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* adding build file

* adding badge fixing inkscape install

* adding pip to environment, adding tex to build pdf workflow

* using chrome to convert pdfs adding pdf badge

* adding sudo

* fixing pdf generating code and forcing draft-status

* updating pdf-building, removing png files

* updating pdf workflow

* adding pdf upload and link

* changing id
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kmader authored Nov 22, 2019
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93 changes: 93 additions & 0 deletions .github/workflows/pdf.yml
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name: make_pdfs

on: [push]

jobs:
build:

runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v1
- name: apt_deps
run: |
sudo apt-get update
sudo apt-get install -y inkscape ghostscript
sudo apt-get install -y --no-install-recommends chromium-browser
- name: Setup environment
run: |
mkdir -p download
cd download
echo "Cached in $HOME/download :"
if [[ ! -f miniconda.sh ]]
then
wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
-O miniconda.sh
fi
chmod +x miniconda.sh && ./miniconda.sh -b
cd ..
export PATH="$HOME/miniconda3/bin:$PATH"
conda update --yes conda
# Configure the conda environment and put it in the path using the
# provided versions
conda create -n testenv --yes python=$PYTHON_VERSION pip nose pytest
conda env update -n testenv -f binder/environment.yml -q
source activate testenv
chmod a+x binder/postBuild
sh binder/postBuild
ipython kernel install --user --name testkernel
jupyter kernelspec list
- name: Build Lectures
run: |
export PATH="$HOME/miniconda3/bin:$PATH";
source activate testenv;
shopt -s globstar;
cd Lectures;
for nb in *ipynb; do
if [[ $nb = *"Kaggle"* ]]; then
echo "skipping kaggle kernel $nb";
else
jupyter nbconvert --ExecutePreprocessor.timeout=3600 --ExecutePreprocessor.kernel_name=testkernel "$nb" --to html
chromium-browser --no-sandbox --headless --disable-gpu --print-to-pdf=$(basename "$nb" .ipynb).pdf $(basename "$nb" .ipynb).html
fi;
done
cd ..
- name: Collect PDFs
run: |
zip -r pdfs.zip */*.pdf
zip -ur pdfs.zip */*.html
- name: Make Combined
run: |
git clone https://github.com/bronson/pdfdir
pdfdir/pdfdir-join Lectures/
zip -ur pdfs.zip Lectures.pdf
- name: Create Release
id: create_release
uses: actions/[email protected]
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
tag_name: ${{ github.ref }}
release_name: Release ${{ github.ref }}
draft: true
prerelease: false
- name: Upload Release Asset
id: upload-zip
uses: actions/[email protected]
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
asset_path: pdfs.zip
asset_name: pdfs.zip
asset_content_type: application/zip
- name: Upload UberPDF
id: upload-pdf
uses: actions/[email protected]
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
asset_path: Lectures.pdf
asset_name: all_lectures.pdf
asset_content_type: application/pdf
2 changes: 1 addition & 1 deletion Lectures/10-ScalingUp.ipynb
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"$$ \\rightarrow 0.975 $$\n",
"\n",
"We could have done these easily without SQL using Excel, Matlab or R\n",
"\n![image.png](attachment:image.png)"
"\n"
],
"metadata": {
"slideshow": {
Expand Down
28 changes: 14 additions & 14 deletions README.md
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[![Build Status](https://travis-ci.org/kmader/Quantitative-Big-Imaging-2019.svg?branch=master)](https://travis-ci.org/kmader/Quantitative-Big-Imaging-2019)
![](https://github.com/kmader/Quantitative-Big-Imaging-2019/workflows/build_notebooks/badge.svg)
[![Make PDF](https://github.com/kmader/Quantitative-Big-Imaging-2019/workflows/make_pdfs/badge.svg)](https://github.com/kmader/Quantitative-Big-Imaging-2019/releases)
[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/kmader/Quantitative-Big-Imaging-2019.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/kmader/Quantitative-Big-Imaging-2019/context:python)
[![Total alerts](https://img.shields.io/lgtm/alerts/g/kmader/Quantitative-Big-Imaging-2019.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/kmader/Quantitative-Big-Imaging-2019/alerts/)

Expand All @@ -9,7 +10,7 @@

Here are the lectures, exercises, and additional course materials corresponding to the spring semester 2019 course at ETH Zurich, [227-0966-00L](http://www.vvz.ethz.ch/Vorlesungsverzeichnis/lerneinheit.view?lerneinheitId=128120&semkez=2019S&ansicht=KATALOGDATEN&lang=en): Quantitative Big Imaging.

The lectures have been prepared and given by Kevin Mader and associated guest lecturers. Please note the Lecture Slides and PDF do not contain source code, this is only available in the handout file. Some of the lectures will be recorded and placed on YouTube on the [QBI Playlist](https://www.youtube.com/playlist?list=PLTWuXgjdOrnmXVVQG5DRkVeOIGOcTmCIw). The lectures are meant to be followed in chronological order and each lecture has a corresponding hands-on exercises in the exercises section.
The lectures have been prepared and given by Kevin Mader and associated guest lecturers. Please note the Lecture Slides and PDF do not contain source code, this is only available in the handout file. Some of the lectures will be recorded and placed on YouTube on the [QBI Playlist](https://www.youtube.com/playlist?list=PLTWuXgjdOrnmXVVQG5DRkVeOIGOcTmCIw). The lectures are meant to be followed in chronological order and each lecture has a corresponding hands-on exercise. The entire lecture set is available as a single PDF file available in the [releases section](https://github.com/kmader/Quantitative-Big-Imaging-2019/releases)

## Learning Objectives

Expand Down Expand Up @@ -61,7 +62,7 @@ For communicating, discussions, asking questions, and everything, we will be try

- [Slides (static)](http://nbviewer.jupyter.org/format/slides/github/kmader/Quantitative-Big-Imaging-2019/blob/master/Lectures/01-Introduction.ipynb) [![slides](https://img.shields.io/badge/interactive-slides-green.svg)](http://mybinder.org/v2/gh/kmader/quantitative-big-imaging-2019/master?filepath=Lectures/01-Introduction.ipynb) [Lecture Handout](http://nbviewer.jupyter.org/github/kmader/Quantitative-Big-Imaging-2019/blob/master/Lectures/01-Introduction.ipynb)
- [Lecture Video](https://www.youtube.com/watch?v=_3UCWECqIHY&list=PLTWuXgjdOrnmXVVQG5DRkVeOIGOcTmCIw&index=3&t=0s)

#### Exercises

- [Getting Started with KNIME](Exercises/01-Description.md)
Expand Down Expand Up @@ -91,19 +92,19 @@ For communicating, discussions, asking questions, and everything, we will be try

- [Slides (static)](http://nbviewer.jupyter.org/format/slides/github/kmader/Quantitative-Big-Imaging-2019/blob/master/Lectures/04-BasicSegmentation.ipynb) [![slides](https://img.shields.io/badge/interactive-slides-green.svg)](http://mybinder.org/v2/gh/kmader/quantitative-big-imaging-2019/master?filepath=Lectures/04-BasicSegmentation.ipynb) [Lecture Handout](http://nbviewer.jupyter.org/github/kmader/Quantitative-Big-Imaging-2019/blob/master/Lectures/04-BasicSegmentation.ipynb)
- Part 2: [Slides (static)](http://nbviewer.jupyter.org/format/slides/github/kmader/Quantitative-Big-Imaging-2018/blob/master/Lectures/04-BasicSegmentation_Part2.ipynb) [![slides](https://img.shields.io/badge/interactive-slides-green.svg)](http://mybinder.org/v2/gh/kmader/quantitative-big-imaging-2019/master?filepath=Lectures/04-BasicSegmentation_Part2.ipynb) [Lecture Handout](http://nbviewer.jupyter.org/github/kmader/Quantitative-Big-Imaging-2019/blob/master/Lectures/04-BasicSegmentation_Part2.ipynb)

- [Lecture Video](https://www.youtube.com/watch?v=LFwHVO5zDzY&index=5&list=PLTWuXgjdOrnmXVVQG5DRkVeOIGOcTmCIw)

#### Exercises

- [Overview](Exercises/04-Overview.md)

### 21th March - Advanced Segmentation

- Part 1: [Slides (static)](http://nbviewer.jupyter.org/format/slides/github/kmader/Quantitative-Big-Imaging-2019/blob/master/Lectures/05-AdvancedSegmentation.ipynb) [![slides](https://img.shields.io/badge/interactive-slides-green.svg)](http://mybinder.org/v2/gh/kmader/quantitative-big-imaging-2019/master?filepath=Lectures/05-AdvancedSegmentation.ipynb) [Lecture Handout](http://nbviewer.jupyter.org/github/kmader/Quantitative-Big-Imaging-2019/blob/master/Lectures/05-AdvancedSegmentation.ipynb)
- Part 2: [Slides (static)](http://nbviewer.jupyter.org/format/slides/github/kmader/Quantitative-Big-Imaging-2019/blob/master/Lectures/05-SupervisedSegmentation.ipynb) [![slides](https://img.shields.io/badge/interactive-slides-green.svg)](http://mybinder.org/v2/gh/kmader/quantitative-big-imaging-2019/master?filepath=Lectures/05-SupervisedSegmentation.ipynb) [Lecture Handout](http://nbviewer.jupyter.org/github/kmader/Quantitative-Big-Imaging-2019/blob/master/Lectures/05-SupervisedSegmentation.ipynb)

- Part 2: [Slides (static)](http://nbviewer.jupyter.org/format/slides/github/kmader/Quantitative-Big-Imaging-2019/blob/master/Lectures/05-SupervisedSegmentation.ipynb) [![slides](https://img.shields.io/badge/interactive-slides-green.svg)](http://mybinder.org/v2/gh/kmader/quantitative-big-imaging-2019/master?filepath=Lectures/05-SupervisedSegmentation.ipynb) [Lecture Handout](http://nbviewer.jupyter.org/github/kmader/Quantitative-Big-Imaging-2019/blob/master/Lectures/05-SupervisedSegmentation.ipynb)

- [Lecture Video](https://www.youtube.com/watch?v=wIEstgKwEro&list=PLTWuXgjdOrnmXVVQG5DRkVeOIGOcTmCIw&index=8&t=0s)

#### Exercises
Expand Down Expand Up @@ -136,9 +137,9 @@ For communicating, discussions, asking questions, and everything, we will be try
### 11th April - Dynamic Experiments

- [Slides (static)](http://nbviewer.jupyter.org/format/slides/github/kmader/Quantitative-Big-Imaging-2019/blob/master/Lectures/08-DynamicExperiments.ipynb) [![slides](https://img.shields.io/badge/interactive-slides-green.svg)](http://mybinder.org/v2/gh/kmader/quantitative-big-imaging-2019/master?filepath=Lectures/08-DynamicExperiments.ipynb) [Lecture Handout](http://nbviewer.jupyter.org/github/kmader/Quantitative-Big-Imaging-2019/blob/master/Lectures/08-DynamicExperiments.ipynb)

- [Feature Points Slides](http://nbviewer.jupyter.org/format/slides/github/kmader/Quantitative-Big-Imaging-2019/blob/master/Lectures/08-FeaturePoints.ipynb)

- [Video](https://www.youtube.com/watch?v=RPHtLaUA1_I&list=PLTWuXgjdOrnmXVVQG5DRkVeOIGOcTmCIw&index=15&t=0s)

#### Exercises
Expand All @@ -155,7 +156,7 @@ For communicating, discussions, asking questions, and everything, we will be try
### 18th April - Statistics, Prediction, and Reproducibility

- [Slides (static)](http://nbviewer.jupyter.org/format/slides/github/kmader/Quantitative-Big-Imaging-2019/blob/master/Lectures/09-Statistics.ipynb) [![slides](https://img.shields.io/badge/interactive-slides-green.svg)](http://mybinder.org/v2/gh/kmader/quantitative-big-imaging-2019/master?filepath=Lectures/09-Statistics.ipynb) [Lecture Handout](http://nbviewer.jupyter.org/github/kmader/Quantitative-Big-Imaging-2019/blob/master/Lectures/09-Statistics.ipynb)

- [Video](https://www.youtube.com/watch?v=ky7tfHkkVd0&list=PLTWuXgjdOrnmXVVQG5DRkVeOIGOcTmCIw&index=17)


Expand All @@ -165,11 +166,11 @@ For communicating, discussions, asking questions, and everything, we will be try
- C. Elegans Dataset on Kaggle [R Notebook](https://www.kaggle.com/kmader/d/kmader/high-content-screening-celegans/qbi-statistics-and-reproducibility-in-r/) or [Python Notebook](https://www.kaggle.com/kmader/d/kmader/high-content-screening-celegans/image-overview)
- Lung Segmentation [https://www.kaggle.com/kmader/dsb-lung-segmentation-algorithm/notebook](Rule-based Image Processing) and [Simple Neural Network](https://www.kaggle.com/kmader/simple-nn-with-keras)


### 2nd May - Scaling Up / Big Data

- [Slides (static)](http://nbviewer.jupyter.org/format/slides/github/kmader/Quantitative-Big-Imaging-2018/blob/master/Lectures/11-ScalingUp.ipynb) [![slides](https://img.shields.io/badge/interactive-slides-green.svg)](http://mybinder.org/v2/gh/kmader/quantitative-big-imaging-2018/master?filepath=Lectures/11-ScalingUp.ipynb) [Lecture Handout](http://nbviewer.jupyter.org/github/kmader/Quantitative-Big-Imaging-2018/blob/master/Lectures/11-ScalingUp.ipynb)

- [Lecture Video](https://www.youtube.com/watch?v=1cSkd2O9bYE&list=PLTWuXgjdOrnmXVVQG5DRkVeOIGOcTmCIw&index=20)

#### Exercises
Expand All @@ -184,7 +185,7 @@ For communicating, discussions, asking questions, and everything, we will be try
### 9th May - Guest Lecture - High Content Screening (M. Prummer)

- [High Content Screening Slides](https://github.com/kmader/Quantitative-Big-Imaging-2019/blob/master/Lectures/11-HCSBigData.pdf) - Michael Prummer / Nexus / Roche

#### Exercises

- [High Content Screening with C. Elegans](https://www.kaggle.com/kmader/high-content-screening-celegans)
Expand Down Expand Up @@ -320,4 +321,3 @@ Javier Montoya / Computer Vision / ScopeM
Presented by Aurelien Lucchi in [Data Analytics Lab](http://www.da.inf.ethz.ch) in D-INFK at ETHZ

- [Slides](https://rawgithub.com/kmader/Quantitative-Big-Imaging-2016/master/Lectures/12-DeepLearning.pdf)

1 change: 1 addition & 0 deletions binder/environment.yml
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Expand Up @@ -35,6 +35,7 @@ dependencies:
- graphviz
- python-graphviz
- tornado
- pip
- pip:
- keras==2.2.5
- fsspec>=0.3.3
Expand Down

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