fixes conversion to pythia citations style as wel as toc ordering

.github/workflows/publish.yaml

@@ -92,21 +92,24 @@ jobs:
           git config --local user.name "$GITHUB_ACTOR"
           git config --local user.email "[email protected]"
           git commit ${NB_PATH[*]} -m "Quarto output" || echo "No changes to commit"
-          git push origin || echo "No changes to commit"
+          git push || echo "No changes to commit"
 
       - name: Commit Files Pythia Book
         if: github.ref == 'refs/heads/main' 
         run: |
-          python src/render_sfinx_toc.py
+          pip install .
+          python src/eo_datascience/render_sfinx_toc.py
+          python src/eo_datascience/clean_nb.py
           cp ./_toc.yml ./pythia/
           cp ./Makefile ./pythia/
+          cp ./chapters/references.bib ./pythia/notebooks/
           cp -R ./notebooks/. ./pythia/notebooks/
           cd ./pythia
           git config --local user.name "$GITHUB_ACTOR"
           git config --local user.email "[email protected]"
           git add .
           git commit -m "Quarto output" || echo "No changes to commit"
-          git push origin || echo "No changes to commit"
+          git push || echo "No changes to commit"
 
       - name: Commit Files Quarto Book Branch dev
         if: github.ref == 'refs/heads/dev'
@@ -115,14 +118,17 @@ jobs:
           git config --local user.name "$GITHUB_ACTOR"
           git config --local user.email "[email protected]"
           git commit ${NB_PATH[*]} -m "Quarto output" || echo "No changes to commit"
-          git push origin dev || echo "No changes to commit"
+          git push || echo "No changes to commit"
 
       - name: Commit Files Pythia Book Branch dev
         if: github.ref == 'refs/heads/dev'
         run: |
-          python src/render_sfinx_toc.py
+          pip install .
+          python src/eo_datascience/render_sfinx_toc.py
+          python src/eo_datascience/clean_nb.py
           cp ./_toc.yml ./pythia/
           cp ./Makefile ./pythia/
+          cp ./chapters/references.bib ./pythia/notebooks/
           cp -R ./notebooks/. ./pythia/notebooks/
           cd ./pythia
           git config --local user.name "$GITHUB_ACTOR"

.gitignore

@@ -54,6 +54,8 @@ docs/_rst/*
 docs/_build/*
 cover/*
 MANIFEST
+/**/*.html
+/**/*_files/
 
 # Per-project virtualenvs
 .venv*/

Makefile

@@ -38,7 +38,6 @@ post-render:
 	for i in $(QMD); do quarto convert $$i; done
 	- mv chapters/*.ipynb notebooks/ >/dev/null 2>&1
 	- for f in chapters/*.quarto_ipynb ; do mv -- "$f" "${f%.quarto_ipynb}.ipynb"  >/dev/null 2>&1; done
-	python src/clean-nb.py
 	cp Makefile notebooks/
 
 data:

chapters/01_classification.qmd

@@ -1,5 +1,5 @@
 ---
-title: Classification
+title: Classification of Sentinel-2 imagery
 subtitle: Finding forests with satelite imagery
 jupyter: 
   kernelspec:

chapters/02_floodmapping.qmd

@@ -10,6 +10,11 @@ jupyter:
 
 ![Image from [wikipedia](https://upload.wikimedia.org/wikipedia/commons/d/d4/Thomas_Bayes.gif)](https://upload.wikimedia.org/wikipedia/commons/d/d4/Thomas_Bayes.gif)
 
+::: {.callout-note}
+This notebooks contains interactive element. These interactive element can only be viewed on Binder by clicking on the Binder badge or 🚀 button.
+:::
+
+
 ```{python}
 %matplotlib widget
 

chapters/references.bib

@@ -9,7 +9,6 @@ @acelik/colors-methods-and-mistakes-in-spatial-data-visualization-60d02e7f09fd
 	author = {Celik, Anil},
 	month = aug,
 	year = {2015},
-	file = {Snapshot:/home/mschobbe/Zotero/storage/BCKHNHID/colors-methods-and-mistakes-in-spatial-data-visualization-60d02e7f09fd.html:text/html},
 }
 
 @article{nguyen_examining_2021,
@@ -134,11 +133,13 @@ @article{bauer-marschallinger_toward_2019
 	file = {IEEE Xplore Abstract Record:/home/mschobbe/Zotero/storage/5QJ4V6PY/8444430.html:text/html},
 }
 
-@software{quast_getting_2024,
-  author       = {Raphael Quast},
-  title        = {EOmaps: A python package to visualize and analyze geographical datasets.},
-  doi          = {10.5281/zenodo.6459598},
-  url          = {https://doi.org/10.5281/zenodo.6459598}
+@article{quast_getting_2024,
+  author = {Raphael Quast},
+  title = {EOmaps: A python package to visualize and analyze geographical datasets.},
+  doi = {10.5281/zenodo.6459598},
+  url = {https://doi.org/10.5281/zenodo.6459598},
+  journal = {},
+  year = {2024}
 }
 
 @article{rouse1974monitoring,
@@ -157,4 +158,5 @@ @online{nasa2020
     year = {2020},
     url = {https://earthobservatory.nasa.gov/features/MeasuringVegetation/measuring_vegetation_2.php},
     urldate = {2024-07-26}
-}
+}
+

environment.yml

@@ -0,0 +1,9 @@
+name: eo-datascience
+channels:
+  - conda-forge
+dependencies:
+  - python=3.10
+  - pip
+  - mamba
+  - jupyter
+  - nbformat