diff --git a/.coveragerc b/.coveragerc deleted file mode 100644 index d207a33..0000000 --- a/.coveragerc +++ /dev/null @@ -1,29 +0,0 @@ -[run] -branch = True -omit = - examples/* - tests/* - tmp.py - setup.py - deker/typings.py - deker/app_types/shell.py - deker/tools/profiling.py - deker/tools/data.py - profiling/* - -[html] -directory = tests/code_coverage - -[report] -fail_under=95 -exclude_lines = - no cov - pragma: no cover - if typing.TYPE_CHECKING: - if TYPE_CHECKING: - if __name__ == .__main__.: - pass - raise NotImplementedError - except ImportError - except ModuleNotFoundError - except Exception diff --git a/.github/workflows/github-actions.yml b/.github/workflows/github-actions.yml deleted file mode 100644 index 1a762ba..0000000 --- a/.github/workflows/github-actions.yml +++ /dev/null @@ -1,284 +0,0 @@ -name: pipeline - -on: - push: - pull_request: - -env: - PYTHON_IMAGE: 3.9 - DOCKER_IMAGE: docker:20.10.23 - PYTHON_PACKAGE_NAME: deker - DOCKER_REG_IMAGE: ${{ secrets.CI_REGISTRY_IMAGE }} - -jobs: - setup: - runs-on: ubuntu-latest - timeout-minutes: 60 - - steps: - - name: Checkout code - uses: actions/checkout@v2 - - - name: Set up Python - uses: actions/setup-python@v3 - with: - python-version: ${{ env.PYTHON_IMAGE }} - - - name: Install dependencies - run: | - pip install --upgrade pip - pip install virtualenv - virtualenv venv - source venv/bin/activate - pip install -r requirements.txt - pip install -r requirements_dev.txt - pip list - - - name: Cache virtual environment - uses: actions/cache@v2 - with: - path: venv - key: ${{ runner.os }}-venv-${{ env.PYTHON_IMAGE }}-${{ hashFiles('requirements.txt', 'requirements_dev.txt') }} - - linters: - needs: setup - runs-on: ubuntu-latest - - steps: - - name: Checkout code - uses: actions/checkout@v2 - - - name: Set up Python - uses: actions/setup-python@v3 - with: - python-version: ${{ env.PYTHON_IMAGE }} - - - name: Load virtual environment - uses: actions/cache@v2 - with: - path: venv - key: ${{ runner.os }}-venv-${{ env.PYTHON_IMAGE }}-${{ hashFiles('requirements.txt', 'requirements_dev.txt') }} - - - name: Run linters and checks - run: | - source venv/bin/activate - isort ./${{ env.PYTHON_PACKAGE_NAME }} - black ./${{ env.PYTHON_PACKAGE_NAME }} - flake8 ./${{ env.PYTHON_PACKAGE_NAME }} - mypy ./${{ env.PYTHON_PACKAGE_NAME }} --install-types --non-interactive --config-file pyproject.toml - doc8 ./docs - env: - PIP_DISABLE_PIP_VERSION_CHECK: 1 - - - name: Save linter reports - if: always() - uses: actions/upload-artifact@v2 - with: - name: linter-reports - path: report.xml - - tests: - needs: setup - runs-on: ubuntu-latest - if: ${{ !startsWith(github.ref, 'refs/tags/v') }} - steps: - - name: Checkout code - uses: actions/checkout@v2 - - - name: Set up Python - uses: actions/setup-python@v2 - with: - python-version: ${{ env.PYTHON_IMAGE }} - - - name: Load virtual environment - uses: actions/cache@v2 - with: - path: venv - key: ${{ runner.os }}-venv-${{ env.PYTHON_IMAGE }}-${{ hashFiles('requirements.txt', 'requirements_dev.txt') }} - - - name: Run shuffled tests - run: | - source venv/bin/activate - pytest --random-order --junitxml=tests.xml - env: - PIP_DISABLE_PIP_VERSION_CHECK: 1 - - - name: Save test reports - if: always() - uses: actions/upload-artifact@v2 - with: - name: test-reports - path: tests.xml - - coverage: - needs: setup - runs-on: ubuntu-latest - if: ${{ !startsWith(github.ref, 'refs/tags/v') }} - steps: - - name: Checkout code - uses: actions/checkout@v2 - - - name: Set up Python - uses: actions/setup-python@v2 - with: - python-version: ${{ env.PYTHON_IMAGE }} - - - name: Load virtual environment - uses: actions/cache@v2 - with: - path: venv - key: ${{ runner.os }}-venv-${{ env.PYTHON_IMAGE }}-${{ hashFiles('requirements.txt', 'requirements_dev.txt') }} - - - name: Run coverage - run: | - source venv/bin/activate - coverage run -m pytest --junitxml=report.xml - coverage report - coverage xml - env: - PIP_DISABLE_PIP_VERSION_CHECK: 1 - - - name: Save coverage reports - if: always() - uses: actions/upload-artifact@v2 - with: - name: coverage-reports - path: coverage.xml - - tox_tests: - needs: setup - runs-on: ubuntu-latest - if: startsWith(github.ref, 'refs/tags/v') - container: - image: ghcr.io/openweathermap/deker/deker-embedded/tox:latest - env: - PACKAGE_VERSION: ${{ github.REF_NAME }} - PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/ - credentials: - username: ${{ github.actor }} - password: ${{ secrets.GITHUB_TOKEN }} - steps: - - name: Set python versions - run: pyenv global 3.9 3.10 3.11 - - - name: Checkout code - uses: actions/checkout@v2 - - name: Install tox - run: | - env - pip install tox - env: - PIP_DISABLE_PIP_VERSION_CHECK: 1 - PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/ - - name: Run tox tests - run: | - env - tox - env: - PIP_DISABLE_PIP_VERSION_CHECK: 1 - PACKAGE_VERSION: ${{ github.REF_NAME }} - PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/ - - build_wheels: - name: Build wheels on ${{ matrix.os }} - needs: tox_tests - if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v') - runs-on: ${{ matrix.os }} - strategy: - matrix: - os: [ubuntu-22.04] - - steps: - - uses: actions/checkout@v3 - - - name: Build wheels - run: | - pip wheel -w ./wheelhouse . - - - build_sdist: - needs: tox_tests - name: Build source distribution - if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v') - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - - name: Build sdist - run: pipx run build --sdist - - - uses: actions/upload-artifact@v3 - with: - path: dist/*.tar.gz - - build_docs: - needs: setup - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - name: Load virtual environment - uses: actions/cache@v2 - with: - path: venv - key: ${{ runner.os }}-venv-${{ env.PYTHON_IMAGE }}-${{ hashFiles('requirements.txt', 'requirements_dev.txt') }} - - name: Make Sphinx docs - run: | - source venv/bin/activate - cd ./docs - make html - ls -la _build/html - - name: Upload artifact - uses: actions/upload-pages-artifact@v2 - with: - path: docs/_build/html - - publish_docs: - needs: build_docs - if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v') - runs-on: ubuntu-latest - permissions: - contents: read - pages: write - id-token: write - concurrency: - group: "pages" - cancel-in-progress: false - environment: - name: github-pages - url: ${{ steps.deployment.outputs.page_url }} - steps: - - name: Deploy to GitHub Pages - uses: actions/deploy-pages@v2 - with: - github_token: ${{ secrets.GITHUB_TOKEN }} - branch: gh-pages - force: true - directory: docs/_build/html - - upload_pypi: - needs: [build_wheels, build_sdist] - runs-on: ubuntu-latest - permissions: - id-token: write - if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v') - environment: - # TODO: next is for prod pypi; comment for tests -# name: pypi -# url: https://pypi.org/p/deker - # TODO: next is for test pypi; comment for prod - name: testpypi - url: https://test.pypi.org/p/deker - - steps: - - uses: actions/download-artifact@v3 - with: - # unpacks default artifact into dist/ - # if `name: artifact` is omitted, the action will create extra parent dir - name: artifact - path: dist - - - name: Publish package distributions to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 - # TODO: next is for test pypi; comment for prod - with: - repository-url: https://test.pypi.org/legacy/ diff --git a/.github/workflows/on_push.yml b/.github/workflows/on_push.yml new file mode 100644 index 0000000..71bf041 --- /dev/null +++ b/.github/workflows/on_push.yml @@ -0,0 +1,14 @@ +name: push + +on: + push: + branches-ignore: + - 'refs/tags/v' + +jobs: + checks: + uses: openweathermap/deker-actions/.github/workflows/checks.yml@master + with: + package-name: ${{ vars.PACKAGE_NAME }} + python-version: '3.9' + min-coverage: 96 diff --git a/.github/workflows/on_release.yml b/.github/workflows/on_release.yml new file mode 100644 index 0000000..5efecad --- /dev/null +++ b/.github/workflows/on_release.yml @@ -0,0 +1,49 @@ +name: build + +on: + push: + tags: + - 'v[1-9]+.[0-9]+.[0-9]+' + +jobs: + tox_tests: + uses: openweathermap/deker-actions/.github/workflows/tox.yml@master + with: + package-name: ${{ vars.PACKAGE_NAME }} + min-coverage: 96 + + build_docs: + needs: tox_tests + uses: openweathermap/deker-actions/.github/workflows/docs_build.yml@master + with: + python-version: '3.9' + + build_sdist: + needs: [tox_tests, build_docs] + name: Build source distribution + uses: openweathermap/deker-actions/.github/workflows/build.yml@master + + publish_docs: + needs: [build_docs, build_sdist] + uses: openweathermap/deker-actions/.github/workflows/docs_publish.yml@master + + upload_pypi: + name: Publish source distribution + needs: [build_docs, build_sdist] + runs-on: ubuntu-latest + permissions: + id-token: write + environment: + name: pypi + url: https://pypi.org/p/${{ vars.PACKAGE_NAME }} + + steps: + - uses: actions/download-artifact@v3 + with: + # unpacks default artifact into dist/ + # if `name: artifact` is omitted, the action will create extra parent dir + name: artifact + path: dist + + - name: Publish package distributions to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.github/workflows/on_test_release.yml b/.github/workflows/on_test_release.yml new file mode 100644 index 0000000..7472e6c --- /dev/null +++ b/.github/workflows/on_test_release.yml @@ -0,0 +1,34 @@ +name: test-build + +on: + push: + tags-ignore: + - 'v[1-9]+.[0-9]+.[0-9]+' + +jobs: + build_sdist: + name: Build test source distribution + uses: openweathermap/deker-actions/.github/workflows/build.yml@master + + upload_test_pypi: + name: Upload test source distribution + needs: build_sdist + runs-on: ubuntu-latest + permissions: + id-token: write + environment: + name: testpypi + url: https://test.pypi.org/p/${{ vars.PACKAGE_NAME }} + + steps: + - uses: actions/download-artifact@v3 + with: + # unpacks default artifact into dist/ + # if `name: artifact` is omitted, the action will create extra parent dir + name: artifact + path: dist + + - name: Publish test source distributions to Test-PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + with: + repository-url: https://test.pypi.org/legacy/ diff --git a/.gitignore b/.gitignore index 446900c..fe7f5b1 100644 --- a/.gitignore +++ b/.gitignore @@ -151,7 +151,6 @@ deker/tmp.py tmp.py tmp/ .DS_Store -.python-version build .ruff_cache/ -dist/ \ No newline at end of file +dist/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 51cf050..c2a1c40 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -96,9 +96,10 @@ repos: name: flake8 files: ^deker/ always_run: false - args: [ --config, setup.cfg, deker] + args: [ deker] verbose: true additional_dependencies: + - Flake8-pyproject - flake8-bugbear - flake8-pytest-style - flake8-docstrings @@ -150,3 +151,11 @@ repos: always_run: true stages: - push + + - id: doc8 + name: doc8 + entry: doc8 --config=pyproject.toml docs/deker + language: python + always_run: true + stages: + - commit diff --git a/CNAME b/CNAME index 23dfcfd..dac007c 100644 --- a/CNAME +++ b/CNAME @@ -1 +1 @@ -docs.deker.io \ No newline at end of file +docs.deker.io diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index f9bd145..0000000 --- a/MANIFEST.in +++ /dev/null @@ -1 +0,0 @@ -include requirements.txt diff --git a/README.md b/README.md index 7cbc74c..86ccedb 100644 --- a/README.md +++ b/README.md @@ -1,136 +1,89 @@ # Deker -![image](docs/deker/images/logo_50.png) - -[![made-with-python](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org/) -[![made-with-sphinx-doc](https://img.shields.io/badge/Made%20with-Sphinx-1f425f.svg)](https://www.sphinx-doc.org/) -[![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square)](http://makeapullrequest.com) -[![PyPI pyversions](https://img.shields.io/pypi/pyversions/deker.svg)](https://pypi.python.org/pypi/deker/) -[![PyPI version shields.io](https://img.shields.io/pypi/v/deker.svg)](https://pypi.python.org/pypi/deker/) -[![GitHub license](https://badgen.net/github/license/openweathermap/deker)](https://github.com/openweathermap/deker/blob/main/LICENSE) -[![pipeline](https://github.com/openweathermap/deker/actions/workflows/github-actions.yml/badge.svg)](https://github.com/openweathermap/deker/actions/workflows/github-actions.yml) -[![docs](https://github.com/openweathermap/deker/actions/workflows/docs.yml/badge.svg)](https://github.com/openweathermap/deker/actions/workflows/docs.yml) +![image](docs/deker/images/logo_50.png) -**Deker** - is a pure-Python NoSQL database framework, which provides storing multidimensional spatial raster -numeric data and its further simple, fast and comfortable accessing and managing. +[![PyPI version shields.io](https://img.shields.io/pypi/v/deker.svg?color=0)](https://pypi.python.org/pypi/deker/) +[![PyPI pyversions](https://img.shields.io/pypi/pyversions/deker.svg)](https://pypi.python.org/pypi/deker/) +[![GitHub license](https://badgen.net/github/license/openweathermap/deker)](https://github.com/openweathermap/deker/blob/main/LICENSE) +[![codecov](https://codecov.io/gh/openweathermap/deker/branch/main/graph/badge.svg?token=Z040BQWIOR)](https://codecov.io/gh/openweathermap/deker) +[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) -It perfectly fits for a vast variety of data: +Deker is pure Python implementation of petabyte-scale highly parallel data storage engine for +multidimensional arrays. -- geospatial data (cartography, geodesy, meteorology, …, even outer space), -- images, -- video, -- audio, -- biomedicine, -- genomics, -- finance, -- ML, -- ... +Deker name comes from term *dekeract*, the [10-cube](https://en.wikipedia.org/wiki/10-cube). -and many others – everything that may be represented and stored as a pack of numbers. +Deker was made with the following major goals in mind: -Deker is not really limited by a number of dimensions – it’s up to you to decide how complicated your structures -shall be and how many dimensions you use _(our current goal is 5, at the moment)_. +* provide intuitive interface for storing and accessing **huge data arrays** +* support **arbitrary number of data dimensions** +* be **thread and process safe** and as **lean on RAM** use as possible -Actually, it is a scalable high-level wrapper over different file formats. -At the moment Deker supports just ``HDF5``, but we’ll be glad to accept PRs with new storage adapters: - ``TIFF``, ``NetCDF``, ``ZARR``, … Any format you like and need, even ``JSON`` or ``TXT``. +Deker empowers users to store and access a wide range of data types, virtually anything that can be +represented as arrays, like **geospacial data**, **satellite images**, **machine learning models**, +**sensors data**, graphs, key-value pairs, tabular data, and more. -Deker uses [NumPy](https://numpy.org/doc/stable/) structures and provides an additional support for -[Xarray](https://docs.xarray.dev/en/stable/), [pandas](https://pandas.pydata.org/docs/) and others. +Deker does not limit your data complexity and size: it supports virtually unlimited number of data +dimensions and provides under the hood mechanisms to **partition** huge amounts of data for +**scalability**. -## Documentation -📖 Check out our [documentation](https://docs.deker.io) for more details! +## Features -## Installation +* **Open source** under GPL 3.0 +* Scalabale storage of huge virtual arrays via **tiling** +* **Parallel processing** of virtual array tiles +* Own **locking** mechanism enabling virtual arrays parallel read and write +* Array level **metadata attributes** +* **Fancy data slicing** using timestamps and named labels +* Support for industry standard [NumPy](https://numpy.org/doc/stable/), [Xarray](https://docs.xarray.dev/en/stable/) +* Storage level data **compression and chunking** (via HDF5) -### Required dependencies +## Code and Documentation - python >= 3.9 +Open source implementation of Deker storage engine is published at -Deker dependencies are external: +* https://github.com/openweathermap/deker -- numpy>=1.18 -- attrs>=23.1.0 -- tqdm>=4.64.1 -- psutil>=5.9.5 +API documentation and tutorials for the current release could be found at -and internal: +* https://docs.deker.io -- deker-tools -- deker-local-adapters - * h5py>=3.8.0 - * hdf5plugin>=4.0.1 +## Quick Start -Deker comes with the above mentioned dependencies out of the box: - ```bash - pip install deker - ``` - -or: - ```bash - python -m pip install deker - ``` +### Dependencies -Extra dependencies ------------------- -- xarray>=2023.5.0 +Minimal Python version for Deker is 3.9. -If you wish to convert your data into Xarray -([xarray installation options](https://docs.xarray.dev/en/stable/getting-started-guide/installing.html)) or pandas -*(or even some other)* objects: +Deker depends on the following third-party packages: -```bash -pip install deker[xarray] -``` +* `numpy` >= 1.18 +* `attrs` >= 23.1.0 +* `tqdm` >= 4.64.1 +* `psutil` >= 5.9.5 +* `h5py` >= 3.8.0 +* `hdf5plugin` >= 4.0.1 -or +Also please not that for flexibility few internal Deker components are published as separate +packages: -```bash -python -m pip install deker[xarray] -``` +* [`deker-local-adapters`](https://github.com/openweathermap/deker-local-adapters) +* [`deker-server-adapters`](https://github.com/openweathermap/deker-server-adapters) +* [`deker-tools`](https://github.com/openweathermap/deker-tools) -Or you can install them separately:: -``` -pip install deker -pip install xarray -``` -or -```bash -python -m pip install deker -python -m pip install xarray -``` -### ARM architecture family -Deker uses NumPy, and some NumPy types are unsupported on current NumPy ARM version. -If you want to run Deker library on your Mac with M1+ chip inside, you need to install **python x86_64** with -[Rosetta](https://support.apple.com/en-us/HT211861). +### Install -Use this [guide](https://towardsdatascience.com/how-to-use-manage-multiple-python-versions-on-an-apple-silicon-m1-mac-d69ee6ed0250) -or follow next steps: +To install Deker run: -1. Install Rosetta (ARM -> x86_64 translator): ```bash - softwareupdate --install-rosetta + pip install deker ``` -2. Create a Rosetta terminal: - 2.1. Duplicate your terminal (`apps -> utilities -> right click -> duplicate`) or `install new`. - 2.2. Click `Get info` on new terminal and set `Open using Rosetta` +Please refer to documentation for advanced topics such as running on Apple silicone or using Xarray +with Deker API. -3. Install homebrew: - ```bash - /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" - ``` -4. Add alias to your `zsh` config file: - ```bash - alias rbrew="arch -x86_64 /usr/local/bin/brew" - ``` -5. Install python: - ```bash - rbrew install python@3.10 - ``` +### First Steps -After that you can install Deker run `pip install deker` +Now you can write simple script to jump into Deker development: -## Usage ```python from deker import Client, ArraySchema, DimensionSchema, TimeDimensionSchema from datetime import datetime, timedelta, timezone @@ -139,7 +92,7 @@ import numpy as np # Where all data will be kept DEKER_URI = "file:///tmp/deker" -# Define dimension schemas +# Define 3-dimensional schema with to numeric and one time dimension dimensions = [ DimensionSchema(name="y", size=128), DimensionSchema(name="x", size=128), @@ -151,20 +104,20 @@ dimensions = [ ) ] -# Define array schema with dtype and dimensions +# Define array schema with float dtype and dimensions array_schema = ArraySchema(dtype=float, dimensions=dimensions) # Instantiate client using context manager with Client(DEKER_URI) as client: # Create collection - collection = client.create_collection("FIRST COLLECTION", array_schema) + collection = client.create_collection("my_collection", array_schema) - # Create array (You can pass primary and/or custom attributes defined in schema here) + # Create array array = collection.create() - # Write data + # Write some data array[:].update(np.ones(shape=array.shape)) - # Read data + # And read the data back data = array[:].read() ``` diff --git a/doc8.ini b/doc8.ini deleted file mode 100644 index 101ec30..0000000 --- a/doc8.ini +++ /dev/null @@ -1,3 +0,0 @@ -[doc8] - -max-line-length=99 diff --git a/docs/conf.py b/docs/conf.py index 9493b78..99b6144 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -10,10 +10,6 @@ import sys -project = "Deker" -copyright = "2023, OpenWeather" -author = "OpenWeather" - # Add support for auto-doc # Ensure that sanic is present in the path, to allow sphinx-apidoc to @@ -22,6 +18,18 @@ sys.path.insert(0, os.path.abspath("..")) +project = "Deker" +copyright = "2023, OpenWeather" +author = "OpenWeather" +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +version = os.getenv("GITHUB_REF_NAME") if os.getenv("GITHUB_REF_TYPE", "") == "tag" else "latest" +# The full version, including alpha/beta/rc tags. +release = version + # -- General configuration ------------------------------------------------ extensions = [ @@ -39,18 +47,6 @@ # The master toctree document. master_doc = "index" -# web page tab logo -# html_logo = "deker/images/logo.png" - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# The short X.Y version. -version = "v1.0.0" -# The full version, including alpha/beta/rc tags. -release = version - # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # This is also used if you do content translation via gettext catalogs. @@ -77,14 +73,10 @@ # a list of builtin themes. html_theme = "sphinx_rtd_theme" html_theme_options = { - # "analytics_id": "G-XXXXXXXXXX", # Provided by Google in your dashboard - # "analytics_anonymize_ip": False, - # "logo_only": False, "display_version": True, "prev_next_buttons_location": "bottom", "style_external_links": True, "vcs_pageview_mode": "", - # "style_nav_header_background": "light-blue", # Toc options "collapse_navigation": False, "sticky_navigation": True, @@ -92,25 +84,23 @@ "includehidden": True, "titles_only": False, } + # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". # html_static_path = ["_static"] # html_css_files = ["custom.css"] + # -- Options for HTMLHelp output ------------------------------------------ # Output file base name for HTML help builder. -htmlhelp_basename = "Dekerdoc" +htmlhelp_basename = "deker-doc" # -- Custom Settings ------------------------------------------------------- suppress_warnings = ["image.nonlocal_uri"] - autodoc_typehints = "description" autodoc_default_options = { "member-order": "groupwise", } -# intersphinx_mapping = { -# "deker": ("http://de1.owm.io:10002", None), -# } diff --git a/docs/deker/collection_schema.rst b/docs/deker/collection_schema.rst index 7cc9534..00bed2f 100755 --- a/docs/deker/collection_schema.rst +++ b/docs/deker/collection_schema.rst @@ -578,19 +578,42 @@ And schema of ``Collection`` of ``VArray``:: VArray Grid ~~~~~~~~~~~ +.. note:: ``arrays_shape`` parameter added in v1.1.0 + Perhaps it is one of the most obscure issues. ``VArray`` shall be split into files, but it cannot decide itself how it shall be done. It's up to you, how you are going to split your data. +There are two ways: ``vgrid`` and ``arrays_shape`` parameters. You can choose any of them, +but not both. Any of these parameters shall be defined as a tuple of integers which quantity +shall be exactly similar to the quantity of the dimensions and its values shall divide ``VArray`` +shape without remainders. + +Our schema has two dimensions with sizes ``100`` and ``200`` correspondingly, what tells us +that the ``VArray`` shape will be ``(100, 200)``. We shall split it either by ``vgrid`` or +with ``arrays_shape``. + +``vgrid`` ++++++++++ + +Let's set ``vgrid`` as ``(50, 20)``. + +.. code-block:: python -``vgrid`` parameter shall be defined as a tuple of integers which quantity shall be exactly similar -to the quantity of the dimensions. Its values shall divide ``VArray`` shape without remainders. + from deker import VArraySchema -Our schema has two dimensions with sizes ``100`` and ``200`` correspondingly, what tells us that -the ``VArray`` shape will be ``(100, 200)``. And we set ``vgrid`` as ``(50, 20)``. What shall -happen? No magic, just a simple math:: + varray_schema = VArraySchema( + dimensions=dimensions, + dtype=np.int64, + fill_value=-99999, + vgrid=(50, 20) + # attributes are not passed as they are optional + ) + +What shall happen? No magic, just a simple math:: (100, 200) / (50, 20) = (2.0, 10.0) -``(2, 10)`` - that will be the shape of all the ``Array``, produced by the ``VArray``. +``(2, 10)`` - that will be the shape of all the ``Array``, produced by the ``VArray``, or the +``arrays_shape``. If we do not want to divide any dimension into pieces and want to keep it in full size in all the ``Array``, we shall pass ``1`` in ``vgrid`` for that dimension:: @@ -600,8 +623,42 @@ If we do not want to divide any dimension into pieces and want to keep it in ful Thus, the first dimension will retain its initial size for all the arrays, and their shape will be ``(100, 10)``. -OK! Now we are finally ready to create our first database and we need ``Client``. +If the ``vgrid`` setting is correct, it will be saved to the collection metadata and applied every +time to all new ``VArrays``. + +``arrays_shape`` ++++++++++++++++++ +`(added in v1.1.0)` + +Sometimes it is easier to decide on the shape of the final ``Arrays`` than on a ``vgrid``. +In this case you can use ``arrays_shape`` parameter. + +.. code-block:: python + from deker import VArraySchema + + varray_schema = VArraySchema( + dimensions=dimensions, + dtype=np.int64, + fill_value=-99999, + arrays_shape=(2, 10) + # attributes are not passed as they are optional + ) + +By providing this parameter you manually set the shape of each inner ``Array`` to the +passed value and produce the ``vgrid`` of your ``VArrays``. + +The ``VArray's`` shape will be divided by this setting:: + + (100, 200) / (2, 10) = (50.0, 20.0) + +``(50, 20)`` - that will be the ``vgrid`` of the ``VArray``. + +If you use ``arrays_shape`` for defining a ``VArraySchema``, not the passed setting, but the +calculated ``vgrid`` will be saved to the collection metadata. On each collection +invocation ``arrays_shape`` is calculated from the ``vgrid`` value restored from the metadata. + +OK! Now we are finally ready to create our first database and we need ``Client``. Creating Collection =================== @@ -733,4 +790,3 @@ Now there is a new path ``/tmp/deker/collections/weather`` on your local drive w store the data relative to the ``Collection`` named ``weather``. Each ``Array`` will contain a pack of daily 24-hours weather data for each entire latitude and longitude degree: ``temperature``, ``humidity``, ``pressure`` and ``wind_speed``. - diff --git a/docs/deker/connecting_to_server.rst b/docs/deker/connecting_to_server.rst new file mode 100644 index 0000000..04ea105 --- /dev/null +++ b/docs/deker/connecting_to_server.rst @@ -0,0 +1,116 @@ +******************** +Connecting to Server +******************** + +.. _OpenWeather: https://openweathermap.org +.. _Installation page: installation.html + +To access remotely the data stored on OpenWeather_ managed Deker server infrastructure, you need +to use server adapters. + +It is an original OpenWeather plugin, based on `httpx `_ +with HTTP 2.0 support, that allows your local client to communicate with remote OpenWeather +public server instances of Deker. + +Deker will automatically find and initialize this plugin if it is installed in current environment. + +.. attention:: + You must install ``deker-server-adapters`` package , for details refer to the `Installation page`_ + + +Usage +========= +To use server version, you have to initialize Deker's Client with an uri which contains +``http/https`` scheme. + +.. code-block:: python + + from deker import Client + client = Client("http://{url-to-deker-server}") # As simple as that + +And now the client will communicate with Deker server. + +If authentication is enabled on the Deker server, you can provide credentials by adding it +to the url like this: + +.. code-block:: python + + from deker import client + client = Client("https://{username}:{password}@{url-to-deker-server}") + +Configuration +============= +Server adapters use ``httpx client`` under the hood. You can configure its behaviour by passing +keyword arguments to the ``httpx_conf`` parameter of the Deker's Client: + +.. code-block:: python + + import httpx + from deker import Client + + limits = httpx.Limits(max_keepalive_connections=5, max_connections=10) + client = Client( + "http://{url-to-deker-server}", + httpx_conf={'http2': False, 'timeout': 10, 'limits': limits} + ) + +By default, adapters' ``httpx client`` has following settings: + +.. list-table:: + :header-rows: 1 + + * - Key + - Type + - Default Value + * - verify + - bool + - True + * - http2 + - bool + - True + * - timeout + - Optional[float] + - None + +The full list of ``httpx`` configuration parameters you can find at `the official website`_. + +.. _the official website: https://www.python-httpx.org/api/#client + +Errors +========= + +.. py:exception:: DekerServerError(response: Response, message: str) + + Bases: :class:`DekerBaseApplicationError` + + Server error, which is raised on any non-specific occasion (like 5xx status from server) + + :param response: Httpx Response + :param message: Message of exception + +.. py:exception:: DekerTimeoutServer + + Bases: :class:`DekerServerError` + + This exception is raised on any timeout (Httpx's Timeout exception or 504 status) + +.. py:exception:: DekerBaseRateLimitError(message: str, limit: Optional[int], remaining: Optional[int], reset: Optional[int]) + + Bases: :class:`DekerBaseApplicationError` + + :param message: Exception message + :param limit: Requests per second limit for the user + :param remaining: How many requests per second are left + :param reset: When limits will be reset + +.. py:exception:: DekerRateLimitError + + Bases: :class:`DekerBaseRateLimitError` + + If user's rate limit is exceeded + +.. py:exception:: DekerDataPointsLimitError + + Bases: :class:`DekerBaseRateLimitError` + + If requested subset exceeds quota diff --git a/docs/deker/installation.rst b/docs/deker/installation.rst index dd1634c..7141f92 100755 --- a/docs/deker/installation.rst +++ b/docs/deker/installation.rst @@ -40,9 +40,12 @@ Also please not that for flexibility few internal Deker components are published packages: * ``deker-local-adapters`` + * ``deker-server-adapters`` * ``deker-tools`` -To install Deker with all the previously mentioned dependencies, run:: +To install Deker run: + +.. code-block:: bash pip install deker @@ -50,38 +53,77 @@ To install Deker with all the previously mentioned dependencies, run:: Optional Packages ----------------- -Deker also supports output of its data as pandas_ or Xarray_ via the following package: +Deker also supports output of its data as Xarray_ via the following package: * ``xarray`` >= 2023.5.0 -To install it with ``xarray`` optional dependency:: +To install it with ``xarray`` optional dependency: + +.. code-block:: bash pip install deker[xarray] .. _Xarray: https://docs.xarray.dev/en/stable/getting-started-guide/installing.html -.. _pandas: https://pandas.pydata.org/getting_started.html + +Deker Tools +=========== + +``deker-tools`` is an out-of-box battery which provides several useful tools and utilities to work +with Deker data. You may find this package useful in your projects, even if they are not related to +Deker. + +To install Deker tools package, run: + +.. code-block:: bash + + pip install deker-tools Interactive Shell ================= ``deker-shell`` is an interactive environment that enables you to manage and access Deker storage -in a convenient way. It requires ``deker`` package to be installed manually before use as described -above. +in a convenient way. It requires ``deker`` package to be installed **manually** before use as +described above. -To install interactive shell package:: +To install interactive shell package, run: - pip install deker deker-shell +.. code-block:: bash + pip install deker deker-shell -Deker Tools -=========== +Or you can install it alongside with Deker by: + +.. code-block:: bash + + pip install deker[shell] + + +Server Adapters +=============== +.. _plugin: connecting_to_server.html + +It is an original OpenWeather plugin_, based on `httpx `_ +with HTTP 2.0 support, that allows your local client to communicate with remote OpenWeather +public server instances of Deker. + +If you don't have Deker yet, run + +.. code-block:: bash + + pip install deker[server-adapters] + +If you have already installed Deker, you can simply install plugin to use it by: + +.. code-block:: bash + + pip install deker-server-adapters -``deker-tools`` is an out-of-box battery which provides several useful tools and utilities to work -with Deker data. You may find this package useful in projects, even if they are not related to -Deker. -To install Deker tools package:: +Install All at Once +================================= +You can install all the above mentioned options at once by: - pip install deker-tools +.. code-block:: bash + pip install deker[all] diff --git a/docs/deker/shell.rst b/docs/deker/shell.rst index 60c4513..bce5989 100644 --- a/docs/deker/shell.rst +++ b/docs/deker/shell.rst @@ -91,4 +91,3 @@ Functions * ``use("collection_name")``: gets collection from client and saves it to ``collection`` variable * ``get_global_coll_variable()``: returns ``collection`` global variable - diff --git a/docs/deker/tools.rst b/docs/deker/tools.rst index 7730bfd..42866b9 100644 --- a/docs/deker/tools.rst +++ b/docs/deker/tools.rst @@ -6,7 +6,7 @@ Deker Tools is a collection of utility functions and classes designed to assist processing tasks. It consists of modules that handle data conversion, path validation, and slice manipulation. -.. attention:: This package is not considered to be part of Deker public API nad could significantly +.. attention:: This package is not considered to be part of Deker public API and can be significantly changed in future versions. For details please refer to the `Deker Tools`_ API documentation. @@ -68,4 +68,3 @@ default:: >>> get_utc(datetime.now()) 2023-07-26 15:42:05.539317+00:00 - diff --git a/docs/index.rst b/docs/index.rst index 7c889c5..6161289 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -8,6 +8,8 @@ Fine Tuning Interactive Shell Deker Tools + Connecting to Server + .. toctree:: :hidden: @@ -63,11 +65,10 @@ Features * Own **locking** mechanism enabling arrays parallel read and write * Array level **metadata attributes** * **Fancy data slicing** using timestamps and named labels -* Support for industry standard NumPy_, pandas_ and Xarray_ +* Support for industry standard NumPy_ and Xarray_ * Storage level data **compression and chunking** (via HDF5) .. _NumPy: https://numpy.org/doc/stable/ -.. _pandas: https://pandas.pydata.org/docs/ .. _Xarray: https://docs.xarray.dev/en/stable/ @@ -81,4 +82,3 @@ Open source implementation of Deker storage engine is published at API documentation and tutorials for 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"nc-time-axis", "netCDF4", "numbagg", "pooch", "pydap", "scanpydoc", "scipy", "seaborn", "sphinx-autosummary-accessors", "sphinx-rtd-theme", "zarr"] +io = ["cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap", "scipy", "zarr"] +parallel = ["dask[complete]"] +viz = ["matplotlib", "nc-time-axis", "seaborn"] + +[[package]] +name = "zipp" +version = "3.16.2" +description = "Backport of pathlib-compatible object wrapper for zip files" +optional = false +python-versions = ">=3.8" +files = [ + {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"}, + {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"}, +] + +[package.extras] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] + +[extras] +all = ["deker-server-adapters", "deker-shell", "xarray"] +server-adapters = ["deker-server-adapters"] +shell = ["deker-shell"] +xarray = ["xarray"] + +[metadata] +lock-version = "2.0" +python-versions = "^3.9" +content-hash = "c6e89a1f69e312422c8099412c661af19d485b9249877824c4b0dc3057503011" diff --git a/pyproject.toml b/pyproject.toml index 9310aae..86ef1ef 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,18 +1,143 @@ -# https://black.readthedocs.io/en/stable/ -[tool.black] -line-length = 100 + ############### + ### PROJECT ### + ############### + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" + +[tool.poetry] +version = "0.0.0" # a placeholder for poetry CI dynamic versionning plugin +name = "deker" +packages = [{ include = "deker" }] +description = "Multidimensional arrays storage engine" +authors = ["OpenWeather "] +license = "GPL-3.0-only" +readme = "README.md" +documentation = 'https://docs.deker.io/' +homepage = 'https://deker.io/' +repository = 'https://github.com/openweathermap/deker' +classifiers = [ + "Development Status :: 4 - Beta", + "Intended Audience :: Developers", + "Intended Audience :: Information Technology", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", + "Topic :: Software Development :: Libraries :: Python Modules", + "Operating System :: Unix", + "Operating System :: POSIX :: Linux", + "Operating System :: MacOS :: MacOS X", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", +] + +[tool.poetry.extras] +xarray = ["xarray"] +server-adapters = ["deker-server-adapters"] +shell = ["deker-shell"] +all = ["deker-shell", "deker-server-adapters", "xarray"] + +[tool.poetry-dynamic-versioning] +vcs = "git" +style = "semver" +metadata = false + +[[tool.poetry.source]] +name = "PyPI" +priority = "primary" + +[[tool.poetry.source]] +name = "testpypi" +url = "https://test.pypi.org/simple/" +priority = "supplemental" + + +[tool.poetry.dependencies] +python = "^3.9" +numpy = "^1.18" +attrs = "^23.1.0" +typing-extensions = "^4.4.0" +tqdm = "^4.64.1" +psutil = "^5.9.5" +deker-local-adapters = "1.0.1" +deker-server-adapters = {version = "^1.0.0", optional = true} +deker-shell = { version = "^1.0.0", optional = true } +xarray = {version = "^2023.5.0", optional = true} + +[tool.poetry.group.dev.dependencies] +black = "23.1.0" +coverage = "7.1.0" +darglint = "1.8.1" +Flake8-pyproject = "1.2.3" +flake8 = "5.0.4" +flake8-bugbear = "23.1.20" +flake8-docstrings = "1.7.0" +flake8-import-order = "0.18.2" +flake8-pytest-style = "1.7.0" +isort = "5.12.0" +mypy = "1.0.0" +mypy-extensions = "1.0.0" +pep8-naming = "0.13.3" +pre-commit = "3.0.4" +pycln = "2.1.3" +pytest = "7.2.1" +pytest-cov = "4.0.0" +pytest-sugar = "0.9.6" +pytest-random-order = "1.1.0" +ssort = "0.11.6" +deepdiff = "6.3.0" +pytest-mock = "3.10.0" +bandit = "1.7.5" +xarray = "^2023.5.0" + + +[tool.poetry.group.docs.dependencies] +docutils = "0.17" +m2r2 = "0.3.2" +sphinx-rtd-theme = "1.2.2" +enum_tools = "0.10.0" +sphinx_toolbox = "3.5.0" +doc8 = "0.11.2" + + ############# + ### TOOLS ### + ############# + + ############## + # FORMATTERS # + ############## + +[tool.black] # code formatter target-version = ['py39'] -include = '\.pyi?$' -extend-exclude = ''' -# A regex preceded with ^/ will apply only to files and ctx -# in the root of the project. -^/foo.py # exclude a file named foo.py in the root of the project (in addition to the defaults) -examples/ -''' +line-length = 100 +[tool.isort] # imports sorter +# https://pycqa.github.io/isort/ +py_version = 39 +sections = ['FUTURE', 'STDLIB', 'THIRDPARTY', 'FIRSTPARTY', 'LOCALFOLDER'] +profile = "black" +atomic = true +include_trailing_comma = true +line_length = 100 +lines_after_imports = 2 +lines_between_types = 1 +multi_line_output = 3 +extend_skip = [".md", ".json"] +known_local_folder = ["deker"] +known_third_party = ["deker_tools"] +extra_standard_library = ["zoneinfo"] +use_parentheses = true + + ########### + # LINTERS # + ########### + +[tool.mypy] # code linter # https://mypy.readthedocs.io/en/stable/ # https://pypi.org/project/mypy-extensions/ -[tool.mypy] python_version = "3.9" ignore_missing_imports = true scripts_are_modules = true @@ -29,6 +154,7 @@ exclude = [ '^setup\.py$', '^tmp\.py$', '^venv/', + '^.venv/', '^test+\.py$', '^conftest\.py$', '^tmp/', @@ -40,34 +166,89 @@ disable_error_code = "misc,no-redef,override,union-attr,index,assignment" module = "tests/*" disallow_untyped_defs = false -# https://pycqa.github.io/isort/ -[tool.isort] -py_version = 39 -sections = ['FUTURE', 'STDLIB', 'THIRDPARTY', 'FIRSTPARTY', 'LOCALFOLDER'] -profile = "black" -atomic = true -include_trailing_comma = true -line_length = 100 -lines_after_imports = 2 -lines_between_types = 1 -multi_line_output = 3 -extend_skip = [".md", ".json"] -known_local_folder = ["deker"] -known_third_party = ["deker_tools"] -extra_standard_library = ["zoneinfo"] -use_parentheses = true +[tool.flake8] # code linter +# https://flake8.pycqa.org/en/latest/ +# https://pypi.org/project/flake8-bugbear +# https://pypi.org/project/flake8-docstrings/ +# https://pypi.org/project/flake8-import-order/ +# https://pypi.org/project/flake8-pytest-style/ +# https://pypi.org/project/pep8-naming/ +min_python_version = 3.9 +max-complexity = 15 +max-doc-length = 120 +max-line-length = 120 +strictness = "full" +docstring_style = "sphinx" +docstring-convention = "pep257" +application_import_names = "deker" +import-order-style = "pycharm" +exclude = [ + "venv/*", + ".venv/*", + ".git/*", + "__pycache__/*", + ".mypy_cache/*", + ".pytest_cache/*", + ".idea/*", + "examples/*", + "tmp/*", + "tests/*", + "tmp.py" +] +extend-select = ["D417"] +per-file-ignores = [ + "__init__.py: D104, F401, F403, F405, I100", + "deker/integrity.py: E501", + "deker/private/types/shell.py: D205, D400", + "deker/collection.py: D401", + "deker/subset.py: DAR101, E203", +] +ignore = [ + "B012", + "B019", + "D100", + "D104", + "D105", + "D106", + "D107", + "D203", + "D401", + "D403", + "D404", + "DAR002", + "DAR003", + "DAR104", + "DAR105", + "DAR201", + "DAR301", + "DAR401", + "DAR501", + "I101", + "I201", + "I202", + "N807", + "N813", + "W503", + "W504", +] + +[tool.pycln] # imports linter # https://hadialqattan.github.io/pycln/#/README -[tool.pycln] all = true diff = true -exclude = "venv/*,.git/*,__pycache__/*,examples/*" +exclude = "venv/*,.venv/*,.git/*,__pycache__/*,examples/*" +[tool.doc8] # RST linter +# https://github.com/PyCQA/doc8 +max-line-length = 99 -[tool.bandit] +[tool.bandit] # security linter +# https://github.com/PyCQA/bandit skips = ["B324"] -[tool.ruff] +[tool.ruff] # code linter +# https://github.com/astral-sh/ruff target-version = "py39" line-length = 120 select = ["ALL"] @@ -86,31 +267,31 @@ ignore = [ "BLE001", "DTZ004", "FIX002", - "C901", # Too complex, refactor files with this error. + "C901", # Too complex, refactor files with this error. "SLF001", "ANN401", "G004", "A003", "TD003", "TD002", - "DTZ003", # .utcnow() is not allowed - "DTZ005", # date time without tz - "DTZ006", # date time without tz - "FA100", # __future__ annotations + "DTZ003", # .utcnow() is not allowed + "DTZ005", # date time without tz + "DTZ006", # date time without tz + "FA100", # __future__ annotations "TRY301", - "PLR0913", # Number of arguments + "PLR0913", # Number of arguments "PERF401", "RUF012", "PLR0912", # Too many branches, - "FBT001", # Boolean positional arg - "FBT002", # Boolean default value + "FBT001", # Boolean positional arg + "FBT002", # Boolean default value "D401", "COM812", "EM101", - "UP006", # Tuple[..] -> tuple[..] - "UP035", # Tuple[..] -> tuple[..] - "UP007", # X | Y instead of Union - "UP037", # Quotes in annotations + "UP006", # Tuple[..] -> tuple[..] + "UP035", # Tuple[..] -> tuple[..] + "UP007", # X | Y instead of Union + "UP037", # Quotes in annotations "RET504", "PIE790", "ERA001", @@ -124,6 +305,7 @@ ignore = [ ] exclude = [ "venv/*", + ".venv/*", ".git/*", "__pycache__/*", ".mypy_cache/*", @@ -144,7 +326,7 @@ exclude = [ "PERF203" # Performance overhead ] "deker/locks.py" = [ - "PERF203",# Performance overhead + "PERF203", # Performance overhead "PTH123", "SIM115" ] @@ -152,7 +334,7 @@ exclude = [ "deker/tools/path.py" = ["S324"] "deker/validators.py" = ["C901", "PLR0912"] "deker/dimensions.py" = ["PLR0915"] # Too many statements -"deker/types/enums.py" = ["A003","A002"] +"deker/types/enums.py" = ["A003", "A002"] "deker/types/shell.py" = ["D205", "D400"] "deker/ABC/base_subset.py" = ["PLW2901"] # overwritten by assignment "deker/ABC/base_array.py" = ["PLW2901"] # overwritten by assignment @@ -174,51 +356,51 @@ known-local-folder = ["deker"] known-third-party = ["deker_tools"] extra-standard-library = ["zoneinfo"] -[build-system] -requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"] + ######### + # TESTS # + ######### -[project] -name = "deker" -requires-python = ">=3.9" -dynamic = ["version", "readme", "dependencies"] -authors = [ - {name = "OpenWeather", email = "info@openweathermap.org"}, -] -maintainers = [ - {name = "OpenWeather", email = "info@openweathermap.org"}, -] -description = "Multidimensional arrays storage engine" -license = {text = "GPL-3.0-only"} -classifiers = [ - "Development Status :: 4 - Beta", - "Intended Audience :: Developers", - "Intended Audience :: Information Technology", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", - "Topic :: Software Development :: Libraries :: Python Modules", - "Operating System :: Unix", - "Operating System :: POSIX :: Linux", - "Operating System :: MacOS :: MacOS X", - "Programming Language :: Python", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", -] -[project.optional-dependencies] -xarray = ["xarray>=2023.5.0"] +[tool.pytest.ini_options] # pytest +# https://docs.pytest.org +# https://pypi.org/project/pytest-asyncio/ +# https://pytest-cov.readthedocs.io/en/latest/ +# https://pypi.org/project/pytest-pythonpath/ +# https://pypi.org/project/pytest-sugar/ +minversion = 7.0 +asyncio_mode = "auto" +addopts = ["--ignore=tmp.py"] +norecursedirs = "data" +testpaths = "./tests" -[project.urls] -'Homepage' = 'https://deker.io/' -'Documentation' = 'https://docs.deker.io/' -'Repository' = 'https://github.com/openweathermap/deker' +#log_cli = true +#log_cli_level = "DEBUG" -[tool.setuptools.dynamic] -readme = {file = ["README.md"], content-type='text/markdown'} -dependencies = {file = ["requirements.txt"]} +pythonpath = ["./deker", "./.venv", "./venv"] +filterwarnings = ["ignore::UserWarning", 'ignore::DeprecationWarning', "ignore::ResourceWarning"] -[tool.setuptools] -packages = ["deker"] -license-files=["LICENSE"] +[tool.coverage.run] # coverage +branch = true +omit = [ + "tests/*", + "tmp.py", + "setup.py", + "deker/types/private/shell.py", +] -[tool.setuptools_scm] +[tool.coverage.html] +directory = "tests/code_coverage" + +[tool.coverage.report] +fail_under=96 +exclude_lines = [ + "no cov", + "pragma: no cover", + "if typing.TYPE_CHECKING:", + "if TYPE_CHECKING:", + "if __name__ == .__main__.:", + "pass", + "raise NotImplementedError", + "except ImportError", + "except ModuleNotFoundError", + "except Exception" +] diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 1110404..0000000 --- a/requirements.txt +++ /dev/null @@ -1,7 +0,0 @@ -numpy>=1.18 -attrs>=23.1.0 -typing-extensions>=4.4.0 -tqdm>=4.64.1 -psutil>=5.9.5 - -deker-local-adapters==1.0.1b diff --git a/requirements_dev.txt b/requirements_dev.txt deleted file mode 100644 index daadfe6..0000000 --- a/requirements_dev.txt +++ /dev/null @@ -1,29 +0,0 @@ -black==23.1.0 -coverage==7.1.0 -darglint==1.8.1 -flake8==5.0.4 # do not upgrade to 6.0.0! -flake8-bugbear==23.1.20 -flake8-docstrings==1.7.0 -flake8-import-order==0.18.2 -flake8-pytest-style==1.7.0 -isort==5.12.0 -mypy==1.0.0 -mypy-extensions==1.0.0 -pep8-naming==0.13.3 -pre-commit==3.0.4 -pycln==2.1.3 -pytest==7.2.1 -pytest-cov==4.0.0 -pytest-sugar==0.9.6 -pytest-random-order==1.1.0 -ssort==0.11.6 -deepdiff==6.3.0 -pytest-mock==3.10.0 -xarray>=2023.5.0 -bandit==1.7.5 -tox==4.6.3 -m2r2 -sphinx-rtd-theme -enum_tools -sphinx_toolbox -doc8 diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 81bcb6b..0000000 --- a/setup.cfg +++ /dev/null @@ -1,100 +0,0 @@ -; https://flake8.pycqa.org/en/latest/ -; https://pypi.org/project/flake8-bugbear -; https://pypi.org/project/flake8-docstrings/ -; https://pypi.org/project/flake8-import-order/ -; https://pypi.org/project/flake8-pytest-style/ -; https://pypi.org/project/pep8-naming/ -[flake8] -min_python_version = 3.9 -max-complexity = 15 -max-doc-length = 120 -max-line-length = 120 -strictness = full -docstring_style = sphinx -docstring-convention = pep257 -application_import_names = deker -import-order-style = pycharm -exclude = - venv/*, - .git/*, - __pycache__/*, - .mypy_cache/*, - .pytest_cache/*, - .idea/*, - examples/*, - tmp/*, - tests/*, - tmp.py - -extend-select = D417 -per-file-ignores = - __init__.py: D104, F401, F403, F405, I100 - deker/integrity.py: E501 - deker/private/types/shell.py: D205, D400 - deker/collection.py: D401 - deker/subset.py: DAR101, E203 - -ignore = - B012, - B019, - D100, - D104, - D105, - D106, - D107, - D203, - D401, - D403, - D404, - DAR002, - DAR003, - DAR104, - DAR105, - DAR201, - DAR301, - DAR401, - DAR501, - I101 - I201, - I202, - N807, - N813, - W503, - W504, - -; https://pypi.org/project/darglint -[darglint] -strictness = full -docstring_style = sphinx -ignore = - DAR003, - DAR104, - DAR105, - DAR201, - DAR401 - -; https://docs.pytest.org -; https://pypi.org/project/pytest-asyncio/ -; https://pytest-cov.readthedocs.io/en/latest/ -; https://pypi.org/project/pytest-pythonpath/ -; https://pypi.org/project/pytest-sugar/ -[tool:pytest] -minversion = 7.0 -asyncio_mode = auto -addopts = --ignore=tmp.py -norecursedirs = data -testpaths = ./tests - -;log_cli = true -;log_cli_level = DEBUG - - -; for pytest < 7.0 -;python_paths = ./deker ./venv -; for pytest >= 7.0 -pythonpath = ./deker ./venv - -filterwarnings = - ignore::UserWarning - ignore::DeprecationWarning - ignore::ResourceWarning diff --git a/tox.ini b/tox.ini deleted file mode 100644 index da607d7..0000000 --- a/tox.ini +++ /dev/null @@ -1,48 +0,0 @@ -[tox] -requires = - tox>=4 -env_list = {py39,py310,py311}-lint, py{39,310,311}-test - -[testenv:{py39,py310,py311}-test] -description = run unit tests -deps = - deepdiff==6.3.0 - pytest>=7 - pytest-sugar - pytest-mock==3.10.0 - xarray>=2023.5.0 - -commands = - pytest {posargs:tests} - -set_env = - PIP_EXTRA_INDEX_URL = {env:PIP_EXTRA_INDEX_URL} - -[testenv:{py39,py310,py311}-lint] -ignore_base_python_conflict = true -description = run linters -deps = black==23.1.0 - coverage==7.1.0 - darglint==1.8.1 - flake8==5.0.4 - flake8-bugbear==23.1.20 - flake8-docstrings==1.7.0 - flake8-import-order==0.18.2 - flake8-pytest-style==1.7.0 - isort==5.12.0 - mypy==1.0.0 - mypy-extensions==1.0.0 - pep8-naming==0.13.3 - bandit==1.7.5 - ssort==0.11.6 - deepdiff==6.3.0 - xarray>=2023.5.0 - -commands = isort {posargs:deker} - black {posargs:deker} - flake8 {posargs:deker} - bandit -r {posargs:deker} -c pyproject.toml - mypy {posargs:deker} --install-types --non-interactive --config-file pyproject.toml - -set_env = - PIP_EXTRA_INDEX_URL = {env:PIP_EXTRA_INDEX_URL}