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Update setup instructions #342

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349df13
replace Anaconda with MiniForge
tobyhodges Apr 1, 2025
55346f2
set up an environment for the workshop
tobyhodges Apr 1, 2025
fb6258b
Apply suggestions from code review
tobyhodges Apr 6, 2025
9ae46f2
Remove mention of Py3 vs Py2
tobyhodges Apr 6, 2025
89f5b47
Apply fixes from review
tobyhodges May 7, 2025
9c8345e
Link to central Python install instructions
tobyhodges May 7, 2025
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11 changes: 11 additions & 0 deletions episodes/files/environment.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
name: dc-image
channels:
- conda-forge
dependencies:
- python>=3.11
- jupyterlab
- numpy
- matplotlib
- scikit-image
- ipympl
- imageio
37 changes: 14 additions & 23 deletions learners/setup.md
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Expand Up @@ -7,7 +7,7 @@ Before joining the workshop or following the lesson, please complete the data an

## Data

The example images used in this lesson are available on [FigShare](https://figshare.com/).
The example images and a description of the Python environment used in this lesson are available on [FigShare](https://figshare.com/).
To download the data, please visit [the dataset page for this workshop][figshare-data]
and click the "Download all" button.
Unzip the downloaded file, and save the contents as a folder called `data` somewhere you will easily find it again,
Expand All @@ -16,30 +16,21 @@ e.g. your Desktop or a folder you have created for using in this workshop.

## Software

1. Download and install the latest [Anaconda
distribution](https://www.anaconda.com/download/) for your
operating system. Make sure to choose the Python 3 version (as
opposed to the one with Python 2). If you wish to use an existing
installation, be sure to upgrade your scikit-image to at least 0.19.
You can upgrade to the latest scikit-image using the shell command that follows.
1. Download and install the latest [MiniForge distribution of Python](https://conda-forge.org/download/) for your operating system.
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I'm not sure it's obvious that, on Unix-like platforms, you need to run

bash Miniforge3-$(uname)-$(uname -m).sh

from the terminal to install Miniforge... I would add a line about this. Is it obvious on Windows? I guess so, if you need to double-click what you just downloaded.

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Yes - on Windows it's an .exe file, so you just double-click the downloaded file.

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I added a link to the central instructions, which are more detailed, in 9c8345e.

If you already have a Python 3 setup that you are happy with, you can continue to use that (we recommend that you make sure your Python version is current).
The next step assumes that `conda` is available to manage your Python environment.
2. Setup an environment to work in during the lesson.
In a terminal (Linux/Mac) or the MiniForge Prompt application (Windows), navigate to the location where you saved the unzipped data for the lesson and run the following command:

::::::::::::::::::::::::::::::::::::::::: callout

## Updating scikit-image in an existing Anaconda distribution

```shell
conda upgrade -y scikit-image
```bash
conda env create -f environment.yml
```

::::::::::::::::::::::::::::::::::::::::::::::::::

2. This lesson uses Matplotlib features to display images, and some
interactive features will be valuable. To enable the interactive
tools in JupyterLab, the `ipympl` package is required. The package
can be installed with the command
If prompted, allow `conda` to install the required libraries.
3. Activate the new environment you just created:

```shell
conda install -c conda-forge ipympl
```bash
conda activate dc-image
```

::::::::::::::::::::::::::::::::::::::::: callout
Expand Down Expand Up @@ -83,9 +74,9 @@ e.g. your Desktop or a folder you have created for using in this workshop.

## Instructions for Windows

Launch the Anaconda Prompt program and type `jupyter lab`.
Launch the MiniForge Prompt program and type `jupyter lab`.
(Running this command on the standard Command Prompt will return an error:
`'conda' is not recognized as an internal or external command, operable program or batch file.`)
`'jupyter' is not recognized as an internal or external command, operable program or batch file.`)


:::::::::::::::::::::::::
Expand Down