From 0048918be952938778a0cd080ce4dbf95df62252 Mon Sep 17 00:00:00 2001 From: seh2 Date: Tue, 27 Oct 2026 17:19:35 +0000 Subject: [PATCH 01/10] Modernise packaging and tooling to match the MetEOR template - Move all package metadata into pyproject.toml and drop setup.py, requirements.txt, tox.ini and environment.yml (dev/docs deps are now the [dev] and [docs] extras; pytest config is in pyproject) - Replace versioneer with setuptools_scm; __version__ now comes from importlib.metadata - Replace black with ruff (lint + format) and mypy in pre-commit, with pinned versions and an explicit ruff rule selection - Replace the old GitHub Actions workflows with tests.yml (pytest on Python 3.11-3.13 plus a ruff/mypy lint job) and publish.yml (tag- triggered PyPI release via trusted publishing) - Update .readthedocs.yaml to install the docs extra and unshallow the clone so setuptools_scm can see tags - Require Python >= 3.11 (3.8-3.10 are end-of-life) - Refresh README badges, development and release instructions, and correct the licence name to LGPLv3 --- .gitattributes | 1 - .github/workflows/publish.yml | 97 ++ .github/workflows/pull_request.yml | 82 - .github/workflows/push_branch.yml | 27 - .github/workflows/tests.yml | 72 + .gitignore | 8 + .pre-commit-config.yaml | 18 +- .readthedocs.yaml | 16 +- MANIFEST.in | 4 +- README.md | 60 +- environment.yml | 20 - obsarray/__init__.py | 9 +- obsarray/_version.py | 716 --------- pyproject.toml | 91 +- requirements.txt | 11 - setup.py | 7 - tox.ini | 12 - versioneer.py | 2334 ---------------------------- 18 files changed, 330 insertions(+), 3255 deletions(-) delete mode 100644 .gitattributes create mode 100644 .github/workflows/publish.yml delete mode 100644 .github/workflows/pull_request.yml delete mode 100644 .github/workflows/push_branch.yml create mode 100644 .github/workflows/tests.yml delete mode 100644 environment.yml delete mode 100644 obsarray/_version.py delete mode 100644 requirements.txt delete mode 100644 setup.py delete mode 100644 tox.ini delete mode 100644 versioneer.py diff --git a/.gitattributes b/.gitattributes deleted file mode 100644 index d5f811c..0000000 --- a/.gitattributes +++ /dev/null @@ -1 +0,0 @@ -obsarray/_version.py export-subst diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 0000000..0ae51c2 --- /dev/null +++ b/.github/workflows/publish.yml @@ -0,0 +1,97 @@ +name: Publish to PyPI + +# Triggered by pushing a v* tag, or manually via the "Run workflow" button. +on: + push: + tags: ["v*"] + workflow_dispatch: + inputs: + confirm: + description: "Type 'publish' to confirm release" + required: true + +jobs: + # ----------------------------------------------------------------------- + # Guard: manual runs require the confirmation input. + # ----------------------------------------------------------------------- + check: + name: Check confirmation + runs-on: ubuntu-latest + if: > + github.event_name == 'push' || + github.event.inputs.confirm == 'publish' + steps: + - run: echo "Confirmed — proceeding with release." + + # ----------------------------------------------------------------------- + # Test gate: don't publish if tests fail. + # ----------------------------------------------------------------------- + test: + name: Tests (Python 3.13) + needs: check + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: "3.13" + cache: pip + - run: pip install -e ".[dev]" + - run: pytest --cov=obsarray + + # ----------------------------------------------------------------------- + # Build source distribution and wheel. + # ----------------------------------------------------------------------- + build: + name: Build distribution + needs: test + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 # full history so setuptools_scm picks up the tag + + - uses: actions/setup-python@v5 + with: + python-version: "3.13" + + - name: Build + run: | + pip install build + python -m build + + - name: Store distribution packages + uses: actions/upload-artifact@v4 + with: + name: dist + path: dist/ + + # ----------------------------------------------------------------------- + # Publish to PyPI via trusted publisher (OIDC — no API token needed). + # + # One-time setup required in the PyPI project settings: + # Publisher: GitHub Actions + # Owner: comet-toolkit + # Repository: obsarray + # Workflow: publish.yml + # Environment: pypi + # ----------------------------------------------------------------------- + publish: + name: Publish to PyPI + needs: build + runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/p/obsarray + permissions: + id-token: write # required for OIDC trusted publishing + + steps: + - name: Download distribution packages + uses: actions/download-artifact@v4 + with: + name: dist + path: dist/ + + - name: Publish to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml deleted file mode 100644 index c8d8415..0000000 --- a/.github/workflows/pull_request.yml +++ /dev/null @@ -1,82 +0,0 @@ -# https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions -name: Pull Request - -on: - pull_request: - branches: - - main - push: - branches: - - main - -jobs: - lint_code: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ["3.11"] - steps: - - uses: actions/checkout@v3 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v3 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install .[dev] - - name: Analysing the code with pre-commit lint checks - run: | - pre-commit run -a - - test_code_python3p8: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ["3.8"] - steps: - - uses: actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v3 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install .[dev] - - name: Test code - run: | - mkdir test_report - tox - - - test_code_and_coverage_report_python3p11: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ["3.11"] - steps: - - uses: actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v3 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install .[dev] - - name: Test code - run: | - mkdir test_report - tox - - name: html to pdf - uses: fifsky/html-to-pdf-action@master - with: - htmlFile: test_report/cov_report/index.html - outputFile: test_report/cov_report/cov_report.pdf - pdfOptions: '{"format": "A4", "margin": {"top": "10mm", "left": "10mm", "right": "10mm", "bottom": "10mm"}}' - - name: Archive code coverage results - uses: actions/upload-artifact@v4 - with: - name: code-coverage-report - path: test_report/cov_report/cov_report.pdf \ No newline at end of file diff --git a/.github/workflows/push_branch.yml b/.github/workflows/push_branch.yml deleted file mode 100644 index 3bb316b..0000000 --- a/.github/workflows/push_branch.yml +++ /dev/null @@ -1,27 +0,0 @@ -# https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions -name: Push to branch - -on: - push: - branches: - - '*' - -jobs: - test_code: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ["3.12"] - steps: - - uses: actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v3 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install .[dev] - - name: Test code - run: | - tox diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml new file mode 100644 index 0000000..4655fae --- /dev/null +++ b/.github/workflows/tests.yml @@ -0,0 +1,72 @@ +name: Tests + +on: + push: + branches: ["main"] + pull_request: + workflow_dispatch: + +jobs: + test: + name: "Python ${{ matrix.python-version }}" + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + python-version: ["3.11", "3.12", "3.13"] + + steps: + - uses: actions/checkout@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + cache: pip + + - name: Install dependencies + run: pip install -e ".[dev]" + + - name: Run tests + run: | + mkdir -p test_report + pytest \ + --html=test_report/report.html \ + --cov-report html:test_report/cov_report \ + --cov-report xml:test_report/coverage.xml \ + --junitxml=test_report/junit.xml \ + --cov=obsarray + + - name: Upload test report + if: always() + uses: actions/upload-artifact@v4 + with: + name: test-report-py${{ matrix.python-version }} + path: test_report/ + retention-days: 7 + + - name: Upload coverage to Codecov + if: matrix.python-version == '3.13' + uses: codecov/codecov-action@v4 + with: + files: test_report/coverage.xml + token: ${{ secrets.CODECOV_TOKEN }} + fail_ci_if_error: false + + lint: + name: Lint + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: "3.13" + cache: pip + - run: pip install -e ".[dev]" + - name: ruff format + run: ruff format --check obsarray + - name: ruff lint + run: ruff check obsarray + - name: mypy + run: mypy obsarray diff --git a/.gitignore b/.gitignore index 4ccc128..36da732 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,12 @@ +# macOS +.DS_Store + # Mypy cache .mypy_cache +# Ruff cache +.ruff_cache + # Compiles docs for gitlab pages public latex @@ -59,6 +65,7 @@ coverage.xml *.cover .hypothesis/ .pytest_cache/ +test_report/ # Translations *.mo @@ -117,4 +124,5 @@ ENV/ # IDE settings .vscode/.git.old + CLAUDE.md diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 29bca3f..c16c553 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,5 +1,17 @@ repos: - - repo: https://github.com/psf/black - rev: stable + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v5.0.0 hooks: - - id: black + - id: check-added-large-files + + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.15.13 + hooks: + - id: ruff + args: [--fix] + - id: ruff-format + + - repo: https://github.com/pre-commit/mirrors-mypy + rev: v2.1.0 + hooks: + - id: mypy diff --git a/.readthedocs.yaml b/.readthedocs.yaml index febb794..d60a279 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -6,15 +6,23 @@ version: 2 # Set the OS, Python version and other tools you might need build: - os: ubuntu-22.04 + os: ubuntu-24.04 tools: - python: "3.10" + python: "3.13" + jobs: + # Read the Docs clones shallowly; setuptools_scm needs the tags to + # derive the version shown in the docs. + post_checkout: + - git fetch --unshallow || true # Build documentation in the "docs/" directory with Sphinx sphinx: configuration: docs/conf.py -# Declare the Python requirements required to build docs +# Install the package with its docs extras from pyproject.toml python: install: - - requirements: requirements.txt + - method: pip + path: . + extra_requirements: + - docs diff --git a/MANIFEST.in b/MANIFEST.in index 783a0ad..04f196a 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,2 +1,2 @@ -include versioneer.py -include obsarray/_version.py +include README.md +include LICENSE diff --git a/README.md b/README.md index 3b32964..3eaede5 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,9 @@ # obsarray: Measurement uncertainty handling in Python -[![Build Status](https://app.travis-ci.com/comet-toolkit/obsarray.svg?branch=main)](https://app.travis-ci.com/comet-toolkit/obsarray) +[![Tests](https://github.com/comet-toolkit/obsarray/actions/workflows/tests.yml/badge.svg?branch=main)](https://github.com/comet-toolkit/obsarray/actions/workflows/tests.yml) [![codecov](https://codecov.io/gh/comet-toolkit/obsarray/branch/main/graph/badge.svg?token=PZTGG03VQY)](https://codecov.io/gh/comet-toolkit/obsarray) [![Documentation Status](https://readthedocs.org/projects/obsarray/badge/?version=latest)](https://obsarray.readthedocs.io/en/latest/?badge=latest) +[![PyPI](https://img.shields.io/pypi/v/obsarray)](https://pypi.org/project/obsarray/) **obsarray** is an extension to [xarray](https://docs.xarray.dev/en/stable/) for defining, storing and interfacing with uncertainty information using standardised metadata. It is particularly designed to work well with [netCDF](https://www.unidata.ucar.edu/software/netcdf/) files and for the Earth Observation community. @@ -10,16 +11,67 @@ obsarray is part of the [CoMet Toolkit](https://www.comet-toolkit.org) (communit ## Installation -obsarray is installable via pip. +obsarray is installable via pip: + +```bash +pip install obsarray +``` ## Documentation For more information visit our [documentation](https://obsarray.readthedocs.io/en/latest). +## Development + +Clone the repository and install it in editable mode with the development +extras: + +```bash +pip install -e ".[dev]" # Development tools (ruff, mypy, pytest, …) +pip install -e ".[docs]" # Documentation build (sphinx, …) +``` + +Install the pre-commit hooks after cloning: + +```bash +pre-commit install +``` + +When you commit, `ruff` will lint and format your code and `mypy` will +type-check it. If it makes corrections the commit will be aborted so you can +review the changes — just commit again once you are happy. + +Run the test suite with: + +```bash +pytest +``` + +### Releasing + +The package version is derived from git tags by +[setuptools_scm](https://setuptools-scm.readthedocs.io), so there is no +version number to edit in the source. To release, tag `main` and push the tag: + +```bash +git tag v +git push origin v +``` + +This triggers the `publish.yml` GitHub Actions workflow, which runs the tests, +builds the sdist and wheel, and publishes them to PyPI via trusted publishing. +The workflow can also be run manually from the GitHub Actions UI (type +`publish` in the confirmation input). + +## Compatibility + +obsarray requires Python 3.11 or later and is tested on Python 3.11, 3.12, +and 3.13. + ## License obsarray is free software licensed under the -[GNU Public License (v3)](./LICENSE). +[GNU Lesser General Public License (v3)](./LICENSE). ## Acknowledgements @@ -32,4 +84,4 @@ The development has been funded by: ## Project status -obsarray is under active development. It is beta software. \ No newline at end of file +obsarray is under active development. It is beta software. diff --git a/environment.yml b/environment.yml deleted file mode 100644 index 090c90a..0000000 --- a/environment.yml +++ /dev/null @@ -1,20 +0,0 @@ -name: obsarray -channels: - - conda-forge - - defaults - - coecms -dependencies: - - python=3.9* - # - # dependencies (in alphabetical order) - # - - numpy - - pip - - xarray - - pip: - - comet_maths - # - # for testing only - # - - pytest >=5.4.1 - - pytest-cov >=2.8.1 \ No newline at end of file diff --git a/obsarray/__init__.py b/obsarray/__init__.py index c085c51..457c846 100644 --- a/obsarray/__init__.py +++ b/obsarray/__init__.py @@ -3,7 +3,8 @@ __author__ = "Sam Hunt " __all__ = [] -from ._version import get_versions +from importlib.metadata import PackageNotFoundError, version + from obsarray import unc_accessor, flag_accessor from obsarray.err_corr import err_corr_forms from obsarray.templater.template_util import create_ds @@ -11,5 +12,7 @@ from obsarray.templater.dswriter import DSWriter from obsarray.utils import append_names -__version__ = get_versions()["version"] -del get_versions +try: + __version__ = version("obsarray") +except PackageNotFoundError: + __version__ = "0.0.0+unknown" diff --git a/obsarray/_version.py b/obsarray/_version.py deleted file mode 100644 index 8e72ef3..0000000 --- a/obsarray/_version.py +++ /dev/null @@ -1,716 +0,0 @@ -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. -# Generated by versioneer-0.29 -# https://github.com/python-versioneer/python-versioneer - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys -from typing import Any, Callable, Dict, List, Optional, Tuple -import functools - - -def get_keywords() -> Dict[str, str]: - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "$Format:%d$" - git_full = "$Format:%H$" - git_date = "$Format:%ci$" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - VCS: str - style: str - tag_prefix: str - parentdir_prefix: str - versionfile_source: str - verbose: bool - - -def get_config() -> VersioneerConfig: - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "pep440" - cfg.tag_prefix = "" - cfg.parentdir_prefix = "" - cfg.versionfile_source = "obsarray/_version.py" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} - - -def register_vcs_handler(vcs: str, method: str) -> Callable: # decorator - """Create decorator to mark a method as the handler of a VCS.""" - - def decorate(f: Callable) -> Callable: - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - - return decorate - - -def run_command( - commands: List[str], - args: List[str], - cwd: Optional[str] = None, - verbose: bool = False, - hide_stderr: bool = False, - env: Optional[Dict[str, str]] = None, -) -> Tuple[Optional[str], Optional[int]]: - """Call the given command(s).""" - assert isinstance(commands, list) - process = None - - popen_kwargs: Dict[str, Any] = {} - if sys.platform == "win32": - # This hides the console window if pythonw.exe is used - startupinfo = subprocess.STARTUPINFO() - startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW - popen_kwargs["startupinfo"] = startupinfo - - for command in commands: - try: - dispcmd = str([command] + args) - # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen( - [command] + args, - cwd=cwd, - env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr else None), - **popen_kwargs, - ) - break - except OSError as e: - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = process.communicate()[0].strip().decode() - if process.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, process.returncode - return stdout, process.returncode - - -def versions_from_parentdir( - parentdir_prefix: str, - root: str, - verbose: bool, -) -> Dict[str, Any]: - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for _ in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return { - "version": dirname[len(parentdir_prefix) :], - "full-revisionid": None, - "dirty": False, - "error": None, - "date": None, - } - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print( - "Tried directories %s but none started with prefix %s" - % (str(rootdirs), parentdir_prefix) - ) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs: str) -> Dict[str, str]: - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords: Dict[str, str] = {} - try: - with open(versionfile_abs, "r") as fobj: - for line in fobj: - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - except OSError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords( - keywords: Dict[str, str], - tag_prefix: str, - verbose: bool, -) -> Dict[str, Any]: - """Get version information from git keywords.""" - if "refnames" not in keywords: - raise NotThisMethod("Short version file found") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = {r.strip() for r in refnames.strip("()").split(",")} - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = {r[len(TAG) :] for r in refs if r.startswith(TAG)} - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r"\d", r)} - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix) :] - # Filter out refs that exactly match prefix or that don't start - # with a number once the prefix is stripped (mostly a concern - # when prefix is '') - if not re.match(r"\d", r): - continue - if verbose: - print("picking %s" % r) - return { - "version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": None, - "date": date, - } - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return { - "version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": "no suitable tags", - "date": None, - } - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs( - tag_prefix: str, root: str, verbose: bool, runner: Callable = run_command -) -> Dict[str, Any]: - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - # GIT_DIR can interfere with correct operation of Versioneer. - # It may be intended to be passed to the Versioneer-versioned project, - # but that should not change where we get our version from. - env = os.environ.copy() - env.pop("GIT_DIR", None) - runner = functools.partial(runner, env=env) - - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=not verbose) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner( - GITS, - [ - "describe", - "--tags", - "--dirty", - "--always", - "--long", - "--match", - f"{tag_prefix}[[:digit:]]*", - ], - cwd=root, - ) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces: Dict[str, Any] = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], cwd=root) - # --abbrev-ref was added in git-1.6.3 - if rc != 0 or branch_name is None: - raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") - branch_name = branch_name.strip() - - if branch_name == "HEAD": - # If we aren't exactly on a branch, pick a branch which represents - # the current commit. If all else fails, we are on a branchless - # commit. - branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) - # --contains was added in git-1.5.4 - if rc != 0 or branches is None: - raise NotThisMethod("'git branch --contains' returned error") - branches = branches.split("\n") - - # Remove the first line if we're running detached - if "(" in branches[0]: - branches.pop(0) - - # Strip off the leading "* " from the list of branches. - branches = [branch[2:] for branch in branches] - if "master" in branches: - branch_name = "master" - elif not branches: - branch_name = None - else: - # Pick the first branch that is returned. Good or bad. - branch_name = branches[0] - - pieces["branch"] = branch_name - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[: git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) - if not mo: - # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % ( - full_tag, - tag_prefix, - ) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix) :] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) - pieces["distance"] = len(out.split()) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces: Dict[str, Any]) -> str: - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces: Dict[str, Any]) -> str: - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_branch(pieces: Dict[str, Any]) -> str: - """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . - - The ".dev0" means not master branch. Note that .dev0 sorts backwards - (a feature branch will appear "older" than the master branch). - - Exceptions: - 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0" - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]: - """Split pep440 version string at the post-release segment. - - Returns the release segments before the post-release and the - post-release version number (or -1 if no post-release segment is present). - """ - vc = str.split(ver, ".post") - return vc[0], int(vc[1] or 0) if len(vc) == 2 else None - - -def render_pep440_pre(pieces: Dict[str, Any]) -> str: - """TAG[.postN.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - if pieces["distance"]: - # update the post release segment - tag_version, post_version = pep440_split_post(pieces["closest-tag"]) - rendered = tag_version - if post_version is not None: - rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"]) - else: - rendered += ".post0.dev%d" % (pieces["distance"]) - else: - # no commits, use the tag as the version - rendered = pieces["closest-tag"] - else: - # exception #1 - rendered = "0.post0.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_post_branch(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . - - The ".dev0" means not master branch. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_old(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces: Dict[str, Any]) -> str: - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces: Dict[str, Any]) -> str: - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]: - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return { - "version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None, - } - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-branch": - rendered = render_pep440_branch(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-post-branch": - rendered = render_pep440_post_branch(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return { - "version": rendered, - "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], - "error": None, - "date": pieces.get("date"), - } - - -def get_versions() -> Dict[str, Any]: - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for _ in cfg.versionfile_source.split("/"): - root = os.path.dirname(root) - except NameError: - return { - "version": "0+unknown", - "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None, - } - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return { - "version": "0+unknown", - "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", - "date": None, - } diff --git a/pyproject.toml b/pyproject.toml index 0c6720d..5237064 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,47 +1,80 @@ [build-system] -requires = ["setuptools>=61", "wheel"] +requires = ["setuptools>=64", "setuptools_scm>=8"] build-backend = "setuptools.build_meta" [project] name = "obsarray" dynamic = ["version"] -description = "Measurement data handling in Python" -authors = [ - { name="CoMet Toolkit Team", email="team@comet-toolkit.org" } -] +description = "Extension to xarray for handling uncertainty-quantified observation data" readme = "README.md" license-files = ["LICENSE"] -requires-python = ">=3.8" +authors = [{name = "CoMet Toolkit Team", email = "team@comet-toolkit.org"}] +requires-python = ">=3.11" +classifiers = [ + "Development Status :: 4 - Beta", + "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)", + "Programming Language :: Python", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", +] dependencies = [ - "comet_maths", - "netcdf4", - "xarray" + "numpy", + "xarray", + "netcdf4", + "comet_maths", ] [project.optional-dependencies] dev = [ - "pre-commit", - "tox", - "sphinx", - "sphinx_design", - "sphinx_book_theme", - "ipython", - "sphinx_autosummary_accessors" + # Pinned: both gate CI. Bump deliberately, not incidentally. + "ruff==0.15.13", + "mypy==2.1.0", + "pre-commit", + "pytest", + "pytest-html", + "pytest-cov", +] +docs = [ + "sphinx", + "sphinx_book_theme", + "sphinx_design", + "sphinx_autosummary_accessors", + "ipython", ] [project.urls] -"Homepage" = "https://github.com/comet-toolkit/obsarray" - -[tool.setuptools] -include-package-data = true +Homepage = "https://github.com/comet-toolkit/obsarray" +Documentation = "https://obsarray.readthedocs.io" [tool.setuptools.packages.find] -exclude = ["tests"] - -[tool.versioneer] -VCS = "git" -style = "pep440" -versionfile_source = "obsarray/_version.py" -versionfile_build = "obsarray/_version.py" -tag_prefix = "v" -parentdir_prefix = "" +include = ["obsarray*"] + +[tool.setuptools_scm] +# version inferred from git tags (e.g. v1.0.3); no extra config needed + +[tool.mypy] +allow_untyped_globals = true +ignore_missing_imports = true + +[[tool.mypy.overrides]] +module = ["obsarray.test.*", "obsarray.*.tests.*"] +ignore_errors = true + +[tool.pytest.ini_options] +testpaths = ["obsarray"] + +[tool.ruff] +# 88 (black's default) rather than the MetEOR template's 120, so switching from +# black to ruff format doesn't reflow the existing codebase. +line-length = 88 +exclude = ["docs"] + +[tool.ruff.lint] +# ruff's historical defaults, stated explicitly so a version bump cannot widen +# the gate without someone choosing to. +select = ["E4", "E7", "E9", "F"] +extend-ignore = ["W291"] + +[tool.ruff.lint.per-file-ignores] +"obsarray/__init__.py" = ["E402", "F401"] diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index d7c2c2f..0000000 --- a/requirements.txt +++ /dev/null @@ -1,11 +0,0 @@ -# required modules -numpy -xarray -comet_maths - -# for docs -sphinx -sphinx_design -ipython -sphinx_autosummary_accessors -sphinx_book_theme \ No newline at end of file diff --git a/setup.py b/setup.py deleted file mode 100644 index d14fa5b..0000000 --- a/setup.py +++ /dev/null @@ -1,7 +0,0 @@ -import versioneer -from setuptools import setup - -setup( - version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), -) diff --git a/tox.ini b/tox.ini deleted file mode 100644 index be89e4b..0000000 --- a/tox.ini +++ /dev/null @@ -1,12 +0,0 @@ - -[testenv] -whitelist_externals = git -setenv = - PYTHONPATH = {toxinidir} -passenv = * -deps = - pytest-html - pytest-cov -commands = - pytest --html=test_report/report.html - pytest --cov-report html:test_report/cov_report --cov=obsarray diff --git a/versioneer.py b/versioneer.py deleted file mode 100644 index de97d90..0000000 --- a/versioneer.py +++ /dev/null @@ -1,2334 +0,0 @@ -# Version: 0.29 - -"""The Versioneer - like a rocketeer, but for versions. - -The Versioneer -============== - -* like a rocketeer, but for versions! -* https://github.com/python-versioneer/python-versioneer -* Brian Warner -* License: Public Domain (Unlicense) -* Compatible with: Python 3.7, 3.8, 3.9, 3.10, 3.11 and pypy3 -* [![Latest Version][pypi-image]][pypi-url] -* [![Build Status][travis-image]][travis-url] - -This is a tool for managing a recorded version number in setuptools-based -python projects. The goal is to remove the tedious and error-prone "update -the embedded version string" step from your release process. Making a new -release should be as easy as recording a new tag in your version-control -system, and maybe making new tarballs. - - -## Quick Install - -Versioneer provides two installation modes. The "classic" vendored mode installs -a copy of versioneer into your repository. The experimental build-time dependency mode -is intended to allow you to skip this step and simplify the process of upgrading. - -### Vendored mode - -* `pip install versioneer` to somewhere in your $PATH - * A [conda-forge recipe](https://github.com/conda-forge/versioneer-feedstock) is - available, so you can also use `conda install -c conda-forge versioneer` -* add a `[tool.versioneer]` section to your `pyproject.toml` or a - `[versioneer]` section to your `setup.cfg` (see [Install](INSTALL.md)) - * Note that you will need to add `tomli; python_version < "3.11"` to your - build-time dependencies if you use `pyproject.toml` -* run `versioneer install --vendor` in your source tree, commit the results -* verify version information with `python setup.py version` - -### Build-time dependency mode - -* `pip install versioneer` to somewhere in your $PATH - * A [conda-forge recipe](https://github.com/conda-forge/versioneer-feedstock) is - available, so you can also use `conda install -c conda-forge versioneer` -* add a `[tool.versioneer]` section to your `pyproject.toml` or a - `[versioneer]` section to your `setup.cfg` (see [Install](INSTALL.md)) -* add `versioneer` (with `[toml]` extra, if configuring in `pyproject.toml`) - to the `requires` key of the `build-system` table in `pyproject.toml`: - ```toml - [build-system] - requires = ["setuptools", "versioneer[toml]"] - build-backend = "setuptools.build_meta" - ``` -* run `versioneer install --no-vendor` in your source tree, commit the results -* verify version information with `python setup.py version` - -## Version Identifiers - -Source trees come from a variety of places: - -* a version-control system checkout (mostly used by developers) -* a nightly tarball, produced by build automation -* a snapshot tarball, produced by a web-based VCS browser, like github's - "tarball from tag" feature -* a release tarball, produced by "setup.py sdist", distributed through PyPI - -Within each source tree, the version identifier (either a string or a number, -this tool is format-agnostic) can come from a variety of places: - -* ask the VCS tool itself, e.g. "git describe" (for checkouts), which knows - about recent "tags" and an absolute revision-id -* the name of the directory into which the tarball was unpacked -* an expanded VCS keyword ($Id$, etc) -* a `_version.py` created by some earlier build step - -For released software, the version identifier is closely related to a VCS -tag. Some projects use tag names that include more than just the version -string (e.g. "myproject-1.2" instead of just "1.2"), in which case the tool -needs to strip the tag prefix to extract the version identifier. For -unreleased software (between tags), the version identifier should provide -enough information to help developers recreate the same tree, while also -giving them an idea of roughly how old the tree is (after version 1.2, before -version 1.3). Many VCS systems can report a description that captures this, -for example `git describe --tags --dirty --always` reports things like -"0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the -0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has -uncommitted changes). - -The version identifier is used for multiple purposes: - -* to allow the module to self-identify its version: `myproject.__version__` -* to choose a name and prefix for a 'setup.py sdist' tarball - -## Theory of Operation - -Versioneer works by adding a special `_version.py` file into your source -tree, where your `__init__.py` can import it. This `_version.py` knows how to -dynamically ask the VCS tool for version information at import time. - -`_version.py` also contains `$Revision$` markers, and the installation -process marks `_version.py` to have this marker rewritten with a tag name -during the `git archive` command. As a result, generated tarballs will -contain enough information to get the proper version. - -To allow `setup.py` to compute a version too, a `versioneer.py` is added to -the top level of your source tree, next to `setup.py` and the `setup.cfg` -that configures it. This overrides several distutils/setuptools commands to -compute the version when invoked, and changes `setup.py build` and `setup.py -sdist` to replace `_version.py` with a small static file that contains just -the generated version data. - -## Installation - -See [INSTALL.md](./INSTALL.md) for detailed installation instructions. - -## Version-String Flavors - -Code which uses Versioneer can learn about its version string at runtime by -importing `_version` from your main `__init__.py` file and running the -`get_versions()` function. From the "outside" (e.g. in `setup.py`), you can -import the top-level `versioneer.py` and run `get_versions()`. - -Both functions return a dictionary with different flavors of version -information: - -* `['version']`: A condensed version string, rendered using the selected - style. This is the most commonly used value for the project's version - string. The default "pep440" style yields strings like `0.11`, - `0.11+2.g1076c97`, or `0.11+2.g1076c97.dirty`. See the "Styles" section - below for alternative styles. - -* `['full-revisionid']`: detailed revision identifier. For Git, this is the - full SHA1 commit id, e.g. "1076c978a8d3cfc70f408fe5974aa6c092c949ac". - -* `['date']`: Date and time of the latest `HEAD` commit. For Git, it is the - commit date in ISO 8601 format. This will be None if the date is not - available. - -* `['dirty']`: a boolean, True if the tree has uncommitted changes. Note that - this is only accurate if run in a VCS checkout, otherwise it is likely to - be False or None - -* `['error']`: if the version string could not be computed, this will be set - to a string describing the problem, otherwise it will be None. It may be - useful to throw an exception in setup.py if this is set, to avoid e.g. - creating tarballs with a version string of "unknown". - -Some variants are more useful than others. Including `full-revisionid` in a -bug report should allow developers to reconstruct the exact code being tested -(or indicate the presence of local changes that should be shared with the -developers). `version` is suitable for display in an "about" box or a CLI -`--version` output: it can be easily compared against release notes and lists -of bugs fixed in various releases. - -The installer adds the following text to your `__init__.py` to place a basic -version in `YOURPROJECT.__version__`: - - from ._version import get_versions - __version__ = get_versions()['version'] - del get_versions - -## Styles - -The setup.cfg `style=` configuration controls how the VCS information is -rendered into a version string. - -The default style, "pep440", produces a PEP440-compliant string, equal to the -un-prefixed tag name for actual releases, and containing an additional "local -version" section with more detail for in-between builds. For Git, this is -TAG[+DISTANCE.gHEX[.dirty]] , using information from `git describe --tags ---dirty --always`. For example "0.11+2.g1076c97.dirty" indicates that the -tree is like the "1076c97" commit but has uncommitted changes (".dirty"), and -that this commit is two revisions ("+2") beyond the "0.11" tag. For released -software (exactly equal to a known tag), the identifier will only contain the -stripped tag, e.g. "0.11". - -Other styles are available. See [details.md](details.md) in the Versioneer -source tree for descriptions. - -## Debugging - -Versioneer tries to avoid fatal errors: if something goes wrong, it will tend -to return a version of "0+unknown". To investigate the problem, run `setup.py -version`, which will run the version-lookup code in a verbose mode, and will -display the full contents of `get_versions()` (including the `error` string, -which may help identify what went wrong). - -## Known Limitations - -Some situations are known to cause problems for Versioneer. This details the -most significant ones. More can be found on Github -[issues page](https://github.com/python-versioneer/python-versioneer/issues). - -### Subprojects - -Versioneer has limited support for source trees in which `setup.py` is not in -the root directory (e.g. `setup.py` and `.git/` are *not* siblings). The are -two common reasons why `setup.py` might not be in the root: - -* Source trees which contain multiple subprojects, such as - [Buildbot](https://github.com/buildbot/buildbot), which contains both - "master" and "slave" subprojects, each with their own `setup.py`, - `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI - distributions (and upload multiple independently-installable tarballs). -* Source trees whose main purpose is to contain a C library, but which also - provide bindings to Python (and perhaps other languages) in subdirectories. - -Versioneer will look for `.git` in parent directories, and most operations -should get the right version string. However `pip` and `setuptools` have bugs -and implementation details which frequently cause `pip install .` from a -subproject directory to fail to find a correct version string (so it usually -defaults to `0+unknown`). - -`pip install --editable .` should work correctly. `setup.py install` might -work too. - -Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in -some later version. - -[Bug #38](https://github.com/python-versioneer/python-versioneer/issues/38) is tracking -this issue. The discussion in -[PR #61](https://github.com/python-versioneer/python-versioneer/pull/61) describes the -issue from the Versioneer side in more detail. -[pip PR#3176](https://github.com/pypa/pip/pull/3176) and -[pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve -pip to let Versioneer work correctly. - -Versioneer-0.16 and earlier only looked for a `.git` directory next to the -`setup.cfg`, so subprojects were completely unsupported with those releases. - -### Editable installs with setuptools <= 18.5 - -`setup.py develop` and `pip install --editable .` allow you to install a -project into a virtualenv once, then continue editing the source code (and -test) without re-installing after every change. - -"Entry-point scripts" (`setup(entry_points={"console_scripts": ..})`) are a -convenient way to specify executable scripts that should be installed along -with the python package. - -These both work as expected when using modern setuptools. When using -setuptools-18.5 or earlier, however, certain operations will cause -`pkg_resources.DistributionNotFound` errors when running the entrypoint -script, which must be resolved by re-installing the package. This happens -when the install happens with one version, then the egg_info data is -regenerated while a different version is checked out. Many setup.py commands -cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into -a different virtualenv), so this can be surprising. - -[Bug #83](https://github.com/python-versioneer/python-versioneer/issues/83) describes -this one, but upgrading to a newer version of setuptools should probably -resolve it. - - -## Updating Versioneer - -To upgrade your project to a new release of Versioneer, do the following: - -* install the new Versioneer (`pip install -U versioneer` or equivalent) -* edit `setup.cfg` and `pyproject.toml`, if necessary, - to include any new configuration settings indicated by the release notes. - See [UPGRADING](./UPGRADING.md) for details. -* re-run `versioneer install --[no-]vendor` in your source tree, to replace - `SRC/_version.py` -* commit any changed files - -## Future Directions - -This tool is designed to make it easily extended to other version-control -systems: all VCS-specific components are in separate directories like -src/git/ . The top-level `versioneer.py` script is assembled from these -components by running make-versioneer.py . In the future, make-versioneer.py -will take a VCS name as an argument, and will construct a version of -`versioneer.py` that is specific to the given VCS. It might also take the -configuration arguments that are currently provided manually during -installation by editing setup.py . Alternatively, it might go the other -direction and include code from all supported VCS systems, reducing the -number of intermediate scripts. - -## Similar projects - -* [setuptools_scm](https://github.com/pypa/setuptools_scm/) - a non-vendored build-time - dependency -* [minver](https://github.com/jbweston/miniver) - a lightweight reimplementation of - versioneer -* [versioningit](https://github.com/jwodder/versioningit) - a PEP 518-based setuptools - plugin - -## License - -To make Versioneer easier to embed, all its code is dedicated to the public -domain. The `_version.py` that it creates is also in the public domain. -Specifically, both are released under the "Unlicense", as described in -https://unlicense.org/. - -[pypi-image]: https://img.shields.io/pypi/v/versioneer.svg -[pypi-url]: https://pypi.python.org/pypi/versioneer/ -[travis-image]: -https://img.shields.io/travis/com/python-versioneer/python-versioneer.svg -[travis-url]: https://travis-ci.com/github/python-versioneer/python-versioneer - -""" -# pylint:disable=invalid-name,import-outside-toplevel,missing-function-docstring -# pylint:disable=missing-class-docstring,too-many-branches,too-many-statements -# pylint:disable=raise-missing-from,too-many-lines,too-many-locals,import-error -# pylint:disable=too-few-public-methods,redefined-outer-name,consider-using-with -# pylint:disable=attribute-defined-outside-init,too-many-arguments - -import configparser -import errno -import json -import os -import re -import subprocess -import sys -from pathlib import Path -from typing import Any, Callable, cast, Dict, List, Optional, Tuple, Union -from typing import NoReturn -import functools - -have_tomllib = True -if sys.version_info >= (3, 11): - import tomllib -else: - try: - import tomli as tomllib - except ImportError: - have_tomllib = False - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - VCS: str - style: str - tag_prefix: str - versionfile_source: str - versionfile_build: Optional[str] - parentdir_prefix: Optional[str] - verbose: Optional[bool] - - -def get_root() -> str: - """Get the project root directory. - - We require that all commands are run from the project root, i.e. the - directory that contains setup.py, setup.cfg, and versioneer.py . - """ - root = os.path.realpath(os.path.abspath(os.getcwd())) - setup_py = os.path.join(root, "setup.py") - pyproject_toml = os.path.join(root, "pyproject.toml") - versioneer_py = os.path.join(root, "versioneer.py") - if not ( - os.path.exists(setup_py) - or os.path.exists(pyproject_toml) - or os.path.exists(versioneer_py) - ): - # allow 'python path/to/setup.py COMMAND' - root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0]))) - setup_py = os.path.join(root, "setup.py") - pyproject_toml = os.path.join(root, "pyproject.toml") - versioneer_py = os.path.join(root, "versioneer.py") - if not ( - os.path.exists(setup_py) - or os.path.exists(pyproject_toml) - or os.path.exists(versioneer_py) - ): - err = ( - "Versioneer was unable to run the project root directory. " - "Versioneer requires setup.py to be executed from " - "its immediate directory (like 'python setup.py COMMAND'), " - "or in a way that lets it use sys.argv[0] to find the root " - "(like 'python path/to/setup.py COMMAND')." - ) - raise VersioneerBadRootError(err) - try: - # Certain runtime workflows (setup.py install/develop in a setuptools - # tree) execute all dependencies in a single python process, so - # "versioneer" may be imported multiple times, and python's shared - # module-import table will cache the first one. So we can't use - # os.path.dirname(__file__), as that will find whichever - # versioneer.py was first imported, even in later projects. - my_path = os.path.realpath(os.path.abspath(__file__)) - me_dir = os.path.normcase(os.path.splitext(my_path)[0]) - vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0]) - if me_dir != vsr_dir and "VERSIONEER_PEP518" not in globals(): - print( - "Warning: build in %s is using versioneer.py from %s" - % (os.path.dirname(my_path), versioneer_py) - ) - except NameError: - pass - return root - - -def get_config_from_root(root: str) -> VersioneerConfig: - """Read the project setup.cfg file to determine Versioneer config.""" - # This might raise OSError (if setup.cfg is missing), or - # configparser.NoSectionError (if it lacks a [versioneer] section), or - # configparser.NoOptionError (if it lacks "VCS="). See the docstring at - # the top of versioneer.py for instructions on writing your setup.cfg . - root_pth = Path(root) - pyproject_toml = root_pth / "pyproject.toml" - setup_cfg = root_pth / "setup.cfg" - section: Union[Dict[str, Any], configparser.SectionProxy, None] = None - if pyproject_toml.exists() and have_tomllib: - try: - with open(pyproject_toml, "rb") as fobj: - pp = tomllib.load(fobj) - section = pp["tool"]["versioneer"] - except (tomllib.TOMLDecodeError, KeyError) as e: - print(f"Failed to load config from {pyproject_toml}: {e}") - print("Try to load it from setup.cfg") - if not section: - parser = configparser.ConfigParser() - with open(setup_cfg) as cfg_file: - parser.read_file(cfg_file) - parser.get("versioneer", "VCS") # raise error if missing - - section = parser["versioneer"] - - # `cast`` really shouldn't be used, but its simplest for the - # common VersioneerConfig users at the moment. We verify against - # `None` values elsewhere where it matters - - cfg = VersioneerConfig() - cfg.VCS = section["VCS"] - cfg.style = section.get("style", "") - cfg.versionfile_source = cast(str, section.get("versionfile_source")) - cfg.versionfile_build = section.get("versionfile_build") - cfg.tag_prefix = cast(str, section.get("tag_prefix")) - if cfg.tag_prefix in ("''", '""', None): - cfg.tag_prefix = "" - cfg.parentdir_prefix = section.get("parentdir_prefix") - if isinstance(section, configparser.SectionProxy): - # Make sure configparser translates to bool - cfg.verbose = section.getboolean("verbose") - else: - cfg.verbose = section.get("verbose") - - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -# these dictionaries contain VCS-specific tools -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} - - -def register_vcs_handler(vcs: str, method: str) -> Callable: # decorator - """Create decorator to mark a method as the handler of a VCS.""" - - def decorate(f: Callable) -> Callable: - """Store f in HANDLERS[vcs][method].""" - HANDLERS.setdefault(vcs, {})[method] = f - return f - - return decorate - - -def run_command( - commands: List[str], - args: List[str], - cwd: Optional[str] = None, - verbose: bool = False, - hide_stderr: bool = False, - env: Optional[Dict[str, str]] = None, -) -> Tuple[Optional[str], Optional[int]]: - """Call the given command(s).""" - assert isinstance(commands, list) - process = None - - popen_kwargs: Dict[str, Any] = {} - if sys.platform == "win32": - # This hides the console window if pythonw.exe is used - startupinfo = subprocess.STARTUPINFO() - startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW - popen_kwargs["startupinfo"] = startupinfo - - for command in commands: - try: - dispcmd = str([command] + args) - # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen( - [command] + args, - cwd=cwd, - env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr else None), - **popen_kwargs, - ) - break - except OSError as e: - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = process.communicate()[0].strip().decode() - if process.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, process.returncode - return stdout, process.returncode - - -LONG_VERSION_PY[ - "git" -] = r''' -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. -# Generated by versioneer-0.29 -# https://github.com/python-versioneer/python-versioneer - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys -from typing import Any, Callable, Dict, List, Optional, Tuple -import functools - - -def get_keywords() -> Dict[str, str]: - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "%(DOLLAR)sFormat:%%d%(DOLLAR)s" - git_full = "%(DOLLAR)sFormat:%%H%(DOLLAR)s" - git_date = "%(DOLLAR)sFormat:%%ci%(DOLLAR)s" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - VCS: str - style: str - tag_prefix: str - parentdir_prefix: str - versionfile_source: str - verbose: bool - - -def get_config() -> VersioneerConfig: - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "%(STYLE)s" - cfg.tag_prefix = "%(TAG_PREFIX)s" - cfg.parentdir_prefix = "%(PARENTDIR_PREFIX)s" - cfg.versionfile_source = "%(VERSIONFILE_SOURCE)s" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} - - -def register_vcs_handler(vcs: str, method: str) -> Callable: # decorator - """Create decorator to mark a method as the handler of a VCS.""" - def decorate(f: Callable) -> Callable: - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - return decorate - - -def run_command( - commands: List[str], - args: List[str], - cwd: Optional[str] = None, - verbose: bool = False, - hide_stderr: bool = False, - env: Optional[Dict[str, str]] = None, -) -> Tuple[Optional[str], Optional[int]]: - """Call the given command(s).""" - assert isinstance(commands, list) - process = None - - popen_kwargs: Dict[str, Any] = {} - if sys.platform == "win32": - # This hides the console window if pythonw.exe is used - startupinfo = subprocess.STARTUPINFO() - startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW - popen_kwargs["startupinfo"] = startupinfo - - for command in commands: - try: - dispcmd = str([command] + args) - # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen([command] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None), **popen_kwargs) - break - except OSError as e: - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %%s" %% dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %%s" %% (commands,)) - return None, None - stdout = process.communicate()[0].strip().decode() - if process.returncode != 0: - if verbose: - print("unable to run %%s (error)" %% dispcmd) - print("stdout was %%s" %% stdout) - return None, process.returncode - return stdout, process.returncode - - -def versions_from_parentdir( - parentdir_prefix: str, - root: str, - verbose: bool, -) -> Dict[str, Any]: - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for _ in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %%s but none started with prefix %%s" %% - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs: str) -> Dict[str, str]: - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords: Dict[str, str] = {} - try: - with open(versionfile_abs, "r") as fobj: - for line in fobj: - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - except OSError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords( - keywords: Dict[str, str], - tag_prefix: str, - verbose: bool, -) -> Dict[str, Any]: - """Get version information from git keywords.""" - if "refnames" not in keywords: - raise NotThisMethod("Short version file found") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = {r.strip() for r in refnames.strip("()").split(",")} - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %%d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r'\d', r)} - if verbose: - print("discarding '%%s', no digits" %% ",".join(refs - tags)) - if verbose: - print("likely tags: %%s" %% ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - # Filter out refs that exactly match prefix or that don't start - # with a number once the prefix is stripped (mostly a concern - # when prefix is '') - if not re.match(r'\d', r): - continue - if verbose: - print("picking %%s" %% r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs( - tag_prefix: str, - root: str, - verbose: bool, - runner: Callable = run_command -) -> Dict[str, Any]: - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - # GIT_DIR can interfere with correct operation of Versioneer. - # It may be intended to be passed to the Versioneer-versioned project, - # but that should not change where we get our version from. - env = os.environ.copy() - env.pop("GIT_DIR", None) - runner = functools.partial(runner, env=env) - - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=not verbose) - if rc != 0: - if verbose: - print("Directory %%s not under git control" %% root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner(GITS, [ - "describe", "--tags", "--dirty", "--always", "--long", - "--match", f"{tag_prefix}[[:digit:]]*" - ], cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces: Dict[str, Any] = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], - cwd=root) - # --abbrev-ref was added in git-1.6.3 - if rc != 0 or branch_name is None: - raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") - branch_name = branch_name.strip() - - if branch_name == "HEAD": - # If we aren't exactly on a branch, pick a branch which represents - # the current commit. If all else fails, we are on a branchless - # commit. - branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) - # --contains was added in git-1.5.4 - if rc != 0 or branches is None: - raise NotThisMethod("'git branch --contains' returned error") - branches = branches.split("\n") - - # Remove the first line if we're running detached - if "(" in branches[0]: - branches.pop(0) - - # Strip off the leading "* " from the list of branches. - branches = [branch[2:] for branch in branches] - if "master" in branches: - branch_name = "master" - elif not branches: - branch_name = None - else: - # Pick the first branch that is returned. Good or bad. - branch_name = branches[0] - - pieces["branch"] = branch_name - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%%s'" - %% describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%%s' doesn't start with prefix '%%s'" - print(fmt %% (full_tag, tag_prefix)) - pieces["error"] = ("tag '%%s' doesn't start with prefix '%%s'" - %% (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) - pieces["distance"] = len(out.split()) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = runner(GITS, ["show", "-s", "--format=%%ci", "HEAD"], cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces: Dict[str, Any]) -> str: - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces: Dict[str, Any]) -> str: - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%%d.g%%s" %% (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_branch(pieces: Dict[str, Any]) -> str: - """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . - - The ".dev0" means not master branch. Note that .dev0 sorts backwards - (a feature branch will appear "older" than the master branch). - - Exceptions: - 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0" - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+untagged.%%d.g%%s" %% (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]: - """Split pep440 version string at the post-release segment. - - Returns the release segments before the post-release and the - post-release version number (or -1 if no post-release segment is present). - """ - vc = str.split(ver, ".post") - return vc[0], int(vc[1] or 0) if len(vc) == 2 else None - - -def render_pep440_pre(pieces: Dict[str, Any]) -> str: - """TAG[.postN.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - if pieces["distance"]: - # update the post release segment - tag_version, post_version = pep440_split_post(pieces["closest-tag"]) - rendered = tag_version - if post_version is not None: - rendered += ".post%%d.dev%%d" %% (post_version + 1, pieces["distance"]) - else: - rendered += ".post0.dev%%d" %% (pieces["distance"]) - else: - # no commits, use the tag as the version - rendered = pieces["closest-tag"] - else: - # exception #1 - rendered = "0.post0.dev%%d" %% pieces["distance"] - return rendered - - -def render_pep440_post(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%%s" %% pieces["short"] - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%%s" %% pieces["short"] - return rendered - - -def render_pep440_post_branch(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . - - The ".dev0" means not master branch. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%%s" %% pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+g%%s" %% pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_old(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces: Dict[str, Any]) -> str: - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces: Dict[str, Any]) -> str: - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]: - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-branch": - rendered = render_pep440_branch(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-post-branch": - rendered = render_pep440_post_branch(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%%s'" %% style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -def get_versions() -> Dict[str, Any]: - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for _ in cfg.versionfile_source.split('/'): - root = os.path.dirname(root) - except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} -''' - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs: str) -> Dict[str, str]: - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords: Dict[str, str] = {} - try: - with open(versionfile_abs, "r") as fobj: - for line in fobj: - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - except OSError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords( - keywords: Dict[str, str], - tag_prefix: str, - verbose: bool, -) -> Dict[str, Any]: - """Get version information from git keywords.""" - if "refnames" not in keywords: - raise NotThisMethod("Short version file found") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = {r.strip() for r in refnames.strip("()").split(",")} - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = {r[len(TAG) :] for r in refs if r.startswith(TAG)} - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r"\d", r)} - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix) :] - # Filter out refs that exactly match prefix or that don't start - # with a number once the prefix is stripped (mostly a concern - # when prefix is '') - if not re.match(r"\d", r): - continue - if verbose: - print("picking %s" % r) - return { - "version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": None, - "date": date, - } - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return { - "version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": "no suitable tags", - "date": None, - } - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs( - tag_prefix: str, root: str, verbose: bool, runner: Callable = run_command -) -> Dict[str, Any]: - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - # GIT_DIR can interfere with correct operation of Versioneer. - # It may be intended to be passed to the Versioneer-versioned project, - # but that should not change where we get our version from. - env = os.environ.copy() - env.pop("GIT_DIR", None) - runner = functools.partial(runner, env=env) - - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=not verbose) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner( - GITS, - [ - "describe", - "--tags", - "--dirty", - "--always", - "--long", - "--match", - f"{tag_prefix}[[:digit:]]*", - ], - cwd=root, - ) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces: Dict[str, Any] = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], cwd=root) - # --abbrev-ref was added in git-1.6.3 - if rc != 0 or branch_name is None: - raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") - branch_name = branch_name.strip() - - if branch_name == "HEAD": - # If we aren't exactly on a branch, pick a branch which represents - # the current commit. If all else fails, we are on a branchless - # commit. - branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) - # --contains was added in git-1.5.4 - if rc != 0 or branches is None: - raise NotThisMethod("'git branch --contains' returned error") - branches = branches.split("\n") - - # Remove the first line if we're running detached - if "(" in branches[0]: - branches.pop(0) - - # Strip off the leading "* " from the list of branches. - branches = [branch[2:] for branch in branches] - if "master" in branches: - branch_name = "master" - elif not branches: - branch_name = None - else: - # Pick the first branch that is returned. Good or bad. - branch_name = branches[0] - - pieces["branch"] = branch_name - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[: git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) - if not mo: - # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % ( - full_tag, - tag_prefix, - ) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix) :] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) - pieces["distance"] = len(out.split()) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def do_vcs_install(versionfile_source: str, ipy: Optional[str]) -> None: - """Git-specific installation logic for Versioneer. - - For Git, this means creating/changing .gitattributes to mark _version.py - for export-subst keyword substitution. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - files = [versionfile_source] - if ipy: - files.append(ipy) - if "VERSIONEER_PEP518" not in globals(): - try: - my_path = __file__ - if my_path.endswith((".pyc", ".pyo")): - my_path = os.path.splitext(my_path)[0] + ".py" - versioneer_file = os.path.relpath(my_path) - except NameError: - versioneer_file = "versioneer.py" - files.append(versioneer_file) - present = False - try: - with open(".gitattributes", "r") as fobj: - for line in fobj: - if line.strip().startswith(versionfile_source): - if "export-subst" in line.strip().split()[1:]: - present = True - break - except OSError: - pass - if not present: - with open(".gitattributes", "a+") as fobj: - fobj.write(f"{versionfile_source} export-subst\n") - files.append(".gitattributes") - run_command(GITS, ["add", "--"] + files) - - -def versions_from_parentdir( - parentdir_prefix: str, - root: str, - verbose: bool, -) -> Dict[str, Any]: - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for _ in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return { - "version": dirname[len(parentdir_prefix) :], - "full-revisionid": None, - "dirty": False, - "error": None, - "date": None, - } - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print( - "Tried directories %s but none started with prefix %s" - % (str(rootdirs), parentdir_prefix) - ) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -SHORT_VERSION_PY = """ -# This file was generated by 'versioneer.py' (0.29) from -# revision-control system data, or from the parent directory name of an -# unpacked source archive. Distribution tarballs contain a pre-generated copy -# of this file. - -import json - -version_json = ''' -%s -''' # END VERSION_JSON - - -def get_versions(): - return json.loads(version_json) -""" - - -def versions_from_file(filename: str) -> Dict[str, Any]: - """Try to determine the version from _version.py if present.""" - try: - with open(filename) as f: - contents = f.read() - except OSError: - raise NotThisMethod("unable to read _version.py") - mo = re.search( - r"version_json = '''\n(.*)''' # END VERSION_JSON", contents, re.M | re.S - ) - if not mo: - mo = re.search( - r"version_json = '''\r\n(.*)''' # END VERSION_JSON", contents, re.M | re.S - ) - if not mo: - raise NotThisMethod("no version_json in _version.py") - return json.loads(mo.group(1)) - - -def write_to_version_file(filename: str, versions: Dict[str, Any]) -> None: - """Write the given version number to the given _version.py file.""" - contents = json.dumps(versions, sort_keys=True, indent=1, separators=(",", ": ")) - with open(filename, "w") as f: - f.write(SHORT_VERSION_PY % contents) - - print("set %s to '%s'" % (filename, versions["version"])) - - -def plus_or_dot(pieces: Dict[str, Any]) -> str: - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces: Dict[str, Any]) -> str: - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_branch(pieces: Dict[str, Any]) -> str: - """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . - - The ".dev0" means not master branch. Note that .dev0 sorts backwards - (a feature branch will appear "older" than the master branch). - - Exceptions: - 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0" - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]: - """Split pep440 version string at the post-release segment. - - Returns the release segments before the post-release and the - post-release version number (or -1 if no post-release segment is present). - """ - vc = str.split(ver, ".post") - return vc[0], int(vc[1] or 0) if len(vc) == 2 else None - - -def render_pep440_pre(pieces: Dict[str, Any]) -> str: - """TAG[.postN.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - if pieces["distance"]: - # update the post release segment - tag_version, post_version = pep440_split_post(pieces["closest-tag"]) - rendered = tag_version - if post_version is not None: - rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"]) - else: - rendered += ".post0.dev%d" % (pieces["distance"]) - else: - # no commits, use the tag as the version - rendered = pieces["closest-tag"] - else: - # exception #1 - rendered = "0.post0.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_post_branch(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . - - The ".dev0" means not master branch. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_old(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces: Dict[str, Any]) -> str: - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces: Dict[str, Any]) -> str: - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]: - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return { - "version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None, - } - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-branch": - rendered = render_pep440_branch(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-post-branch": - rendered = render_pep440_post_branch(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return { - "version": rendered, - "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], - "error": None, - "date": pieces.get("date"), - } - - -class VersioneerBadRootError(Exception): - """The project root directory is unknown or missing key files.""" - - -def get_versions(verbose: bool = False) -> Dict[str, Any]: - """Get the project version from whatever source is available. - - Returns dict with two keys: 'version' and 'full'. - """ - if "versioneer" in sys.modules: - # see the discussion in cmdclass.py:get_cmdclass() - del sys.modules["versioneer"] - - root = get_root() - cfg = get_config_from_root(root) - - assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg" - handlers = HANDLERS.get(cfg.VCS) - assert handlers, "unrecognized VCS '%s'" % cfg.VCS - verbose = verbose or bool(cfg.verbose) # `bool()` used to avoid `None` - assert ( - cfg.versionfile_source is not None - ), "please set versioneer.versionfile_source" - assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix" - - versionfile_abs = os.path.join(root, cfg.versionfile_source) - - # extract version from first of: _version.py, VCS command (e.g. 'git - # describe'), parentdir. This is meant to work for developers using a - # source checkout, for users of a tarball created by 'setup.py sdist', - # and for users of a tarball/zipball created by 'git archive' or github's - # download-from-tag feature or the equivalent in other VCSes. - - get_keywords_f = handlers.get("get_keywords") - from_keywords_f = handlers.get("keywords") - if get_keywords_f and from_keywords_f: - try: - keywords = get_keywords_f(versionfile_abs) - ver = from_keywords_f(keywords, cfg.tag_prefix, verbose) - if verbose: - print("got version from expanded keyword %s" % ver) - return ver - except NotThisMethod: - pass - - try: - ver = versions_from_file(versionfile_abs) - if verbose: - print("got version from file %s %s" % (versionfile_abs, ver)) - return ver - except NotThisMethod: - pass - - from_vcs_f = handlers.get("pieces_from_vcs") - if from_vcs_f: - try: - pieces = from_vcs_f(cfg.tag_prefix, root, verbose) - ver = render(pieces, cfg.style) - if verbose: - print("got version from VCS %s" % ver) - return ver - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - ver = versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - if verbose: - print("got version from parentdir %s" % ver) - return ver - except NotThisMethod: - pass - - if verbose: - print("unable to compute version") - - return { - "version": "0+unknown", - "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", - "date": None, - } - - -def get_version() -> str: - """Get the short version string for this project.""" - return get_versions()["version"] - - -def get_cmdclass(cmdclass: Optional[Dict[str, Any]] = None): - """Get the custom setuptools subclasses used by Versioneer. - - If the package uses a different cmdclass (e.g. one from numpy), it - should be provide as an argument. - """ - if "versioneer" in sys.modules: - del sys.modules["versioneer"] - # this fixes the "python setup.py develop" case (also 'install' and - # 'easy_install .'), in which subdependencies of the main project are - # built (using setup.py bdist_egg) in the same python process. Assume - # a main project A and a dependency B, which use different versions - # of Versioneer. A's setup.py imports A's Versioneer, leaving it in - # sys.modules by the time B's setup.py is executed, causing B to run - # with the wrong versioneer. Setuptools wraps the sub-dep builds in a - # sandbox that restores sys.modules to it's pre-build state, so the - # parent is protected against the child's "import versioneer". By - # removing ourselves from sys.modules here, before the child build - # happens, we protect the child from the parent's versioneer too. - # Also see https://github.com/python-versioneer/python-versioneer/issues/52 - - cmds = {} if cmdclass is None else cmdclass.copy() - - # we add "version" to setuptools - from setuptools import Command - - class cmd_version(Command): - description = "report generated version string" - user_options: List[Tuple[str, str, str]] = [] - boolean_options: List[str] = [] - - def initialize_options(self) -> None: - pass - - def finalize_options(self) -> None: - pass - - def run(self) -> None: - vers = get_versions(verbose=True) - print("Version: %s" % vers["version"]) - print(" full-revisionid: %s" % vers.get("full-revisionid")) - print(" dirty: %s" % vers.get("dirty")) - print(" date: %s" % vers.get("date")) - if vers["error"]: - print(" error: %s" % vers["error"]) - - cmds["version"] = cmd_version - - # we override "build_py" in setuptools - # - # most invocation pathways end up running build_py: - # distutils/build -> build_py - # distutils/install -> distutils/build ->.. - # setuptools/bdist_wheel -> distutils/install ->.. - # setuptools/bdist_egg -> distutils/install_lib -> build_py - # setuptools/install -> bdist_egg ->.. - # setuptools/develop -> ? - # pip install: - # copies source tree to a tempdir before running egg_info/etc - # if .git isn't copied too, 'git describe' will fail - # then does setup.py bdist_wheel, or sometimes setup.py install - # setup.py egg_info -> ? - - # pip install -e . and setuptool/editable_wheel will invoke build_py - # but the build_py command is not expected to copy any files. - - # we override different "build_py" commands for both environments - if "build_py" in cmds: - _build_py: Any = cmds["build_py"] - else: - from setuptools.command.build_py import build_py as _build_py - - class cmd_build_py(_build_py): - def run(self) -> None: - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - _build_py.run(self) - if getattr(self, "editable_mode", False): - # During editable installs `.py` and data files are - # not copied to build_lib - return - # now locate _version.py in the new build/ directory and replace - # it with an updated value - if cfg.versionfile_build: - target_versionfile = os.path.join(self.build_lib, cfg.versionfile_build) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - cmds["build_py"] = cmd_build_py - - if "build_ext" in cmds: - _build_ext: Any = cmds["build_ext"] - else: - from setuptools.command.build_ext import build_ext as _build_ext - - class cmd_build_ext(_build_ext): - def run(self) -> None: - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - _build_ext.run(self) - if self.inplace: - # build_ext --inplace will only build extensions in - # build/lib<..> dir with no _version.py to write to. - # As in place builds will already have a _version.py - # in the module dir, we do not need to write one. - return - # now locate _version.py in the new build/ directory and replace - # it with an updated value - if not cfg.versionfile_build: - return - target_versionfile = os.path.join(self.build_lib, cfg.versionfile_build) - if not os.path.exists(target_versionfile): - print( - f"Warning: {target_versionfile} does not exist, skipping " - "version update. This can happen if you are running build_ext " - "without first running build_py." - ) - return - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - cmds["build_ext"] = cmd_build_ext - - if "cx_Freeze" in sys.modules: # cx_freeze enabled? - from cx_Freeze.dist import build_exe as _build_exe # type: ignore - - # nczeczulin reports that py2exe won't like the pep440-style string - # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g. - # setup(console=[{ - # "version": versioneer.get_version().split("+", 1)[0], # FILEVERSION - # "product_version": versioneer.get_version(), - # ... - - class cmd_build_exe(_build_exe): - def run(self) -> None: - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _build_exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write( - LONG - % { - "DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - } - ) - - cmds["build_exe"] = cmd_build_exe - del cmds["build_py"] - - if "py2exe" in sys.modules: # py2exe enabled? - try: - from py2exe.setuptools_buildexe import py2exe as _py2exe # type: ignore - except ImportError: - from py2exe.distutils_buildexe import py2exe as _py2exe # type: ignore - - class cmd_py2exe(_py2exe): - def run(self) -> None: - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _py2exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write( - LONG - % { - "DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - } - ) - - cmds["py2exe"] = cmd_py2exe - - # sdist farms its file list building out to egg_info - if "egg_info" in cmds: - _egg_info: Any = cmds["egg_info"] - else: - from setuptools.command.egg_info import egg_info as _egg_info - - class cmd_egg_info(_egg_info): - def find_sources(self) -> None: - # egg_info.find_sources builds the manifest list and writes it - # in one shot - super().find_sources() - - # Modify the filelist and normalize it - root = get_root() - cfg = get_config_from_root(root) - self.filelist.append("versioneer.py") - if cfg.versionfile_source: - # There are rare cases where versionfile_source might not be - # included by default, so we must be explicit - self.filelist.append(cfg.versionfile_source) - self.filelist.sort() - self.filelist.remove_duplicates() - - # The write method is hidden in the manifest_maker instance that - # generated the filelist and was thrown away - # We will instead replicate their final normalization (to unicode, - # and POSIX-style paths) - from setuptools import unicode_utils - - normalized = [ - unicode_utils.filesys_decode(f).replace(os.sep, "/") - for f in self.filelist.files - ] - - manifest_filename = os.path.join(self.egg_info, "SOURCES.txt") - with open(manifest_filename, "w") as fobj: - fobj.write("\n".join(normalized)) - - cmds["egg_info"] = cmd_egg_info - - # we override different "sdist" commands for both environments - if "sdist" in cmds: - _sdist: Any = cmds["sdist"] - else: - from setuptools.command.sdist import sdist as _sdist - - class cmd_sdist(_sdist): - def run(self) -> None: - versions = get_versions() - self._versioneer_generated_versions = versions - # unless we update this, the command will keep using the old - # version - self.distribution.metadata.version = versions["version"] - return _sdist.run(self) - - def make_release_tree(self, base_dir: str, files: List[str]) -> None: - root = get_root() - cfg = get_config_from_root(root) - _sdist.make_release_tree(self, base_dir, files) - # now locate _version.py in the new base_dir directory - # (remembering that it may be a hardlink) and replace it with an - # updated value - target_versionfile = os.path.join(base_dir, cfg.versionfile_source) - print("UPDATING %s" % target_versionfile) - write_to_version_file( - target_versionfile, self._versioneer_generated_versions - ) - - cmds["sdist"] = cmd_sdist - - return cmds - - -CONFIG_ERROR = """ -setup.cfg is missing the necessary Versioneer configuration. You need -a section like: - - [versioneer] - VCS = git - style = pep440 - versionfile_source = src/myproject/_version.py - versionfile_build = myproject/_version.py - tag_prefix = - parentdir_prefix = myproject- - -You will also need to edit your setup.py to use the results: - - import versioneer - setup(version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), ...) - -Please read the docstring in ./versioneer.py for configuration instructions, -edit setup.cfg, and re-run the installer or 'python versioneer.py setup'. -""" - -SAMPLE_CONFIG = """ -# See the docstring in versioneer.py for instructions. Note that you must -# re-run 'versioneer.py setup' after changing this section, and commit the -# resulting files. - -[versioneer] -#VCS = git -#style = pep440 -#versionfile_source = -#versionfile_build = -#tag_prefix = -#parentdir_prefix = - -""" - -OLD_SNIPPET = """ -from ._version import get_versions -__version__ = get_versions()['version'] -del get_versions -""" - -INIT_PY_SNIPPET = """ -from . import {0} -__version__ = {0}.get_versions()['version'] -""" - - -def do_setup() -> int: - """Do main VCS-independent setup function for installing Versioneer.""" - root = get_root() - try: - cfg = get_config_from_root(root) - except (OSError, configparser.NoSectionError, configparser.NoOptionError) as e: - if isinstance(e, (OSError, configparser.NoSectionError)): - print("Adding sample versioneer config to setup.cfg", file=sys.stderr) - with open(os.path.join(root, "setup.cfg"), "a") as f: - f.write(SAMPLE_CONFIG) - print(CONFIG_ERROR, file=sys.stderr) - return 1 - - print(" creating %s" % cfg.versionfile_source) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write( - LONG - % { - "DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - } - ) - - ipy = os.path.join(os.path.dirname(cfg.versionfile_source), "__init__.py") - maybe_ipy: Optional[str] = ipy - if os.path.exists(ipy): - try: - with open(ipy, "r") as f: - old = f.read() - except OSError: - old = "" - module = os.path.splitext(os.path.basename(cfg.versionfile_source))[0] - snippet = INIT_PY_SNIPPET.format(module) - if OLD_SNIPPET in old: - print(" replacing boilerplate in %s" % ipy) - with open(ipy, "w") as f: - f.write(old.replace(OLD_SNIPPET, snippet)) - elif snippet not in old: - print(" appending to %s" % ipy) - with open(ipy, "a") as f: - f.write(snippet) - else: - print(" %s unmodified" % ipy) - else: - print(" %s doesn't exist, ok" % ipy) - maybe_ipy = None - - # Make VCS-specific changes. For git, this means creating/changing - # .gitattributes to mark _version.py for export-subst keyword - # substitution. - do_vcs_install(cfg.versionfile_source, maybe_ipy) - return 0 - - -def scan_setup_py() -> int: - """Validate the contents of setup.py against Versioneer's expectations.""" - found = set() - setters = False - errors = 0 - with open("setup.py", "r") as f: - for line in f.readlines(): - if "import versioneer" in line: - found.add("import") - if "versioneer.get_cmdclass()" in line: - found.add("cmdclass") - if "versioneer.get_version()" in line: - found.add("get_version") - if "versioneer.VCS" in line: - setters = True - if "versioneer.versionfile_source" in line: - setters = True - if len(found) != 3: - print("") - print("Your setup.py appears to be missing some important items") - print("(but I might be wrong). Please make sure it has something") - print("roughly like the following:") - print("") - print(" import versioneer") - print(" setup( version=versioneer.get_version(),") - print(" cmdclass=versioneer.get_cmdclass(), ...)") - print("") - errors += 1 - if setters: - print("You should remove lines like 'versioneer.VCS = ' and") - print("'versioneer.versionfile_source = ' . This configuration") - print("now lives in setup.cfg, and should be removed from setup.py") - print("") - errors += 1 - return errors - - -def setup_command() -> NoReturn: - """Set up Versioneer and exit with appropriate error code.""" - errors = do_setup() - errors += scan_setup_py() - sys.exit(1 if errors else 0) - - -if __name__ == "__main__": - cmd = sys.argv[1] - if cmd == "setup": - setup_command() From 0f28472a078dd879d2f799dd1c061ae97fdd07c9 Mon Sep 17 00:00:00 2001 From: seh2 Date: Tue, 27 Oct 2026 17:19:48 +0000 Subject: [PATCH 02/10] Reformat with ruff format and apply safe ruff autofixes Mechanical only: ruff format at black's line length (removes blank lines at the start of blocks and rejoins a few split expressions) and removes unused imports flagged by ruff --fix. No behaviour change. --- notebook/test_register_err_corr_form.py | 3 --- obsarray/err_corr.py | 6 +----- obsarray/flag_accessor.py | 2 -- obsarray/templater/template_util.py | 1 - obsarray/test/test_unc_accessor.py | 3 +-- obsarray/test/test_utils.py | 24 ++++++++---------------- obsarray/unc_accessor.py | 3 --- 7 files changed, 10 insertions(+), 32 deletions(-) diff --git a/notebook/test_register_err_corr_form.py b/notebook/test_register_err_corr_form.py index 4bf2a62..725f362 100644 --- a/notebook/test_register_err_corr_form.py +++ b/notebook/test_register_err_corr_form.py @@ -1,12 +1,9 @@ from obsarray.err_corr import register_err_corr_form, BaseErrCorrForm -import xarray as xr import numpy as np -import obsarray @register_err_corr_form("new") class NewForm(BaseErrCorrForm): - form = "new" is_systematic = True diff --git a/obsarray/err_corr.py b/obsarray/err_corr.py index dc7aa69..edf3254 100644 --- a/obsarray/err_corr.py +++ b/obsarray/err_corr.py @@ -1,7 +1,7 @@ """err_corr_forms - module for the defintion of error-correlation parameterisation forms""" import abc -from typing import Callable, Type, Union, List +from typing import Callable, Type, Union import numpy as np from comet_maths.linear_algebra.matrix_conversion import expand_errcorr_dims @@ -201,7 +201,6 @@ def decorator(form_cls: Type) -> Type: @register_err_corr_form("random") class RandomCorrelation(BaseErrCorrForm): - form = "random" is_random = True @@ -226,7 +225,6 @@ def build_matrix(self, sli: tuple) -> np.ndarray: @register_err_corr_form("systematic") class SystematicCorrelation(BaseErrCorrForm): - form = "systematic" is_systematic = True @@ -251,7 +249,6 @@ def build_matrix(self, sli: tuple) -> np.ndarray: @register_err_corr_form("err_corr_matrix") class ErrCorrMatrixCorrelation(BaseErrCorrForm): - form = "err_corr_matrix" def build_matrix(self, sli: tuple) -> np.ndarray: @@ -278,7 +275,6 @@ def build_matrix(self, sli: tuple) -> np.ndarray: @register_err_corr_form("ensemble") class EnsembleCorrelation(BaseErrCorrForm): - form = "ensemble" def build_matrix(self, sli: tuple) -> np.ndarray: diff --git a/obsarray/flag_accessor.py b/obsarray/flag_accessor.py index c12b587..afce03b 100644 --- a/obsarray/flag_accessor.py +++ b/obsarray/flag_accessor.py @@ -319,7 +319,6 @@ def __setitem__( # add uncertainty variable if type(flag_def) == xr.DataArray: - # add necessary flag metadata if missing from provided data array flag_meanings, flag_masks = DatasetUtil.unpack_flag_attrs(flag_def.attrs) flag_def.attrs.update(DatasetUtil.pack_flag_attrs(flag_meanings)) @@ -328,7 +327,6 @@ def __setitem__( # use templater functionality if var defined with tuple elif type(flag_def) == tuple: - attrs = flag_def[1] if "flag_meanings" not in attrs: diff --git a/obsarray/templater/template_util.py b/obsarray/templater/template_util.py index 38d858e..8c17de5 100644 --- a/obsarray/templater/template_util.py +++ b/obsarray/templater/template_util.py @@ -91,7 +91,6 @@ def add_variables( """ for var_name in template.keys(): - var = TemplateUtil._create_var(var_name, template[var_name], size) ds[var_name] = var diff --git a/obsarray/test/test_unc_accessor.py b/obsarray/test/test_unc_accessor.py index d162433..b390fa2 100644 --- a/obsarray/test/test_unc_accessor.py +++ b/obsarray/test/test_unc_accessor.py @@ -48,8 +48,7 @@ def create_ds(var_suffix="", dim_suffix="", coord_dim_suffix_extra=""): ds = xr.Dataset( data_vars={ - "temperature" - + var_suffix: ( + "temperature" + var_suffix: ( [ "x" + dim_suffix, "y" + dim_suffix, diff --git a/obsarray/test/test_utils.py b/obsarray/test/test_utils.py index fb1537a..da37151 100644 --- a/obsarray/test/test_utils.py +++ b/obsarray/test/test_utils.py @@ -12,8 +12,7 @@ def create_test_ds(suffix): # define ds variables template = { - "temperature" - + suffix: { + "temperature" + suffix: { "dtype": np.float32, "dim": ["x" + suffix, "y" + suffix, "time" + suffix], "attributes": { @@ -24,8 +23,7 @@ def create_test_ds(suffix): ], }, }, - "u_ran_temperature" - + suffix: { + "u_ran_temperature" + suffix: { "dtype": np.float32, "dim": ["x" + suffix, "y" + suffix, "time" + suffix], "attributes": { @@ -42,8 +40,7 @@ def create_test_ds(suffix): ], }, }, - "u_sys_temperature" - + suffix: { + "u_sys_temperature" + suffix: { "dtype": np.float32, "dim": ["x" + suffix, "y" + suffix, "time" + suffix], "attributes": { @@ -70,14 +67,12 @@ def create_test_ds(suffix): ], }, }, - "pressure" - + suffix: { + "pressure" + suffix: { "dtype": np.float32, "dim": ["x" + suffix, "y" + suffix, "time" + suffix], "attributes": {"units": "Pa", "unc_comps": ["u_str_pressure" + suffix]}, }, - "u_str_pressure" - + suffix: { + "u_str_pressure" + suffix: { "dtype": np.float32, "dim": ["x" + suffix, "y" + suffix, "time" + suffix], "attributes": { @@ -99,20 +94,17 @@ def create_test_ds(suffix): ], }, }, - "err_corr_str_pressure_y" - + suffix: { + "err_corr_str_pressure_y" + suffix: { "dtype": np.float32, "dim": ["y" + suffix, "y" + suffix], "attributes": {"units": ""}, }, - "n_moles" - + suffix: { + "n_moles" + suffix: { "dtype": np.float32, "dim": ["x" + suffix, "y" + suffix, "time" + suffix], "attributes": {"units": "", "unc_comps": ["u_ran_n_moles" + suffix]}, }, - "u_ran_n_moles" - + suffix: { + "u_ran_n_moles" + suffix: { "dtype": np.float32, "dim": ["x" + suffix, "y" + suffix, "time" + suffix], "attributes": { diff --git a/obsarray/unc_accessor.py b/obsarray/unc_accessor.py index a94aed5..95f5443 100644 --- a/obsarray/unc_accessor.py +++ b/obsarray/unc_accessor.py @@ -139,7 +139,6 @@ def err_corr(self) -> List[Tuple[Union[str, List[str]], BaseErrCorrForm]]: # as a two element tuple (as described in doc string) err_corr = [] for i in err_corr_idxs: - dim_i = self._obj[self._unc_var_name].attrs[ DatasetUtil.return_err_corr_dim_str(i) ] @@ -150,7 +149,6 @@ def err_corr(self) -> List[Tuple[Union[str, List[str]], BaseErrCorrForm]]: # continue if parmeterisation dimension in slice dimensions if [dim_i_j for dim_i_j in list_dim_i if dim_i_j in sli_dims]: - form_i = self._obj[self._unc_var_name].attrs[ DatasetUtil.return_err_corr_form_str(i) ] @@ -862,7 +860,6 @@ def _add_unc_var( # use templater functionality if var defined with tuple elif type(unc_def) == tuple: - attrs = {} if len(unc_def) == 3: attrs = unc_def[2] From 40ac44a6ae62e3a3669727e642a62b255f3118b0 Mon Sep 17 00:00:00 2001 From: mattgoalen Date: Mon, 25 Nov 2024 11:55:19 +0000 Subject: [PATCH 03/10] update tests for numpy change (cherry picked from commit 7b8f9bf29a76ebc2848ba53807d6ffe646578d0c) --- obsarray/templater/tests/test_dataset_util.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/obsarray/templater/tests/test_dataset_util.py b/obsarray/templater/tests/test_dataset_util.py index 5a93255..60cb65a 100644 --- a/obsarray/templater/tests/test_dataset_util.py +++ b/obsarray/templater/tests/test_dataset_util.py @@ -471,7 +471,7 @@ def test_get_default_fill_value(self): self.assertEqual(-127, DatasetUtil.get_default_fill_value(np.int8)) self.assertEqual(-32767, DatasetUtil.get_default_fill_value(np.int16)) - self.assertEqual(np.uint16(-1), DatasetUtil.get_default_fill_value(np.uint16)) + self.assertEqual(np.array(-1).astype("uint16"), DatasetUtil.get_default_fill_value(np.uint16)) self.assertEqual(-2147483647, DatasetUtil.get_default_fill_value(np.int32)) self.assertEqual( -9223372036854775806, DatasetUtil.get_default_fill_value(np.int64) From c9f5c33b602bff09df50cab1847383c4a589fa02 Mon Sep 17 00:00:00 2001 From: mattgoalen Date: Mon, 25 Nov 2024 11:58:06 +0000 Subject: [PATCH 04/10] update for overflow error (cherry picked from commit 61fc7843b0902b1e741ed6a94b58942b2393721c) --- obsarray/flag_accessor.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/obsarray/flag_accessor.py b/obsarray/flag_accessor.py index afce03b..62daeb3 100644 --- a/obsarray/flag_accessor.py +++ b/obsarray/flag_accessor.py @@ -83,8 +83,8 @@ def __setitem__(self, sli: tuple, flag_value): ) else: self._obj[self._flag_var_name].values[self._sli] = ( - self._obj[self._flag_var_name][self._sli].values & ~flag_mask - ) + self._obj[self._flag_var_name][self._sli].values & np.array(~flag_mask) + ).astype(self._obj[self._flag_var_name].values[self._sli].dtype) # else apply mask else: @@ -99,8 +99,8 @@ def __setitem__(self, sli: tuple, flag_value): ) self._obj[self._flag_var_name][self._sli].values[i_false] = np.array( - self._obj[self._flag_var_name][self._sli].values[i_false] & ~flag_mask - ) + self._obj[self._flag_var_name][self._sli].values[i_false] & np.array(~flag_mask) + ).astype(self._obj[self._flag_var_name].values[self._sli].dtype) def _expand_sli(self, sli: Optional[tuple] = None) -> tuple: """ From a873467ce26ffc116f327211e854ad0059d6ae27 Mon Sep 17 00:00:00 2001 From: seh2 Date: Tue, 27 Oct 2026 17:22:03 +0000 Subject: [PATCH 05/10] Fix ruff lint findings and an xarray-related test failure - E721: compare exact types with `is` rather than `==` (same semantics) - E712: mark the intentional elementwise numpy `== True/False` comparisons with noqa rather than changing their behaviour - F841: use the already-computed sliced_dims rather than recomputing it, and drop unused variables from the create_ds test fixture - F811: remove a verbatim duplicate of test___setitem___new_mask - Reformat the cherry-picked overflow fix to the project line length - test_rename_dims: newer xarray's assert_identical also compares indexes, and rename_dims keeps the index on the renamed "time" coordinate, so drop it before comparing with the expected dataset --- obsarray/flag_accessor.py | 14 ++++++++------ obsarray/templater/dataset_util.py | 4 ++-- obsarray/templater/template_util.py | 2 +- obsarray/templater/tests/test_dataset_util.py | 4 +++- obsarray/test/test_flag_accessor.py | 16 ---------------- obsarray/test/test_unc_accessor.py | 8 +++----- obsarray/unc_accessor.py | 12 ++++++------ 7 files changed, 23 insertions(+), 37 deletions(-) diff --git a/obsarray/flag_accessor.py b/obsarray/flag_accessor.py index 62daeb3..08b06f3 100644 --- a/obsarray/flag_accessor.py +++ b/obsarray/flag_accessor.py @@ -83,7 +83,8 @@ def __setitem__(self, sli: tuple, flag_value): ) else: self._obj[self._flag_var_name].values[self._sli] = ( - self._obj[self._flag_var_name][self._sli].values & np.array(~flag_mask) + self._obj[self._flag_var_name][self._sli].values + & np.array(~flag_mask) ).astype(self._obj[self._flag_var_name].values[self._sli].dtype) # else apply mask @@ -91,15 +92,16 @@ def __setitem__(self, sli: tuple, flag_value): if flag_value.dtype is not np.dtype(bool): TypeError("Flag mask must of boolean type") - i_true = np.where(flag_value == True) - i_false = np.where(flag_value == False) + i_true = np.where(flag_value == True) # noqa: E712 (elementwise) + i_false = np.where(flag_value == False) # noqa: E712 (elementwise) self._obj[self._flag_var_name][self._sli].values[i_true] = np.array( self._obj[self._flag_var_name][self._sli].values[i_true] | flag_mask ) self._obj[self._flag_var_name][self._sli].values[i_false] = np.array( - self._obj[self._flag_var_name][self._sli].values[i_false] & np.array(~flag_mask) + self._obj[self._flag_var_name][self._sli].values[i_false] + & np.array(~flag_mask) ).astype(self._obj[self._flag_var_name].values[self._sli].dtype) def _expand_sli(self, sli: Optional[tuple] = None) -> tuple: @@ -318,7 +320,7 @@ def __setitem__( """ # add uncertainty variable - if type(flag_def) == xr.DataArray: + if type(flag_def) is xr.DataArray: # add necessary flag metadata if missing from provided data array flag_meanings, flag_masks = DatasetUtil.unpack_flag_attrs(flag_def.attrs) flag_def.attrs.update(DatasetUtil.pack_flag_attrs(flag_meanings)) @@ -326,7 +328,7 @@ def __setitem__( self._obj[flag_var_name] = flag_def # use templater functionality if var defined with tuple - elif type(flag_def) == tuple: + elif type(flag_def) is tuple: attrs = flag_def[1] if "flag_meanings" not in attrs: diff --git a/obsarray/templater/dataset_util.py b/obsarray/templater/dataset_util.py index 812752f..09d33e9 100644 --- a/obsarray/templater/dataset_util.py +++ b/obsarray/templater/dataset_util.py @@ -569,7 +569,7 @@ def set_flag(da, flag_name, error_if_set=False): set_flags = DatasetUtil.unpack_flags(da)[flag_name] - if numpy.any(set_flags == True) and error_if_set: + if numpy.any(set_flags == True) and error_if_set: # noqa: E712 raise ValueError( "Flag " + flag_name + " already set for variable " + da.name ) @@ -597,7 +597,7 @@ def unset_flag(da, flag_name, error_if_unset=False): set_flags = DatasetUtil.unpack_flags(da)[flag_name] - if numpy.any(set_flags == False) and error_if_unset: + if numpy.any(set_flags == False) and error_if_unset: # noqa: E712 raise ValueError( "Flag " + flag_name + " already set for variable " + da.name ) diff --git a/obsarray/templater/template_util.py b/obsarray/templater/template_util.py index 8c17de5..aedf102 100644 --- a/obsarray/templater/template_util.py +++ b/obsarray/templater/template_util.py @@ -172,7 +172,7 @@ def _check_variable_definition(variable_name: str, variable_attrs: Dict): """ # Variable name must be type str - if type(variable_name) != str: + if type(variable_name) is not str: raise TypeError( "Invalid variable name: " + str(variable_name) + " (must be string)" ) diff --git a/obsarray/templater/tests/test_dataset_util.py b/obsarray/templater/tests/test_dataset_util.py index 60cb65a..b5c78b9 100644 --- a/obsarray/templater/tests/test_dataset_util.py +++ b/obsarray/templater/tests/test_dataset_util.py @@ -471,7 +471,9 @@ def test_get_default_fill_value(self): self.assertEqual(-127, DatasetUtil.get_default_fill_value(np.int8)) self.assertEqual(-32767, DatasetUtil.get_default_fill_value(np.int16)) - self.assertEqual(np.array(-1).astype("uint16"), DatasetUtil.get_default_fill_value(np.uint16)) + self.assertEqual( + np.array(-1).astype("uint16"), DatasetUtil.get_default_fill_value(np.uint16) + ) self.assertEqual(-2147483647, DatasetUtil.get_default_fill_value(np.int32)) self.assertEqual( -9223372036854775806, DatasetUtil.get_default_fill_value(np.int64) diff --git a/obsarray/test/test_flag_accessor.py b/obsarray/test/test_flag_accessor.py index 4ef330d..dd3b138 100644 --- a/obsarray/test/test_flag_accessor.py +++ b/obsarray/test/test_flag_accessor.py @@ -231,22 +231,6 @@ def test___setitem___new_mask(self, mdu, mf): mf.assert_called_with(slice(None, None, None), True) - @patch("obsarray.flag_accessor.Flag.__setitem__") - @patch("obsarray.flag_accessor.DatasetUtil.add_flag_meaning_to_attrs") - def test___setitem___new_mask(self, mdu, mf): - - original_attrs = deepcopy(self.ds["temperature_flags"].attrs) - - self.ds.flag["temperature_flags"]["test_flag"] = True - - mdu.assert_called_once_with( - original_attrs, "test_flag", self.ds["temperature_flags"].dtype - ) - - self.assertDictEqual(self.ds["temperature_flags"].attrs, {}) - - mf.assert_called_with(slice(None, None, None), True) - @patch("obsarray.flag_accessor.Flag.__setitem__") @patch("obsarray.flag_accessor.DatasetUtil.rm_flag_meaning_from_attrs") def test___delitem__(self, mdu, mf): diff --git a/obsarray/test/test_unc_accessor.py b/obsarray/test/test_unc_accessor.py index b390fa2..9c4a38d 100644 --- a/obsarray/test/test_unc_accessor.py +++ b/obsarray/test/test_unc_accessor.py @@ -37,10 +37,6 @@ def compare_err_corr_form(self, form, exp_form): def create_ds(var_suffix="", dim_suffix="", coord_dim_suffix_extra=""): np.random.seed(0) temperature = 15 + 8 * np.random.randn(2, 2, 3) - u_r_temperature = temperature * 0.02 - u_s_temperature = temperature * 0.01 - precipiation = 15 + 8 * np.random.randn(2, 2, 3) - u_r_precipiation = temperature * 0.02 lon = [[-99.83, -99.32], [-99.79, -99.23]] lat = [[42.25, 42.21], [42.63, 42.59]] time = pd.date_range("2014-09-06", periods=3) @@ -799,7 +795,9 @@ def test_rename_dims(self): exp_ds = create_ds(dim_suffix=dim_suffix) - xr.testing.assert_identical(ds, exp_ds) + # xarray keeps the index on the renamed "time" coordinate, whereas a + # freshly built non-dimension coordinate has none - compare without it + xr.testing.assert_identical(ds.drop_indexes("time"), exp_ds) if __name__ == "__main__": diff --git a/obsarray/unc_accessor.py b/obsarray/unc_accessor.py index 95f5443..b4bb2a0 100644 --- a/obsarray/unc_accessor.py +++ b/obsarray/unc_accessor.py @@ -348,7 +348,7 @@ def err_corr_matrix(self) -> xr.DataArray: # parameterisation object for dim_err_corr in self.err_corr: sliced_dims = dim_err_corr[1].get_sliced_dims_errcorr(self._sli) - if len(dim_err_corr[1].get_sliced_dims_errcorr(self._sli)) > 0: + if len(sliced_dims) > 0: err_corr_matrix.values = err_corr_matrix.values.dot( dim_err_corr[1].build_dot_matrix(self._sli) ) @@ -752,7 +752,7 @@ def unc_vars(self) -> xr.core.dataset.DataVariables: for var_name in self.obs_vars: var_unc_var_names = self._var_unc_var_names(var_name) - if type(var_unc_var_names) == str: + if type(var_unc_var_names) is str: var_unc_var_names = [var_unc_var_names] unc_var_names |= set(var_unc_var_names) @@ -774,7 +774,7 @@ def _var_unc_var_names( all_unc_var_names = [] if "unc_comps" in self._obj[obs_var_name].attrs: all_unc_var_names = self._obj[obs_var_name].attrs["unc_comps"] - if type(all_unc_var_names) == str: + if type(all_unc_var_names) is str: all_unc_var_names = [all_unc_var_names] # Filter returned names if unc_type defined @@ -855,11 +855,11 @@ def _add_unc_var( """ # add uncertainty variable - if type(unc_def) == xr.DataArray: + if type(unc_def) is xr.DataArray: self._obj[unc_var] = unc_def # use templater functionality if var defined with tuple - elif type(unc_def) == tuple: + elif type(unc_def) is tuple: attrs = {} if len(unc_def) == 3: attrs = unc_def[2] @@ -882,7 +882,7 @@ def _add_unc_var( # add variable to uncertainty components attribute if self._is_obs_var(obs_var): - if type(self._obj[obs_var].attrs["unc_comps"]) == str: + if type(self._obj[obs_var].attrs["unc_comps"]) is str: self._obj[obs_var].attrs["unc_comps"] = [ self._obj[obs_var].attrs["unc_comps"] ] From ccc75f87010653e79ce3f771d5abcc69299431a5 Mon Sep 17 00:00:00 2001 From: seh2 Date: Tue, 27 Oct 2026 17:26:50 +0000 Subject: [PATCH 06/10] Fix mypy findings Annotation fixes so the new mypy gate passes: - Use numpy.typing.DTypeLike for dtype arguments (numpy.typecodes is a string constant, not a type) - Make implicit-Optional defaults explicit and widen fill_value to accept numpy scalars, which get_default_fill_value returns - Accept Hashable variable names where xarray hands them to us, and return xr.Dataset rather than an unbound TypeVar from rename methods - Annotate err-corr slices as tuples, matching all callers and subclasses, and accept slices/ints in Flag indexing (e.g. ``[:]``) - Build _expand_sli's list under its own name instead of retyping out_sli Small behaviour changes that fall out of this: - A "flag" template variable without attributes now raises a clear ValueError rather than AttributeError on None.pop - An uncertainty tuple definition with attrs=None is treated as having no attrs rather than raising TypeError - append_names/empty_err_corr_matrix format non-str names with str() rather than failing on string concatenation --- obsarray/err_corr.py | 6 +++--- obsarray/flag_accessor.py | 20 ++++++++++--------- obsarray/templater/dataset_util.py | 26 ++++++++++++++---------- obsarray/templater/dstemplater.py | 2 +- obsarray/templater/template_util.py | 4 ++++ obsarray/unc_accessor.py | 31 ++++++++++++++--------------- obsarray/utils.py | 8 +++++--- 7 files changed, 54 insertions(+), 43 deletions(-) diff --git a/obsarray/err_corr.py b/obsarray/err_corr.py index edf3254..5079d10 100644 --- a/obsarray/err_corr.py +++ b/obsarray/err_corr.py @@ -1,7 +1,7 @@ """err_corr_forms - module for the defintion of error-correlation parameterisation forms""" import abc -from typing import Callable, Type, Union +from typing import Callable, Type import numpy as np from comet_maths.linear_algebra.matrix_conversion import expand_errcorr_dims @@ -150,7 +150,7 @@ def slice_errcorr_matrix(self, err_corr_matrix, variable_shape, sli) -> np.ndarr ) @abc.abstractmethod - def build_matrix(self, sli: Union[np.ndarray, tuple]) -> np.ndarray: + def build_matrix(self, sli: tuple) -> np.ndarray: """ Returns uncertainty effect error-correlation matrix, populated with error-correlation values defined in this parameterisation @@ -161,7 +161,7 @@ def build_matrix(self, sli: Union[np.ndarray, tuple]) -> np.ndarray: """ pass - def build_dot_matrix(self, sli: Union[np.ndarray, tuple]) -> np.ndarray: + def build_dot_matrix(self, sli: tuple) -> np.ndarray: """ Returns expanded error correlation matrix for use in dot product with error correlation in other dimensions. diff --git a/obsarray/flag_accessor.py b/obsarray/flag_accessor.py index 08b06f3..7269373 100644 --- a/obsarray/flag_accessor.py +++ b/obsarray/flag_accessor.py @@ -2,7 +2,7 @@ import numpy as np import xarray as xr -from typing import List, Optional, Union, Tuple +from typing import Hashable, List, Optional, Union, Tuple from obsarray.templater.template_util import create_var from obsarray.templater.dataset_util import DatasetUtil @@ -45,7 +45,7 @@ def __repr__(self): """Custom __repr__""" return str(self) - def __getitem__(self, sli: tuple): + def __getitem__(self, sli: Union[tuple, slice, int]): """ Defines variable slice @@ -58,7 +58,7 @@ def __getitem__(self, sli: tuple): return self - def __setitem__(self, sli: tuple, flag_value): + def __setitem__(self, sli: Union[tuple, slice, int], flag_value): """ Sets flag values @@ -104,7 +104,7 @@ def __setitem__(self, sli: tuple, flag_value): & np.array(~flag_mask) ).astype(self._obj[self._flag_var_name].values[self._sli].dtype) - def _expand_sli(self, sli: Optional[tuple] = None) -> tuple: + def _expand_sli(self, sli: Optional[Union[tuple, slice, int]] = None) -> tuple: """ Function to expand the provided sli so that it always has the right number of dimensions @@ -120,12 +120,14 @@ def _expand_sli(self, sli: Optional[tuple] = None) -> tuple: # E.g. if providing [0] for a variable with 3 dimensions, this becomes # [0,slice(None),slice(None)] else: - out_sli = list([slice(None)] * self._obj[self._flag_var_name].ndim) + out_sli_list: list = list( + [slice(None)] * self._obj[self._flag_var_name].ndim + ) sli_list = list(sli) if isinstance(sli, tuple) else [sli] for i in range(len(sli_list)): if not sli_list[i] == ":": - out_sli[i] = sli_list[i] - out_sli = tuple(out_sli) + out_sli_list[i] = sli_list[i] + out_sli = tuple(out_sli_list) return out_sli @@ -415,7 +417,7 @@ def flag_vars(self) -> xr.core.dataset.DataVariables: return self._obj[list(flag_var_names)].data_vars - def _is_data_var(self, var_name: str) -> bool: + def _is_data_var(self, var_name: Hashable) -> bool: """ Returns true if named dataset variable is an data variable (i.e. not a flag variable) @@ -426,7 +428,7 @@ def _is_data_var(self, var_name: str) -> bool: return True return False - def _is_flag_var(self, var_name: str) -> bool: + def _is_flag_var(self, var_name: Hashable) -> bool: """ Returns true if named dataset variable is an flag variable diff --git a/obsarray/templater/dataset_util.py b/obsarray/templater/dataset_util.py index 09d33e9..4a170c9 100644 --- a/obsarray/templater/dataset_util.py +++ b/obsarray/templater/dataset_util.py @@ -6,6 +6,7 @@ from copy import deepcopy import xarray import numpy +from numpy.typing import DTypeLike from typing import Union, Optional, List, Dict, Tuple @@ -34,9 +35,9 @@ class DatasetUtil: @staticmethod def create_default_array( dim_sizes: List[int], - dtype: numpy.typecodes, + dtype: DTypeLike, dim_names: Optional[List[str]] = None, - fill_value: Optional[Union[int, float]] = None, + fill_value: Optional[Union[int, float, numpy.number]] = None, ) -> xarray.DataArray: """ Return default empty xarray DataArray @@ -66,10 +67,10 @@ def create_default_array( @staticmethod def create_variable( dim_sizes: List[int], - dtype: numpy.typecodes, + dtype: DTypeLike, dim_names: Optional[List[str]] = None, - attributes: Dict = None, - fill_value: Optional[Union[int, float]] = None, + attributes: Optional[Dict] = None, + fill_value: Optional[Union[int, float, numpy.number]] = None, ) -> xarray.Variable: """ Return default empty xarray Variable @@ -107,7 +108,7 @@ def create_variable( @staticmethod def create_unc_variable( dim_sizes: List[int], - dtype: numpy.typecodes, + dtype: DTypeLike, dim_names: List[str], attributes: Optional[Dict] = None, pdf_shape: str = "gaussian", @@ -315,7 +316,7 @@ def unpack_flag_attrs(attrs: dict) -> Tuple[list, list]: @staticmethod def add_flag_meaning_to_attrs( - attrs: dict, flag_meaning: str, dtype: numpy.typecodes + attrs: dict, flag_meaning: str, dtype: DTypeLike ) -> dict: """ Add new meaning to flag variable attributes @@ -384,7 +385,7 @@ def rm_flag_meaning_from_attrs(attrs: dict, flag_meaning: str) -> dict: return updated_attrs @staticmethod - def return_flags_dtype(n_masks: int) -> numpy.typecodes: + def return_flags_dtype(n_masks: int) -> DTypeLike: """ Return required flags array data type @@ -404,10 +405,10 @@ def return_flags_dtype(n_masks: int) -> numpy.typecodes: @staticmethod def add_encoding( variable: xarray.Variable, - dtype: numpy.typecodes, + dtype: DTypeLike, scale_factor: Optional[float] = 1.0, offset: Optional[float] = 0.0, - fill_value: Optional[Union[int, float]] = None, + fill_value: Optional[Union[int, float, numpy.number]] = None, chunksizes: Optional[float] = None, ): """ @@ -442,7 +443,9 @@ def add_encoding( variable.encoding = encoding_dict @staticmethod - def get_default_fill_value(dtype: numpy.typecodes) -> Union[int, float]: + def get_default_fill_value( + dtype: DTypeLike, + ) -> Optional[Union[int, float, numpy.number]]: """ Returns default fill_value for given data type @@ -469,6 +472,7 @@ def get_default_fill_value(dtype: numpy.typecodes) -> Union[int, float]: return numpy.float32(9.96921e36) elif dtype == numpy.float64: return numpy.float64(9.969209968386869e36) + return None @staticmethod def _get_flag_encoding(da): diff --git a/obsarray/templater/dstemplater.py b/obsarray/templater/dstemplater.py index c4784d3..018e203 100644 --- a/obsarray/templater/dstemplater.py +++ b/obsarray/templater/dstemplater.py @@ -122,7 +122,7 @@ def create_size_dict(self, ds_format: str) -> Dict[str, None]: :return: empty sizes dictionary """ - dim_sizes_dict = dict() + dim_sizes_dict: Dict[str, None] = dict() for dim in self.return_template_dim_names(ds_format): dim_sizes_dict[dim] = None diff --git a/obsarray/templater/template_util.py b/obsarray/templater/template_util.py index aedf102..f8eca37 100644 --- a/obsarray/templater/template_util.py +++ b/obsarray/templater/template_util.py @@ -130,6 +130,10 @@ def _create_var( # Create variable and add to dataset if isinstance(dtype, str): if dtype == "flag": + if attributes is None: + raise ValueError( + "Flag variable " + var_name + " must define flag_meanings" + ) flag_meanings = attributes.pop("flag_meanings") variable = du.create_flags_variable( dim_sizes, diff --git a/obsarray/unc_accessor.py b/obsarray/unc_accessor.py index b4bb2a0..3b18559 100644 --- a/obsarray/unc_accessor.py +++ b/obsarray/unc_accessor.py @@ -3,13 +3,12 @@ from copy import deepcopy import numpy as np import xarray as xr -from typing import Union, Tuple, List, Optional +from typing import Hashable, Union, Tuple, List, Optional from comet_maths import convert_corr_to_cov, correlation_from_covariance from obsarray.templater.template_util import create_var from obsarray.templater.dataset_util import DatasetUtil from obsarray.err_corr import err_corr_forms, BaseErrCorrForm from obsarray.utils import empty_err_corr_matrix -from xarray.core.types import T_Dataset __author__ = "Sam Hunt " @@ -28,7 +27,7 @@ class Uncertainty: def __init__( self, xarray_obj: xr.Dataset, - var_name: str, + var_name: Hashable, unc_var_name: str, sli: Optional[tuple] = None, ): @@ -84,12 +83,12 @@ def _expand_sli(self, sli: Optional[tuple] = None) -> tuple: # E.g. if providing [0] for a variable with 3 dimensions, this becomes # [0,slice(None),slice(None)] else: - out_sli = list([slice(None)] * self._obj[self._unc_var_name].ndim) + out_sli_list = list([slice(None)] * self._obj[self._unc_var_name].ndim) sli_list = list(sli) if isinstance(sli, tuple) else [sli] for i in range(len(sli_list)): if not sli_list[i] == ":": - out_sli[i] = sli_list[i] - out_sli = tuple(out_sli) + out_sli_list[i] = sli_list[i] + out_sli = tuple(out_sli_list) return out_sli @@ -379,7 +378,7 @@ class VariableUncertainty: :param var_name: name of dataset variable """ - def __init__(self, xarray_obj: xr.Dataset, var_name: str): + def __init__(self, xarray_obj: xr.Dataset, var_name: Hashable): self._obj = xarray_obj self._var_name = var_name self._sli = tuple([slice(None)] * self._obj[self._var_name].ndim) @@ -452,7 +451,7 @@ def __iter__(self): self.i = 0 # Define counter return self - def __next__(self) -> Uncertainty: + def __next__(self) -> Union[Uncertainty, "VariableUncertainty"]: """ Returns ith variable uncertainty @@ -677,7 +676,7 @@ def __repr__(self) -> str: """Custom __repr__""" return str(self) - def __getitem__(self, var_name: str) -> VariableUncertainty: + def __getitem__(self, var_name: Hashable) -> VariableUncertainty: """ Returns :py:class:`~obsarray.unc_accessor.VariableUncertainty` object to interface with uncertainty information for a given observation variable @@ -759,7 +758,7 @@ def unc_vars(self) -> xr.core.dataset.DataVariables: return self._obj[list(unc_var_names)].data_vars def _var_unc_var_names( - self, obs_var_name: str, unc_type: Optional[str] = None + self, obs_var_name: Hashable, unc_type: Optional[str] = None ) -> List[str]: """ Returns the names of uncertainty variables associated with specified observation variable @@ -796,7 +795,7 @@ def _var_unc_var_names( return unc_var_names - def _is_obs_var(self, var_name: str) -> bool: + def _is_obs_var(self, var_name: Hashable) -> bool: """ Returns true if named dataset variable is an observation variable @@ -823,7 +822,7 @@ def _var_unc_vars( obs_var_name: str, sli: Optional[tuple] = None, unc_type: Optional[str] = None, - ) -> xr.core.dataset.DataVariables: + ) -> Optional[xr.core.dataset.DataVariables]: """ Returns uncertainty data variables for specified observation variable @@ -860,8 +859,8 @@ def _add_unc_var( # use templater functionality if var defined with tuple elif type(unc_def) is tuple: - attrs = {} - if len(unc_def) == 3: + attrs: dict = {} + if len(unc_def) == 3 and unc_def[2] is not None: attrs = unc_def[2] if "err_corr" not in attrs: @@ -904,7 +903,7 @@ def _remove_unc_var(self, obs_var: str, unc_var: str) -> None: del self._obj[unc_var] self._obj[obs_var].attrs["unc_comps"].remove(unc_var) - def rename(self, vars_dict: dict[str, str]) -> T_Dataset: + def rename(self, vars_dict: dict[str, str]) -> xr.Dataset: """ Returns a new dataset with renamed variables - safely handling `unc_vars` and related metadata @@ -953,7 +952,7 @@ def rename(self, vars_dict: dict[str, str]) -> T_Dataset: return ds - def rename_dims(self, dims_dict: dict[str, str]) -> T_Dataset: + def rename_dims(self, dims_dict: dict[str, str]) -> xr.Dataset: """ Returns a new dataset with renamed dimensions - safely handling `unc_vars` related metadata diff --git a/obsarray/utils.py b/obsarray/utils.py index 17e1fe0..276be74 100644 --- a/obsarray/utils.py +++ b/obsarray/utils.py @@ -20,7 +20,7 @@ def empty_err_corr_matrix(obs_var: xr.DataArray): dim_lens = [len(obs_var[dim]) for dim in dim_names] n_elems = int(np.prod(dim_lens)) - erc_dim_name = ".".join(dim_names) + erc_dim_name = ".".join(str(dim) for dim in dim_names) err_corr_matrix = xr.DataArray(np.eye(n_elems), dims=[erc_dim_name, erc_dim_name]) @@ -47,12 +47,14 @@ def append_names( # update variable names if not skip_vars: - var_rename = {var_name: var_name + suffix for var_name in ds.variables.keys()} + var_rename = { + var_name: f"{var_name}{suffix}" for var_name in ds.variables.keys() + } ds = ds.unc.rename(var_rename) # update dimension names if not skip_dims: - dim_rename = {dim_name: dim_name + suffix for dim_name in ds.dims.keys()} + dim_rename = {dim_name: f"{dim_name}{suffix}" for dim_name in ds.dims.keys()} ds = ds.unc.rename_dims(dim_rename) # update attribute names From 862c2370d7c415ea00fd4cc46b6d9df799e0cfea Mon Sep 17 00:00:00 2001 From: seh2 Date: Tue, 27 Oct 2026 17:26:50 +0000 Subject: [PATCH 07/10] Align the pre-commit mypy hook with the CI lint job Install numpy and xarray into the hook environment so type narrowing behaves as it does in CI, restrict the hook to the package (as CI does), and use the ruff-check hook id in place of the legacy ruff alias. --- .pre-commit-config.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c16c553..50e565c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,7 +7,7 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit rev: v0.15.13 hooks: - - id: ruff + - id: ruff-check args: [--fix] - id: ruff-format @@ -15,3 +15,7 @@ repos: rev: v2.1.0 hooks: - id: mypy + # Match the CI lint job: check the package only, with numpy/xarray + # type information available (CI installs the package). + files: ^obsarray/ + additional_dependencies: [numpy, xarray] From 1bf8a9f4c0e1ffb0a71ff62cf2f8b4ad7a8543c8 Mon Sep 17 00:00:00 2001 From: seh2 Date: Tue, 27 Oct 2026 17:27:12 +0000 Subject: [PATCH 08/10] docs: set Sphinx language to "en" language = None is no longer valid in current Sphinx. --- docs/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 1df86cc..9cafd60 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -79,7 +79,7 @@ # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. -language = None +language = "en" # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. From 6b476d77a332046562118fb16d755740604b9df2 Mon Sep 17 00:00:00 2001 From: seh2 Date: Tue, 27 Oct 2026 17:41:24 +0000 Subject: [PATCH 09/10] Bump GitHub Actions to Node 24 versions checkout v7, setup-python v7, upload-artifact v7, download-artifact v8 and codecov-action v7, clearing the Node.js 20 deprecation warnings. None of their breaking changes affect these workflows (artifacts are downloaded by name, no pull_request_target, no pip-install input). --- .github/workflows/publish.yml | 12 ++++++------ .github/workflows/tests.yml | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 0ae51c2..b71d38a 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -31,8 +31,8 @@ jobs: needs: check runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 + - uses: actions/checkout@v7 + - uses: actions/setup-python@v7 with: python-version: "3.13" cache: pip @@ -47,11 +47,11 @@ jobs: needs: test runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v7 with: fetch-depth: 0 # full history so setuptools_scm picks up the tag - - uses: actions/setup-python@v5 + - uses: actions/setup-python@v7 with: python-version: "3.13" @@ -61,7 +61,7 @@ jobs: python -m build - name: Store distribution packages - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@v7 with: name: dist path: dist/ @@ -88,7 +88,7 @@ jobs: steps: - name: Download distribution packages - uses: actions/download-artifact@v4 + uses: actions/download-artifact@v8 with: name: dist path: dist/ diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 4655fae..39b17ae 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -17,10 +17,10 @@ jobs: python-version: ["3.11", "3.12", "3.13"] steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v7 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 + uses: actions/setup-python@v7 with: python-version: ${{ matrix.python-version }} cache: pip @@ -40,7 +40,7 @@ jobs: - name: Upload test report if: always() - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@v7 with: name: test-report-py${{ matrix.python-version }} path: test_report/ @@ -48,7 +48,7 @@ jobs: - name: Upload coverage to Codecov if: matrix.python-version == '3.13' - uses: codecov/codecov-action@v4 + uses: codecov/codecov-action@v7 with: files: test_report/coverage.xml token: ${{ secrets.CODECOV_TOKEN }} @@ -58,8 +58,8 @@ jobs: name: Lint runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 + - uses: actions/checkout@v7 + - uses: actions/setup-python@v7 with: python-version: "3.13" cache: pip From 5681e769c7f47a75b8c5bfbc91809fc008a3626c Mon Sep 17 00:00:00 2001 From: seh2 Date: Tue, 27 Oct 2026 17:43:12 +0000 Subject: [PATCH 10/10] README: credit the CoMet Toolkit Team in acknowledgements --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3eaede5..d2023d3 100644 --- a/README.md +++ b/README.md @@ -75,7 +75,7 @@ obsarray is free software licensed under the ## Acknowledgements -obsarray has been developed by [Sam Hunt](https://github.com/shunt16). +obsarray has been developed by the [CoMet Toolkit Team](mailto:team@comet-toolkit.org). The development has been funded by: