diff --git a/.devcontainer/scipy2024/devcontainer.json b/.devcontainer/scipy2024/devcontainer.json index 1abbd53e..8c7934c0 100644 --- a/.devcontainer/scipy2024/devcontainer.json +++ b/.devcontainer/scipy2024/devcontainer.json @@ -12,7 +12,7 @@ }, "customizations": { "codespaces": { - "openFiles": ["workshops/scipy2024/README.md"] + "openFiles": ["workshops/scipy2024/index.ipynb"] }, "vscode": { "extensions": ["ms-toolsai.jupyter", "ms-python.python"] diff --git a/README.md b/README.md index fdc1b5c1..859df993 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![CI](https://github.com/xarray-contrib/xarray-tutorial/workflows/CI/badge.svg?branch=main)](https://github.com/xarray-contrib/xarray-tutorial/actions?query=branch%3Amain) [![Jupyter Book Badge](https://jupyterbook.org/badge.svg)](https://tutorial.xarray.dev) -[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/xarray-contrib/xarray-tutorial/HEAD?labpath=overview/fundamental-path/index.ipynb) +[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/xarray-contrib/xarray-tutorial/HEAD?labpath=workshops/scipy2024/index.ipynb) This is the repository for a Jupyter Book website with tutorial material for [Xarray](https://github.com/pydata/xarray), _an open source project and Python package that makes working with labelled multi-dimensional arrays simple, efficient, and fun!_ diff --git a/fundamentals/01_data_structures.md b/fundamentals/01_data_structures.md index e4cc74a0..389f1f4d 100644 --- a/fundamentals/01_data_structures.md +++ b/fundamentals/01_data_structures.md @@ -54,7 +54,7 @@ powerful and concise interface. For example: Although the Xarray library was originally developed with Earth Science datasets in mind, the datastructures work well across many other domains! For example, below is a side-by-side view of a data schematic on the left and Xarray Dataset representation on the right taken from a mosquito genetics analysis: - +![malaria_dataset](../images/malaria_dataset.png) The data can be stored as a 3-dimensional array, where one dimension of the array corresponds to positions (**variants**) within a reference genome, another dimension corresponds to the individual mosquitoes that were sequenced (**samples**), and a third dimension corresponds to the number of genomes within each individual (**ploidy**)." diff --git a/fundamentals/01_datastructures.ipynb b/fundamentals/01_datastructures.ipynb index e3131c77..fa3875de 100644 --- a/fundamentals/01_datastructures.ipynb +++ b/fundamentals/01_datastructures.ipynb @@ -6,14 +6,12 @@ "source": [ "# Xarray's Data structures\n", "\n", - "In this lesson, we cover the basics of Xarray data structures. Our\n", - "learning goals are as follows. By the end of the lesson, we will be able to:\n", + "In this lesson, we cover the basics of Xarray data structures. By the end of the lesson, we will be able to:\n", "\n", ":::{admonition} Learning Goals\n", - "- Understand the basic data structures (`DataArray` and `Dataset` objects) in Xarray\n", - "- Customize the display of Xarray objects\n", - "- Access variables, coordinates, and arbitrary metadata\n", - "- Transform to tabular Pandas data structures\n", + "- Understand the basic Xarray data structures `DataArray` and `Dataset` \n", + "- Customize the display of Xarray data structures\n", + "- The connection between Pandas and Xarray data structures\n", ":::" ] }, @@ -130,18 +128,13 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The output consists of:\n", + "☝️ From top to bottom the output consists of:\n", "\n", - "- a summary of all *dimensions* of the `Dataset` `(lat: 25, time: 2920, lon: 53)`: this tells us that the first\n", - " dimension is named `lat` and has a size of `25`, the second dimension is named\n", - " `time` and has a size of `2920`, and the third dimension is named `lon` and has a size\n", - " of `53`. Because we will access the dimensions by name, the order doesn't matter.\n", - "- an unordered list of *coordinates* or dimensions with coordinates with one item\n", - " per line. Each item has a name, one or more dimensions in parentheses, a dtype\n", - " and a preview of the values. Also, if it is a dimension coordinate, it will be\n", - " printed in **bold** font.\n", - "- an alphabetically sorted list of *dimensions without coordinates* (if there are any)\n", - "- an unordered list of *attributes*, or metadata" + "- **Dimensions**: summary of all *dimensions* of the `Dataset` `(lat: 25, time: 2920, lon: 53)`: this tells us that the first dimension is named `lat` and has a size of `25`, the second dimension is named `time` and has a size of `2920`, and the third dimension is named `lon` and has a size of `53`. Because we will access the dimensions by name, the order doesn't matter.\n", + "- **Coordinates**: an unordered list of *coordinates* or dimensions with coordinates with one item per line. Each item has a name, one or more dimensions in parentheses, a dtype and a preview of the values. Also, if it is a dimension coordinate, it will be printed in **bold** font. *dimensions without coordinates* appear in plain font (there are none in this example, but you might imagine a 'mask' coordinate that has a value assigned at every point).\n", + "- **Data variables**: names of each nD *measurement* in the dataset, followed by its dimensions `(time, lat, lon)`, dtype, and a preview of values.\n", + "- **Indexes**: Each dimension with coordinates is backed by an \"Index\". In this example, each dimension is backed by a `PandasIndex`\n", + "- **Attributes**: an unordered list of metadata (for example, a paragraph describing the dataset)" ] }, { diff --git a/images/malaria_dataset.png b/images/malaria_dataset.png new file mode 100644 index 00000000..b360a198 Binary files /dev/null and b/images/malaria_dataset.png differ diff --git a/workshops/scipy2024/index.ipynb b/workshops/scipy2024/index.ipynb index de817e0b..9cf8f355 100644 --- a/workshops/scipy2024/index.ipynb +++ b/workshops/scipy2024/index.ipynb @@ -13,7 +13,7 @@ "\n", "**Xarray**: *Friendly, Interactive, and Scalable Scientific Data Analysis*\n", "\n", - "July 8, 13:30–17:30 (US/Pacific), Room 317\n", + "July 8, 13:30–17:30 (US/Pacific), Tacoma Convention Center Ballroom B/C\n", "\n", "This *4-hour* workshop will explore content from [the Xarray tutorial](https://tutorial.xarray.dev), which contains a comprehensive collection of hands-on tutorial Jupyter Notebooks. We will review a curated set of examples that will prepare you for increasingly complex real-world data analysis tasks!\n", "\n", @@ -33,13 +33,13 @@ "| Topic | Time | Notebook Links | \n", "| :- | - | - | \n", "| Introduction and Setup | 1:30 (10 min) | --- | \n", - "| The Xarray Data Model | 1:40 (40 min) | [Data structures](../../fundamentals/01_datastructures.ipynb)
[Basic Indexing](../../fundamentals/02.1_indexing_Basic.ipynb) | \n", + "| The Xarray Data Model | 1:40 (40 min) | [Data structures](../../fundamentals/01_data_structures.md)
[Basic Indexing](../../fundamentals/02.1_indexing_Basic.ipynb) | \n", "| *10 minute Break* \n", "| Indexing & Computational Patterns | 2:30 (50 min) | [Advanced Indexing](../../intermediate/indexing/indexing.md)
[Computational Patterns](../../intermediate/01-high-level-computation-patterns.ipynb)
| \n", "| *10 minute Break* | \n", "| Xarray Integrations and Extensions | 3:30 (50 min) | [The Xarray Ecosystem](../../intermediate/xarray_ecosystem.ipynb) | \n", "| *10 minute Break* | \n", - "| Backends & Practice with your Data | 4:30 (50 min) | TODO: [Backends](../../advanced/backends/1.Backend_without_Lazy_Loading.ipynb) or Luis' remote data notebook |\n", + "| Backends & Remote data| 4:30 (50 min) | [Remote Data](../../intermediate/remote_data/remote-data.ipynb) |\n", "| | End 5:30 | |\n", "\n", "\n", @@ -66,6 +66,9 @@ "- Once you see a url to click within the terminal, simply `cmd + click` the given url.\n", "- This will open up another tab in your browser, leading to a [Jupyter Lab](https://jupyterlab.readthedocs.io/en/latest/) Interface.\n", "\n", + ":::{warning}\n", + "Consider Codespaces as ephemeral environments. You may lose your connection and any edits you make.\n", + ":::\n", "\n", "\n", "## Thanks for attending!\n", @@ -81,14 +84,6 @@ "- Max Jones (CarbonPlan)\n", "- Wietze Suijker (Space Intelligence)" ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "1", - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": {