obsarray 1.0.3__tar.gz → 1.1__tar.gz

obsarray-1.1/.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@v7
+      - uses: actions/setup-python@v7
+        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@v7
+        with:
+          fetch-depth: 0  # full history so setuptools_scm picks up the tag
+
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.13"
+
+      - name: Build
+        run: |
+          pip install build
+          python -m build
+
+      - name: Store distribution packages
+        uses: actions/upload-artifact@v7
+        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@v8
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

obsarray-1.1/.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@v7
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install dependencies
+        run: pip install -e ".[dev]"
+
+      - name: Run tests
+        run: |
+          mkdir -p test_report
+          pytest \
+            --html=test_report/report.html \
+            --cov-report html:test_report/cov_report \
+            --cov-report xml:test_report/coverage.xml \
+            --junitxml=test_report/junit.xml \
+            --cov=obsarray
+
+      - name: Upload test report
+        if: always()
+        uses: actions/upload-artifact@v7
+        with:
+          name: test-report-py${{ matrix.python-version }}
+          path: test_report/
+          retention-days: 7
+
+      - name: Upload coverage to Codecov
+        if: matrix.python-version == '3.13'
+        uses: codecov/codecov-action@v7
+        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@v7
+      - uses: actions/setup-python@v7
+        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

obsarray-1.1/.gitignore

@@ -0,0 +1,128 @@
+# macOS
+.DS_Store
+
+# Mypy cache
+.mypy_cache
+
+# Ruff cache
+.ruff_cache
+
+# Compiles docs for gitlab pages
+public
+latex
+
+# Visual studio / pycharm folders
+.idea
+.vscode
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+docs/_build
+docs/content/api
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+test_report/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/content/user/generated/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# IDE settings
+.vscode/.git.old
+
+CLAUDE.md

obsarray-1.1/.pre-commit-config.yaml

@@ -0,0 +1,21 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.13
+    hooks:
+      - id: ruff-check
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    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]

obsarray-1.1/.readthedocs.yaml

@@ -0,0 +1,28 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-24.04
+  tools:
+    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
+
+# Install the package with its docs extras from pyproject.toml
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

obsarray-1.1/MANIFEST.in

@@ -0,0 +1,2 @@
+include README.md
+include LICENSE

obsarray-1.1/PKG-INFO

@@ -0,0 +1,130 @@
+Metadata-Version: 2.4
+Name: obsarray
+Version: 1.1
+Summary: Extension to xarray for handling uncertainty-quantified observation data
+Author-email: CoMet Toolkit Team <team@comet-toolkit.org>
+Project-URL: Homepage, https://github.com/comet-toolkit/obsarray
+Project-URL: Documentation, https://obsarray.readthedocs.io
+Classifier: Development Status :: 4 - Beta
+Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: xarray
+Requires-Dist: netcdf4
+Requires-Dist: comet_maths
+Provides-Extra: dev
+Requires-Dist: ruff==0.15.13; extra == "dev"
+Requires-Dist: mypy==2.1.0; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-html; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx_book_theme; extra == "docs"
+Requires-Dist: sphinx_design; extra == "docs"
+Requires-Dist: sphinx_autosummary_accessors; extra == "docs"
+Requires-Dist: ipython; extra == "docs"
+Dynamic: license-file
+
+# obsarray: Measurement uncertainty handling in Python
+
+[![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.
+
+> **Upcoming change:** obsarray currently follows v0.1 of the
+> [UNC specification](https://comet-toolkit.github.io/unc_website/) for
+> uncertainty metadata. A future release will default to
+> [draft v0.2](https://comet-toolkit.github.io/unc_website/specification/draft-v0.2/unc_specification.html),
+> which is proposed for inclusion in the CF conventions and is not backwards
+> compatible with v0.1. See
+> [what this means for you](https://obsarray.readthedocs.io/en/latest/content/user/unc_conventions.html).
+
+obsarray is part of the [CoMet Toolkit](https://www.comet-toolkit.org) (community metrology toolkit), and can combined with the [punpy](https://punpy.readthedocs.io/en/latest/) (propagating uncertainties in python) module for very simple propagation of defined data uncertainties through arbitrary python functions.
+
+## Installation
+
+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<X.Y.Z>
+git push origin v<X.Y.Z>
+```
+
+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 Lesser General Public License (v3)](./LICENSE).
+
+## Acknowledgements
+
+obsarray has been developed by the [CoMet Toolkit Team](mailto:team@comet-toolkit.org).
+
+The development has been funded by:
+
+* The UK's Department for Business, Energy and Industrial Strategy's (BEIS) National Measurement System (NMS) programme
+* The IDEAS-QA4EO project funded by the European Space Agency.
+
+## Project status
+
+obsarray is under active development. It is beta software.

obsarray-1.1/README.md

@@ -0,0 +1,95 @@
+# obsarray: Measurement uncertainty handling in Python
+
+[![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.
+
+> **Upcoming change:** obsarray currently follows v0.1 of the
+> [UNC specification](https://comet-toolkit.github.io/unc_website/) for
+> uncertainty metadata. A future release will default to
+> [draft v0.2](https://comet-toolkit.github.io/unc_website/specification/draft-v0.2/unc_specification.html),
+> which is proposed for inclusion in the CF conventions and is not backwards
+> compatible with v0.1. See
+> [what this means for you](https://obsarray.readthedocs.io/en/latest/content/user/unc_conventions.html).
+
+obsarray is part of the [CoMet Toolkit](https://www.comet-toolkit.org) (community metrology toolkit), and can combined with the [punpy](https://punpy.readthedocs.io/en/latest/) (propagating uncertainties in python) module for very simple propagation of defined data uncertainties through arbitrary python functions.
+
+## Installation
+
+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<X.Y.Z>
+git push origin v<X.Y.Z>
+```
+
+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 Lesser General Public License (v3)](./LICENSE).
+
+## Acknowledgements
+
+obsarray has been developed by the [CoMet Toolkit Team](mailto:team@comet-toolkit.org).
+
+The development has been funded by:
+
+* The UK's Department for Business, Energy and Industrial Strategy's (BEIS) National Measurement System (NMS) programme
+* The IDEAS-QA4EO project funded by the European Space Agency.
+
+## Project status
+
+obsarray is under active development. It is beta software.

obsarray-1.1/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = obsarray
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

obsarray-1.1/docs/_static/custom.css

@@ -0,0 +1,4 @@
+code.literal {
+    color: #404040 !important;
+    background-color: #fbfbfb !important;
+}

obsarray-1.1/docs/_templates/autosummary/attribute.rst

@@ -0,0 +1,5 @@
+{{ objname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. auto{{ objtype }}:: {{ objname }}

obsarray-1.1/docs/_templates/autosummary/base.rst

@@ -0,0 +1,5 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. auto{{ objtype }}:: {{ objname }}

obsarray-1.1/docs/_templates/autosummary/class.rst

@@ -0,0 +1,33 @@
+{{ objname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+
+   {% block methods %}
+   .. automethod:: __init__
+
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+   {% for item in methods %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

obsarray-1.1/docs/_templates/autosummary/function.rst

@@ -0,0 +1,5 @@
+{{ objname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. auto{{ objtype }}:: {{ objname }}

obsarray-1.1/docs/_templates/autosummary/method.rst

@@ -0,0 +1,5 @@
+{{ objname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. auto{{ objtype }}:: {{ objname }}