Merge pull request #727 from NEUBIAS/master

Update the ome-zarr channel

.github/workflows/test-python-scripts.yml

@@ -0,0 +1,44 @@
+name: test-python-scripts
+
+on:
+  push:
+    branches:
+      - gh-pages
+      - master
+  pull_request: []
+
+jobs:
+  test-python-scripts:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest, windows-latest, ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: install xvfb/deps
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -yy mesa-utils libgl1-mesa-dev xvfb curl
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: false
+          auto-activate-base: true
+          activate-environment: ""
+          channel-priority: strict
+          miniforge-version: latest
+      - name: install common conda dependencies
+        run: conda install -c conda-forge -c euro-bioimaging python=3.10 napari=0.4.17 pytest notebook matplotlib jupytext "scikit-image>=0.20" openijtiff -y
+      - name: linux test
+        if: matrix.os == 'ubuntu-latest'
+        shell: bash -l {0}
+        run: xvfb-run --server-args="-screen 0 1024x768x24" pytest -v test_python
+      - name: osx test
+        if: matrix.os == 'macos-latest'
+        shell: bash -l {0}
+        run: pytest -v test_python
+      - name: windows test
+        if: matrix.os == 'windows-latest'
+        shell: cmd /C CALL {0}
+        run: pytest -v test_python

.github/workflows/website.yml

@@ -16,7 +16,7 @@ jobs:
       - name: Set up Ruby
         uses: ruby/setup-ruby@v1
         with:
-          ruby-version: '2.7'
+          ruby-version: '3.0'
 
       - name: Set up Python
         uses: actions/setup-python@v2

.gitignore

@@ -10,5 +10,7 @@ _site*
 .idea
 Thumbs.db
 ~$*
+*.ipynb
 .ipynb_checkpoints
 **/__pycache__/
+Untitl*

CONTRIBUTING.md

@@ -1,15 +1,12 @@
----
-layout: page
-title: Guidelines for Contributing
----
+# Contribute
 
-Contributions to this project are very welcome.
-Changes should be submitted by merge request from a new branch to `master`.
-Merge requests should be reviewed by at least one Maintainer before merging.
+There are already [numerous contributors](https://github.com/NEUBIAS/training-resources/graphs/contributors) to this project and we are always welcoming more!
 
-See `README.md` for information on the structure of the repository.
+If you are a first time contributor we recommend expressing your interest by [creating an issue](https://github.com/NEUBIAS/training-resources/issues) where you describe how you would like to contribute. 
+We will then get in touch with you to discuss the details, e.g. by having a zoom with you.
 
-## Step by step guide
+
+## Step by step technical contribution guide
 
 To contribute to this project, please follow those steps:
 
@@ -23,21 +20,26 @@ To contribute to this project, please follow those steps:
 1. Thank you for your contribution!
 
 ### Editor
+
 [Visual Studio Code](https://code.visualstudio.com/) supports code formating and highlighting with the [Liquid](https://marketplace.visualstudio.com/items?itemName=sissel.shopify-liquid) and [Jekyll Syntax Support](https://marketplace.visualstudio.com/items?itemName=ginfuru.ginfuru-vscode-jekyll-syntax) extensions (available via VSCode marketplace).
 
 After the extensions are installed the document type can be changed to "Liquid" in the bottom right corner.
 ![Set document type to liquid.](image_data/contribute/doc_type_liquid.png)
 
 This should enable syntax highlighting. By pressing `Ctrl + Shift + p` you can search for `Liquid: Enable Formatting` and `Liquid: Format Document`.
 
-## Adding a new module
+### Adding a new module
 
 Each module page is built from a template (`_layouts/module.html`),
 ensuring a consistent structure and style for the whole collection.
 To create a new module, you will need to add a few files
-in a few different places in this repository.
+in a few different places in this repository. 
+
+For convenience there is the [add_new_module.sh](https://github.com/NEUBIAS/training-resources/blob/master/add_new_module.sh) shell script that will automatically create the file and folder skeleton for a new module. Example usage: `./add_new_module.sh distance_transform`
+
+
+#### Module file
 
-### Module file
 Most important is the module file itself.
 This module file should be saved with a short, descriptive name (no spaces!)
 ending with the `.md` (Markdown) extension.
@@ -49,7 +51,7 @@ beneath the closing `---` of this header.
 Any content written there will appear in the rendered page after
 the concept map and/or figure, and before the _Activity_ section.
 
-#### YAML Header Specification
+##### YAML Header Specification
 
 All fields not marked as optional are required for the page to build.
 You can check that your YAML is valid with [this tool](http://www.yamllint.com/).
@@ -58,45 +60,42 @@ You can check that your YAML is valid with [this tool](http://www.yamllint.com/)
 ---
 title:     Title of the Module
 layout:    module               # don't change this
+
 prerequisites:
   - "a list of things that learners should know"
   - "in order to understand this module"
+
 objectives:
   - "a list of learning objectives"
   - "see note 1 below for more info"
+
 motivation: |
   A description of *why* you would want to learn this.
   Can be written in
   (GitHub-flavoured) [Markdown](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet).
   Line breaks will be respected, so you can add lists etc using Markdown syntax.
+
 concept_map: > # see note 2
   graph TD
       A[Christmas] -->|Get money| B(Go shopping)
       B --> C{Let me think}
       C -->|One| D[Laptop]
       C -->|Two| E[iPhone]
       C -->|Three| F[fa:fa-car Car];
+
 figure: /figures/mymodule.png # store the example image for your module in the `figures` folder and provide the absolute path from the root of the site here.
 figure_legend: Some description of the figure. (optional)
-activity_preface: |
-  Some general description of the activity for
-  that learners will do while studying the module.
-  It will be followed by platform-specific instructions/example code.
-  (optional)
-activities: # platform-specific activity instruction/example code files (see note 3) (optional)
-  - ["ImageJ GUI", "mymodule/activities/mymodule_imagejgui.md", "markdown"]
-  - ["ImageJ Macro": "mymodule/activities/mymodule_imagejmacro.ijm", "java"]
-  - ["Jython", "mymodule/activities/mymodule_jython.py", "python"]
-exercises: # platform-specific exercises (in Markdown files) (see note 4) (optional)
-  "ImageJ GUI": "mymodule/exercises/mymodule_imagejgui.md"
-  "ImageJ Macro": "mymodule/exercises/mymodule_imagejmacro.md"
-  "Jython": "mymodule/exercises/mymodule_jython.md"
-  "MATLAB": "mymodule/exercises/mymodule_matlab.md"
+
+multiactivities: # see note 3
+  - ["mymodule/mymodule_act1.md", [["ImageJ GUI", "mymodule/mymodule_act1_imagejgui.md"], ["ImageJ Macro", "mymodule/mymodule_act1_imagejmacro.ijm"], ["ImageJ Jython", "mymodule/mymodule_act1_jython.py"], ["skimage napari", "mymodule/mymodule_act1_skimage_napari.py", "python"]]]
+  - ["mymodule/mymodule_act2.md", [["ImageJ GUI", "mymodule/mymodule_act2_imagejgui.md"], ["ImageJ Macro", "mymodule/mymodule_act2_imagejmacro.ijm"], ["ImageJ Jython", "mymodule/mymodule_act2_jython.py"]
+  ["skimage napari", "mymodule/mymodule_act2_skimage_napari.py"]]]
+
 assessment: |
   Language-agnostic questions to assess learner understanding of the key concept
   covered in the module.
   (optional)
-learn_next: # see note 5
+learn_next: # see note 4
   - "[name_of_one](calibration)"
   - "[or_more_modules](object_splitting)"
   - "[to link to next](display)"
@@ -109,53 +108,36 @@ Notes:
 
 1. Learning objectives should be worded as endings to a sentence beginning "After completing this lesson, learners should be able to...". We recommend starting each learning objective with a verb from [Bloom's Taxonomy](https://cft.vanderbilt.edu/guides-sub-pages/blooms-taxonomy/)
 2. Concept maps are drawn with [Mermaid.js](https://mermaidjs.github.io/flowchart.html). The indentation of the chart description is important, so be careful!
-3. The `activities` field should be populated with three-entry arrays, where the first value is the name of the platform, the second value is the path to the instructions or script for the activity, and the third is a lower-case language identifier to tell GitHub Pages if and how the content of the file should be highlighted. For files containing activity instructions written in Markdown - as opposed to a script written in some programming language - the value in the third position should be `"markdown"`.
-4. The `exercises` field should be populated with key-value pairs, where the key is the name of the platform (e.g. "ImageJ GUI", "Python", etc) and the value is the path (relative to `_includes/`) to the file containing the exercises for that platform.
-5. The points in "Learn Next" are Markdown links, which should be formed as `[Module Title](modulefilename)`, where the extension has been removed from the filename.
+3. The `multiactivities` fields should be nested arrays: `["header.md", [["analysis_platform1_name", "mymodule/analysis_platform1_impl"],["analysis_platform2_name", "mymodule/analysis_platform2_impl"], ... ]]` 
+4. The points in "Learn Next" are Markdown links, which should be formed as `[Module Title](modulefilename)`, where the extension has been removed from the filename.
 
-### Associated files
-**THIS HAS NOW CHANGED 2023.04.25 AP. TODO: Review this section** 
-Below is a list of all the other files that you should provide
+##### Associated files
+
+Below is a list of all the other files that one should provide
 to accompany a new module,
 as well as the appropriate location for each
 (relative to the top level of the repository).
 Examples are given for a `/modules/mymodule.md`
 
-- The `figure` image
+- The `figure` image:
   - an file containing an example image to illustrate the concept being taught in the module
-  - location: `/figures/mymodule.md`
-- The `activities` files
-  - Markdown files containing instructions and/or example code for an activity that learners should follow to learn how to apply the concept on a particular platform (ImageJ Macro, MATLAB, etc)
-  - location: `_includes/mymodule/activities/mymodule_platformnospaces.md`
-- The `exercises` files
-  - Markdown files containing exercises to test the learner's understanding of applying the concept on a particular platform
-  - location: `_includes/mymodule/exercises/mymodule_platformnospaces.md`
-
-## Adding exercises/activity instructions for a new platform
-
-Contributions of instructions and exercises for more platforms are very welcome - please see the "Associated files" subsection above for details of where these contributed files should be added.
-
-## Customising the material for a course
-
-This repository is designed to work as a central reference point for all modules and platforms. However, we expect that instructors will want to prepare more specific material to be used in individual workshops/courses.
-
-To do this, fork or import\* this repository and follow the steps described below.
-
-\* Each GitHub user can only have a single fork of a repository so importing may be the better choice if you expect to make multiple customised sites from this material.
-
-### Setting a defualt platform
+  - location: `/figures/mymodule.png`
+  - if the figure is hard to make, please consider also adding a corresponding a PPTX file
+  - location: `/figures/resources/mymodule.pptx`
+- The `activities` files:
+  - There may be multiple activities for each module
+  - Each activity needs:
+    - a markdown header file that explains in general terms what the activity is about
+    - location: `_includes/mymodule/mymodule_myactivity.md` 
+    - files that implement the activity header in a specific platform, e.g.
+    - location: `_includes/mymodule/mymodule_myactivity_imagejgui.md`
+    - location: `_includes/mymodule/mymodule_myactivity_skimage.py`
 
-You can specify a default plaform for your site by adjusting the `default-platform` field in the site `_config.yml`. Beware: your choices will be limited by the availability of platform options for exercises and activities throughout the material! If you want to set a default platform that does not have exercises/activities prepared for every module, you should add the paths to any module files missing exercises/activities for your given platform to the `exclude` list in `_config.yml`. This will prevent any errors being raised due to a missing parameter for those modules.
+## Building the website locally
 
-### Adjusting module set and order
+It is important to test locally whether the website builds correctly before submitting changes to the repo.
 
-Use the `module_order` field in `_config.yml` to specify which modules should appear in your site and in what order. Other modules not mentioned in this list will still be built (unless you add their paths to the `exclude` field) but will not be included in the page navigation i.e. via dropdown menu, next/previous buttons, etc.
-
-## Questions about the module layout
-
-If you have questions about the module layout, please contact [email protected].
-
-## Building locally OSX
+### Building locally OSX
 
 To test your changes locally, install `jekyll` on your system. Instructions for Mac OSX are here: [https://jekyllrb.com/docs/installation/macos/](https://jekyllrb.com/docs/installation/macos/).
 
@@ -175,7 +157,7 @@ Now you can navigate around the locally-built version of the pages
 and check whether you're happy to submit your changes to be merged into `master` :+1:
 
 
-## Building locally Windows (without make)
+### Building locally Windows (without make)
 
 You need to install several tools (`ruby` and then `jekyll`). Please follow the instructions
 [https://jekyllrb.com/docs/installation/windows/] follow step 1-4
@@ -227,7 +209,8 @@ and check whether you're happy to submit your changes to be merged into `master`
 
 Caveat: Some users must run their ``gem install`` commands as administrator. We do not know exactly why, but it may depend on their respective Windows installation. 
 
-## See your new module
+### See your new module
+
 To see a module edit the file *_config.yml*  and add your module (the file name in _modules with .md) to the 
 list and the appropriate location
 ```markdown
@@ -252,3 +235,8 @@ module_order:
 ```
 
 Note that when jekyll is serving your page, changes on existing files are automatically updated.
+
+
+## Questions
+
+If you have any questions please ask us in [an issue](https://github.com/NEUBIAS/training-resources/issues).

Gemfile

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 
-source 'https://rubygems.org'
+source 'http://rubygems.org'
 
 git_source(:github) { |repo_name| "https://github.com/#{repo_name}" }
 

README.md

@@ -1,14 +1,28 @@
-# Image Analysis Training Resources
+# Bioimage Analysis Training Resource
 
 [![Gitpod ready-to-code](https://img.shields.io/badge/Gitpod-ready--to--code-blue?logo=gitpod)](https://gitpod.io/#https://github.com/neubias/training-resources)
 
 **[Module overview](https://neubias.github.io/training-resources/all-modules)**
 
 **[Home page](https://neubias.github.io/training-resources)**
 
+
 This project is intended to collect together various resources
 that can be useful when planning/delivering training in image analysis.
 
+## About 
+
+- [Google slides presentation](https://docs.google.com/presentation/d/1x5euj3p4hoAdOONQbzFA5xf3rnsNeTjC1rpadCbwbQk/edit?usp=sharing)
+- [Recorded webinar](https://www.youtube.com/watch?v=xtm7DAiXtr0)
+
+## Teach
+
+The material in this repository can be flexibly used in many ways.
+
+Some guidance and tips can be found in [`TEACHING_TIPS`](TEACHING_TIPS.md)
+
+## Contribute
+
 Detailed guidance for contributing can be found in [`CONTRIBUTING.md`](CONTRIBUTING.md).
 
 ## Repository