Add GitHub Pages workflow & rename to index.html (#20)

### Description
This will mean that the slides appear at
https://scikit-surgery.github.io/cmicHACKS2 rather than
https://scikit-surgery.github.io/cmicHACKS2/slides/slides.html. And
means any new change will be deployed.


## Type of change
Please delete options accordingly to the description.

<!-- Write an `x` in all the boxes that apply -->
- [ ] Bug fix (non-breaking change which fixes an issue)
- [X] New feature (non-breaking change which adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to not work as expected)
- [ ] This change requires a documentation update


### Checklist
<!-- You do not need to complete all the items by the time you submit
the pull request, but most likely the changes will only be merged if all
the tasks are done. -->

<!-- Write an `x` in all the boxes that apply -->
- [X] I have read the
[`CONTRIBUTING`](https://github.com/CONTRIBUTING.rst) docs and have a
developer setup (especially important are `pre-commit`and `pytest`)
- [X] My code is properly tested
- [X] My code follows the style guidelines 
- [X] My code does not contain unused elements. If so, I documented why
it needs to.
- [X] My changes generate no new warnings 
- [X] I have performed a self-review of my own code
- [X] I have commented my code, particularly in hard-to-understand areas
- [X] I have made corresponding changes to the documentation
- [X] This pull request is ready to be reviewed
- [X] My branch is up-to-date with master (with use of rebase if needed)
- [X] If the PR is ready and there are multiple commits, I have
[squashed them and
force-pushed](https://www.w3docs.com/snippets/git/how-to-combine-multiple-commits-into-one-with-3-steps.html#force-pushing-commits-7)

.github/workflows/slides.yml

@@ -0,0 +1,43 @@
+name: Deploy Slides
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+concurrency:
+  cancel-in-progress: true
+  group: >-
+    ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+
+jobs:
+  deploy-slides:
+    env:
+      BUNDLE_GEMFILE: ${{ github.workspace }}/slides/Gemfile
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+
+      - name: Set up Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: "3.2"
+          bundler-cache: true
+
+      - name: Install and Build
+        working-directory: ./slides
+        run: >-
+            JEKYLL_GITHUB_TOKEN=${{ secrets.GITHUB_TOKEN }}
+            JEKYLL_ENV=production
+            bundle exec jekyll build
+
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./slides/_site
+          publish_branch: gh-pages
+          user_name: github-actions[bot]
+          user_email: github-actions[bot]@users.noreply.github.com

.gitignore

@@ -11,7 +11,7 @@
 
 ## site
 .jekyll-cache/ 
-_site/ 
+_site/
 Gemfile.lock
 
 ## Kvasir-SEG dataset

README.md

@@ -16,7 +16,7 @@ In this hackathon, instructors aim to engage with participants to bring three le
 
 We hope to bring together researchers, engineers and clinicians across different departments to hack workflows for real-time AI for Surgery (development, evaluation and integration) and hopefully to sparking future collaborations.
 
-See slides for a quick introduction: https://scikit-surgery.github.io/cmicHACKS2/slides/slides.html
+See slides for a quick introduction: https://scikit-surgery.github.io/cmicHACKS2
 
 ## :sparkles: Project leaders and organisers 
 Leaders: [Zhehua Mao](https://github.com/ZH-Mao) and [Miguel Xochicale](https://github.com/mxochicale)    

slides/README.md

@@ -37,7 +37,7 @@ bundle exec jekyll serve
 ```
 2. Open hmtl slides using firefox on a local server.
 ```
-firefox http://127.0.0.1:4000/slides.html #or google-chrome http://127.0.0.1:4000/slides.html
+firefox http://127.0.0.1:4000 #or google-chrome http://127.0.0.1:4000
 ```
 3. You might like to remove build files
 ```
@@ -46,9 +46,9 @@ rm -rf .jekyll-cache/ _site/ Gemfile.lock
 
 ## 🎒 Steps to create github pages 
 1. Setting up pages at https://github.com/SciKit-Surgery/cmicHACKS2/settings/pages
-2. Select deploy from a branch, select branch `7-slides` with path `/root` and[SAVE]. Then, you might need to select `main` branch for the final version of the slides.
+2. Select deploy from a branch, select branch `gh-pages` with path `/root` and[SAVE]. Then, you might need to select `main` branch for the final version of the slides.
 3. First GitHub action:  https://github.com/SciKit-Surgery/cmicHACKS2/actions/runs/6747753816
-4. Online slides should be available here https://scikit-surgery.github.io/cmicHACKS2/slides/slides.html
+4. Online slides should be available here https://scikit-surgery.github.io/cmicHACKS2
 
 
 ## References 

slides/figures/agenda/Makefile

@@ -0,0 +1,55 @@
+
+OS_VERSION:=$(shell lsb_release -a 2>/dev/null | grep Description | awk '{ print $$2 "-" $$3 }')
+$(eval $(shell grep VERSION_ID /etc/os-release))
+#ifeq ($(VERSION_ID), 22.04)
+ifeq ($(OS_VERSION), Ubuntu-22.04.1)
+EXPORT_ID = --export-png
+else
+EXPORT_ID = --export-filename
+endif
+# https://stackoverflow.com/questions/714100/os-detecting-makefile
+
+INKSCAPE?=inkscape --export-dpi=200 $(EXPORT_ID)
+
+
+#dPDFSETTINGS=screen #lower quality, smaller size. (72 dpi)
+#dPDFSETTINGS=ebook #for better quality, but slightly larger pdfs. (150 dpi)
+#dPDFSETTINGS=prepress #output similar to Acrobat Distiller "Prepress Optimized" setting (300 dpi)
+#dPDFSETTINGS=printer #selects output similar to the Acrobat Distiller "Print Optimized" setting (300 dpi)
+dPDFSETTINGS=default #selects output intended to be useful across a wide variety of uses, possibly at the expense of a larger output file
+
+GS?=gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/$(dPDFSETTINGS) -dNOPAUSE -dQUIET -dBATCH -sOutputFile=
+
+FIGURES_SVG=$(wildcard vectors/*.svg)
+FIGURES_PNG=$(subst vectors/,outputs/,$(FIGURES_SVG:.svg=.png))
+FIGURES_PDF=$(subst vectors/,outputs/,$(FIGURES_SVG:.svg=.pdf))
+FIGURES_PDF_REDUCED_SIZE=$(subst vectors/,outputs/,$(FIGURES_SVG:.svg=_reduced_size.pdf))
+
+# Pattern rule for converting SVG to PNG and PDF
+png:	$(FIGURES_PNG)
+outputs/%.png: vectors/%.svg
+	$(INKSCAPE) $(@) $(<)
+
+pdf:	$(FIGURES_PDF)
+outputs/%.pdf: vectors/%.svg
+	$(INKSCAPE) $(@) $(<)
+
+edit:
+	inkscape $(FIGURES_SVG)
+
+view-png:
+	eog $(FIGURES_PNG)
+
+view-pdf:
+	evince $(FIGURES_PDF)
+
+reduce-pdf-size:
+	$(GS)$(FIGURES_PDF_REDUCED_SIZE) $(FIGURES_PDF)
+
+clean:  ##  output figure files
+	rm -f $(FIGURES_PNG) $(FIGURES_PDF) outputs/*.pdf
+
+test:
+	echo $(VERSION_ID)
+	echo $(OS_VERSION)
+	echo $(EXPORT_ID)

slides/figures/agenda/README.md

@@ -0,0 +1,44 @@
+# Vector figures
+
+## Notes
+
+## Usage 
+```
+make png
+make pdf
+make view-png #eog *.png
+make view-pdf #evince *.pdf
+make reduce-pdf-size dPDFSETTING=book # screen, ebook, prepress, printer and default
+make edit # inkscape vector/drawing-v$NN.svg
+make clean
+```
+
+## tree file and file size
+```
+tree -s
+[       4096]  .
+├── [       1771]  Makefile
+├── [       4096]  outputs
+│   ├── [       8378]  drawing-v00.pdf
+│   ├── [      30203]  drawing-v00.png
+│   ├── [       9015]  drawing-v00_reduced_size.pdf
+│   └── [         70]  README.md
+├── [        508]  README.md
+├── [       4096]  references
+│   └── [         15]  README.md
+└── [       4096]  vectors
+    └── [       6982]  drawing-v00.svg
+
+3 directories, 8 files
+
+```
+
+## Download template
+Open a terminal and type:
+```
+cd ~/Desktop &&svn checkout https://github.com/mxochicale/figures/trunk/00_template-vector-images
+cd 00_template-vector-images && rm -rf .svn
+```
+
+# References
+https://stackoverflow.com/questions/7106012/download-a-single-folder-or-directory-from-a-github-repo

slides/figures/agenda/outputs/README.md

@@ -0,0 +1,6 @@
+# Versions
+## v01
+![v](drawing-v01.png)
+
+## v00
+![v](drawing-v00.png)

slides/figures/agenda/references/README.md

@@ -0,0 +1,3 @@
+# References
+
+