ["dtypes"] +__all__ = ["dtypes", "read"] +__version__ = "1.0.0rc1" # dependencies from . import dtypes +from . import read diff --git a/sam45/dtypes.py b/sam45/dtypes.py index 8df9067..75a7cd4 100644 --- a/sam45/dtypes.py +++ b/sam45/dtypes.py @@ -4,13 +4,14 @@ # standard library from importlib.resources import files from tomli import loads +from typing import Any # dependencies import numpy as np -def _get_dtype(name: str, /) -> np.dtype: +def _get_dtype(name: str, /) -> np.dtype[Any]: with (files("sam45") / "dtypes.toml").open() as f: text = f.read() @@ -20,13 +21,13 @@ def _get_dtype(name: str, /) -> np.dtype: ctl = _get_dtype("ctl") -"""Data type of the SAM45/CTL information.""" +"""Structured data type of the SAM45/CTL information.""" obs = _get_dtype("obs") -"""Data type of the SAM45/OBS information.""" +"""Structured data type of the SAM45/OBS information.""" dat = _get_dtype("dat") -"""Data type of the SAM45/DAT information.""" +"""Structured data type of the SAM45/DAT information.""" end = _get_dtype("end") -"""Data type of the SAM45/END information.""" +"""Structured data type of the SAM45/END information.""" diff --git a/sam45/read.py b/sam45/read.py new file mode 100644 index 0000000..bf3d9ba --- /dev/null +++ b/sam45/read.py @@ -0,0 +1,125 @@ +__all__ = ["ctl", "obs", "dat", "end"] + + +# standard library +from mmap import mmap +from os import PathLike +from typing import Any + + +# dependencies +from numpy import frombuffer +from numpy.typing import NDArray +from . import dtypes + + +def ctl(log: PathLike[str] | str, /, *, validate: bool = True) -> NDArray[Any]: + """Read a SAM45 log to extract the SAM45/CTL information. + + Args: + log: Path to the SAM45 log. + validate: Whether to validate the content of the read information. + + Returns: + NumPy structured array containing the SAM45/CTL information. + + Raises: + ValueError: Raised if the read information is invalid, + i.e., the ``crec_type`` field of it is not ``b"L0"``. + + """ + start = None + stop = dtypes.ctl.itemsize + + with open(log, "r+b") as f: + mm = mmap(f.fileno(), 0) + data = frombuffer(mm[start:stop], dtype=dtypes.ctl) + + if not validate or (data["crec_type"] == b"L0").all(): + return data + else: + raise ValueError("Invalid SAM45/CTL information (maybe truncated).") + + +def obs(log: PathLike[str] | str, /, *, validate: bool = True) -> NDArray[Any]: + """Read a SAM45 log to extract the SAM45/OBS information. + + Args: + log: Path to the SAM45 log. + validate: Whether to validate the content of the read information. + + Returns: + NumPy structured array containing the SAM45/OBS information. + + Raises: + ValueError: Raised if the read information is invalid, + i.e., the ``crec_type`` field of it is not ``b"L1"``. + + """ + start = dtypes.ctl.itemsize + stop = dtypes.ctl.itemsize + dtypes.obs.itemsize + + with open(log, "r+b") as f: + mm = mmap(f.fileno(), 0) + data = frombuffer(mm[start:stop], dtype=dtypes.obs) + + if not validate or (data["crec_type"] == b"L1").all(): + return data + else: + raise ValueError("Invalid SAM45/OBS information (maybe truncated).") + + +def dat(log: PathLike[str] | str, /, *, validate: bool = True) -> NDArray[Any]: + """Read a SAM45 log to extract the SAM45/DAT information. + + Args: + log: Path to the SAM45 log. + validate: Whether to validate the content of the read information. + + Returns: + NumPy structured array containing the SAM45/DAT information. + + Raises: + ValueError: Raised if the read information is invalid, + i.e., the ``crec_type`` field of it is not ``b"L2"``. + + """ + start = dtypes.ctl.itemsize + dtypes.obs.itemsize + stop = -dtypes.end.itemsize + + with open(log, "r+b") as f: + mm = mmap(f.fileno(), 0) + data = frombuffer(mm[start:stop], dtype=dtypes.dat) + + if not validate or (data["crec_type"] == b"L2").all(): + return data + else: + raise ValueError("Invalid SAM45/DAT information (maybe truncated).") + + +def end(log: PathLike[str] | str, /, *, validate: bool = True) -> NDArray[Any]: + """Read a SAM45 log to extract the SAM45/END information. + + Args: + log: Path to the SAM45 log. + validate: Whether to validate the content of the read information. + + Returns: + NumPy structured array containing the SAM45/END information. + + Raises: + ValueError: Raised if the read information is invalid, + i.e., the ``crec_type`` field of it is not ``b"ED"``. + + """ + start = -dtypes.end.itemsize + stop = None + + with open(log, "r+b") as f: + mm = mmap(f.fileno(), 0) + data = frombuffer(mm[start:stop], dtype=dtypes.end) + + if not validate or (data["crec_type"] == b"ED").all(): + return data + else: + raise ValueError("Invalid SAM45/END information 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