initial commit

.gitignore

+*~
+.ipynb_checkpoints
+site
+docs
+*.pyc
+__pycache__

.gitlab-ci.yml

+image: quantumtinkerer/research
+
+stages:
+  - build
+  - deploy
+
+build lectures:
+  stage: build
+  before_script:
+    - pip install -U mkdocs mkdocs-material python-markdown-math notedown
+  script:
+    - python execute.py
+    - mkdocs build
+  artifacts:
+    paths:
+      - site
+    expire_in: 1 week
+
+.prepare_deploy: &prepare_deploy
+  stage: deploy
+  only:
+    - branches@sconesaboj/qm1-notes
+  before_script:
+    ## Install ssh-agent if not already installed, it is required by Docker.
+    ## (change apt-get to yum if you use an RPM-based image)
+    - 'which ssh-agent || ( apt-get update -y && apt-get install openssh-client -y )'
+
+    ## Run ssh-agent (inside the build environment)
+    - eval $(ssh-agent -s)
+
+    ## Add the SSH key stored in SSH_PRIVATE_KEY variable to the agent store
+    ## We're using tr to fix line endings which makes ed25519 keys work
+    ## without extra base64 encoding.
+    ## https://gitlab.com/gitlab-examples/ssh-private-key/issues/1#note_48526556
+    - echo "$WEBSITE_UPLOAD_KEY" | tr -d '\r' | ssh-add - > /dev/null
+
+    ## Create the SSH directory and give it the right permissions
+    - mkdir -p ~/.ssh
+    - chmod 700 ~/.ssh
+    - ssh-keyscan tnw-tn1.tudelft.net >> ~/.ssh/known_hosts
+    - chmod 644 ~/.ssh/known_hosts
+  script:
+    - "rsync -rv site/* qm1@tnw-tn1.tudelft.net:$DEPLOY_PATH"
+
+deploy master version:
+  <<: *prepare_deploy
+  only:
+    - master@sconesaboj/qm1-notes
+  variables:
+    DEPLOY_PATH: ""
+  environment:
+    name: $CI_COMMIT_REF_NAME
+    url: "https://qm1.quantumtinkerer.tudelft.nl"
+
+deploy test version:
+  <<: *prepare_deploy
+  except:
+    - master@sconesaboj/qm1-notes
+  variables:
+    DEPLOY_PATH: "test_builds/$CI_COMMIT_REF_NAME"
+  environment:
+    name: $CI_COMMIT_REF_NAME
+    url: "https://qm1.quantumtinkerer.tudelft.nl/test_builds/$CI_COMMIT_REF_NAME"
+    on_stop: undeploy test version
+
+undeploy test version:
+  <<: *prepare_deploy
+  except:
+    - master@sconesaboj/qm1-notes
+  when: manual
+  variables:
+    DEPLOY_PATH: "test_builds/$CI_COMMIT_REF_NAME"
+  script:
+    - mkdir empty/
+    - "rsync -rlv --delete empty/ solidstate@tnw-tn1.tudelft.net:$DEPLOY_PATH"
+  environment:
+    name: $CI_COMMIT_REF_NAME
+    action: stop

.gitlab/issue_templates/typo.md

+<!--
+Thanks for providing feedback!
+
+Please provide the information below.
+-->
+
+## File in which the problem appears
+
+## Problematic sentence
+
+## Correct version

AUTHORS.md

+The following people contributed to making of these lecture notes:
+
+* Sonia Conesa Boj
+
+<!--
+Execute
+git shortlog -s | sed -e "s/^ *[0-9\t ]*//"| xargs -i sh -c 'grep -q "{}" AUTHORS.md || echo "{}"'
+
+To check if any authors are missing from this list.
+ -->

LICENSE.md

+Copyright Delft University of Technology and contributors 2019.
+
+## Contents
+
+[![Creative Commons License](https://i.creativecommons.org/l/cc-by-sa-nc/4.0/88x31.png)](http://creativecommons.org/licenses/cc-by-sa-nc/4.0/ "Creative Commons License")
+
+This work is licensed under a [Creative Commons Attribution-ShareAlike 4.0 International License](http://creativecommons.org/licenses/cc-by-sa-nc/4.0/).
+
+## Source code
+
+The source code for building the website and producing the plots is available under BSD license.
+
+Copyright (c) 2019, Delft University of Technology and contributors  
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright
+  notice, this list of conditions and the following disclaimer.
+* Redistributions in binary form must reproduce the above copyright
+  notice, this list of conditions and the following disclaimer in the
+  documentation and/or other materials provided with the distribution.
+* Neither the name of the <organization> nor the
+  names of its contributors may be used to endorse or promote products
+  derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL DELFT UNIVERSITY OF TECHNOLOGY BE LIABLE FOR ANY
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

+# Quantum mechanics 1 lecture notes
+
+Lecture notes and teaching material used for the Delft University of Technology course awesome course.
+
+The compiled materials are available at https://qm1.quantumtinkerer.tudelft.nl
+
+# Origin and technical support
+
+This repository is based on a template for publishing lecture notes, developed
+by Anton Akhmerov, who also hosts such repositories for other courses.

execute.py

+from pathlib import Path
+import shutil
+import mimetypes
+
+import nbconvert
+import notedown
+from traitlets.config import Config
+
+from nbconvert_fix import ExtractOutputPreprocessor
+
+
+reader = notedown.MarkdownReader(code_regex='fenced')
+
+mimetypes.add_type('application/vnd.plotly.v1+json', '.json')
+
+src = Path('src')
+target = Path('docs')
+shutil.rmtree(target, ignore_errors=True)
+target.mkdir(exist_ok=True)
+shutil.copytree(src / 'figures', target / 'figures')
+shutil.copytree(src / 'scripts', target / 'scripts')
+
+output_extractor = ExtractOutputPreprocessor()
+output_extractor.extract_output_types = (
+    output_extractor.extract_output_types
+    | {'application/vnd.plotly.v1+json'}
+)
+
+exporter = nbconvert.MarkdownExporter(
+    config=Config(dict(
+        MarkdownExporter=dict(
+            preprocessors=[
+                nbconvert.preprocessors.ExecutePreprocessor,
+                output_extractor,
+            ],
+            exclude_input=True,
+            template_file='extra_markdown.tpl',
+        ),
+        NbConvertBase=dict(
+            display_data_priority=[
+                'text/html',
+                'text/markdown',
+                'image/svg+xml',
+                'text/latex',
+                'image/png',
+                'application/vnd.plotly.v1+json',
+                'image/jpeg',
+                'text/plain'
+            ]
+        ),
+    ))
+)
+
+writer = nbconvert.writers.FilesWriter(build_directory=str(target))
+
+for source_file in src.glob('*.md'):
+    fname = source_file.name[:-len('.md')]
+    notebook = reader.reads(source_file.read_text())
+
+    output, resources = exporter.from_notebook_node(
+        notebook,
+        resources={
+            'unique_key': fname,
+            'output_files_dir': 'figures',
+        }
+    )
+
+    writer.write(output, resources, fname)

extra_markdown.tpl

+{% extends 'markdown.tpl' %}
+
+{%- block data_other -%}
+{%- for type in output.data | filter_data_type -%}
+{%- if type == 'application/vnd.plotly.v1+json' -%}
+{%- set fname = output.metadata.filenames['application/vnd.plotly.v1+json'] -%}
+{%- set plotly_url = fname | path2url -%}
+{%- set div_id = fname.split('/') | last -%}
+<div id="{{cookiecutter.div_id}}"><img ></img></div>
+
+<script>
+window.addEventListener('load', function() {
+  Plotly.d3.json('../{{cookiecutter.plotly_url}}', function(error, fig) {
+    Plotly.plot('{{cookiecutter.div_id}}', fig.data, fig.layout).then(
+      function(value) {Plotly.relayout('{{cookiecutter.div_id}}', {height: ' '})}
+    );
+  });
+});
+</script>
+{%- endif -%}
+{%- endfor -%}
+{%- endblock -%}
+
+{% block error %}
+{% endblock error %}
+
+{% block stream %}
+{%- if output.name == 'stdout' -%}
+{{cookiecutter. output.text | indent }}
+{%- endif -%}
+{% endblock stream %}

mkdocs.yml

+site_name: Quantum mechanics 1 lecture notes
+repo_url: https://gitlab.kwant-project.org/sconesaboj/qm1-notes
+repo_name: source
+edit_uri: edit/master/src/
+site_description: |
+  Lecture notes for QM1
+nav:
+  - Intro: 'index.md'
+
+theme:
+  name: material
+  palette:
+    primary: 'white'
+    accent: 'indigo'
+
+markdown_extensions:
+  - mdx_math:
+      enable_dollar_delimiter: True
+  - toc:
+      permalink: True
+  - admonition
+  - pymdownx.details
+  - abbr
+  - footnotes
+  - meta
+
+extra_javascript:
+  - 'https://cdn.plot.ly/plotly-latest.min.js'
+  - 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.3/MathJax.js?config=TeX-AMS_HTML'
+  - 'scripts/mathjaxhelper.js'
+copyright: "Copyright © 2019 Delft University of Technology, CC-BY-SA-NC 4.0."

nbconvert_fix.py

+import sys
+import os
+import json
+from mimetypes import guess_extension
+from binascii import a2b_base64
+
+from nbformat.notebooknode import NotebookNode
+import nbconvert
+from nbconvert.preprocessors.extractoutput import guess_extension_without_jpe
+
+
+class ExtractOutputPreprocessor(nbconvert.preprocessors.ExtractOutputPreprocessor):
+    # Patches against gh-846 following
+    # https://github.com/jupyter/nbconvert/pull/847
+
+    def preprocess_cell(self, cell, resources, cell_index):
+        """
+        Apply a transformation on each cell,
+
+        Parameters
+        ----------
+        cell : NotebookNode cell
+            Notebook cell being processed
+        resources : dictionary
+            Additional resources used in the conversion process.  Allows
+            preprocessors to pass variables into the Jinja engine.
+        cell_index : int
+            Index of the cell being processed (see base.py)
+        """
+
+        #Get the unique key from the resource dict if it exists.  If it does not
+        #exist, use 'output' as the default.  Also, get files directory if it
+        #has been specified
+        unique_key = resources.get('unique_key', 'output')
+        output_files_dir = resources.get('output_files_dir', None)
+
+        #Make sure outputs key exists
+        if not isinstance(resources['outputs'], dict):
+            resources['outputs'] = {}
+
+        #Loop through all of the outputs in the cell
+        for index, out in enumerate(cell.get('outputs', [])):
+            if out.output_type not in {'display_data', 'execute_result'}:
+                continue
+            #Get the output in data formats that the template needs extracted
+            for mime_type in self.extract_output_types:
+                if mime_type in out.data:
+                    data = out.data[mime_type]
+
+                    # If data was JSON, it will become a NotebookNode at this point.
+                    if isinstance(data, NotebookNode):
+                        data = json.dumps(data)
+
+                    #Binary files are base64-encoded, SVG is already XML
+                    if mime_type in {'image/png', 'image/jpeg', 'application/pdf'}:
+                        # data is b64-encoded as text (str, unicode),
+                        # we want the original bytes
+                        data = a2b_base64(data)
+                    elif sys.platform == 'win32':
+                        data = data.replace('\n', '\r\n').encode("UTF-8")
+                    else:
+                        data = data.encode("UTF-8")
+
+                    ext = guess_extension_without_jpe(mime_type)
+                    if ext is None:
+                        ext = '.' + mime_type.rsplit('/')[-1]
+                    if out.metadata.get('filename', ''):
+                        filename = out.metadata['filename']
+                        if not filename.endswith(ext):
+                            filename+=ext
+                    else:
+                        filename = self.output_filename_template.format(
+                                    unique_key=unique_key,
+                                    cell_index=cell_index,
+                                    index=index,
+                                    extension=ext)
+
+                    # On the cell, make the figure available via
+                    #   cell.outputs[i].metadata.filenames['mime/type']
+                    # where
+                    #   cell.outputs[i].data['mime/type'] contains the data
+                    if output_files_dir is not None:
+                        filename = os.path.join(output_files_dir, filename)
+                    out.metadata.setdefault('filenames', {})
+                    out.metadata['filenames'][mime_type] = filename
+
+                    if filename in resources['outputs']:
+                        raise ValueError(
+                            "Your outputs have filename metadata associated "
+                            "with them. Nbconvert saves these outputs to "
+                            "external files using this filename metadata. "
+                            "Filenames need to be unique across the notebook, "
+                            "or images will be overwritten. The filename {} is "
+                            "associated with more than one output. The second "
+                            "output associated with this filename is in cell "
+                            "{}.".format(filename, cell_index)
+                            )
+                    #In the resources, make the figure available via
+                    #   resources['outputs']['filename'] = data
+                    resources['outputs'][filename] = data
+
+        return cell, resources

src/index.md

+# Nice title
+
+!!! summary "Learning goals"
+
+    After following this course you will be able to:
+
+    - Solve awesome problems
+    - Tell exciting stories
+
+In these notes our aim is to provide learning materials which are:
+
+- self-contained
+- easy to modify and remix, so we provide the full source, including the code
+- open for reuse: see the license below.
+
+Whether you are a student taking this course, or an instructor reusing the materials, we welcome all contributions, so check out the [course repository](https://gitlab.kwant-project.org/sconesaboj/qm1-notes), especially do [let us know](https://gitlab.kwant-project.org/sconesaboj/qm1-notes/issues/new?issuable_template=typo) if you see a typo!

src/scripts/mathjaxhelper.js

+MathJax.Hub.Config({
+  config: ["MMLorHTML.js"],
+  jax: ["input/TeX", "output/HTML-CSS", "output/NativeMML"],
+  tex2jax: {
+    inlineMath: [ ['$','$'] ],
+    processEscapes: true
+  },
+  extensions: ["MathMenu.js", "MathZoom.js"]
+});