Skip to content

Add Jupyter notebooks using nbsphinx #33

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
michael-petersen merged 23 commits into from
Apr 7, 2025
Merged

Add Jupyter notebooks using nbsphinx #33

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
23 commits
Select commit Hold shift + click to select a range
8d3902a
Added Jupyter notebooks rather than Markdown examples
Mar 12, 2025
fe0aa45
Add nbsphinx to requirements
Mar 12, 2025
f3e3ad9
XML update
Mar 12, 2025
d8371a7
Some missing files from the XML update
Mar 12, 2025
da356cc
Turn off notebook execution
Mar 12, 2025
237a8bf
Turn off notebook execution
Mar 12, 2025
9450531
Explicit reference in pyEXP-tutorial.rst to ipynb files
Mar 12, 2025
4e29e75
Downgrade Sphinx version to match Ubuntu
Mar 12, 2025
14cc2f0
Added notebook directory
Mar 12, 2025
0b48dcd
Some minor wording updates
Mar 12, 2025
71d3e1e
Another slight reorganization
Mar 12, 2025
b3010b9
Some additional edits
Mar 12, 2025
95e3111
Some additional edits
Mar 12, 2025
bf4a31a
Additions to prevent dangling links
Mar 12, 2025
9d16eb3
Move extra links to the correct location
Mar 12, 2025
cd424f6
Fix dangling links
Mar 12, 2025
8e4df6b
Add a note about the data directory
Mar 12, 2025
ea8c9a1
'Data' is the name of the data directory, not 'data'
Mar 12, 2025
814dd87
Update pyEXP-tutorial.rst
The9Cat Mar 12, 2025
307f77c
Update to relase note
Mar 12, 2025
7c3d96d
Merge branch 'Jupyter' of github.com:EXP-code/EXP-docs into Jupyter
Mar 12, 2025
fd42153
Update inline example
Mar 13, 2025
b68528b
Version bump
Apr 6, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
19 changes: 15 additions & 4 deletions conf.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,9 @@
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information

project = 'EXP'
copyright = '2023-2024, EXP-code collaboration'
copyright = '2023-2025, EXP-code collaboration'
author = 'EXP-code collaboration'
release = '0.15'
release = '0.16'
version = '7.x'

# -- General configuration ---------------------------------------------------
Expand All @@ -27,7 +27,9 @@
'sphinx.ext.inheritance_diagram',
'sphinx.ext.graphviz',
'breathe',
'sphinx_copybutton'
'sphinx_copybutton',
'nbsphinx',
'nbsphinx_link'
]


Expand All @@ -44,5 +46,14 @@
html_logo = 'exp_logo_white.png'
html_static_path = ['_static']

# Turn on figure numering
# -- Turn on figure numering -------------------------------------------------
numfig = True

# -- Extension configuration -------------------------------------------------
nbsphinx_execute = 'never'

# -- Grab files from pyEXP-examples -----------------------------------------
import os

os.system("cd intro/Tutorials; rm *ipynb*; wget -L https://raw.githubusercontent.com/EXP-code/pyEXP-examples/refs/heads/main/Tutorials/Introduction/Part1-Coefficients.ipynb; wget -L https://raw.githubusercontent.com/EXP-code/pyEXP-examples/refs/heads/main/Tutorials/Introduction/Part2-Analysis.ipynb")

4 changes: 1 addition & 3 deletions doxyxml/Doxyfile.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
<doxyfile xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="doxyfile.xsd" version="1.9.8" xml:lang="en-US">
<option id='DOXYFILE_ENCODING' default='yes' type='string'><value><![CDATA[UTF-8]]></value></option>
<option id='PROJECT_NAME' default='no' type='string'><value><![CDATA[EXP]]></value></option>
<option id='PROJECT_NUMBER' default='no' type='string'><value><![CDATA[7.7.30]]></value></option>
<option id='PROJECT_NUMBER' default='no' type='string'><value><![CDATA[7.8.0]]></value></option>
<option id='PROJECT_BRIEF' default='no' type='string'><value><![CDATA[Basis-function-EXP-ansionCode]]></value></option>
<option id='PROJECT_LOGO' default='no' type='string'><value><![CDATA[exp_logo.png]]></value></option>
<option id='OUTPUT_DIRECTORY' default='no' type='string'><value><![CDATA[.]]></value></option>
Expand Down Expand Up @@ -132,8 +132,6 @@
<option id='INPUT_FILE_ENCODING' default='yes' type='stringlist'>
</option>
<option id='FILE_PATTERNS' default='no' type='stringlist'>
<value><![CDATA[*.doc]]></value>
<value><![CDATA[*.dox]]></value>
<value><![CDATA[*.py]]></value>
<value><![CDATA[*.h]]></value>
<value><![CDATA[*.H]]></value>
Expand Down
52 changes: 29 additions & 23 deletions doxyxml/_axisymmetric_basis_8_h.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -116,11 +116,9 @@
</childnode>
<childnode refid="4" relation="include">
</childnode>
<childnode refid="6" relation="include">
</childnode>
<childnode refid="7" relation="include">
</childnode>
<childnode refid="13" relation="include">
<childnode refid="8" relation="include">
</childnode>
<childnode refid="14" relation="include">
</childnode>
Expand All @@ -132,26 +130,32 @@
</childnode>
<childnode refid="18" relation="include">
</childnode>
<childnode refid="19" relation="include">
</childnode>
</node>
<node id="8">
<node id="9">
<label>/home/weinberg/Projects/EXP/src/Bessel.H</label>
<link refid="_bessel_8_h"/>
<childnode refid="9" relation="include">
<childnode refid="10" relation="include">
</childnode>
</node>
<node id="5">
<label>/home/weinberg/Projects/EXP/src/CBDisk.H</label>
<link refid="_c_b_disk_8_h"/>
</node>
<node id="2">
<label>/home/weinberg/Projects/EXP/src/Direct.H</label>
<link refid="_direct_8_h"/>
</node>
<node id="10">
<node id="11">
<label>/home/weinberg/Projects/EXP/src/EJcom.H</label>
<link refid="_e_jcom_8_h"/>
</node>
<node id="5">
<node id="6">
<label>/home/weinberg/Projects/EXP/src/FlatDisk.H</label>
<link refid="_flat_disk_8_h"/>
</node>
<node id="11">
<node id="12">
<label>/home/weinberg/Projects/EXP/src/MixtureBasis.H</label>
<link refid="_mixture_basis_8_h"/>
</node>
Expand All @@ -164,54 +168,56 @@
<link refid="_polar_basis_8_h"/>
<childnode refid="5" relation="include">
</childnode>
<childnode refid="6" relation="include">
</childnode>
</node>
<node id="6">
<node id="7">
<label>/home/weinberg/Projects/EXP/src/Shells.H</label>
<link refid="_shells_8_h"/>
</node>
<node id="12">
<node id="13">
<label>/home/weinberg/Projects/EXP/src/Sphere.H</label>
<link refid="_sphere_8_h"/>
<childnode refid="9" relation="include">
<childnode refid="10" relation="include">
</childnode>
</node>
<node id="7">
<node id="8">
<label>/home/weinberg/Projects/EXP/src/SphericalBasis.H</label>
<link refid="_spherical_basis_8_h"/>
<childnode refid="8" relation="include">
<childnode refid="9" relation="include">
</childnode>
<childnode refid="12" relation="include">
<childnode refid="13" relation="include">
</childnode>
</node>
<node id="9">
<node id="10">
<label>/home/weinberg/Projects/EXP/src/TwoCenter.H</label>
<link refid="_two_center_8_h"/>
<childnode refid="10" relation="include">
</childnode>
<childnode refid="11" relation="include">
</childnode>
<childnode refid="12" relation="include">
</childnode>
</node>
<node id="13">
<node id="14">
<label>/home/weinberg/Projects/EXP/src/user/UserBar.H</label>
<link refid="_user_bar_8_h"/>
</node>
<node id="14">
<node id="15">
<label>/home/weinberg/Projects/EXP/src/user/UserDisk.H</label>
<link refid="_user_disk_8_h"/>
</node>
<node id="15">
<node id="16">
<label>/home/weinberg/Projects/EXP/src/user/UserHalo.H</label>
<link refid="_user_halo_8_h"/>
</node>
<node id="16">
<node id="17">
<label>/home/weinberg/Projects/EXP/src/user/UserLogPot.H</label>
<link refid="_user_log_pot_8_h"/>
</node>
<node id="17">
<node id="18">
<label>/home/weinberg/Projects/EXP/src/user/UserMNdisk.H</label>
<link refid="_user_m_ndisk_8_h"/>
</node>
<node id="18">
<node id="19">
<label>/home/weinberg/Projects/EXP/src/user/UserMW.H</label>
<link refid="_user_m_w_8_h"/>
</node>
Expand Down
62 changes: 34 additions & 28 deletions doxyxml/_basis_8_h.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -100,11 +100,9 @@
</childnode>
<childnode refid="5" relation="include">
</childnode>
<childnode refid="7" relation="include">
</childnode>
<childnode refid="8" relation="include">
</childnode>
<childnode refid="14" relation="include">
<childnode refid="9" relation="include">
</childnode>
<childnode refid="15" relation="include">
</childnode>
Expand All @@ -116,46 +114,52 @@
</childnode>
<childnode refid="19" relation="include">
</childnode>
<childnode refid="20" relation="include">
</childnode>
</node>
<node id="1">
<label>/home/weinberg/Projects/EXP/src/Basis.H</label>
<link refid="_basis_8_h"/>
<childnode refid="2" relation="include">
</childnode>
<childnode refid="20" relation="include">
</childnode>
<childnode refid="21" relation="include">
</childnode>
<childnode refid="22" relation="include">
</childnode>
</node>
<node id="9">
<node id="10">
<label>/home/weinberg/Projects/EXP/src/Bessel.H</label>
<link refid="_bessel_8_h"/>
<childnode refid="10" relation="include">
<childnode refid="11" relation="include">
</childnode>
</node>
<node id="20">
<node id="6">
<label>/home/weinberg/Projects/EXP/src/CBDisk.H</label>
<link refid="_c_b_disk_8_h"/>
</node>
<node id="21">
<label>/home/weinberg/Projects/EXP/src/CylTwoD.H</label>
<link refid="_cyl_two_d_8_h"/>
</node>
<node id="21">
<node id="22">
<label>/home/weinberg/Projects/EXP/src/Cylinder.H</label>
<link refid="_cylinder_8_h"/>
<childnode refid="10" relation="include">
<childnode refid="11" relation="include">
</childnode>
</node>
<node id="3">
<label>/home/weinberg/Projects/EXP/src/Direct.H</label>
<link refid="_direct_8_h"/>
</node>
<node id="11">
<node id="12">
<label>/home/weinberg/Projects/EXP/src/EJcom.H</label>
<link refid="_e_jcom_8_h"/>
</node>
<node id="6">
<node id="7">
<label>/home/weinberg/Projects/EXP/src/FlatDisk.H</label>
<link refid="_flat_disk_8_h"/>
</node>
<node id="12">
<node id="13">
<label>/home/weinberg/Projects/EXP/src/MixtureBasis.H</label>
<link refid="_mixture_basis_8_h"/>
</node>
Expand All @@ -168,54 +172,56 @@
<link refid="_polar_basis_8_h"/>
<childnode refid="6" relation="include">
</childnode>
<childnode refid="7" relation="include">
</childnode>
</node>
<node id="7">
<node id="8">
<label>/home/weinberg/Projects/EXP/src/Shells.H</label>
<link refid="_shells_8_h"/>
</node>
<node id="13">
<node id="14">
<label>/home/weinberg/Projects/EXP/src/Sphere.H</label>
<link refid="_sphere_8_h"/>
<childnode refid="10" relation="include">
<childnode refid="11" relation="include">
</childnode>
</node>
<node id="8">
<node id="9">
<label>/home/weinberg/Projects/EXP/src/SphericalBasis.H</label>
<link refid="_spherical_basis_8_h"/>
<childnode refid="9" relation="include">
<childnode refid="10" relation="include">
</childnode>
<childnode refid="13" relation="include">
<childnode refid="14" relation="include">
</childnode>
</node>
<node id="10">
<node id="11">
<label>/home/weinberg/Projects/EXP/src/TwoCenter.H</label>
<link refid="_two_center_8_h"/>
<childnode refid="11" relation="include">
</childnode>
<childnode refid="12" relation="include">
</childnode>
<childnode refid="13" relation="include">
</childnode>
</node>
<node id="14">
<node id="15">
<label>/home/weinberg/Projects/EXP/src/user/UserBar.H</label>
<link refid="_user_bar_8_h"/>
</node>
<node id="15">
<node id="16">
<label>/home/weinberg/Projects/EXP/src/user/UserDisk.H</label>
<link refid="_user_disk_8_h"/>
</node>
<node id="16">
<node id="17">
<label>/home/weinberg/Projects/EXP/src/user/UserHalo.H</label>
<link refid="_user_halo_8_h"/>
</node>
<node id="17">
<node id="18">
<label>/home/weinberg/Projects/EXP/src/user/UserLogPot.H</label>
<link refid="_user_log_pot_8_h"/>
</node>
<node id="18">
<node id="19">
<label>/home/weinberg/Projects/EXP/src/user/UserMNdisk.H</label>
<link refid="_user_m_ndisk_8_h"/>
</node>
<node id="19">
<node id="20">
<label>/home/weinberg/Projects/EXP/src/user/UserMW.H</label>
<link refid="_user_m_w_8_h"/>
</node>
Expand Down
16 changes: 12 additions & 4 deletions doxyxml/_biorth_cube_8_h.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -58,6 +58,10 @@
<childnode refid="11" relation="include">
</childnode>
</node>
<node id="36">
<label>EXPmath.H</label>
<link refid="_e_x_pmath_8_h"/>
</node>
<node id="31">
<label>EmpCyl2d.H</label>
<link refid="_emp_cyl2d_8_h"/>
Expand All @@ -77,16 +81,20 @@
</childnode>
<childnode refid="35" relation="include">
</childnode>
<childnode refid="21" relation="include">
</childnode>
<childnode refid="26" relation="include">
</childnode>
<childnode refid="10" relation="include">
</childnode>
<childnode refid="21" relation="include">
</childnode>
<childnode refid="36" relation="include">
</childnode>
<childnode refid="8" relation="include">
</childnode>
<childnode refid="37" relation="include">
</childnode>
<childnode refid="38" relation="include">
</childnode>
</node>
<node id="17">
<label>MonotCubicInterpolator.H</label>
Expand Down Expand Up @@ -228,10 +236,10 @@
<node id="27">
<label>highfive/H5File.hpp</label>
</node>
<node id="37">
<node id="38">
<label>highfive/eigen.hpp</label>
</node>
<node id="36">
<node id="37">
<label>highfive/highfive.hpp</label>
</node>
<node id="9">
Expand Down
Loading