diff --git a/docs/notebooks/cookbook/units.ipynb b/docs/notebooks/cookbook/units.ipynb deleted file mode 100644 index 4c2bfa38..00000000 --- a/docs/notebooks/cookbook/units.ipynb +++ /dev/null @@ -1,179 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "id": "6641d87c-46a2-4877-b25b-42b40c038bc8", - "metadata": {}, - "source": [ - "# Loading data with units\n", - "Pass **units=True** as keyword. This will load as code units by default. Alternatively, we can use units=\"cgs\". Units are introduced via the [pint](https://pint.readthedocs.io/en/latest/) package, see there for more details." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "8144380b-2729-40cc-8bfb-af6e15e702fd", - "metadata": {}, - "outputs": [], - "source": [ - "from scida import load\n", - "ds = load(\"testdata://TNG50-4_snapshot\", units=True) # units=True equals units=\"code\"\n", - "gas = ds.data[\"PartType0\"]" - ] - }, - { - "cell_type": "markdown", - "id": "08ee5a74-c69c-4a35-b1b0-01dbfdfcc850", - "metadata": {}, - "source": [ - "Instead of just an array of values, fields now consist of a magnitude and unit, this also shows in the dask arrays representation" - ] - }, - { - "cell_type": "markdown", - "id": "530fd69e-b037-440b-9a62-0be70198ad74", - "metadata": {}, - "source": [ - "# Basics\n", - "## Evaluating fields and their units" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "236a4279-9f23-4090-abf1-102c333cd5c4", - "metadata": {}, - "outputs": [], - "source": [ - "gas[\"Coordinates\"]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "19174d80-bebd-41ff-bc2c-60c65e205b80", - "metadata": {}, - "outputs": [], - "source": [ - "# calculate magnitude (of first entry) and units\n", - "gas[\"Coordinates\"][0].magnitude.compute(), gas[\"Coordinates\"].units" - ] - }, - { - "cell_type": "markdown", - "id": "86c7996e-c965-4ae8-bc73-4be50f45a67d", - "metadata": {}, - "source": [ - "We can change units for evaluation as desired" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "376d0077-b641-433d-8549-2cb51d464fef", - "metadata": {}, - "outputs": [], - "source": [ - "coords = gas[\"Coordinates\"]\n", - "coords.to(\"cm\") \n", - "# here the default system is cgs, thus we get the same result from\n", - "coords.to_base_units()" - ] - }, - { - "cell_type": "markdown", - "id": "1da60b22-93ad-424c-a1e4-bc56dab6abec", - "metadata": {}, - "source": [ - "## The unit registry\n", - "The unit registry keeps all units. There is no global registry, but each dataset has its own registry as attribute **ureg**." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "d2bea295-ed26-41ac-8855-2783ac5f64c9", - "metadata": {}, - "outputs": [], - "source": [ - "ureg = ds.ureg\n", - "# get the unit meter\n", - "ureg(\"m\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "fb5caf1d-703c-47c9-9050-7ddfd9383ba9", - "metadata": {}, - "outputs": [], - "source": [ - "# define an array with units meter (dask arrays analogously)\n", - "import numpy as np\n", - "np.arange(10) * ureg(\"m\")" - ] - }, - { - "cell_type": "markdown", - "id": "de75ec74-219c-429b-957d-98826cdfe41e", - "metadata": {}, - "source": [ - "## Synthesize new dask arrays with units\n", - "Defining new arrays from existing arrays will keep their units accordingly." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "1803db7d-51aa-406b-be96-81909837f0fe", - "metadata": {}, - "outputs": [], - "source": [ - "energy_restframe = (gas[\"Masses\"]*ureg(\"c\")**2).to(\"erg\") # E=mc^2\n", - "energy_restframe" - ] - }, - { - "cell_type": "markdown", - "id": "a28057b5-36cc-4496-bc4e-efa6935b638a", - "metadata": {}, - "source": [ - "## Custom units\n", - "We can introduce and evaluate to custom units." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "37c6a353-04ca-4622-acd4-d188292cb0f2", - "metadata": {}, - "outputs": [], - "source": [ - "ureg.define(\"halfmeter = 0.5 * m\")\n", - "# first particle coordinates in halfmeters\n", - "coords.to(\"halfmeter\")[0].compute()" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "scida", - "language": "python", - "name": "scida" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.9.2" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/docs/stylesheets/code_select.css b/docs/stylesheets/code_select.css new file mode 100644 index 00000000..22007671 --- /dev/null +++ b/docs/stylesheets/code_select.css @@ -0,0 +1,4 @@ +.language-pycon .gp, .language-pycon .go { /* Generic.Prompt, Generic.Output */ + user-select: none; +} +.language-pycon .md-clipboard { display: none; } diff --git a/docs/tutorial/observations.md b/docs/tutorial/observations.md index 4aaf153a..40c7cebc 100644 --- a/docs/tutorial/observations.md +++ b/docs/tutorial/observations.md @@ -2,7 +2,7 @@ This package is designed to aid in the efficient analysis of large datasets, such as GAIA DR3. -!!! note "Tutorial dataset" +!!! info "Tutorial dataset" In the following, we will subset from the [GAIA data release 3](https://www.cosmos.esa.int/web/gaia/dr3). The reduced dataset contains 100000 randomly selected entries only. The reduced dataset can be downloaded [here](https://heibox.uni-heidelberg.de/f/3b05069b1b524c0fa57e/?dl=1). Check [Supported Datasets](../supported_data.md) for an incomplete list of supported datasets and requirements for support of new datasets. @@ -19,8 +19,7 @@ It uses the [dask](https://dask.org/) library to perform computations, which has Here, we choose the [GAIA data release 3](https://www.cosmos.esa.int/web/gaia/dr3) as an example. The dataset is obtained in HDF5 format as used at ITA Heidelberg. We intentionally select a small subset of the data to work with. -Choosing a subset means that the data size in the snapshot is small and easy to work with. -We demonstrate how to work with larger data sets at a later stage. +Choosing a subset means that the data size is small and easy to work with. We demonstrate how to work with larger data sets at a later stage. First, we load the dataset using the convenience function `load()` that will determine the appropriate dataset class for us: @@ -110,10 +109,10 @@ and dimensionality checks are performed. Importantly, the unit calculation is do to directly see the resulting units and any dimensionality mismatches. -## Analyzing snapshot data -### Computing a simple statistic on (all) particles +## Analyzing the data +### Computing a simple statistic on (all) objects -The fields in our snapshot object behave similar to actual numpy arrays. +The fields in our data object behave similar to actual numpy arrays. As a first simple example, let's calculate the mean declination of the stars. Just as in numpy we can write @@ -148,26 +147,32 @@ We discuss more advanced and interactive visualization methods [here](../visuali >>> x = ds.data["l"] >>> y = ds.data["b"] >>> nbins = (360, 180) ->>> xbins = np.linspace(0.0, 360.0, nbins[0] + 1) ->>> ybins = np.linspace(-90, 90.0, nbins[1] + 1) +>>> extent = [0.0, 360.0, -90.0, 90.0] +>>> xbins = np.linspace(*extent[:2], nbins[0] + 1) +>>> ybins = np.linspace(*extent[-2:], nbins[1] + 1) >>> hist, xbins, ybins = da.histogram2d(x, y, bins=[xbins, ybins]) >>> im2d = hist.compute() #(1)! >>> import matplotlib.pyplot as plt >>> from matplotlib.colors import LogNorm ->>> plt.imshow(im2d.T, norm=LogNorm(), extent=[0.0, 360.0, -90.0, 90.0]) ->>> plt.xlabel("l (deg)") ->>> plt.ylabel("b (deg)") +>>> plt.imshow(im2d.T, origin="lower", norm=LogNorm(), extent=extent, interpolation="none") +>>> plt.xlabel("l [deg]") +>>> plt.ylabel("b [deg]") >>> plt.show() ``` 1. The *compute()* on `im2d` results in a two-dimensional array which we can display. + ![2D histogram example](../images/simple_hist2d_obs.png) +!!! info + + Above image shows the histogram obtained for the full data set. + ## FITS files -Observations are often stored in [FITS](https://en.wikipedia.org/wiki/FITS) files. Support in scida work-in-progress +Observations are often stored in [FITS](https://en.wikipedia.org/wiki/FITS) files. Support in scida is work-in-progress and requires the [astropy](https://www.astropy.org/) package. Here we show use of the SDSS DR16: diff --git a/docs/tutorial/simulations.md b/docs/tutorial/simulations.md index 31ac77c0..7c7cd395 100644 --- a/docs/tutorial/simulations.md +++ b/docs/tutorial/simulations.md @@ -1,6 +1,6 @@ ## Getting started -!!! note "Tutorial dataset" +!!! info "Tutorial dataset" In the following, we will use a small test dataset from the [TNG50](https://www.tng-project.org/) simulation. This is a cosmological galaxy formation simulation. This dataset is still a gigabyte in size and can be downloaded [here](https://heibox.uni-heidelberg.de/f/dc65a8c75220477eb62d/). Note that analysis is not limited to simulations, but also observational data. @@ -208,6 +208,6 @@ We discuss more advanced and interactive visualization methods [here](../visuali ![2D histogram example](../images/simple_hist2d.png) ## Catalogs -Many cosmological simulations have a catalog of halos, subhalos, galaxies, etc. +Many cosmological simulations have a catalog of halos, subhalos, galaxies, etc. -For AREPO/Gadget based simulations, we support use of this information. Find more find more information on how to use catalogs [here](../halocatalogs.md). \ No newline at end of file +For AREPO/Gadget based simulations, we support use of this information. Find more find more information on how to use catalogs [here](../halocatalogs.md). diff --git a/mkdocs.yml b/mkdocs.yml index 70f69596..577a7dca 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -4,6 +4,7 @@ theme: name: material features: - content.code.annotate + - content.code.copy - navigation.sections - navigation.indexes @@ -29,8 +30,6 @@ nav: - 'Advanced Topics': - 'Arepo Simulations': - 'Halo Catalogs': halocatalogs.md - # - 'Cookbook': - # - 'Units': notebooks/cookbook/units.ipynb - 'Configuration': configuration.md - 'FAQ': faq.md - api_docs.md @@ -49,6 +48,9 @@ markdown_extensions: - name: mermaid class: mermaid format: !!python/name:pymdownx.superfences.fence_code_format + - pymdownx.highlight: + use_pygments: true + pygments_lang_class: true - admonition - pymdownx.details - pymdownx.superfences @@ -57,8 +59,8 @@ markdown_extensions: - attr_list - footnotes - pymdownx.emoji: - emoji_index: !!python/name:materialx.emoji.twemoji - emoji_generator: !!python/name:materialx.emoji.to_svg + emoji_index: !!python/name:material.extensions.emoji.twemoji + emoji_generator: !!python/name:material.extensions.emoji.to_svg - pymdownx.arithmatex: generic: true - md_in_html @@ -87,16 +89,16 @@ plugins: width: 12.172vw - mkdocs-jupyter: execute: !ENV [JUPYTER_EXECUTE, true] - execute_ignore: "notebooks/static/*.ipynb" # waiting for list support (https://github.com/danielfrg/mkdocs-jupyter/issues/119) + execute_ignore: + - "notebooks/static/*.ipynb" kernel_name: scida - mkdocstrings: default_handler: python handlers: python: options: - show_signature_annotations: true - show_source: true show_submodules: true + docstring_style: numpy watch: - src/scida @@ -108,3 +110,4 @@ extra_javascript: extra_css: - stylesheets/gridview.css + - stylesheets/code_select.css diff --git a/poetry.lock b/poetry.lock index 74102c36..03c79288 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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python-versions = ">=3.6" files = [ @@ -1495,7 +1468,6 @@ testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"] name = "jinja2" version = "3.1.2" description = "A very fast and expressive template engine." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1513,18 +1485,17 @@ i18n = ["Babel (>=2.7)"] name = "jsonpointer" version = "2.4" description = "Identify specific nodes in a JSON document (RFC 6901)" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" files = [ {file = "jsonpointer-2.4-py2.py3-none-any.whl", hash = "sha256:15d51bba20eea3165644553647711d150376234112651b4f1811022aecad7d7a"}, + {file = "jsonpointer-2.4.tar.gz", hash = "sha256:585cee82b70211fa9e6043b7bb89db6e1aa49524340dde8ad6b63206ea689d88"}, ] [[package]] name = "jsonschema" version = "4.19.0" description = "An implementation of JSON Schema validation for Python" -category = "main" optional = 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{file = "mkdocstrings-python-legacy-0.2.3.tar.gz", hash = "sha256:3fb58fdabe19c6b52b8bb1d3bb1540b1cd527b562865468d6754e8cd1201050c"}, - {file = "mkdocstrings_python_legacy-0.2.3-py3-none-any.whl", hash = "sha256:1b04d71a4064b0bb8ea9448debab89868a752c7e7bfdd11de480dfbcb9751a00"}, + {file = "mkdocstrings_python-1.7.5-py3-none-any.whl", hash = "sha256:5f6246026353f0c0785135db70c3fe9a5d9318990fc7ceb11d62097b8ffdd704"}, + {file = "mkdocstrings_python-1.7.5.tar.gz", hash = "sha256:c7d143728257dbf1aa550446555a554b760dcd40a763f077189d298502b800be"}, ] [package.dependencies] -mkdocstrings = ">=0.19" -pytkdocs = ">=0.14" +griffe = ">=0.37" +mkdocstrings = ">=0.20" [[package]] name = "msgpack" version = "1.0.5" description = "MessagePack serializer" -category = "main" optional = false python-versions = "*" files = [ @@ -2762,7 +2714,6 @@ files = [ name = "multipledispatch" version = "1.0.0" description = "Multiple dispatch" -category = "dev" optional = false python-versions = "*" files = [ @@ -2774,7 +2725,6 @@ files = [ name = "mypy" version = "1.5.1" description = "Optional static typing for Python" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2821,7 +2771,6 @@ reports = ["lxml"] name = "mypy-extensions" version = "1.0.0" description = "Type system extensions for programs checked with the mypy type checker." -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -2833,7 +2782,6 @@ files = [ name = "nbclassic" version = "1.0.0" description = "Jupyter Notebook as a Jupyter Server extension." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2869,7 +2817,6 @@ test = ["coverage", "nbval", "pytest", "pytest-cov", "pytest-jupyter", "pytest-p name = "nbclient" version = "0.8.0" description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor." -category = "main" optional = false python-versions = ">=3.8.0" files = [ @@ -2879,7 +2826,7 @@ files = [ [package.dependencies] jupyter-client = ">=6.1.12" -jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" +jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" nbformat = ">=5.1" traitlets = ">=5.4" @@ -2890,47 +2837,46 @@ test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>= [[package]] name = "nbconvert" -version = "6.5.4" +version = "7.12.0" description = "Converting Jupyter Notebooks" -category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "nbconvert-6.5.4-py3-none-any.whl", hash = "sha256:d679a947f849a966cbbd0bf6e7fedcfdb64be3b20ce7cef11ad55c13f5820e19"}, - {file = "nbconvert-6.5.4.tar.gz", hash = "sha256:9e3c7c6d491374cbdd5f35d268c05809357716d346f4573186bbeab32ee50bc1"}, + {file = "nbconvert-7.12.0-py3-none-any.whl", hash = "sha256:5b6c848194d270cc55fb691169202620d7b52a12fec259508d142ecbe4219310"}, + {file = "nbconvert-7.12.0.tar.gz", hash = "sha256:b1564bd89f69a74cd6398b0362da94db07aafb991b7857216a766204a71612c0"}, ] [package.dependencies] beautifulsoup4 = "*" -bleach = "*" +bleach = "!=5.0.0" defusedxml = "*" -entrypoints = ">=0.2.2" +importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""} jinja2 = ">=3.0" jupyter-core = ">=4.7" jupyterlab-pygments = "*" -lxml = "*" -MarkupSafe = ">=2.0" -mistune = ">=0.8.1,<2" +markupsafe = ">=2.0" +mistune = ">=2.0.3,<4" nbclient = ">=0.5.0" -nbformat = ">=5.1" +nbformat = ">=5.7" packaging = "*" pandocfilters = ">=1.4.1" pygments = ">=2.4.1" tinycss2 = "*" -traitlets = ">=5.0" +traitlets = ">=5.1" [package.extras] -all = ["ipykernel", "ipython", "ipywidgets (>=7)", "nbsphinx (>=0.2.12)", "pre-commit", "pyppeteer (>=1,<1.1)", "pytest", "pytest-cov", "pytest-dependency", "sphinx (>=1.5.1)", "sphinx-rtd-theme", "tornado (>=6.1)"] -docs = ["ipython", "nbsphinx (>=0.2.12)", "sphinx (>=1.5.1)", "sphinx-rtd-theme"] +all = ["nbconvert[docs,qtpdf,serve,test,webpdf]"] +docs = ["ipykernel", "ipython", "myst-parser", "nbsphinx (>=0.2.12)", "pydata-sphinx-theme", "sphinx (==5.0.2)", "sphinxcontrib-spelling"] +qtpdf = ["nbconvert[qtpng]"] +qtpng = ["pyqtwebengine (>=5.15)"] serve = ["tornado (>=6.1)"] -test = ["ipykernel", "ipywidgets (>=7)", "pre-commit", "pyppeteer (>=1,<1.1)", "pytest", "pytest-cov", "pytest-dependency"] -webpdf = ["pyppeteer (>=1,<1.1)"] +test = ["flaky", "ipykernel", "ipywidgets (>=7)", "pytest"] +webpdf = ["playwright"] [[package]] name = "nbformat" version = "5.9.2" description = "The Jupyter Notebook format" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2952,7 +2898,6 @@ test = ["pep440", "pre-commit", "pytest", "testpath"] name = "nest-asyncio" version = "1.5.7" description = "Patch asyncio to allow nested event loops" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -2964,7 +2909,6 @@ files = [ name = "nodeenv" version = "1.8.0" description = "Node.js virtual environment builder" -category = "dev" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*" files = [ @@ -2979,7 +2923,6 @@ setuptools = "*" name = "notebook" version = "6.5.5" description = "A web-based notebook environment for interactive computing" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3014,7 +2957,6 @@ test = ["coverage", "nbval", "pytest", "pytest-cov", "requests", "requests-unixs name = "notebook-shim" version = "0.2.3" description = "A shim layer for notebook traits and config" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3032,7 +2974,6 @@ test = ["pytest", "pytest-console-scripts", "pytest-jupyter", "pytest-tornasync" name = "numba" version = "0.57.1" description = "compiling Python code using LLVM" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3063,14 +3004,13 @@ files = [ ] [package.dependencies] -llvmlite = ">=0.40.0dev0,<0.41" +llvmlite = "==0.40.*" numpy = ">=1.21,<1.25" [[package]] name = "numcodecs" version = "0.11.0" description = "A Python package providing buffer compression and transformation codecs for use" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3103,7 +3043,6 @@ zfpy = ["zfpy (>=1.0.0)"] name = "numpy" version = "1.24.4" description = "Fundamental package for array computing in Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3141,7 +3080,6 @@ files = [ name = "overrides" version = "7.4.0" description = "A decorator to automatically detect mismatch when overriding a method." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3153,7 +3091,6 @@ files = [ name = "packaging" version = "23.1" description = "Core utilities for Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3161,11 +3098,20 @@ files = [ {file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"}, ] +[[package]] +name = "paginate" +version = "0.5.6" +description = "Divides large result sets into pages for easier browsing" +optional = false +python-versions = "*" +files = [ + {file = "paginate-0.5.6.tar.gz", hash = "sha256:5e6007b6a9398177a7e1648d04fdd9f8c9766a1a945bceac82f1929e8c78af2d"}, +] + [[package]] name = "pandas" version = "2.0.3" description = "Powerful data structures for data analysis, time series, and statistics" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3199,8 +3145,8 @@ files = [ [package.dependencies] numpy = [ {version = ">=1.20.3", markers = "python_version < \"3.10\""}, - {version = ">=1.21.0", markers = "python_version >= \"3.10\""}, {version = ">=1.23.2", markers = "python_version >= \"3.11\""}, + {version = ">=1.21.0", markers = "python_version >= \"3.10\" and python_version < \"3.11\""}, ] python-dateutil = ">=2.8.2" pytz = ">=2020.1" @@ -3233,7 +3179,6 @@ xml = ["lxml (>=4.6.3)"] name = "pandocfilters" version = "1.5.0" description = "Utilities for writing pandoc filters in python" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -3245,7 +3190,6 @@ files = [ name = "panel" version = "1.2.1" description = "The powerful data exploration & web app framework for Python." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3282,7 +3226,6 @@ ui = ["jupyter-server", "playwright", "pytest-playwright"] name = "param" version = "1.13.0" description = "Make your Python code clearer and more reliable by declaring Parameters." -category = "dev" optional = false python-versions = ">=2.7" files = [ @@ -3299,7 +3242,6 @@ tests = ["coverage", "flake8", "pytest"] name = "parso" version = "0.8.3" description = "A Python Parser" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3315,7 +3257,6 @@ testing = ["docopt", "pytest (<6.0.0)"] name = "partd" version = "1.4.0" description = "Appendable key-value storage" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3334,7 +3275,6 @@ complete = ["blosc", "numpy (>=1.9.0)", "pandas (>=0.19.0)", "pyzmq"] name = "pathspec" version = "0.11.2" description = "Utility library for gitignore style pattern matching of file paths." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3346,7 +3286,6 @@ files = [ name = "pexpect" version = "4.8.0" description = "Pexpect allows easy control of interactive console applications." -category = "main" optional = false python-versions = "*" files = [ @@ -3361,7 +3300,6 @@ ptyprocess = ">=0.5" name = "pickleshare" version = "0.7.5" description = "Tiny 'shelve'-like database with concurrency support" -category = "main" optional = false python-versions = "*" files = [ @@ -3373,7 +3311,6 @@ files = [ name = "pillow" version = "10.0.0" description = "Python Imaging Library (Fork)" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3443,7 +3380,6 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa name = "pint" version = "0.22" description = "Physical quantities module" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -3468,7 +3404,6 @@ xarray = ["xarray"] name = "platformdirs" version = "3.10.0" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3484,7 +3419,6 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-co name = "pluggy" version = "1.2.0" description = "plugin and hook calling mechanisms for python" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3500,7 +3434,6 @@ testing = ["pytest", "pytest-benchmark"] name = "pre-commit" version = "3.3.3" description = "A framework for managing and maintaining multi-language pre-commit hooks." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3519,7 +3452,6 @@ virtualenv = ">=20.10.0" name = "prometheus-client" version = "0.17.1" description = "Python client for the Prometheus monitoring system." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3534,7 +3466,6 @@ twisted = ["twisted"] name = "prompt-toolkit" version = "3.0.39" description = "Library for building powerful interactive command lines in Python" -category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -3549,7 +3480,6 @@ wcwidth = "*" name = "psutil" version = "5.9.5" description = "Cross-platform lib for process and system monitoring in Python." -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -3576,7 +3506,6 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"] name = "ptyprocess" version = "0.7.0" description = "Run a subprocess in a pseudo terminal" -category = "main" optional = false python-versions = "*" files = [ @@ -3588,7 +3517,6 @@ files = [ name = "pure-eval" version = "0.2.2" description = "Safely evaluate AST nodes without side effects" -category = "main" optional = false python-versions = "*" files = [ @@ -3603,7 +3531,6 @@ tests = ["pytest"] name = "py" version = "1.11.0" description = "library with cross-python path, ini-parsing, io, code, log facilities" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -3615,7 +3542,6 @@ files = [ name = "pycodestyle" version = "2.11.0" description = "Python style guide checker" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3627,7 +3553,6 @@ files = [ name = "pycparser" version = "2.21" description = "C parser in Python" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -3639,7 +3564,6 @@ files = [ name = "pyct" version = "0.5.0" description = "Python package common tasks for users (e.g. copy examples, fetch data, ...)" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3660,7 +3584,6 @@ tests = ["flake8", "pytest"] name = "pyerfa" version = "2.0.0.3" description = "Python bindings for ERFA" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3717,7 +3640,6 @@ test = ["pytest", "pytest-doctestplus (>=0.7)"] name = "pyflakes" version = "3.1.0" description = "passive checker of Python programs" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3729,7 +3651,6 @@ files = [ name = "pygments" version = "2.16.1" description = "Pygments is a syntax highlighting package written in Python." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3744,7 +3665,6 @@ plugins = ["importlib-metadata"] name = "pyinstrument" version = "4.5.1" description = "Call stack profiler for Python. Shows you why your code is slow!" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3805,25 +3725,26 @@ jupyter = ["ipython"] [[package]] name = "pymdown-extensions" -version = "10.1" +version = "10.4" description = "Extension pack for Python Markdown." -category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "pymdown_extensions-10.1-py3-none-any.whl", hash = "sha256:ef25dbbae530e8f67575d222b75ff0649b1e841e22c2ae9a20bad9472c2207dc"}, - {file = "pymdown_extensions-10.1.tar.gz", hash = "sha256:508009b211373058debb8247e168de4cbcb91b1bff7b5e961b2c3e864e00b195"}, + {file = "pymdown_extensions-10.4-py3-none-any.whl", hash = "sha256:cfc28d6a09d19448bcbf8eee3ce098c7d17ff99f7bd3069db4819af181212037"}, + {file = "pymdown_extensions-10.4.tar.gz", hash = "sha256:bc46f11749ecd4d6b71cf62396104b4a200bad3498cb0f5dad1b8502fe461a35"}, ] [package.dependencies] markdown = ">=3.2" pyyaml = "*" +[package.extras] +extra = ["pygments (>=2.12)"] + [[package]] name = "pynvml" version = "11.5.0" description = "Python Bindings for the NVIDIA Management Library" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -3835,7 +3756,6 @@ files = [ name = "pyparsing" version = "3.0.9" description = "pyparsing module - Classes and methods to define and execute parsing grammars" -category = "dev" optional = false python-versions = ">=3.6.8" files = [ @@ -3850,7 +3770,6 @@ diagrams = ["jinja2", "railroad-diagrams"] name = "pytest" version = "7.4.0" description = "pytest: simple powerful testing with Python" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3873,7 +3792,6 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no name = "pytest-mock" version = "3.11.1" description = "Thin-wrapper around the mock package for easier use with pytest" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3891,7 +3809,6 @@ dev = ["pre-commit", "pytest-asyncio", "tox"] name = "pytest-profiling" version = "1.7.0" description = "Profiling plugin for py.test" -category = "dev" optional = false python-versions = "*" files = [ @@ -3911,7 +3828,6 @@ tests = ["pytest-virtualenv"] name = "pytest-xdist" version = "3.3.1" description = "pytest xdist plugin for distributed testing, most importantly across multiple CPUs" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3933,7 +3849,6 @@ testing = ["filelock"] name = "python-dateutil" version = "2.8.2" description = "Extensions to the standard Python datetime module" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ @@ -3948,7 +3863,6 @@ six = ">=1.5" name = "python-json-logger" version = "2.0.7" description = "A python library adding a json log formatter" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3956,26 +3870,10 @@ files = [ {file = "python_json_logger-2.0.7-py3-none-any.whl", hash 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false python-versions = "*" files = [ @@ -4921,7 +4885,6 @@ files = [ name = "webcolors" version = "1.13" description = "A library for working with the color formats defined by HTML and CSS." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4937,7 +4900,6 @@ tests = ["pytest", "pytest-cov"] name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" -category = "main" optional = false python-versions = "*" files = [ @@ -4949,7 +4911,6 @@ files = [ name = "websocket-client" version = "1.6.1" description = "WebSocket client for Python with low level API options" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4966,7 +4927,6 @@ test = ["websockets"] name = "wheel" version = "0.41.1" description = "A built-package format for Python" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4981,7 +4941,6 @@ test = ["pytest (>=6.0.0)", "setuptools (>=65)"] name = "widgetsnbextension" version = "4.0.8" description = "Jupyter interactive widgets for Jupyter Notebook" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4993,7 +4952,6 @@ files = [ name = "xarray" version = "2022.12.0" description = "N-D labeled arrays and datasets in Python" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -5018,7 +4976,6 @@ viz = ["matplotlib", "nc-time-axis", "seaborn"] name = "xyzservices" version = "2023.7.0" description = "Source of XYZ tiles providers" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -5030,7 +4987,6 @@ files = [ name = "zarr" version = "2.16.0" description = "An implementation of chunked, compressed, N-dimensional arrays for Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -5051,7 +5007,6 @@ jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"] name = "zict" version = "3.0.0" description = "Mutable mapping tools" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -5063,7 +5018,6 @@ files = [ name = "zipp" version = "3.16.2" description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -5078,4 +5032,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "67223321a71e9b95e70471fc605c22ac02eb69573f254309f90c26eb2f8b6cd1" +content-hash = "83b9adee21c1bc46bd51d7bb02b837dfd4c406a05efc293c66cefadd7993f617" diff --git a/pyproject.toml b/pyproject.toml index 960b6b11..72d6a49d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,10 +30,10 @@ coverage = "^7.0.1" pytest-xdist = {extras = ["psutil"], version = "^3.1.0"} pytest-profiling = "^1.7.0" mypy = ">=0.930" -mkdocs = "^1.3.0" -mkdocs-material = "^8.0.0" -mkdocstrings = {version = "^0.19.0", extras = ["python-legacy"]} -mkdocs-jupyter = "^0.22.0" +mkdocs = "^1.5.3" +mkdocs-material = "^9.5.1" +mkdocstrings = {extras = ["python"], version = "^0.24.0"} +mkdocs-jupyter = "^0.24.6" ipykernel = "^6.19.4" matplotlib = "^3.6.2" ipywidgets = "^8.0.4"