switch to jupyter book

Author: akhmerov

.gitattributes

@@ -1 +0,0 @@
-*.ipynb filter=nb-filters

.gitignore

@@ -24,6 +24,7 @@ auto
 
 # Cached output
 .nb_output_cache
+_build
 
 # Misc
 .DS_Store

.gitlab-ci.yml

@@ -1,34 +1,23 @@
 image: topocourse/topocourse
 stages:
-  - execute
   - build
   - deploy
 
 
 execute_ipynbs:
-  stage: execute
+  stage: build
   before_script:
-    - pip install ruamel.yaml git+https://gitlab.kwant-project.org/anton-akhmerov/publist.git
+    - pip install ruamel.yaml git+https://gitlab.kwant-project.org/anton-akhmerov/publist.git jupyter-book
   script:
-    - export PYTHONPATH=$PYTHONPATH:${PWD}/code
-    - export OPENBLAS_NUM_THREADS=1 OMP_NUM_THREADS=1 MKL_NUM_THREADS=1 MKL_DYNAMIC=FALSE
-    - export MARKDOWN=generated/markdown
-    - mkdir -p $MARKDOWN
-    - cp -r src/* $MARKDOWN
-    - python scripts/preprocess_markdown.py
-    - export WITH_OUTPUT=generated/with_output
-    - cp -r data $WITH_OUTPUT
-    - cp -r $MARKDOWN/* $WITH_OUTPUT
-    - find $WITH_OUTPUT -name '*.md' | parallel --delay 3 --jobs 32 notedown -o --run --timeout -1 --match fenced
-    - rm -rf $WITH_OUTPUT/data
+    - jupyter-book build src
   artifacts:
     paths:
-      - generated/with_output
+      - src/_build/html
     expire_in: 7d
 
 
 mirror to github:
-  stage: execute
+  stage: build
   allow_failure: true
   only:
     - branches@qt/topocm
@@ -47,55 +36,13 @@ mirror to github:
     - for REPO in $REPOS; do git push --mirror $REPO; done
 
 
-edx archive:
-  stage: build
-  before_script:
-    - pip install ruamel.yaml
-  script: ./scripts/converter.py ./generated/with_output
-  artifacts:
-    paths:
-      - generated/import_to_edx.tar.gz
-      - generated/html/edx
-    expire_in: 7d
-
-
-pelican website:
-  stage: build
-  variables:
-    DEST: "generated/html"
-  before_script:
-    - pip install ruamel.yaml
-  script:
-    - python scripts/converter_pelican.py
-    - pelican -o $DEST/ -s website_assets/pelicanconf.py generated/pelican_content
-  artifacts:
-    paths:
-      - generated/html
-    expire_in: 30d
-
-
-ocw website:
-  stage: build
-  before_script:
-    - pip install ruamel.yaml
-  script:
-    - python scripts/converter_ocw.py
-    - mv website_assets/iframes.txt generated/html/ocw
-  artifacts:
-    paths:
-      - generated/html/ocw
-    expire_in: 1d
-
-
 .upload_website: &upload_website
   stage: deploy
   before_script:
     - mkdir -p ~/.ssh && ssh-keyscan tnw-tn1.tudelft.net >> ~/.ssh/known_hosts
     - echo $WEBSITE_KEY | base64 -d > ~/.ssh/id_rsa && chmod 600 ~/.ssh/id_rsa
   script:
-    - cp -r generated/with_output generated/html/notebooks
-    - "rsync -ravz --delete generated/html/* [email protected]:"
-    - "rsync -ravz --delete website_assets/static [email protected]:"
+    - "rsync -ravz src/_build/html/* [email protected]:"
   after_script:
     - rm -rf ~/.ssh
 

src/_config.yml

@@ -0,0 +1,18 @@
+title: 'Topology in condensed matter: tying quantum knots'
+author: Topology course team
+execute:
+  execute_notebooks: cache
+  timeout: -1
+  stderr_output: remove-warn
+sphinx:
+  config:
+    html_js_files:
+    - https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js
+    - - https://cdn.bokeh.org/bokeh/release/bokeh-2.2.3.min.js
+      - crossorigin: anonymous
+    - - https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.2.3.min.js
+      - crossorigin: anonymous
+    - - https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.2.3.min.js
+      - crossorigin: anonymous
+    - - https://unpkg.com/@holoviz/[email protected]/dist/panel.min.js
+      - crossorigin: anonymous

src/_toc.yml

@@ -0,0 +1,69 @@
+format: jb-book
+root: syllabus
+parts:
+- caption: Before you begin
+  chapters:
+  - file: w0_background/intro
+  - file: w0_background/band_structures
+- caption: Topology in toy models
+  chapters:
+  - file: w1_topointro/0d
+  - file: w1_topointro/1D
+  - file: w1_topointro/w1_assignments
+- caption: Majoranas I
+  chapters:
+  - file: w2_majorana/nanowire
+  - file: w2_majorana/signatures
+  - file: w2_majorana/braiding
+  - file: w2_majorana/w2_assignments
+- caption: 'More parameters: charge pumping'
+  chapters:
+  - file: w3_pump_QHE/pumps
+  - file: w3_pump_QHE/Laughlinargument
+  - file: w3_pump_QHE/QHEedgestates
+  - file: w3_pump_QHE/w3_assignments
+- caption: Chern insulators
+  chapters:
+  - file: w4_haldane/QHE_lattice
+  - file: w4_haldane/haldane_model
+  - file: w4_haldane/w4_assignments
+- caption: Quantum spin Hall effect
+  chapters:
+  - file: w5_qshe/fermion_parity_pump
+  - file: w5_qshe/qshe_experiments
+  - file: w5_qshe/w5_assignments
+- caption: Three-dimensional topological insulators
+  chapters:
+  - file: w6_3dti/bhz
+  - file: w6_3dti/3dti_signatures
+  - file: w6_3dti/w6_assignments
+- caption: Topological defects
+  chapters:
+  - file: w7_defects/ti_majoranas
+  - file: w7_defects/crystalline_defects
+  - file: w7_defects/w7_assignments
+- caption: General approach to topological classification
+  chapters:
+  - file: w8_general/classification
+  - file: w8_general/invariants
+  - file: w8_general/w8_assignments
+- caption: Anderson localization and topology
+  chapters:
+  - file: w9_disorder/scaling
+  - file: w9_disorder/topoflow
+  - file: w9_disorder/w9_assignments
+- caption: Extensions of classification I
+  chapters:
+  - file: w10_extensions/gapless
+  - file: w10_extensions/mechanics
+  - file: w10_extensions/w10_assignments
+- caption: Extensions of classification II
+  chapters:
+  - file: w11_extensions2/floquet
+  - file: w11_extensions2/cti
+  - file: w11_extensions2/w11_assignments
+- caption: Beyond single-particle physics
+  chapters:
+  - file: w12_manybody/fqhe
+  - file: w12_manybody/topoorder
+  - file: w12_manybody/w12_assignments

src/code

@@ -0,0 +1 @@
+../code

src/syllabus.md.j2 src/syllabus.md

@@ -1,15 +1,25 @@
-# Syllabus
+---
+jupytext:
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.11.4
+kernelspec:
+  display_name: Python 3
+  language: python
+  name: python3
+---
+
+# Introduction
+
++++
 
-{% for chapter in chapters -%}
-* **{{chapter.title}}**
-{% for section in chapter.sections %}  * [{{section.title}}]({{section.location}}.ipynb)
-{% endfor -%}
-{%- endfor %}
 ## Course structure
 
 Each section consists of several relatively self-contained topics, each introduced and summarized by an expert.
 
-## Current course team
+### Current course team
 
 **Anton Akhmerov** is an assistant professor in Kavli Institute of Nanoscience of Delft University of Technology and QuTech.
 
@@ -19,7 +29,7 @@ Each section consists of several relatively self-contained topics, each introduc
 
 **Bas Nijholt, Irfan Muhammad, Tómas Örn Rosdahl** are PhD students working in Kavli Institute for Nanoscience at TU Delft supervised by Anton Akhmerov.
 
-## Other course developers
+### Other course developers
 
 The initial verison of the course was created by:
 * Anton Akhmerov
@@ -28,7 +38,7 @@ The initial verison of the course was created by:
 * Sebastian Rubbert
 * Rafał Skolasiński
 
-## Acknowledgements
+### Acknowledgements
 
 When working on the course, we greatly benefitted from support of
 
@@ -48,7 +58,7 @@ For the support with implementing the technical aspects of the course we thank
 
 Finally, we thank all the external speakers for contributing the videos for the course.
 
-## License
+### License
 
 Unless otherwise specified the **Course Materials** of TU
 Delft TOPOCMx are Copyright [Delft University of Technology](http://www.tudelft.nl/en/) and are licensed under