From 67d5d5667ef610e4f8c7a6f3b77b3e1d0604426d Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Wed, 27 Sep 2023 21:05:35 +0300 Subject: [PATCH 01/19] notebooks: Remove `BBox_filtering.ipynb` it has been superseeded by `crop()` --- notebooks/BBox_filtering.ipynb | 309 --------------------------------- 1 file changed, 309 deletions(-) delete mode 100644 notebooks/BBox_filtering.ipynb diff --git a/notebooks/BBox_filtering.ipynb b/notebooks/BBox_filtering.ipynb deleted file mode 100644 index 065e9b9..0000000 --- a/notebooks/BBox_filtering.ipynb +++ /dev/null @@ -1,309 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": null, - "id": "871b1568-5742-46dd-9072-8e3785f8475c", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "%load_ext autoreload\n", - "%autoreload 2\n", - "\n", - "from __future__ import annotations" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "98ba7fda-b961-450c-b885-75176c8609dc", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "# debug\n", - "import sys\n", - "\n", - "print(sys.executable)\n", - "print(sys.version_info)" - ] - }, - { - "cell_type": "markdown", - "id": "09b3a22a-1c7d-457b-973c-7ea35d65e22a", - "metadata": { - "tags": [] - }, - "source": [ - "## Subsetting an unstructured mesh using a BBox \n", - "\n", - "In unstructured meshes the `longitude` and `latitude` are data variables instead of dimensions.\n", - "This means that filtering/subsetting a mesh using a Bounding Box (BBox) is somewhat more challenging.\n", - "Nevertheless it is still possible to do it using `numpy` and `xarray`.\n", - "\n", - "This notebook describes how to achieve this.\n", - "\n", - "For convenience, we are going to use an ADCIRC netcdf file which has been converted to the \"Thalassa schema\".\n", - "\n", - "We will also need an additional library which the following cell will take care of importing." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "5090d13b-e185-4155-8801-692ff511a829", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "try:\n", - " import numpy_indexed\n", - "except ImportError:\n", - " %pip install numpy_indexed" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "95c5af35-560d-4222-8e8d-6f680a9d24b3", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "import holoviews as hv\n", - "import numpy as np\n", - "import numpy_indexed as npi\n", - "import pandas as pd\n", - "import xarray as xr\n", - "\n", - "from thalassa import api\n", - "\n", - "hv.extension(\"bokeh\")" - ] - }, - { - "cell_type": "markdown", - "id": "567728b6-300e-4f86-b80f-56f70d49dfe3", - "metadata": { - "tags": [] - }, - "source": [ - "### Sample file\n", - "\n", - "As an example let's download a netcdf file containing the output of an ADCIRC model." - ] - }, - { - "cell_type": "markdown", - "id": "39d407a6-b810-4571-ac5b-6145c81df5cc", - "metadata": { - "tags": [] - }, - "source": [ - "Let's load the file and convert it to the thalassa schema." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "2802b2dc-a45f-4da2-9e62-62eaafab63d9", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "from thalassa import api\n", - "\n", - "filename = \"../tests/data/fort.63.nc\"\n", - "ds = api.open_dataset(filename)\n", - "ds = ds.assign(zeta_max=ds.zeta.max(\"time\"))\n", - "ds" - ] - }, - { - "cell_type": "markdown", - "id": "195cb344-61c0-429b-b648-d739180a819e", - "metadata": { - "tags": [] - }, - "source": [ - "As we can see the model has 3070 `nodes` and 5780 `trifaces` (i.e. triangles)\n", - "\n", - "Note: The reason why the thalassa schema defines `triface` is because `face` might be referring to quad elements, too (in Schism models; ADCIRC does not support them). `triface` always refers to triangles." - ] - }, - { - "cell_type": "markdown", - "id": "b9b19fd4-0c43-4cc1-9019-7abee26d591e", - "metadata": { - "tags": [] - }, - "source": [ - "### Filtering \n", - "\n", - "Now let's define the function that does the filtering by BBox" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "0ff5f2aa-cc49-486f-a407-4d90e962bc33", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "def filter_thalassa_by_bbox(\n", - " ds: xr.Dataset,\n", - " lon_min: float = -180,\n", - " lon_max: float = 180,\n", - " lat_min: float = -90,\n", - " lat_max: float = 90,\n", - ") -> xr.Dataset:\n", - " indices_of_nodes_in_bbox = np.where(\n", - " True \n", - " & (ds.lat >= lat_min)\n", - " & (ds.lat <= lat_max) \n", - " & (ds.lon >= lon_min) \n", - " & (ds.lon <= lon_max)\n", - " )[0]\n", - " indices_of_triface_nodes_in_bbox = np.where(\n", - " ds.triface_nodes.isin(indices_of_nodes_in_bbox).all(axis=1)\n", - " )[0]\n", - " ds = ds.isel(node=indices_of_nodes_in_bbox, triface=indices_of_triface_nodes_in_bbox)\n", - " remapped_nodes = np.arange(len(indices_of_nodes_in_bbox))\n", - " remapped_triface_nodes = np.c_[\n", - " npi.remap(ds.triface_nodes[:,0], indices_of_nodes_in_bbox, remapped_nodes),\n", - " npi.remap(ds.triface_nodes[:,1], indices_of_nodes_in_bbox, remapped_nodes),\n", - " npi.remap(ds.triface_nodes[:,2], indices_of_nodes_in_bbox, remapped_nodes),\n", - " ]\n", - " ds[\"triface_nodes\"] = ((\"triface\", \"three\"), remapped_triface_nodes)\n", - " return ds" - ] - }, - { - "cell_type": "markdown", - "id": "77ee052d-6b60-4f68-a2c0-66d1341584f6", - "metadata": { - "tags": [] - }, - "source": [ - "Let's see it in action!\n", - "\n", - "The original Dataset depicts the Hampton port/Bay. \n", - "The BBox we used centers in the inner harbor area. \n", - "\n", - "`fds` is the filtered Dataset and as we can see it only contains 798 nodes and 1325 trifaces" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "926aa112-f444-4718-a5af-87605b3ee0ae", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "fds = filter_thalassa_by_bbox(\n", - " ds=ds,\n", - " lon_min=-72.6,\n", - " lon_max=-72.4,\n", - " lat_min=40.8,\n", - " lat_max=41.0,\n", - ")\n", - "\n", - "ds.dims\n", - "fds.dims" - ] - }, - { - "cell_type": "markdown", - "id": "c234f1c5-0ad2-41e9-87ab-5cfe0e482ebf", - "metadata": { - "tags": [] - }, - "source": [ - "### Visual diff\n", - "Let's use `thalassa` to visualize the difference:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "4f810fb2-140f-44b2-999d-16deab9c07ca", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "# The full dataset\n", - "trimesh = api.create_trimesh(\n", - " ds,\n", - " variable=\"zeta_max\",\n", - ")\n", - "dmap = api.get_tiles() * api.get_raster(trimesh=trimesh) #* api.get_wireframe(trimesh=trimesh)\n", - "dmap.opts(width=600, title=\"Full dataset\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "850bf0f0-24b3-4158-abd1-5bfe2283a40b", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "# The filtered dataset\n", - "ftrimesh = api.create_trimesh(\n", - " ds=fds,\n", - " variable=\"zeta_max\",\n", - ")\n", - "fdmap = api.get_tiles() * api.get_raster(trimesh=ftrimesh) * api.get_wireframe(trimesh=ftrimesh)\n", - "fdmap.opts(width=600, title=\"Filtered Dataset\")" - ] - }, - { - "cell_type": "markdown", - "id": "afa61cf4-1bf1-466e-b89c-1020f927d38f", - "metadata": { - "tags": [] - }, - "source": [ - "### Further development\n", - "\n", - "It should not be too difficult to extend/modify the function so that: \n", - "\n", - "1. it supports different Dataset schemas (e.g. vanilla ADCIRC, vanilla SCHISM) but this is left as an exercise to the reader.\n", - "2. it filters using a vector object (e.g. a shapefile) instead of a simple BBox." - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "thalassa", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.12" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} From 13465bf8a89e02dec2565dbf9ce5c429c786cbc5 Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Tue, 3 Oct 2023 16:40:46 +0300 Subject: [PATCH 02/19] pre-commit: Auto-update --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6894f3a..61b3dee 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -35,7 +35,7 @@ repos: - id: "python-use-type-annotations" - repo: "https://github.com/asottile/reorder_python_imports" - rev: "v3.11.0" + rev: "v3.12.0" hooks: - id: "reorder-python-imports" args: @@ -48,7 +48,7 @@ repos: - repo: "https://github.com/charliermarsh/ruff-pre-commit" # Ruff version. - rev: 'v0.0.291' + rev: 'v0.0.292' hooks: - id: "ruff" From 1de4e847e6bf3300525aea0ae6336814f916c897 Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Tue, 3 Oct 2023 16:41:27 +0300 Subject: [PATCH 03/19] docs: Update mkdocs configuration --- Makefile | 3 + docs/api.md | 4 +- mkdocs.yml | 116 +++++- poetry.lock | 596 ++++++++++++++++-------------- pyproject.toml | 3 + requirements/requirements-dev.txt | 43 +-- requirements/requirements.txt | 27 +- 7 files changed, 456 insertions(+), 336 deletions(-) diff --git a/Makefile b/Makefile index bcb08a8..9fcce9e 100644 --- a/Makefile +++ b/Makefile @@ -32,3 +32,6 @@ exec_notebooks: deps: pre-commit run poetry-lock -a pre-commit run poetry-export -a + +docs: + mkdocs serve diff --git a/docs/api.md b/docs/api.md index 9a06eab..834f036 100644 --- a/docs/api.md +++ b/docs/api.md @@ -1,6 +1,8 @@ # Reference -::: thalassa.api +::: thalassa + + diff --git a/mkdocs.yml b/mkdocs.yml index 89e002b..58bd5d8 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -43,26 +43,110 @@ watch: plugins: - "search" + - "autorefs" - "mkdocstrings": default_handler: python handlers: python: options: - # General - allow_inspection: true - show_source: false - # Headings - show_root_toc_entry: true - show_root_full_path: true - show_object_full_path: true - show_root_members_full_path: true - # members - members_order: "source" + ### General + # Whether to allow inspecting modules when visiting them is not possible. Default: True. + allow_inspection: True + # Show the base classes of a class. Default: True. + show_bases: True + # Show the source code of this object. Default: True. + show_source: True + # Pre-load modules that are not specified directly in autodoc instructions (::: identifier). It is useful when you want to render documentation for a particular member of an object, and this member is imported from another package than its parent. + # For an imported member to be rendered, you need to add it to the __all__ attribute of the importing module. + # The modules must be listed as an array of strings. Default: None. + preload_modules: null - annotations_path: "brief" - show_signature: true - show_signature_annotations: true - separate_signature: true + ### Headings + # The initial heading level to use. Default: 2. + heading_level: 2 + # Show the heading of the object at the root of the documentation tree (i.e. the object referenced by the identifier after :::). Default: False. + show_root_heading: True + # If the root heading is not shown, at least add a ToC entry for it. Default: True. + show_root_toc_entry: True + # Show the full Python path for the root object heading. Default: True. + show_root_full_path: True + # Show the full Python path of the root members. Default: False. + show_root_members_full_path: False + # Show the full Python path of every object. Default: False. + show_object_full_path: False + # When grouped by categories, show a heading for each category. Default: False. + show_category_heading: False + # Show the symbol type in headings (e.g. mod, class, meth, func and attr). Default: False. + show_symbol_type_heading: False + # Show the symbol type in the Table of Contents (e.g. mod, class, methd, func and attr). Default: False + show_symbol_type_toc: False + + ### Members + # A boolean, or an explicit list of inherited members to render. If true, select all inherited members, which can then be filtered with members. If false or empty list, do not select any inherited member. Default: False. + inherited_members: False + # A boolean, or an explicit list of members to render. If true, select all members without further filtering. If false or empty list, do not render members. If none, select all members and apply further filtering with filters and docstrings. Default: None. + members: null + # The members ordering to use. Options: alphabetical - order by the members names, source - order members as they appear in the source file. Default: "alphabetical". + members_order: "alphabetical" + # A list of filters applied to filter objects based on their name. A filter starting with ! will exclude matching objects instead of including them. The members option takes precedence over filters (filters will still be applied recursively to lower members in the hierarchy). Default: ["!^_[^_]"]. + filters: ["!^_[^_]"] + # Group the object's children by categories: attributes, classes, functions, and modules. Default: True. + group_by_category: True + # When rendering a module, show its submodules recursively. Default: False. + show_submodules: False + # Whether to render summaries of modules, classes, functions (methods) and attributes. + summary: True + + ### Docstrings + # The docstring style to use: google, numpy, sphinx, or None. Default: "google". + docstring_style: "google" + # The options for the docstring parser. See parsers under griffe.docstrings. + # docstring_options: + # The style used to render docstring sections. Options: table, list, spacy. Default: "table". + docstring_section_style: "spacy" + # Whether to merge the __init__ method into the class' signature and docstring. Default: False. + merge_init_into_class: False + # Show the object heading even if it has no docstring or children with docstrings. Default: False. + show_if_no_docstring: False + # Whether to display the "Attributes" section in the object's docstring. Default: True. + show_docstring_attributes: True + # Whether to display the "Functions" or "Methods" sections in the object's docstring. Default: True. + show_docstring_functions: True + # Whether to display the "Classes" section in the object's docstring. Default: True. + show_docstring_classes: True + # Whether to display the "Modules" section in the object's docstring. Default: True. + show_docstring_modules: True + # Whether to display the textual block (including admonitions) in the object's docstring. Default: True. + show_docstring_description: True + # Whether to display the "Examples" section in the object's docstring. Default: True. + show_docstring_examples: True + # Whether to display the "Other Parameters" section in the object's docstring. Default: True. + show_docstring_other_parameters: True + # Whether to display the "Parameters" section in the object's docstring. Default: True. + show_docstring_parameters: True + # Whether to display the "Raises" section in the object's docstring. Default: True. + show_docstring_raises: True + # Whether to display the "Receives" section in the object's docstring. Default: True. + show_docstring_receives: True + # Whether to display the "Returns" section in the object's docstring. Default: True. + show_docstring_returns: True + # Whether to display the "Warns" section in the object's docstring. Default: True. + show_docstring_warns: True + # Whether to display the "Yields" section in the object's docstring. Default: True. + show_docstring_yields: True + + ### Signature/annotations + # The verbosity for annotations path: brief (recommended), or source (as written in the source). Default: "brief". + annotations_path: "full" + # Maximum line length when formatting code/signatures. Default: 60. line_length: 88 - signature_crossrefs: true - show_root_heading: true + # Show methods and functions signatures. Default: True. + show_signature: True + # Show the type annotations in methods and functions signatures. Default: False. + show_signature_annotations: True + # Whether to render cross-references for type annotations in signatures. Default: False. + signature_crossrefs: True + # Whether to put the whole signature in a code block below the heading. If Black is installed, the signature is also formatted using it. Default: False. + separate_signature: True + # Whether to unwrap Annotated types to show only the type without the annotations. 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"sha256:fc7f93ded930c92394ef2cb6f04a8aabab4117a91449e72dcc8dfa646a508be8"}, ] [[package]] @@ -2099,13 +2114,13 @@ mkdocs = ">=1.1" [[package]] name = "mkdocs-material" -version = "9.4.2" +version = "9.4.3" description = "Documentation that simply works" optional = false python-versions = ">=3.8" files = [ - {file = "mkdocs_material-9.4.2-py3-none-any.whl", hash = "sha256:8651ff451f84681df9d2e3388906eee63c866576d98d6bb542826f83a091b289"}, - {file = "mkdocs_material-9.4.2.tar.gz", hash = "sha256:d53b17d058e70efd04c281f9b384ca10fb1f0bfecfe85dacdadad891bb826e3d"}, + {file = "mkdocs_material-9.4.3-py3-none-any.whl", hash = "sha256:3274a47a4e55a541b25bd8fa4937cf3f3c82a51763453511661e0052062758b9"}, + {file = "mkdocs_material-9.4.3.tar.gz", hash = "sha256:5c9abc3f6ba8f88be1f9f13df23d695ca4dddbdd8a3538e4e6279c055c3936bc"}, ] [package.dependencies] @@ -2165,13 +2180,13 @@ python-legacy = ["mkdocstrings-python-legacy (>=0.2.1)"] [[package]] name = "mkdocstrings-python" -version = "1.7.0" +version = "1.7.1" description = "A Python handler for mkdocstrings." optional = false python-versions = ">=3.8" files = [ - {file = "mkdocstrings_python-1.7.0-py3-none-any.whl", hash = "sha256:85c5f009a5a0ebb6076b7818c82a2bb0eebd0b54662628fa8b25ee14a6207951"}, - {file = "mkdocstrings_python-1.7.0.tar.gz", hash = "sha256:5dac2712bd38a3ff0812b8650a68b232601d1474091b380a8b5bc102c8c0d80a"}, + {file = "mkdocstrings_python-1.7.1-py3-none-any.whl", hash = "sha256:cb1651fba8423324b861fe38ce881cf56f30738770a2119f007a0a4ffcb00777"}, + {file = "mkdocstrings_python-1.7.1.tar.gz", hash = "sha256:90d838dc7861674794e3ca79f64c23c5d8fa76b9aa29db834b246771964c0881"}, ] [package.dependencies] @@ -2528,13 +2543,13 @@ numpy = "*" [[package]] name = "packaging" -version = "23.1" +version = "23.2" description = "Core utilities for Python packages" optional = false python-versions = ">=3.7" files = [ - {file = "packaging-23.1-py3-none-any.whl", hash = "sha256:994793af429502c4ea2ebf6bf664629d07c1a9fe974af92966e4b8d2df7edc61"}, - {file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"}, + {file = "packaging-23.2-py3-none-any.whl", hash = "sha256:8c491190033a9af7e1d931d0b5dacc2ef47509b34dd0de67ed209b5203fc88c7"}, + {file = "packaging-23.2.tar.gz", hash = "sha256:048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5"}, ] [[package]] @@ -2873,13 +2888,13 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa [[package]] name = "platformdirs" -version = "3.10.0" +version = "3.11.0" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." optional = false python-versions = ">=3.7" files = [ - {file = "platformdirs-3.10.0-py3-none-any.whl", hash = "sha256:d7c24979f292f916dc9cbf8648319032f551ea8c49a4c9bf2fb556a02070ec1d"}, - {file = "platformdirs-3.10.0.tar.gz", hash = "sha256:b45696dab2d7cc691a3226759c0d3b00c47c8b6e293d96f6436f733303f77f6d"}, + {file = "platformdirs-3.11.0-py3-none-any.whl", hash = "sha256:e9d171d00af68be50e9202731309c4e658fd8bc76f55c11c7dd760d023bda68e"}, + {file = "platformdirs-3.11.0.tar.gz", hash = "sha256:cf8ee52a3afdb965072dcc652433e0c7e3e40cf5ea1477cd4b3b1d2eb75495b3"}, ] [package.extras] @@ -3724,25 +3739,25 @@ testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jar [[package]] name = "setuptools-scm" -version = "8.0.3" +version = "8.0.4" description = "the blessed package to manage your versions by scm tags" optional = false python-versions = ">=3.8" files = [ - {file = "setuptools-scm-8.0.3.tar.gz", hash = "sha256:0169fd70197efda2f8c4d0b2a7a3d614431b488116f37b79d031e9e7ec884d8c"}, - {file = "setuptools_scm-8.0.3-py3-none-any.whl", hash = "sha256:813822234453438a13c78d05c8af29918fbc06f88efb33d38f065340bbb48c39"}, + {file = "setuptools-scm-8.0.4.tar.gz", hash = "sha256:b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7"}, + {file = "setuptools_scm-8.0.4-py3-none-any.whl", hash = "sha256:b47844cd2a84b83b3187a5782c71128c28b4c94cad8bfb871da2784a5cb54c4f"}, ] [package.dependencies] packaging = ">=20" setuptools = "*" tomli = {version = ">=1", markers = "python_version < \"3.11\""} -typing-extensions = {version = "*", markers = "python_version < \"3.11\""} +typing-extensions = "*" [package.extras] docs = ["entangled-cli[rich]", "mkdocs", "mkdocs-entangled-plugin", "mkdocs-material", "mkdocstrings[python]", "pygments"] rich = ["rich"] -test = ["pytest", "rich", "virtualenv (>20)"] +test = ["build", "pytest", "rich", "wheel"] [[package]] name = "shapely" @@ -3822,13 +3837,13 @@ files = [ [[package]] name = "stack-data" -version = "0.6.2" +version = "0.6.3" description = "Extract data from python stack frames and tracebacks for informative displays" optional = false python-versions = "*" files = [ - {file = "stack_data-0.6.2-py3-none-any.whl", hash = "sha256:cbb2a53eb64e5785878201a97ed7c7b94883f48b87bfb0bbe8b623c74679e4a8"}, - {file = "stack_data-0.6.2.tar.gz", hash = "sha256:32d2dd0376772d01b6cb9fc996f3c8b57a357089dec328ed4b6553d037eaf815"}, + {file = "stack_data-0.6.3-py3-none-any.whl", hash = "sha256:d5558e0c25a4cb0853cddad3d77da9891a08cb85dd9f9f91b9f8cd66e511e695"}, + {file = "stack_data-0.6.3.tar.gz", hash = "sha256:836a778de4fec4dcd1dcd89ed8abff8a221f58308462e1c4aa2a3cf30148f0b9"}, ] [package.dependencies] @@ -3934,6 +3949,17 @@ files = [ docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] test = ["argcomplete (>=3.0.3)", "mypy (>=1.5.1)", "pre-commit", "pytest (>=7.0,<7.5)", "pytest-mock", "pytest-mypy-testing"] +[[package]] +name = "types-decorator" +version = "5.1.8.4" +description = "Typing stubs for decorator" +optional = false +python-versions = "*" +files = [ + {file = "types-decorator-5.1.8.4.tar.gz", hash = "sha256:a8c39024634e99834bef146cec2e36c585f47884addf4dc65d6d0b7b1f627517"}, + {file = "types_decorator-5.1.8.4-py3-none-any.whl", hash = "sha256:e411203e0ec0116964dcd491e162a951e4a68cd2d4a946172690bee43c4ebe6e"}, +] + [[package]] name = "typing-extensions" version = "4.8.0" @@ -3972,13 +3998,13 @@ test = ["coverage", "pytest", "pytest-cov"] [[package]] name = "urllib3" -version = "2.0.5" +version = "2.0.6" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false python-versions = ">=3.7" files = [ - {file = "urllib3-2.0.5-py3-none-any.whl", hash = "sha256:ef16afa8ba34a1f989db38e1dbbe0c302e4289a47856990d0682e374563ce35e"}, - {file = "urllib3-2.0.5.tar.gz", hash = "sha256:13abf37382ea2ce6fb744d4dad67838eec857c9f4f57009891805e0b5e123594"}, + {file = "urllib3-2.0.6-py3-none-any.whl", hash = "sha256:7a7c7003b000adf9e7ca2a377c9688bbc54ed41b985789ed576570342a375cd2"}, + {file = "urllib3-2.0.6.tar.gz", hash = "sha256:b19e1a85d206b56d7df1d5e683df4a7725252a964e3993648dd0fb5a1c157564"}, ] [package.extras] @@ -4028,13 +4054,13 @@ watchmedo = ["PyYAML (>=3.10)"] [[package]] name = "wcwidth" -version = "0.2.6" +version = "0.2.8" description = "Measures the displayed width of unicode strings in a terminal" optional = false python-versions = "*" files = [ - {file = "wcwidth-0.2.6-py2.py3-none-any.whl", hash = "sha256:795b138f6875577cd91bba52baf9e445cd5118fd32723b460e30a0af30ea230e"}, - {file = "wcwidth-0.2.6.tar.gz", hash = "sha256:a5220780a404dbe3353789870978e472cfe477761f06ee55077256e509b156d0"}, + {file = "wcwidth-0.2.8-py2.py3-none-any.whl", hash = "sha256:77f719e01648ed600dfa5402c347481c0992263b81a027344f3e1ba25493a704"}, + {file = "wcwidth-0.2.8.tar.gz", hash = "sha256:8705c569999ffbb4f6a87c6d1b80f324bd6db952f5eb0b95bc07517f4c1813d4"}, ] [[package]] @@ -4158,4 +4184,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.9, <4.0" -content-hash = "935e583ff1b84e54d2e12d41ade4f4a4c9a2d994f21ca2f4700719d5b1d545e7" +content-hash = "c8282f41f3b2b81685c9df2a948cc9f7788e01ffbac8f8f92f187c2d48c8b968" diff --git a/pyproject.toml b/pyproject.toml index 40eea0a..ca39228 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,6 +27,7 @@ bokeh = ">=3.0" Cartopy = "*" dask = "*" datashader = "*" +decorator = "*" geopandas = "*" geoviews = ">=1.10" holoviews = "*" @@ -35,7 +36,9 @@ numba = ">0.52" numpy = "*" numpy-indexed = "*" pandas = "*" +scipy = "*" shapely = "*" +types-decorator = "*" xarray = {version = "*", extras = ["io", "accel"]} [tool.poetry.group.dev.dependencies] diff --git a/requirements/requirements-dev.txt b/requirements/requirements-dev.txt index 947ee26..967c603 100644 --- a/requirements/requirements-dev.txt +++ b/requirements/requirements-dev.txt @@ -11,9 +11,9 @@ bokeh==3.2.2 ; python_version >= "3.9" and python_version < "4.0" bottleneck==1.3.7 ; python_version >= "3.9" and python_version < "4.0" cartopy==0.22.0 ; python_version >= "3.9" and python_version < "4.0" certifi==2023.7.22 ; python_version >= "3.9" and python_version < "4.0" -cffi==1.15.1 ; python_version >= "3.9" and python_version < "4.0" and implementation_name == "pypy" +cffi==1.16.0 ; python_version >= "3.9" and python_version < "4.0" and implementation_name == "pypy" cftime==1.6.2 ; python_version >= "3.9" and python_version < "4.0" -charset-normalizer==3.2.0 ; python_version >= "3.9" and python_version < "4.0" +charset-normalizer==3.3.0 ; python_version >= "3.9" and python_version < "4.0" click-plugins==1.1.1 ; python_version >= "3.9" and python_version < "4.0" click==8.1.7 ; python_version >= "3.9" and python_version < "4.0" cligj==0.7.2 ; python_version >= "3.9" and python_version < "4" @@ -23,10 +23,10 @@ colorcet==3.0.1 ; python_version >= "3.9" and python_version < "4.0" comm==0.1.4 ; python_version >= "3.9" and python_version < "4.0" contourpy==1.1.1 ; python_version >= "3.9" and python_version < "4.0" covdefaults==2.3.0 ; python_version >= "3.9" and python_version < "4.0" -coverage==7.3.1 ; python_version >= "3.9" and python_version < "4.0" -coverage[toml]==7.3.1 ; python_version >= "3.9" and python_version < "4.0" -cycler==0.11.0 ; python_version >= "3.9" and python_version < "4.0" -dask==2023.9.2 ; python_version >= "3.9" and python_version < "4.0" +coverage==7.3.2 ; python_version >= "3.9" and python_version < "4.0" +coverage[toml]==7.3.2 ; python_version >= "3.9" and python_version < "4.0" +cycler==0.12.0 ; python_version >= "3.9" and python_version < "4.0" +dask==2023.9.3 ; python_version >= "3.9" and python_version < "4.0" datashader==0.15.2 ; python_version >= "3.9" and python_version < "4.0" datashape==0.5.2 ; python_version >= "3.9" and python_version < "4.0" debugpy==1.8.0 ; python_version >= "3.9" and python_version < "4.0" @@ -35,18 +35,18 @@ defusedxml==0.7.1 ; python_version >= "3.9" and python_version < "4.0" docopt==0.6.2 ; python_version < "3.10" and python_version >= "3.9" entrypoints==0.4 ; python_version >= "3.9" and python_version < "4.0" exceptiongroup==1.1.3 ; python_version >= "3.9" and python_version < "3.11" -executing==1.2.0 ; python_version >= "3.9" and python_version < "4.0" +executing==2.0.0 ; python_version >= "3.9" and python_version < "4.0" fasteners==0.19 ; python_version >= "3.9" and python_version < "4.0" -fastjsonschema==2.18.0 ; python_version >= "3.9" and python_version < "4.0" +fastjsonschema==2.18.1 ; python_version >= "3.9" and python_version < "4.0" fiona==1.9.4.post1 ; python_version >= "3.9" and python_version < "4.0" flox==0.7.2 ; python_version >= "3.9" and python_version < "4.0" -fonttools==4.42.1 ; python_version >= "3.9" and python_version < "4.0" +fonttools==4.43.0 ; python_version >= "3.9" and python_version < "4.0" fsspec==2023.9.2 ; python_version >= "3.9" and python_version < "4.0" future==0.18.3 ; python_version >= "3.9" and python_version < "4.0" geopandas==0.14.0 ; python_version >= "3.9" and python_version < "4.0" geoviews==1.10.1 ; python_version >= "3.9" and python_version < "4.0" ghp-import==2.1.0 ; python_version >= "3.9" and python_version < "4.0" -griffe==0.36.2 ; python_version >= "3.9" and python_version < "4.0" +griffe==0.36.4 ; python_version >= "3.9" and python_version < "4.0" h5netcdf==1.2.0 ; python_version >= "3.9" and python_version < "4.0" h5py==3.9.0 ; python_version >= "3.9" and python_version < "4.0" holoviews==1.17.1 ; python_version >= "3.9" and python_version < "4.0" @@ -55,9 +55,9 @@ importlib-metadata==6.8.0 ; python_version >= "3.9" and python_version < "4.0" importlib-resources==6.1.0 ; python_version >= "3.9" and python_version < "3.10" iniconfig==2.0.0 ; python_version >= "3.9" and python_version < "4.0" ipykernel==6.25.2 ; python_version >= "3.9" and python_version < "4.0" -ipython==8.15.0 ; python_version >= "3.9" and python_version < "4.0" +ipython==8.16.1 ; python_version >= "3.9" and python_version < "4.0" ipywidgets==8.1.1 ; python_version >= "3.9" and python_version < "4.0" -jedi==0.19.0 ; python_version >= "3.9" and python_version < "4.0" +jedi==0.19.1 ; python_version >= "3.9" and python_version < "4.0" jinja2==3.1.2 ; python_version >= "3.9" and python_version < "4.0" jsonschema-specifications==2023.7.1 ; python_version >= "3.9" and python_version < "4.0" jsonschema==4.19.1 ; python_version >= "3.9" and python_version < "4.0" @@ -77,12 +77,12 @@ matplotlib==3.8.0 ; python_version >= "3.9" and python_version < "4.0" mdit-py-plugins==0.4.0 ; python_version >= "3.9" and python_version < "4.0" mdurl==0.1.2 ; python_version >= "3.9" and python_version < "4.0" mergedeep==1.3.4 ; python_version >= "3.9" and python_version < "4.0" -mistune==3.0.1 ; python_version >= "3.9" and python_version < "4.0" +mistune==3.0.2 ; python_version >= "3.9" and python_version < "4.0" mkdocs-autorefs==0.5.0 ; python_version >= "3.9" and python_version < "4.0" mkdocs-material-extensions==1.2 ; python_version >= "3.9" and python_version < "4.0" -mkdocs-material==9.4.2 ; python_version >= "3.9" and python_version < "4.0" +mkdocs-material==9.4.3 ; python_version >= "3.9" and python_version < "4.0" mkdocs==1.5.3 ; python_version >= "3.9" and python_version < "4.0" -mkdocstrings-python==1.7.0 ; python_version >= "3.9" and python_version < "4.0" +mkdocstrings-python==1.7.1 ; python_version >= "3.9" and python_version < "4.0" mkdocstrings==0.23.0 ; python_version >= "3.9" and python_version < "4.0" multipledispatch==1.0.0 ; python_version >= "3.9" and python_version < "4.0" mypy-extensions==1.0.0 ; python_version >= "3.9" and python_version < "4.0" @@ -98,7 +98,7 @@ numcodecs==0.11.0 ; python_version >= "3.9" and python_version < "4.0" numpy-groupies==0.10.1 ; python_version >= "3.9" and python_version < "4.0" numpy-indexed==0.3.7 ; python_version >= "3.9" and python_version < "4.0" numpy==1.25.2 ; python_version >= "3.9" and python_version < "4.0" -packaging==23.1 ; python_version >= "3.9" and python_version < "4.0" +packaging==23.2 ; python_version >= "3.9" and python_version < "4.0" paginate==0.5.6 ; python_version >= "3.9" and python_version < "4.0" pandas==2.1.1 ; python_version >= "3.9" and python_version < "4.0" pandocfilters==1.5.0 ; python_version >= "3.9" and python_version < "4.0" @@ -110,7 +110,7 @@ pathspec==0.11.2 ; python_version >= "3.9" and python_version < "4.0" pexpect==4.8.0 ; python_version >= "3.9" and python_version < "4.0" and sys_platform != "win32" pickleshare==0.7.5 ; python_version >= "3.9" and python_version < "4.0" pillow==10.0.1 ; python_version >= "3.9" and python_version < "4.0" -platformdirs==3.10.0 ; python_version >= "3.9" and python_version < "4.0" +platformdirs==3.11.0 ; python_version >= "3.9" and python_version < "4.0" pluggy==1.3.0 ; python_version >= "3.9" and python_version < "4.0" pooch==1.7.0 ; python_version >= "3.9" and python_version < "4.0" prompt-toolkit==3.0.39 ; python_version >= "3.9" and python_version < "4.0" @@ -139,24 +139,25 @@ regex==2023.8.8 ; python_version >= "3.9" and python_version < "4.0" requests==2.31.0 ; python_version >= "3.9" and python_version < "4.0" rpds-py==0.10.3 ; python_version >= "3.9" and python_version < "4.0" scipy==1.9.3 ; python_version >= "3.9" and python_version < "4.0" -setuptools-scm==8.0.3 ; python_version >= "3.9" and python_version < "4.0" +setuptools-scm==8.0.4 ; python_version >= "3.9" and python_version < "4.0" setuptools==68.2.2 ; python_version >= "3.9" and python_version < "4.0" shapely==2.0.1 ; python_version >= "3.9" and python_version < "4.0" six==1.16.0 ; python_version >= "3.9" and python_version < "4.0" soupsieve==2.5 ; python_version >= "3.9" and python_version < "4.0" -stack-data==0.6.2 ; python_version >= "3.9" and python_version < "4.0" +stack-data==0.6.3 ; python_version >= "3.9" and python_version < "4.0" tinycss2==1.2.1 ; python_version >= "3.9" and python_version < "4.0" tomli==2.0.1 ; python_version >= "3.9" and python_full_version <= "3.11.0a6" toolz==0.12.0 ; python_version >= "3.9" and python_version < "4.0" tornado==6.3.3 ; python_version >= "3.9" and python_version < "4.0" tqdm==4.66.1 ; python_version >= "3.9" and python_version < "4.0" traitlets==5.10.1 ; python_version >= "3.9" and python_version < "4.0" +types-decorator==5.1.8.4 ; python_version >= "3.9" and python_version < "4.0" typing-extensions==4.8.0 ; python_version >= "3.9" and python_version < "4.0" tzdata==2023.3 ; python_version >= "3.9" and python_version < "4.0" uc-micro-py==1.0.2 ; python_version >= "3.9" and python_version < "4.0" -urllib3==2.0.5 ; python_version >= "3.9" and python_version < "4.0" +urllib3==2.0.6 ; python_version >= "3.9" and python_version < "4.0" watchdog==3.0.0 ; python_version >= "3.9" and python_version < "4.0" -wcwidth==0.2.6 ; python_version >= "3.9" and python_version < "4.0" +wcwidth==0.2.8 ; python_version >= "3.9" and python_version < "4.0" webencodings==0.5.1 ; python_version >= "3.9" and python_version < "4.0" webob==1.8.7 ; python_version >= "3.9" and python_version < "3.10" widgetsnbextension==4.0.9 ; python_version >= "3.9" and python_version < "4.0" diff --git a/requirements/requirements.txt b/requirements/requirements.txt index b96ffea..7df1b30 100644 --- a/requirements/requirements.txt +++ b/requirements/requirements.txt @@ -10,7 +10,7 @@ bottleneck==1.3.7 ; python_version >= "3.9" and python_version < "4.0" cartopy==0.22.0 ; python_version >= "3.9" and python_version < "4.0" certifi==2023.7.22 ; python_version >= "3.9" and python_version < "4.0" cftime==1.6.2 ; python_version >= "3.9" and python_version < "4.0" -charset-normalizer==3.2.0 ; python_version >= "3.9" and python_version < "4.0" +charset-normalizer==3.3.0 ; python_version >= "3.9" and python_version < "4.0" click-plugins==1.1.1 ; python_version >= "3.9" and python_version < "4.0" click==8.1.7 ; python_version >= "3.9" and python_version < "4.0" cligj==0.7.2 ; python_version >= "3.9" and python_version < "4" @@ -19,19 +19,19 @@ colorama==0.4.6 ; python_version >= "3.9" and python_version < "4.0" and (platfo colorcet==3.0.1 ; python_version >= "3.9" and python_version < "4.0" comm==0.1.4 ; python_version >= "3.9" and python_version < "4.0" contourpy==1.1.1 ; python_version >= "3.9" and python_version < "4.0" -cycler==0.11.0 ; python_version >= "3.9" and python_version < "4.0" -dask==2023.9.2 ; python_version >= "3.9" and python_version < "4.0" +cycler==0.12.0 ; python_version >= "3.9" and python_version < "4.0" +dask==2023.9.3 ; python_version >= "3.9" and python_version < "4.0" datashader==0.15.2 ; python_version >= "3.9" and python_version < "4.0" datashape==0.5.2 ; python_version >= "3.9" and python_version < "4.0" decorator==5.1.1 ; python_version >= "3.9" and python_version < "4.0" docopt==0.6.2 ; python_version < "3.10" and python_version >= "3.9" entrypoints==0.4 ; python_version >= "3.9" and python_version < "4.0" exceptiongroup==1.1.3 ; python_version >= "3.9" and python_version < "3.11" -executing==1.2.0 ; python_version >= "3.9" and python_version < "4.0" +executing==2.0.0 ; python_version >= "3.9" and python_version < "4.0" fasteners==0.19 ; python_version >= "3.9" and python_version < "4.0" fiona==1.9.4.post1 ; python_version >= "3.9" and python_version < "4.0" flox==0.7.2 ; python_version >= "3.9" and python_version < "4.0" -fonttools==4.42.1 ; python_version >= "3.9" and python_version < "4.0" +fonttools==4.43.0 ; python_version >= "3.9" and python_version < "4.0" fsspec==2023.9.2 ; python_version >= "3.9" and python_version < "4.0" future==0.18.3 ; python_version >= "3.9" and python_version < "4.0" geopandas==0.14.0 ; python_version >= "3.9" and python_version < "4.0" @@ -42,9 +42,9 @@ holoviews==1.17.1 ; python_version >= "3.9" and python_version < "4.0" idna==3.4 ; python_version >= "3.9" and python_version < "4.0" importlib-metadata==6.8.0 ; python_version >= "3.9" and python_version < "4.0" importlib-resources==6.1.0 ; python_version >= "3.9" and python_version < "3.10" -ipython==8.15.0 ; python_version >= "3.9" and python_version < "4.0" +ipython==8.16.1 ; python_version >= "3.9" and python_version < "4.0" ipywidgets==8.1.1 ; python_version >= "3.9" and python_version < "4.0" -jedi==0.19.0 ; python_version >= "3.9" and python_version < "4.0" +jedi==0.19.1 ; python_version >= "3.9" and python_version < "4.0" jinja2==3.1.2 ; python_version >= "3.9" and python_version < "4.0" jupyterlab-widgets==3.0.9 ; python_version >= "3.9" and python_version < "4.0" kiwisolver==1.4.5 ; python_version >= "3.9" and python_version < "4.0" @@ -66,7 +66,7 @@ numcodecs==0.11.0 ; python_version >= "3.9" and python_version < "4.0" numpy-groupies==0.10.1 ; python_version >= "3.9" and python_version < "4.0" numpy-indexed==0.3.7 ; python_version >= "3.9" and python_version < "4.0" numpy==1.25.2 ; python_version >= "3.9" and python_version < "4.0" -packaging==23.1 ; python_version >= "3.9" and python_version < "4.0" +packaging==23.2 ; python_version >= "3.9" and python_version < "4.0" pandas==2.1.1 ; python_version >= "3.9" and python_version < "4.0" panel==1.2.3 ; python_version >= "3.9" and python_version < "4.0" param==1.13.0 ; python_version >= "3.9" and python_version < "4.0" @@ -75,7 +75,7 @@ partd==1.4.1 ; python_version >= "3.9" and python_version < "4.0" pexpect==4.8.0 ; python_version >= "3.9" and python_version < "4.0" and sys_platform != "win32" pickleshare==0.7.5 ; python_version >= "3.9" and python_version < "4.0" pillow==10.0.1 ; python_version >= "3.9" and python_version < "4.0" -platformdirs==3.10.0 ; python_version >= "3.9" and python_version < "4.0" +platformdirs==3.11.0 ; python_version >= "3.9" and python_version < "4.0" pooch==1.7.0 ; python_version >= "3.9" and python_version < "4.0" prompt-toolkit==3.0.39 ; python_version >= "3.9" and python_version < "4.0" ptyprocess==0.7.0 ; python_version >= "3.9" and python_version < "4.0" and sys_platform != "win32" @@ -92,22 +92,23 @@ pyviz-comms==3.0.0 ; python_version >= "3.9" and python_version < "4.0" pyyaml==6.0.1 ; python_version >= "3.9" and python_version < "4.0" requests==2.31.0 ; python_version >= "3.9" and python_version < "4.0" scipy==1.9.3 ; python_version >= "3.9" and python_version < "4.0" -setuptools-scm==8.0.3 ; python_version >= "3.9" and python_version < "4.0" +setuptools-scm==8.0.4 ; python_version >= "3.9" and python_version < "4.0" setuptools==68.2.2 ; python_version >= "3.9" and python_version < "4.0" shapely==2.0.1 ; python_version >= "3.9" and python_version < "4.0" six==1.16.0 ; python_version >= "3.9" and python_version < "4.0" soupsieve==2.5 ; python_version < "3.10" and python_version >= "3.9" -stack-data==0.6.2 ; python_version >= "3.9" and python_version < "4.0" +stack-data==0.6.3 ; python_version >= "3.9" and python_version < "4.0" tomli==2.0.1 ; python_version >= "3.9" and python_version < "3.11" toolz==0.12.0 ; python_version >= "3.9" and python_version < "4.0" tornado==6.3.3 ; python_version >= "3.9" and python_version < "4.0" tqdm==4.66.1 ; python_version >= "3.9" and python_version < "4.0" traitlets==5.10.1 ; python_version >= "3.9" and python_version < "4.0" +types-decorator==5.1.8.4 ; python_version >= "3.9" and python_version < "4.0" typing-extensions==4.8.0 ; python_version >= "3.9" and python_version < "4.0" tzdata==2023.3 ; python_version >= "3.9" and python_version < "4.0" uc-micro-py==1.0.2 ; python_version >= "3.9" and python_version < "4.0" -urllib3==2.0.5 ; python_version >= "3.9" and python_version < "4.0" -wcwidth==0.2.6 ; python_version >= "3.9" and python_version < "4.0" +urllib3==2.0.6 ; python_version >= "3.9" and python_version < "4.0" +wcwidth==0.2.8 ; python_version >= "3.9" and python_version < "4.0" webencodings==0.5.1 ; python_version >= "3.9" and python_version < "4.0" webob==1.8.7 ; python_version >= "3.9" and python_version < "3.10" widgetsnbextension==4.0.9 ; python_version >= "3.9" and python_version < "4.0" From fb05864323b62e2a86290b44e0c4973c45d77e7e Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Tue, 3 Oct 2023 16:44:56 +0300 Subject: [PATCH 04/19] plotting: Add `plot_ts()` --- thalassa/__init__.py | 2 ++ thalassa/plotting.py | 15 +++++++++++++++ 2 files changed, 17 insertions(+) diff --git a/thalassa/__init__.py b/thalassa/__init__.py index 0ece6e6..f8f731d 100644 --- a/thalassa/__init__.py +++ b/thalassa/__init__.py @@ -3,6 +3,7 @@ from .api import open_dataset from .plotting import plot from .plotting import plot_mesh +from .plotting import plot_ts from .utils import crop __all__: list[str] = [ @@ -10,4 +11,5 @@ "open_dataset", "plot", "plot_mesh", + "plot_ts", ] diff --git a/thalassa/plotting.py b/thalassa/plotting.py index 1c8505e..1fd55e2 100644 --- a/thalassa/plotting.py +++ b/thalassa/plotting.py @@ -64,3 +64,18 @@ def plot( else: overlay = hv.Overlay((tiles, raster)) return overlay.collate() + + +def plot_ts( + ds: xr.Dataset, + variable: str, + source_plot: gv.DynamicMap, +) -> gv.DynamicMap: + """ + Return an `hv.Curve` with the full timeseries of a specific node. + + The node is selected by clicking on `source_plot`. + """ + ds = normalization.normalize_dataset(ds) + ts = api.get_tap_timeseries(ds, variable, source_plot._raster) + return ts From 6bdfce0cbac062acdf6d98acc4d5094323addeea Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Tue, 3 Oct 2023 16:46:24 +0300 Subject: [PATCH 05/19] utils: minor: Update `typing` imports --- thalassa/utils.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/thalassa/utils.py b/thalassa/utils.py index 4e298f8..9ac69f5 100644 --- a/thalassa/utils.py +++ b/thalassa/utils.py @@ -1,7 +1,7 @@ from __future__ import annotations import logging.config -import typing +import typing as T import geopandas as gpd import geoviews as gv @@ -69,7 +69,7 @@ def generate_thalassa_ds( if time_range is not None: coords["time"] = (("time"), time_range) # Data Variables - data_vars: dict[str, typing.Any] = { + data_vars: dict[str, T.Any] = { "triface_nodes": (("triface", "three"), triface_nodes), **kwargs, } @@ -100,7 +100,7 @@ def is_variable_visualizable(ds: xr.Dataset, variable: str) -> bool: return ds[variable].dims in _VISUALIZABLE_DIMS -def filter_visualizable_data_vars(ds: xr.Dataset, variables: typing.Iterable[str]) -> list[str]: +def filter_visualizable_data_vars(ds: xr.Dataset, variables: T.Iterable[str]) -> list[str]: visualizable = [] for var in variables: if is_variable_visualizable(ds=ds, variable=var): @@ -132,7 +132,7 @@ def split_quads(face_nodes: npt.NDArray[np.int_]) -> npt.NDArray[np.int_]: # Append new triangles to the existing ones # Also cast to the proper type for Mypy - new_face_nodes = typing.cast( + new_face_nodes = T.cast( npt.NDArray[np.int_], np.r_[existing_triangles, new_triangles].astype(int), ) @@ -144,7 +144,7 @@ def get_index_of_nearest_node(ds: xr.Dataset, lon: float, lat: float) -> int: # https://www.unidata.ucar.edu/blogs/developer/en/entry/accessing_netcdf_data_by_coordinates # https://github.com/Unidata/python-workshop/blob/fall-2016/notebooks/netcdf-by-coordinates.ipynb dist = abs(ds.lon - lon) ** 2 + abs(ds.lat - lat) ** 2 - index_of_nearest_node = typing.cast(int, dist.argmin()) + index_of_nearest_node = T.cast(int, dist.argmin()) return index_of_nearest_node @@ -244,7 +244,7 @@ def is_point_in_the_raster(raster: gv.DynamicMap, lon: float, lat: float) -> boo raster_dataset = raster.values()[0].data data_var_name = raster.ddims[-1].name interpolated = raster_dataset[data_var_name].interp(dict(lon=lon, lat=lat)).data - return typing.cast(bool, ~np.isnan(interpolated)) + return T.cast(bool, ~np.isnan(interpolated)) def generate_mesh_polygon(ds: xr.Dataset) -> gpd.GeoDataFrame: From 5c458e4d4d4fd60621f8e97c12daa478afa59bca Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Tue, 3 Oct 2023 16:48:09 +0300 Subject: [PATCH 06/19] minor --- thalassa/api.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/thalassa/api.py b/thalassa/api.py index 4e1c431..2fda3d4 100644 --- a/thalassa/api.py +++ b/thalassa/api.py @@ -191,7 +191,10 @@ def callback(x: float, y: float) -> hv.Curve: ) # setup hover hover = HoverTool( - tooltips=[("time", "@time{%F %T}"), (f"{variable}", f"@{variable}")], + tooltips=[ + ("time", "@time{%F %T}"), + (f"{variable}", f"@{variable}"), + ], formatters={ "@time": "datetime", }, From 056b14ed1b66d8ff5a6f6f87eb15648a930a2d7c Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Tue, 3 Oct 2023 16:46:44 +0300 Subject: [PATCH 07/19] docs: Add a docstring to `crop()` --- thalassa/utils.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/thalassa/utils.py b/thalassa/utils.py index 9ac69f5..a3696ec 100644 --- a/thalassa/utils.py +++ b/thalassa/utils.py @@ -30,6 +30,13 @@ def crop( ds: xr.Dataset, bbox: shapely.Polygon | tuple[float, float, float, float], ) -> xr.Dataset: + """ + Crop the dataset using the provided `bbox` + + Parameters: + ds: The dataset we want to crop. + bbox: A Shapely polygon which will be used to (on-the-fly) crop the `dataset`. + """ bbox = resolve_bbox(bbox) indices_of_nodes_in_bbox = np.where( True From 5d6873de3ad17590229468f97a63ec5f72e8094d Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Tue, 3 Oct 2023 16:48:39 +0300 Subject: [PATCH 08/19] docs: Add docstring to `normalize_dataset()` --- thalassa/normalization.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/thalassa/normalization.py b/thalassa/normalization.py index 1027751..ede4576 100644 --- a/thalassa/normalization.py +++ b/thalassa/normalization.py @@ -179,6 +179,12 @@ def normalize_adcirc(ds: xr.Dataset) -> xr.Dataset: def normalize_dataset(ds: xr.Dataset) -> xr.Dataset: + """ + Normalize the `dataset` i.e. convert it to the "Thalassa Schema". + + Parameters: + ds: The dataset we want to convert. + """ logger.debug("Dataset normalization: Started") fmt = infer_format(ds) normalizer_func = NORMALIZE_DISPATCHER[fmt] From 797bb40f0fb44246c7bd4be66efde0d119ef414d Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Tue, 3 Oct 2023 16:49:30 +0300 Subject: [PATCH 09/19] docs: Add docstring to `plot_mesh()` --- thalassa/plotting.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/thalassa/plotting.py b/thalassa/plotting.py index 1fd55e2..70d4f80 100644 --- a/thalassa/plotting.py +++ b/thalassa/plotting.py @@ -19,6 +19,15 @@ def plot_mesh( bbox: shapely.Polygon | None = None, title: str = "Mesh", ) -> gv.DynamicMap: + """ + Plot the mesh of the dataset + + Parameters: + ds: The dataset whose mesh we want to visualize. + bbox: A Shapely polygon which will be used to (on-the-fly) crop the `dataset`. + title: The title of the plot + + """ ds = normalization.normalize_dataset(ds) if bbox: ds = utils.crop(ds, bbox) From 4690925eaa716286839e442833dcae37943b9554 Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Tue, 3 Oct 2023 16:53:16 +0300 Subject: [PATCH 10/19] docs: Add docstring to `plot()` --- thalassa/plotting.py | 21 ++++++++++++++++++++- 1 file changed, 20 insertions(+), 1 deletion(-) diff --git a/thalassa/plotting.py b/thalassa/plotting.py index 70d4f80..df9eff1 100644 --- a/thalassa/plotting.py +++ b/thalassa/plotting.py @@ -51,7 +51,26 @@ def plot( y_range: tuple[float, float] | None = None, show_mesh: bool = False, ) -> gv.DynamicMap: - ds = normalization.normalize_dataset(ds) + """ + Return the plot of the specified `variable`. + + Parameters: + ds: The dataset which will get rendered. It must adhere to the "thalassa schema" + variable: The `dataset`'s variable which we want to visualize. + bbox: A Shapely polygon which will be used to (on-the-fly) crop the `dataset`. + title: The title of the plot. Defaults to `variable`. + cmap: The colormap to use. + colorbar: Boolean flag indicating whether the plot should have an integrated colorbar. + clabel: A caption for the colorbar. Useful for indicating e.g. units + clim_min: The lower limit for the colorbar. + clim_max: The upper limit for the colorbar. + x_range: A tuple indicating the minimum and maximum longitude to be displayed. + y_range: A tuple indicating the minimum and maximum latitude to be displayed. + show_mesh: A boolean flag indicating whether the mesh should be overlayed on the rendered variable. + Enabling this makes rendering slower. + + """ + ds = normalization.normalize(ds) if bbox: ds = utils.crop(ds, bbox) trimesh = api.create_trimesh(ds=ds, variable=variable) From 3bb325638d1f995cde2202540e960ff1cc88daed Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Tue, 3 Oct 2023 16:52:56 +0300 Subject: [PATCH 11/19] refactor: Rename `normalize_dataset()` -> `normalize()` --- thalassa/__init__.py | 2 ++ thalassa/api.py | 2 +- thalassa/normalization.py | 2 +- thalassa/plotting.py | 4 ++-- 4 files changed, 6 insertions(+), 4 deletions(-) diff --git a/thalassa/__init__.py b/thalassa/__init__.py index f8f731d..88dba4c 100644 --- a/thalassa/__init__.py +++ b/thalassa/__init__.py @@ -1,6 +1,7 @@ from __future__ import annotations from .api import open_dataset +from .normalization import normalize from .plotting import plot from .plotting import plot_mesh from .plotting import plot_ts @@ -8,6 +9,7 @@ __all__: list[str] = [ "crop", + "normalize", "open_dataset", "plot", "plot_mesh", diff --git a/thalassa/api.py b/thalassa/api.py index 2fda3d4..e91290c 100644 --- a/thalassa/api.py +++ b/thalassa/api.py @@ -65,7 +65,7 @@ def open_dataset( with warnings.catch_warnings(record=True): ds = xr.open_dataset(path, **(default_kwargs | kwargs)) # type: ignore[arg-type] if normalize: - ds = normalization.normalize_dataset(ds) + ds = normalization.normalize(ds) return ds diff --git a/thalassa/normalization.py b/thalassa/normalization.py index ede4576..7ef1c6a 100644 --- a/thalassa/normalization.py +++ b/thalassa/normalization.py @@ -178,7 +178,7 @@ def normalize_adcirc(ds: xr.Dataset) -> xr.Dataset: } -def normalize_dataset(ds: xr.Dataset) -> xr.Dataset: +def normalize(ds: xr.Dataset) -> xr.Dataset: """ Normalize the `dataset` i.e. convert it to the "Thalassa Schema". diff --git a/thalassa/plotting.py b/thalassa/plotting.py index df9eff1..1fd221e 100644 --- a/thalassa/plotting.py +++ b/thalassa/plotting.py @@ -28,7 +28,7 @@ def plot_mesh( title: The title of the plot """ - ds = normalization.normalize_dataset(ds) + ds = normalization.normalize(ds) if bbox: ds = utils.crop(ds, bbox) tiles = api.get_tiles() @@ -104,6 +104,6 @@ def plot_ts( The node is selected by clicking on `source_plot`. """ - ds = normalization.normalize_dataset(ds) + ds = normalization.normalize(ds) ts = api.get_tap_timeseries(ds, variable, source_plot._raster) return ts From 3850ea4d43d4e2756196359027053cd75efb9677 Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Tue, 3 Oct 2023 16:54:46 +0300 Subject: [PATCH 12/19] api: Let API function accept either a `Dataset` or a `TriMesh` object. --- notebooks/API.ipynb | 2 +- thalassa/api.py | 19 ++++++++++++------- thalassa/plotting.py | 18 +++++++++++------- 3 files changed, 24 insertions(+), 15 deletions(-) diff --git a/notebooks/API.ipynb b/notebooks/API.ipynb index b9516b5..22005d4 100644 --- a/notebooks/API.ipynb +++ b/notebooks/API.ipynb @@ -138,7 +138,7 @@ "\n", "# The trimesh is the most basic object. This is what you need to create all the others graphs\n", "# It is on this object that you specify the timestamp and/or the layer.\n", - "trimesh = api.create_trimesh(ds=ds.sel(time=timestamp), variable=variable)\n", + "trimesh = api.create_trimesh(ds.sel(time=timestamp), variable=variable)\n", "\n", "# The wireframe is the representation of the mesh\n", "wireframe = api.get_wireframe(trimesh)\n", diff --git a/thalassa/api.py b/thalassa/api.py index e91290c..c0ee5ee 100644 --- a/thalassa/api.py +++ b/thalassa/api.py @@ -80,16 +80,22 @@ def get_dtf() -> DatetimeTickFormatter: def create_trimesh( - ds: xr.Dataset, + ds_or_trimesh: gv.TriMesh | xr.Dataset, variable: str | None = None, ) -> gv.TriMesh: """ Create a ``gv.TriMesh`` object from the provided dataset. Parameters: - ds: The dataset containing the variable we want to visualize + ds_or_trimesh: The dataset containing the variable we want to visualize. + If a trimesh object is passed, then return it immediately. variable: The data variable we want to visualize """ + if isinstance(ds_or_trimesh, gv.TriMesh): + # This is already a trimesh, nothing to do + return ds_or_trimesh + # create the trimesh object + ds = ds_or_trimesh columns = ["lon", "lat"] if variable is not None: columns.append(variable) @@ -118,10 +124,7 @@ def get_wireframe( ds_or_trimesh: gv.TriMesh | xr.Dataset, ) -> gv.DynamicMap: """Return a ``DynamicMap`` with a wireframe of the mesh.""" - if not isinstance(ds_or_trimesh, gv.TriMesh): - trimesh = create_trimesh(ds=ds_or_trimesh) - else: - trimesh = ds_or_trimesh + trimesh = create_trimesh(ds_or_trimesh) kwargs = dict(element=trimesh.edgepaths, precompute=True) wireframe = rasterize(**kwargs).opts(tools=["hover"], cmap=["black"], title="Mesh") wireframe = dynspread(wireframe) @@ -129,7 +132,8 @@ def get_wireframe( def get_raster( - trimesh: gv.TriMesh, + ds_or_trimesh: gv.TriMesh | xr.Dataset, + variable: str | None = None, title: str = "", cmap: str = "plasma", colorbar: bool = True, @@ -144,6 +148,7 @@ def get_raster( Uses ``datashader`` behind the scenes. """ + trimesh = create_trimesh(ds_or_trimesh=ds_or_trimesh, variable=variable) kwargs = dict(element=trimesh, precompute=True) if x_range: kwargs["x_range"] = x_range diff --git a/thalassa/plotting.py b/thalassa/plotting.py index 1fd221e..41f3810 100644 --- a/thalassa/plotting.py +++ b/thalassa/plotting.py @@ -73,9 +73,10 @@ def plot( ds = normalization.normalize(ds) if bbox: ds = utils.crop(ds, bbox) - trimesh = api.create_trimesh(ds=ds, variable=variable) + trimesh = api.create_trimesh(ds_or_trimesh=ds, variable=variable) raster = api.get_raster( - trimesh=trimesh, + ds_or_trimesh=trimesh, + variable=variable, x_range=x_range, y_range=y_range, cmap=cmap, @@ -86,12 +87,15 @@ def plot( clabel=clabel, ) tiles = api.get_tiles() + components = [tiles, raster] if show_mesh: - mesh = api.get_wireframe(ds_or_trimesh=trimesh) - overlay = hv.Overlay((tiles, raster, mesh)) - else: - overlay = hv.Overlay((tiles, raster)) - return overlay.collate() + mesh = api.get_wireframe(ds) + components.append(mesh) + overlay = hv.Overlay(components) + dmap = overlay.collate() + # Keep a reference of the raster DynamicMap, in order to be able to retrieve it from plot_ts + dmap._raster = raster + return dmap def plot_ts( From 7dab0fc4c8c2c918906d6d241027a4a32e920a3f Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Tue, 3 Oct 2023 16:55:24 +0300 Subject: [PATCH 13/19] plotting: Add some sanity checks in `plot()` --- thalassa/plotting.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/thalassa/plotting.py b/thalassa/plotting.py index 41f3810..86d5ec2 100644 --- a/thalassa/plotting.py +++ b/thalassa/plotting.py @@ -14,6 +14,23 @@ logger = logging.getLogger(__name__) +def _sanity_check(ds: xr.Dataset, variable: str) -> None: + dims = ds[variable].dims + if "node" not in dims: + msg = ( + f"Only variables whose dimensions include 'node' can be plotted. " + f"The dimensions of variable '{variable}' are: {ds[variable].dims}" + ) + raise ValueError(msg) + if dims != ("node",): + msg = ( + f"In order to plot variable '{variable}', the dataset must be filtered in such a way " + f"that the only dimension of '{variable}' is `node`. Please use `.sel()` or `.isel()` " + f"to filter the dataset accordingly. Current dimensions are: {ds[variable].dims}" + ) + raise ValueError(msg) + + def plot_mesh( ds: xr.Dataset, bbox: shapely.Polygon | None = None, @@ -71,6 +88,7 @@ def plot( """ ds = normalization.normalize(ds) + _sanity_check(ds=ds, variable=variable) if bbox: ds = utils.crop(ds, bbox) trimesh = api.create_trimesh(ds_or_trimesh=ds, variable=variable) From e4e5b6e18a9e28cbbfa889dfbb41acc7f90fe533 Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Tue, 3 Oct 2023 16:55:51 +0300 Subject: [PATCH 14/19] plotting: Stop hardcoding `max_elev` as the default variable for `plot()` --- thalassa/plotting.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/thalassa/plotting.py b/thalassa/plotting.py index 86d5ec2..7574316 100644 --- a/thalassa/plotting.py +++ b/thalassa/plotting.py @@ -56,7 +56,7 @@ def plot_mesh( def plot( ds: xr.Dataset, - variable: str = "max_elev", + variable: str, bbox: shapely.Polygon | None = None, title: str = "", cmap: str = "plasma", From 1f317e9113762df4fbc9fa677913610642a79046 Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Wed, 4 Oct 2023 10:20:23 +0300 Subject: [PATCH 15/19] docs: Add examples in the docstrings --- thalassa/api.py | 24 +++++++++-- thalassa/normalization.py | 11 +++++ thalassa/plotting.py | 87 ++++++++++++++++++++++++++++++++++++--- thalassa/utils.py | 16 +++++-- 4 files changed, 126 insertions(+), 12 deletions(-) diff --git a/thalassa/api.py b/thalassa/api.py index c0ee5ee..3e436e7 100644 --- a/thalassa/api.py +++ b/thalassa/api.py @@ -48,13 +48,31 @@ def open_dataset( **kwargs: dict[str, typing.Any], ) -> xr.Dataset: """ - Open the file specified in ``path`` using ``xarray`` and return an ``xr.Dataset`` + Open the file specified at ``path`` using ``xarray`` and return an ``xarray.Dataset``. + + If `normalize` is `True` then convert the dataset to the "Thalassa schema", too. + Additional `kwargs` are passed on to `xarray.open_dataset()`. + + !!! note + + This function is just a wrapper around `xarray.open_dataset()`. The reason we need + it is because the netcdfs files created by ADCIRC are not compatible with `xarray`, + at least not when using the defaults. This function automatically detects the + problematic variables (e.g. `neta` and `nvel`) and drops them. + + Examples: + ``` python + import thalassa + + ds = thalassa.open_dataset("some_netcdf.nc") + print(ds) + ``` Parameters: path: The path to the dataset file (netCDF, zarr, grib) - normalize: Boolean flag indicating whether the dataset should be converted/normalized to the ``Thalassa`` schema. + normalize: Boolean flag indicating whether the dataset should be converted/normalized to the "Thalassa schema". Normalization is currently only supported for ``SCHISM`` and ``ADCIRC`` netcdf files. - kwargs: The ``kwargs`` are being passed through to ``xr.open_dataset``. + kwargs: The ``kwargs`` are being passed through to ``xarray.open_dataset``. """ default_kwargs: dict[str, typing.Any] = dict( diff --git a/thalassa/normalization.py b/thalassa/normalization.py index 7ef1c6a..2a84bef 100644 --- a/thalassa/normalization.py +++ b/thalassa/normalization.py @@ -182,8 +182,19 @@ def normalize(ds: xr.Dataset) -> xr.Dataset: """ Normalize the `dataset` i.e. convert it to the "Thalassa Schema". + Examples: + ``` python + import thalassa + import xarray as xr + + ds = xr.open_dataset("some_netcdf.nc") + ds = thalassa.normalize(ds) + print(ds) + ``` + Parameters: ds: The dataset we want to convert. + """ logger.debug("Dataset normalization: Started") fmt = infer_format(ds) diff --git a/thalassa/plotting.py b/thalassa/plotting.py index 7574316..a032702 100644 --- a/thalassa/plotting.py +++ b/thalassa/plotting.py @@ -39,10 +39,29 @@ def plot_mesh( """ Plot the mesh of the dataset + Examples: + ``` python + import thalassa + + ds = thalassa.open_dataset("some_netcdf.nc") + thalassa.plot_mesh(ds) + ``` + + If we want to on-the-fly crop the dataset we can pass `bbox`, too: + + ``` python + import shapely + import thalassa + + bbox = shapely.box(0, 0, 1, 1) + ds = thalassa.open_dataset("some_netcdf.nc") + thalassa.plot_mesh(ds, bbox=bbox) + ``` + Parameters: - ds: The dataset whose mesh we want to visualize. + ds: The dataset whose mesh we want to visualize. It must adhere to the "thalassa schema" bbox: A Shapely polygon which will be used to (on-the-fly) crop the `dataset`. - title: The title of the plot + title: The title of the plot. """ ds = normalization.normalize(ds) @@ -71,9 +90,48 @@ def plot( """ Return the plot of the specified `variable`. + Examples: + ``` python + import thalassa + + ds = thalassa.open_dataset("some_netcdf.nc") + thalassa.plot(ds, variable="zeta_max") + ``` + + When we plot time dependent variables we need to filter the data + in such a way that `time` is no longer a dimension. + For example to plot the map of the first timestamp of variable `zeta`: + + ``` python + import thalassa + + ds = thalassa.open_dataset("some_netcdf.nc") + thalassa.plot(ds.isel(time=0), variable="zeta") + ``` + + Often, it is quite useful to limit the range of the colorbar: + + ``` python + import thalassa + + ds = thalassa.open_dataset("some_netcdf.nc") + thalassa.plot(ds, variable="zeta", clim_min=1, clim_max=3, clabel="meter") + ``` + + If we want to on-the-fly crop the dataset we can pass `bbox`, too: + + ``` python + import shapely + import thalassa + + bbox = shapely.box(0, 0, 1, 1) + ds = thalassa.open_dataset("some_netcdf.nc") + thalassa.plot(ds, variable="depth", bbox=bbox) + ``` + Parameters: - ds: The dataset which will get rendered. It must adhere to the "thalassa schema" - variable: The `dataset`'s variable which we want to visualize. + ds: The dataset which will get visualized. It must adhere to the "thalassa schema". + variable: The dataset's variable which we want to visualize. bbox: A Shapely polygon which will be used to (on-the-fly) crop the `dataset`. title: The title of the plot. Defaults to `variable`. cmap: The colormap to use. @@ -122,9 +180,26 @@ def plot_ts( source_plot: gv.DynamicMap, ) -> gv.DynamicMap: """ - Return an `hv.Curve` with the full timeseries of a specific node. + Return a plot with the full timeseries of a specific node. - The node is selected by clicking on `source_plot`. + The node that will be visualized is selected by clicking on `source_plot`. + + Examples: + ``` python + import thalassa + + ds = thalassa.open_dataset("some_netcdf.nc") + main_plot = thalassa.plot(ds, variable="zeta_max") + ts_plot = thalassa.plot_ts(ds, variable="zeta", source_plot=main_plot) + + (main_plot.opts(width=600) + ts_plot.opts(width=600)).cols(1) + ``` + + Parameters: + ds: The dataset which will get visualized. It must adhere to the "thalassa schema" + variable: The dataset's variable which we want to visualize. + source_plot: The plot instance which be used to select the coordinates of the node. + Normally, you get this instance by calling `plot()`. """ ds = normalization.normalize(ds) ts = api.get_tap_timeseries(ds, variable, source_plot._raster) diff --git a/thalassa/utils.py b/thalassa/utils.py index a3696ec..65667df 100644 --- a/thalassa/utils.py +++ b/thalassa/utils.py @@ -28,14 +28,24 @@ def resolve_bbox( def crop( ds: xr.Dataset, - bbox: shapely.Polygon | tuple[float, float, float, float], + bbox: shapely.Polygon, ) -> xr.Dataset: """ - Crop the dataset using the provided `bbox` + Crop the dataset using the provided `bbox`. + + Examples: + ``` python + import thalassa + import shapely + + ds = thalassa.open_dataset("some_netcdf.nc") + bbox = shapely.box(0, 0, 1, 1) + ds = thalassa.crop(ds, bbox) + ``` Parameters: ds: The dataset we want to crop. - bbox: A Shapely polygon which will be used to (on-the-fly) crop the `dataset`. + bbox: A Shapely polygon whose boundary will be used to crop `ds`. """ bbox = resolve_bbox(bbox) indices_of_nodes_in_bbox = np.where( From f833e4f5acd313847ecf8aa93ffad4546b7a1636 Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Wed, 4 Oct 2023 10:35:31 +0300 Subject: [PATCH 16/19] poetry: Update requirements --- poetry.lock | 580 ++++++++++++++---------------- pyproject.toml | 4 +- requirements/requirements-dev.txt | 29 +- requirements/requirements.txt | 7 +- 4 files changed, 290 insertions(+), 330 deletions(-) diff --git a/poetry.lock b/poetry.lock index 54f9695..c63ae70 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,5 +1,19 @@ # This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +[[package]] +name = "ansiwrap" +version = "0.8.4" +description = "textwrap, but savvy to ANSI colors and styles" +optional = false +python-versions = "*" +files = [ + {file = "ansiwrap-0.8.4-py2.py3-none-any.whl", hash = "sha256:7b053567c88e1ad9eed030d3ac41b722125e4c1271c8a99ade797faff1f49fb1"}, + {file = "ansiwrap-0.8.4.zip", hash = "sha256:ca0c740734cde59bf919f8ff2c386f74f9a369818cdc60efe94893d01ea8d9b7"}, +] + +[package.dependencies] +textwrap3 = ">=0.9.2" + [[package]] name = "appnope" version = "0.1.3" @@ -58,15 +72,18 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte [[package]] name = "babel" -version = "2.12.1" +version = "2.13.0" description = "Internationalization utilities" optional = false python-versions = ">=3.7" files = [ - {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"}, - {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"}, + {file = "Babel-2.13.0-py3-none-any.whl", hash = "sha256:fbfcae1575ff78e26c7449136f1abbefc3c13ce542eeb13d43d50d8b047216ec"}, + {file = "Babel-2.13.0.tar.gz", hash = "sha256:04c3e2d28d2b7681644508f836be388ae49e0cfe91465095340395b60d00f210"}, ] +[package.extras] +dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] + [[package]] name = "backcall" version = "0.2.0" @@ -943,17 +960,6 @@ files = [ {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"}, ] -[[package]] -name = "defusedxml" -version = "0.7.1" -description = "XML bomb protection for Python stdlib modules" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" -files = [ - {file = "defusedxml-0.7.1-py2.py3-none-any.whl", hash = "sha256:a352e7e428770286cc899e2542b6cdaedb2b4953ff269a210103ec58f6198a61"}, - {file = "defusedxml-0.7.1.tar.gz", hash = "sha256:1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69"}, -] - [[package]] name = "docopt" version = "0.6.2" @@ -1640,17 +1646,6 @@ traitlets = ">=5.3" docs = ["myst-parser", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"] test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"] -[[package]] -name = "jupyterlab-pygments" -version = "0.2.2" -description = "Pygments theme using JupyterLab CSS variables" -optional = false -python-versions = ">=3.7" -files = [ - {file = "jupyterlab_pygments-0.2.2-py2.py3-none-any.whl", hash = "sha256:2405800db07c9f770863bcf8049a529c3dd4d3e28536638bd7c1c01d2748309f"}, - {file = "jupyterlab_pygments-0.2.2.tar.gz", hash = "sha256:7405d7fde60819d905a9fa8ce89e4cd830e318cdad22a0030f7a901da705585d"}, -] - [[package]] name = "jupyterlab-widgets" version = "3.0.9" @@ -2055,17 +2050,6 @@ files = [ {file = "mergedeep-1.3.4.tar.gz", hash = "sha256:0096d52e9dad9939c3d975a774666af186eda617e6ca84df4c94dec30004f2a8"}, ] -[[package]] -name = "mistune" -version = "3.0.2" -description = "A sane and fast Markdown parser with useful plugins and renderers" -optional = false -python-versions = ">=3.7" -files = [ - {file = "mistune-3.0.2-py3-none-any.whl", hash = "sha256:71481854c30fdbc938963d3605b72501f5c10a9320ecd412c121c163a1c7d205"}, - {file = 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hash = "sha256:18d5ff7fbd305a1d564273e9eb22de83ae3cd9cd6329fddc8f12f6428a711a6a"}, ] [[package]] @@ -3855,22 +3825,29 @@ pure-eval = "*" tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"] [[package]] -name = "tinycss2" -version = "1.2.1" -description = "A tiny CSS parser" +name = "tenacity" +version = "8.2.3" +description = "Retry code until it succeeds" optional = false python-versions = ">=3.7" files = [ - {file = "tinycss2-1.2.1-py3-none-any.whl", hash = "sha256:2b80a96d41e7c3914b8cda8bc7f705a4d9c49275616e886103dd839dfc847847"}, - {file = "tinycss2-1.2.1.tar.gz", hash = "sha256:8cff3a8f066c2ec677c06dbc7b45619804a6938478d9d73c284b29d14ecb0627"}, + {file = "tenacity-8.2.3-py3-none-any.whl", hash = "sha256:ce510e327a630c9e1beaf17d42e6ffacc88185044ad85cf74c0a8887c6a0f88c"}, + {file = "tenacity-8.2.3.tar.gz", hash = "sha256:5398ef0d78e63f40007c1fb4c0bff96e1911394d2fa8d194f77619c05ff6cc8a"}, ] -[package.dependencies] -webencodings = ">=0.4" - [package.extras] -doc = ["sphinx", "sphinx_rtd_theme"] -test = ["flake8", "isort", "pytest"] +doc = ["reno", "sphinx", "tornado (>=4.5)"] + +[[package]] +name = "textwrap3" +version = "0.9.2" +description = "textwrap from Python 3.6 backport (plus a few tweaks)" +optional = false +python-versions = "*" +files = [ + {file = "textwrap3-0.9.2-py2.py3-none-any.whl", hash = "sha256:bf5f4c40faf2a9ff00a9e0791fed5da7415481054cef45bb4a3cfb1f69044ae0"}, + {file = "textwrap3-0.9.2.zip", hash = "sha256:5008eeebdb236f6303dcd68f18b856d355f6197511d952ba74bc75e40e0c3414"}, +] [[package]] name = "tomli" @@ -3936,30 +3913,19 @@ telegram = ["requests"] [[package]] name = "traitlets" -version = "5.10.1" +version = "5.11.2" description = "Traitlets Python configuration system" optional = false python-versions = ">=3.8" files = [ - {file = "traitlets-5.10.1-py3-none-any.whl", hash = "sha256:07ab9c5bf8a0499fd7b088ba51be899c90ffc936ffc797d7b6907fc516bcd116"}, - {file = "traitlets-5.10.1.tar.gz", hash = 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"4.8.0" @@ -4136,13 +4102,13 @@ viz = ["matplotlib", "nc-time-axis", "seaborn"] [[package]] name = "xyzservices" -version = "2023.7.0" +version = "2023.10.0" description = "Source of XYZ tiles providers" optional = false python-versions = ">=3.8" files = [ - {file = "xyzservices-2023.7.0-py3-none-any.whl", hash = "sha256:88e9cbf22b31a2f9c1b242e2b18690f5c705f0e539c9bfd37a10399e1037731b"}, - {file = "xyzservices-2023.7.0.tar.gz", hash = "sha256:0ec928742227d6f5d4367ea7b457fcfed943429f4de2949b5b02a82cdf5569d6"}, + {file = "xyzservices-2023.10.0-py3-none-any.whl", hash = "sha256:70b9910f6c8e46f6ca92dea21e9b8cf89edf0ead35a870198fb59a7d63579525"}, + {file = "xyzservices-2023.10.0.tar.gz", hash = "sha256:eee203e91955782fd8bfc2f05846830c289139dc0ab4eaf733bfa8f0be71861f"}, ] [[package]] @@ -4184,4 +4150,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.9, <4.0" -content-hash = "c8282f41f3b2b81685c9df2a948cc9f7788e01ffbac8f8f92f187c2d48c8b968" +content-hash = "1d507fb94fcd4c5fa3bcd91b3b7829d3b02224b12ffd4a13a495d58fde379fd8" diff --git a/pyproject.toml b/pyproject.toml index ca39228..dc19382 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,7 +27,6 @@ bokeh = ">=3.0" Cartopy = "*" dask = "*" datashader = "*" -decorator = "*" geopandas = "*" geoviews = ">=1.10" holoviews = "*" @@ -38,7 +37,6 @@ numpy-indexed = "*" pandas = "*" scipy = "*" shapely = "*" -types-decorator = "*" xarray = {version = "*", extras = ["io", "accel"]} [tool.poetry.group.dev.dependencies] @@ -48,7 +46,7 @@ pytest = "*" pytest-cov = ">=3.0" ipykernel = "*" ipython = "*" -nbconvert = "*" +papermill = "*" [tool.poetry.group.docs.dependencies] mkdocs = "*" diff --git a/requirements/requirements-dev.txt b/requirements/requirements-dev.txt index 967c603..e9e4083 100644 --- a/requirements/requirements-dev.txt +++ b/requirements/requirements-dev.txt @@ -1,10 +1,11 @@ +ansiwrap==0.8.4 ; python_version >= "3.9" and python_version < "4.0" appnope==0.1.3 ; python_version >= "3.9" and python_version < "4.0" and (platform_system == "Darwin" or sys_platform == "darwin") asciitree==0.3.3 ; python_version >= "3.9" and python_version < "4.0" asttokens==2.4.0 ; python_version >= "3.9" and python_version < "4.0" attrs==23.1.0 ; python_version >= "3.9" and python_version < "4.0" -babel==2.12.1 ; python_version >= "3.9" and python_version < "4.0" +babel==2.13.0 ; python_version >= "3.9" and python_version < "4.0" backcall==0.2.0 ; python_version >= "3.9" and python_version < "4.0" -beautifulsoup4==4.12.2 ; python_version >= "3.9" and python_version < "4.0" +beautifulsoup4==4.12.2 ; python_version < "3.10" and python_version >= "3.9" black==23.9.1 ; python_version >= "3.9" and python_version < "4.0" bleach==6.0.0 ; python_version >= "3.9" and python_version < "4.0" bokeh==3.2.2 ; python_version >= "3.9" and python_version < "4.0" @@ -31,7 +32,6 @@ datashader==0.15.2 ; python_version >= "3.9" and python_version < "4.0" datashape==0.5.2 ; python_version >= "3.9" and python_version < "4.0" debugpy==1.8.0 ; python_version >= "3.9" and python_version < "4.0" decorator==5.1.1 ; python_version >= "3.9" and python_version < "4.0" -defusedxml==0.7.1 ; python_version >= "3.9" and python_version < "4.0" docopt==0.6.2 ; python_version < "3.10" and python_version >= "3.9" entrypoints==0.4 ; python_version >= "3.9" and python_version < "4.0" exceptiongroup==1.1.3 ; python_version >= "3.9" and python_version < "3.11" @@ -63,7 +63,6 @@ jsonschema-specifications==2023.7.1 ; python_version >= "3.9" and python_version jsonschema==4.19.1 ; python_version >= "3.9" and python_version < "4.0" jupyter-client==8.3.1 ; python_version >= "3.9" and python_version < "4.0" jupyter-core==5.3.2 ; python_version >= "3.9" and python_version < "4.0" -jupyterlab-pygments==0.2.2 ; python_version >= "3.9" and python_version < "4.0" jupyterlab-widgets==3.0.9 ; python_version >= "3.9" and python_version < "4.0" kiwisolver==1.4.5 ; python_version >= "3.9" and python_version < "4.0" linkify-it-py==2.0.2 ; python_version >= "3.9" and python_version < "4.0" @@ -77,32 +76,30 @@ matplotlib==3.8.0 ; python_version >= "3.9" and python_version < "4.0" mdit-py-plugins==0.4.0 ; python_version >= "3.9" and python_version < "4.0" mdurl==0.1.2 ; python_version >= "3.9" and python_version < "4.0" mergedeep==1.3.4 ; python_version >= "3.9" and python_version < "4.0" -mistune==3.0.2 ; python_version >= "3.9" and python_version < "4.0" mkdocs-autorefs==0.5.0 ; python_version >= "3.9" and python_version < "4.0" mkdocs-material-extensions==1.2 ; python_version >= "3.9" and python_version < "4.0" mkdocs-material==9.4.3 ; python_version >= "3.9" and python_version < "4.0" mkdocs==1.5.3 ; python_version >= "3.9" and python_version < "4.0" -mkdocstrings-python==1.7.1 ; python_version >= "3.9" and python_version < "4.0" +mkdocstrings-python==1.7.2 ; python_version >= "3.9" and python_version < "4.0" mkdocstrings==0.23.0 ; python_version >= "3.9" and python_version < "4.0" multipledispatch==1.0.0 ; python_version >= "3.9" and python_version < "4.0" mypy-extensions==1.0.0 ; python_version >= "3.9" and python_version < "4.0" mypy==1.5.1 ; python_version >= "3.9" and python_version < "4.0" nbclient==0.8.0 ; python_version >= "3.9" and python_version < "4.0" -nbconvert==7.8.0 ; python_version >= "3.9" and python_version < "4.0" nbformat==5.9.2 ; python_version >= "3.9" and python_version < "4.0" nest-asyncio==1.5.8 ; python_version >= "3.9" and python_version < "4.0" netcdf4==1.6.4 ; python_version >= "3.9" and python_version < "4.0" numba==0.58.0 ; python_version >= "3.9" and python_version < "4.0" numbagg==0.2.2 ; python_version >= "3.9" and python_version < "4.0" numcodecs==0.11.0 ; python_version >= "3.9" and python_version < "4.0" -numpy-groupies==0.10.1 ; python_version >= "3.9" and python_version < "4.0" +numpy-groupies==0.10.2 ; python_version >= "3.9" and python_version < "4.0" numpy-indexed==0.3.7 ; python_version >= "3.9" and python_version < "4.0" numpy==1.25.2 ; python_version >= "3.9" and python_version < "4.0" packaging==23.2 ; python_version >= "3.9" and python_version < "4.0" paginate==0.5.6 ; python_version >= "3.9" and python_version < "4.0" pandas==2.1.1 ; python_version >= "3.9" and python_version < "4.0" -pandocfilters==1.5.0 ; python_version >= "3.9" and python_version < "4.0" panel==1.2.3 ; python_version >= "3.9" and python_version < "4.0" +papermill==2.4.0 ; python_version >= "3.9" and python_version < "4.0" param==1.13.0 ; python_version >= "3.9" and python_version < "4.0" parso==0.8.3 ; python_version >= "3.9" and python_version < "4.0" partd==1.4.1 ; python_version >= "3.9" and python_version < "4.0" @@ -135,23 +132,23 @@ pyyaml-env-tag==0.1 ; python_version >= "3.9" and python_version < "4.0" pyyaml==6.0.1 ; python_version >= "3.9" and python_version < "4.0" pyzmq==25.1.1 ; python_version >= "3.9" and python_version < "4.0" referencing==0.30.2 ; python_version >= "3.9" and python_version < "4.0" -regex==2023.8.8 ; python_version >= "3.9" and python_version < "4.0" +regex==2023.10.3 ; python_version >= "3.9" and python_version < "4.0" requests==2.31.0 ; python_version >= "3.9" and python_version < "4.0" -rpds-py==0.10.3 ; python_version >= "3.9" and python_version < "4.0" +rpds-py==0.10.4 ; python_version >= "3.9" and python_version < "4.0" scipy==1.9.3 ; python_version >= "3.9" and python_version < "4.0" setuptools-scm==8.0.4 ; python_version >= "3.9" and python_version < "4.0" setuptools==68.2.2 ; python_version >= "3.9" and python_version < "4.0" shapely==2.0.1 ; python_version >= "3.9" and python_version < "4.0" six==1.16.0 ; python_version >= "3.9" and python_version < "4.0" -soupsieve==2.5 ; python_version >= "3.9" and python_version < "4.0" +soupsieve==2.5 ; python_version < "3.10" and python_version >= "3.9" stack-data==0.6.3 ; python_version >= "3.9" and python_version < "4.0" -tinycss2==1.2.1 ; python_version >= "3.9" and python_version < "4.0" +tenacity==8.2.3 ; python_version >= "3.9" and python_version < "4.0" +textwrap3==0.9.2 ; python_version >= "3.9" and python_version < "4.0" tomli==2.0.1 ; python_version >= "3.9" and python_full_version <= "3.11.0a6" toolz==0.12.0 ; python_version >= "3.9" and python_version < "4.0" tornado==6.3.3 ; python_version >= "3.9" and python_version < "4.0" tqdm==4.66.1 ; python_version >= "3.9" and python_version < "4.0" -traitlets==5.10.1 ; python_version >= "3.9" and python_version < "4.0" -types-decorator==5.1.8.4 ; python_version >= "3.9" and python_version < "4.0" +traitlets==5.11.2 ; python_version >= "3.9" and python_version < "4.0" typing-extensions==4.8.0 ; python_version >= "3.9" and python_version < "4.0" tzdata==2023.3 ; python_version >= "3.9" and python_version < "4.0" uc-micro-py==1.0.2 ; python_version >= "3.9" and python_version < "4.0" @@ -163,6 +160,6 @@ webob==1.8.7 ; python_version >= "3.9" and python_version < "3.10" widgetsnbextension==4.0.9 ; python_version >= "3.9" and python_version < "4.0" xarray==2023.9.0 ; python_version >= "3.9" and python_version < "4.0" xarray[accel,io]==2023.9.0 ; python_version >= "3.9" and python_version < "4.0" -xyzservices==2023.7.0 ; python_version >= "3.9" and python_version < "4.0" +xyzservices==2023.10.0 ; python_version >= "3.9" and python_version < "4.0" zarr==2.16.1 ; python_version >= "3.9" and python_version < "4.0" zipp==3.17.0 ; python_version >= "3.9" and python_version < "4.0" diff --git a/requirements/requirements.txt b/requirements/requirements.txt index 7df1b30..146ee6a 100644 --- a/requirements/requirements.txt +++ b/requirements/requirements.txt @@ -63,7 +63,7 @@ netcdf4==1.6.4 ; python_version >= "3.9" and python_version < "4.0" numba==0.58.0 ; python_version >= "3.9" and python_version < "4.0" numbagg==0.2.2 ; python_version >= "3.9" and python_version < "4.0" numcodecs==0.11.0 ; python_version >= "3.9" and python_version < "4.0" -numpy-groupies==0.10.1 ; python_version >= "3.9" and python_version < "4.0" +numpy-groupies==0.10.2 ; python_version >= "3.9" and python_version < "4.0" numpy-indexed==0.3.7 ; python_version >= "3.9" and python_version < "4.0" numpy==1.25.2 ; python_version >= "3.9" and python_version < "4.0" packaging==23.2 ; python_version >= "3.9" and python_version < "4.0" @@ -102,8 +102,7 @@ tomli==2.0.1 ; python_version >= "3.9" and python_version < "3.11" toolz==0.12.0 ; python_version >= "3.9" and python_version < "4.0" tornado==6.3.3 ; python_version >= "3.9" and python_version < "4.0" tqdm==4.66.1 ; python_version >= "3.9" and python_version < "4.0" -traitlets==5.10.1 ; python_version >= "3.9" and python_version < "4.0" -types-decorator==5.1.8.4 ; python_version >= "3.9" and python_version < "4.0" +traitlets==5.11.2 ; python_version >= "3.9" and python_version < "4.0" typing-extensions==4.8.0 ; python_version >= "3.9" and python_version < "4.0" tzdata==2023.3 ; python_version >= "3.9" and python_version < "4.0" uc-micro-py==1.0.2 ; python_version >= "3.9" and python_version < "4.0" @@ -114,6 +113,6 @@ webob==1.8.7 ; python_version >= "3.9" and python_version < "3.10" widgetsnbextension==4.0.9 ; python_version >= "3.9" and python_version < "4.0" xarray==2023.9.0 ; python_version >= "3.9" and python_version < "4.0" xarray[accel,io]==2023.9.0 ; python_version >= "3.9" and python_version < "4.0" -xyzservices==2023.7.0 ; python_version >= "3.9" and python_version < "4.0" +xyzservices==2023.10.0 ; python_version >= "3.9" and python_version < "4.0" zarr==2.16.1 ; python_version >= "3.9" and python_version < "4.0" zipp==3.17.0 ; python_version >= "3.9" and python_version < "4.0" From fba79ab47847b393997c02fa4efd42a34de88db7 Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Thu, 5 Oct 2023 10:26:24 +0300 Subject: [PATCH 17/19] notebooks: minor: Rename notebook Replace space with an underscore. --- .../{Public API.ipynb => Public_API.ipynb} | 41 ------------------- 1 file changed, 41 deletions(-) rename notebooks/{Public API.ipynb => Public_API.ipynb} (90%) diff --git a/notebooks/Public API.ipynb b/notebooks/Public_API.ipynb similarity index 90% rename from notebooks/Public API.ipynb rename to notebooks/Public_API.ipynb index af98906..66f33ff 100644 --- a/notebooks/Public API.ipynb +++ b/notebooks/Public_API.ipynb @@ -419,47 +419,6 @@ " bbox=bbox\n", ")" ] - }, - { - "cell_type": "markdown", - "id": "28f5ee84-fdc7-43cf-b54b-bd27ced49ce3", - "metadata": { - "tags": [] - }, - "source": [ - "## Global models\n", - "\n", - "Global models are supported but you must post-process their output in order to handle elements that cross the International Date Line\n", - "\n", - "One way of doing this is to use pyPoseidon: https://pyposeidon.readthedocs.io/en/latest/utils.html#seam\n", - "\n", - "For further discussion please chere here: https://github.com/ec-jrc/Thalassa/issues/58" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "f91dd93d-cf19-4467-b916-226d9e12c894", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "ds = thalassa.open_dataset(\"/tmp/ds2d.zarr\")\n", - "ds" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "676db643-3645-48d6-9d27-087b1afd4498", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "thalassa.plot(ds, \"max_elev\", clim_min=-50, clim_max=100)" - ] } ], "metadata": { From 6aa57e695e4fdddc5a811bb1c8e787aacb80912b Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Thu, 5 Oct 2023 17:51:27 +0300 Subject: [PATCH 18/19] notebooks: Switch to papermill for `exec_notebooks` --- Makefile | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 9fcce9e..c1b44fb 100644 --- a/Makefile +++ b/Makefile @@ -27,7 +27,11 @@ clean_notebooks: pre-commit run nbstripout exec_notebooks: - python -m nbconvert --to notebook --execute --stdout notebooks/* >/dev/null + set -e; \ + for file in $$(git -C notebooks ls-files); do \ + echo $$file; \ + timeout 600 papermill --start-timeout 1 --cwd notebooks notebooks/$$file --progress-bar /dev/null; \ + done deps: pre-commit run poetry-lock -a From 188965bd064d64cc4b59ef1b64ce6390d36ba916 Mon Sep 17 00:00:00 2001 From: Panos Mavrogiorgos Date: Thu, 5 Oct 2023 19:34:11 +0300 Subject: [PATCH 19/19] ci: Cache the netcdf files for `Public_API.ipynb` --- .github/workflows/run_tests.yml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index 608d571..8e5347b 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -38,6 +38,14 @@ jobs: with: path: ${{ env.pythonLocation }} key: test-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml', 'requirements/*') }} + - uses: actions/cache@main + id: cache-netcdfs + with: + path: | + notebooks/schout_adcirc_20230828.nc + notebooks/schout_adcirc_20230829.nc + notebooks/schout_adcirc_20230830.nc + key: test-stofs-3d-atl-netcdf-files - run: python --version - run: python -m pip install --upgrade pip - run: python -m pip --version