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Convert website to Sphinx #263

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Dec 18, 2024
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ce38ab6
Use Sphinx for building
bryanwweber Jun 17, 2022
96a65d1
Add sphinx-design extension for Bootstrap support
bryanwweber Jun 19, 2022
eb4a718
Update dependencies and instructions
bryanwweber Mar 18, 2023
804e5fd
Formatting
bryanwweber Mar 18, 2023
a38b3da
add python 3.9 support for type hints
bryanwweber Apr 5, 2023
50f0f38
Update pdm and dependencies
bryanwweber Jul 2, 2023
bf7b1c4
More or less reproduce the home page
bryanwweber Jul 2, 2023
40ca92e
Some content reformatting
bryanwweber Jul 3, 2023
97a40dc
Bump api-docs submodule
speth Feb 25, 2024
aacb13d
Add tool for copying API docs into place
speth Feb 26, 2024
97918cf
Add header links to versioned sections and make styling more consistent
speth Feb 26, 2024
af0f35c
Ignore pdm.lock file
speth Feb 26, 2024
6c701e5
Delete content that was migrated to the Cantera/cantera repo
speth Feb 26, 2024
a2f7053
Delete Nikola plugin and theme files
speth Feb 26, 2024
2663431
Improve formatting of cards on homepage
speth Feb 27, 2024
f84d11b
Convert "Community" page to Markdown and update formatting
speth Feb 28, 2024
22fecba
Convert "affiliated" page to Markdown and update formatting
speth Feb 28, 2024
3d56a5e
Convert "Governance" page to Markdown and update formatting
speth Feb 28, 2024
0e3887b
Convert Dave Goodwin memorial page to Markdown and update formatting
speth Feb 29, 2024
27c9bfb
Use ABlog to handle news posts
speth Feb 29, 2024
f7c57dc
Clean up formatting of all news posts
speth Mar 2, 2024
4b44a66
Fix some warnings and display issues on index and community pages
speth Mar 4, 2024
5bcdf55
Redirect search to stable docs on most pages
speth Mar 7, 2024
7463476
Match style of navbar icons in current docs
speth Mar 7, 2024
bed0d03
Fix header links to stable docs from subdirectories
speth Mar 7, 2024
31c7e2a
Remove unused local Sphinx extensions
speth Mar 7, 2024
cffb509
Use updated favicon
speth Mar 8, 2024
cd6fc33
Add "assets" directory needed for legacy doc landing pages
speth Mar 8, 2024
d28d656
[CI] Update CI for Sphinx-built site
speth Dec 11, 2024
b137e7f
Read intersphinx inventories from cantera.org
speth Dec 12, 2024
c67d727
Configure PDM as an "application"
speth Dec 12, 2024
d1f8c2e
Remove obsolete use of api-docs repository
speth Dec 13, 2024
8c3c9bb
Merge branch 'main' into website-reformat-sphinx-myst
speth Dec 14, 2024
836d872
Increase minimum Python version to 3.10
speth Dec 14, 2024
d23216a
Log more from pdm
speth Dec 14, 2024
4c1d386
Fix pdm configuration
speth Dec 14, 2024
ac6da52
Fix Sphinx config issues
speth Dec 16, 2024
3892bc4
Don't set a misleading version number
speth Dec 16, 2024
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Clean up formatting of all news posts
  • Loading branch information
speth authored and bryanwweber committed Mar 8, 2024
commit f7c57dc27efe848f71af9a4ef6667fa85aacebfc
1 change: 1 addition & 0 deletions pyproject.toml
Original file line number Diff line number Diff line change
@@ -9,6 +9,7 @@ dependencies = [
"sphinx-design>=0.4.1",
"sphinx-autobuild>=2021.3.14",
"ablog>=0.11.6",
"sphinxcontrib.mermaid",
]
requires-python = ">=3.9"
license = { text = "BSD-3-Clause" }
4 changes: 4 additions & 0 deletions source/_static/css/custom.css
Original file line number Diff line number Diff line change
@@ -32,6 +32,10 @@ p + div.math {
}
}

.mermaid {
text-align: center;
}

/* Make "tip" background color different from "versionadded" */
.admonition.tip,
div.admonition.tip {
15 changes: 13 additions & 2 deletions source/conf.py
Original file line number Diff line number Diff line change
@@ -48,13 +48,17 @@
"myst_parser",
"sphinx.ext.duration",
"sphinx.ext.mathjax",
"_extension.bootstrap",
"_extension.gallery_extension",
"sphinxcontrib.mermaid",
"ablog",
"sphinx.ext.intersphinx",
]

myst_enable_extensions = ["colon_fence", "deflist", "attrs_block"]
myst_url_schemes = {
"http": None,
"https": None,
"mailto": {"url": "mailto:{{path}}", "title": "{{path}}"},
}
# Add any paths that contain templates here, relative to this directory.
templates_path = ["_templates"]

@@ -69,6 +73,13 @@
# -- Internationalization ---------------------------------------------------
language = "en"

intersphinx_mapping = {
'stable': ('/stable', '../dev-docs/objects.inv'),
'dev': ('/dev', '../dev-docs/objects.inv'),
'ct30': ('/3.0', '../api-docs/docs-3.0/sphinx/html/objects.inv'),
'ct26': ('/2.6', '../api-docs/docs-2.6/sphinx/html/objects.inv'),
}

# -- Options for HTML output -------------------------------------------------

# The theme to use for HTML and HTML Help pages. See the documentation for
1 change: 1 addition & 0 deletions source/governance.md
Original file line number Diff line number Diff line change
@@ -24,6 +24,7 @@ Cantera Users' Group moderators
: Members of the moderators team moderate the Users' Group, and have power to
enable/disable posting of community members at their discretion.

(current-steering-committee)=
## Current Steering Committee

The role of the steering committee is to ensure the long-term health of the Cantera
55 changes: 34 additions & 21 deletions source/news/GSoC_2019_Fourth_Blog.md
Original file line number Diff line number Diff line change
@@ -1,48 +1,61 @@
---
title: GSoC 2019 Fourth Blog
date: 2019-07-20 15:03
slug: GSoC_2019_Fourth_Blog
tags: GSoC 2019
description: 2019 Google Summer of Code Cantera Project Blog
type: text
author: Chao Xu
---

# GSoC 2019 Fourth Blog

After two months, the functions of ChemCheck are fairly robust. We improved editing and ck2yaml error reporting pages this week, and we
added pages for user account management.

<!-- TEASER_END -->
After two months, the functions of ChemCheck are fairly robust. We improved editing and ck2yaml error reporting pages this week, and we added pages for user account management.

We have included a download function for the editing page, so users can download the edited file to their local directory. It would be more convenient
if changes can be saved to the original file online, so that users do not have to re-upload their files, but we will leave it for now since an
editing function is not the most important part. The current exception handling (how to handle unrecognized character) for the editing page is stripping out all the characters in encodings that cannot
be recognized by ace-editor, and it could also be improved by implementing some Python library to guess the encoding of the file in the future.
Here is what the page looks like:

{{% thumbnail "/images/GSoC_2019_images/updated_editor.png" alt="Updated Editor Page" align="center" %}}<p class="text-center">Editor Page</p>{{% /thumbnail %}}
:::{card} Updated Editor Page
```{image} /_static/images/GSoC_2019_images/updated_editor.png
:align: center
:width: 100%
```
:::


The page shown when conversion fails is also improved. Logging messages are added to error messages if a conversion failed. In addition, ChemCheck looks through
four lines ahead and after the line where the error occurs, so that users could have an idea about how to fix the error. Here is the page:

{{% thumbnail "/images/GSoC_2019_images/convert_fail_page.png" alt="Convert Fail Page" align="center" %}}<p class="text-center">Convert Fail Page</p>{{% /thumbnail %}}
:::{card} Convert Fail Page
```{image} /_static/images/GSoC_2019_images/convert_fail_page.png
:align: center
:width: 100%
```
:::

A series of account management pages including signup page, login page, logout page, password change page (changing password for users who are logged in), and password reset (for users who forget their password) pages, among others.
have been included. The signup function will be used only if users want to retrieve their uploaded files. A built-in Django module (`django.contrib.auth.urls`) is implemented for this part; however, the password reset page did not work as expected, because it did not send an email to the user to reset the password.
I am working on getting this part to work. Except the password reset function, other pages work well.

Signup Page:

{{% thumbnail "/images/GSoC_2019_images/signup.png" alt="Signup Page" align="center" %}}<p class="text-center">Signup Page</p>{{% /thumbnail %}}

Login Page:

{{% thumbnail "/images/GSoC_2019_images/login.png" alt="Login Page" align="center" %}}<p class="text-center">Login Page</p>{{% /thumbnail %}}

Password Change Page:

{{% thumbnail "/images/GSoC_2019_images/password_change.png" alt="Password Change Page" align="center" %}}<p class="text-center">Password Change Page</p>{{% /thumbnail %}}
:::{card} Signup Page
```{image} /_static/images/GSoC_2019_images/signup.png
:align: center
:width: 100%
```
:::

:::{card} Login Page
```{image} /_static/images/GSoC_2019_images/login.png
:align: center
:width: 100%
```
:::

:::{card} Password Change Page
```{image} /_static/images/GSoC_2019_images/password_change.png
:align: center
:width: 100%
```
:::

## Goals in next two weeks

41 changes: 30 additions & 11 deletions source/news/GSoC_2019_Project_First_Evaluation.md
Original file line number Diff line number Diff line change
@@ -1,10 +1,6 @@
---
title: GSoC 2019 First Evaluation
date: 2019-06-22 17:41
slug: GSoC_2019_Project_First_Evaluation
tags: GSoC 2019
description: 2019 Google Summer of Code Cantera Project Blog
type: text
author: Chao Xu
---

@@ -17,39 +13,62 @@ web-based application for visualizing and diagnosing syntax and chemical errors
functions that allow users to convert their mechanism files to Cantera YAML input files easily (Cantera input file is going to be changed
from CTI file to YAML file, so we made some adjustments as well).

<!-- TEASER_END -->

## Upload Page

Users will upload their files to ChemCheck for checking, so we created an upload page which allows users to upload their mechanism, transport,
thermo, and surface file. Here is the view of upload page.

{{% thumbnail "/images/GSoC_2019_images/upload_page.png" alt="Upload Page" align="center" %}}<p class="text-center">Upload Page</p>{{% /thumbnail %}}
:::{card} Upload Page
```{image} /_static/images/GSoC_2019_images/upload_page.png
:align: center
:width: 100%
```
:::

## List Page

After files are uploaded, ChemCheck returns to a list page which lists all uploaded files in the app with id for each group of files.
Users are able to either click on "Details" button to do further operation to their files or hit "Upload new mechanism" button to upload new files.

{{% thumbnail "/images/GSoC_2019_images/list_page.png" alt="List Page" align="center" %}}<p class="text-center">List Page</p>{{% /thumbnail %}}
:::{card} List Page
```{image} /_static/images/GSoC_2019_images/list_page.png
:align: center
:width: 100%
```
:::

## Detail Page

In this page, users can either edit their files or hit the "convert to YAML" button to convert files. The editing function is still in development.
Also, there is a "Back to mechanism list" link for users going back to list view.

{{% thumbnail "/images/GSoC_2019_images/detail_page.png" alt="Detail Page" align="center" %}}<p class="text-center">Detail Page</p>{{% /thumbnail %}}
:::{card} Detail Page
```{image} /_static/images/GSoC_2019_images/detail_page.png
:align: center
:width: 100%
```
:::

## Convert Page

If the file is converted successfully, a success message will be shown on the page.
Users can see details and download the files from this page.

{{% thumbnail "/images/GSoC_2019_images/convert_success.png" alt="Convert Success Page" align="center" %}}<p class="text-center">Convert Success Page</p>{{% /thumbnail %}}
:::{card} Convert Success Page
```{image} /_static/images/GSoC_2019_images/convert_success.png
:align: center
:width: 100%
```
:::

However, if the file is not converted successfully, the error message will be shown.

{{% thumbnail "/images/GSoC_2019_images/convert_fail.png" alt="Convert Fail Page" align="center" %}}<p class="text-center">Convert Fail Page</p>{{% /thumbnail %}}
:::{card} Convert Fail Page
```{image} /_static/images/GSoC_2019_images/convert_fail.png
:align: center
:width: 100%
```
:::

## Future Improvement

20 changes: 10 additions & 10 deletions source/news/GSoC_2019_Project_Introduction.md
Original file line number Diff line number Diff line change
@@ -1,18 +1,12 @@
---
title: GSoC 2019 PyCanChemAndYouCan2
date: 2019-06-07 12:33
slug: GSoC_2019_Project_Introduction
tags: GSoC 2019
description: 2019 Google Summer of Code Cnatera Project Blog
type: text
author: Chao Xu
---

# GSoC 2019 PyCanChemAndYouCan2 (ChemCheck)
# GSoC 2019: PyCanChemAndYouCan2 (ChemCheck)

Hi everyone! I'm Chao Xu, a master student in Chemical Engineering at Northeastern University. I am working on a Cantera project in GSoC 2019 with my mentor Richard West([@rwest](https://github.com/rwest)) and other Cantera committee members([@bryanwweber](https://github.com/bryanwweber), [@kyleniemeyer](https://github.com/kyleniemeyer)). I am glad to introduce my project here!

<!-- TEASER_END -->
Hi everyone! I'm Chao Xu, a master student in Chemical Engineering at Northeastern University. I am working on a Cantera project in GSoC 2019 with my mentor Richard West ([@rwest](https://github.com/rwest)) and other Cantera committee members ([@bryanwweber](https://github.com/bryanwweber), [@kyleniemeyer](https://github.com/kyleniemeyer)). I am glad to introduce my project here!

## What is PyCanChemAndYouCan2(ChemCheck)

@@ -53,8 +47,14 @@ The debugging tool PyCanChemAndYouCan2 is a web-based application developed in D

Here is the workflow of the application:

[upload files] --> [list files] --> [choose one and execute by ck2cti.py and wrapper script]
--> [show input file with added comments on ACE editor] --> [edit file] --> [download edited file]
```{mermaid}
flowchart TB
A[upload files] --> B[list files]
B --> C[choose one and execute by ck2cti.py and wrapper script]
C --> D[show input file with added comments on ACE editor]
D --> E[edit file]
E --> F[download edited file]
```

My project code will be posted on <https://github.com/comocheng/ChemCheck>.

47 changes: 34 additions & 13 deletions source/news/GSoC_2019_Third_Blog.md
Original file line number Diff line number Diff line change
@@ -1,10 +1,6 @@
---
title: GSoC 2019 Third Blog
date: 2019-07-06 13:59
slug: GSoC_2019_Third_Blog
tags: GSoC 2019
description: 2019 Google Summer of Code Cantera Project Blog
type: text
author: Chao Xu
---

@@ -13,29 +9,54 @@ author: Chao Xu
As we planned after the first evaluation, the functionality of ChemCheck should be more robust. File replacement was added, and users are able to
update and delete files arbitrarily.

<!-- TEASER_END -->

The page looks like this:

{{% thumbnail "/images/GSoC_2019_images/detail_page2.png" alt="Updated Detail Page" align="center" %}}<p class="text-center">Updated Detail Page</p>{{% /thumbnail %}}
:::{card} Updated Detail Page
```{image} /_static/images/GSoC_2019_images/detail_page2.png
:align: center
:width: 100%
```
:::

The delete button leads to a delete page, which will delete files in both the database and the directory.

{{% thumbnail "/images/GSoC_2019_images/delete_page.png" alt="Delete Page" align="center" %}}<p class="text-center">Delete Page</p>{{% /thumbnail %}}
:::{card} Delete Page
```{image} /_static/images/GSoC_2019_images/delete_page.png
:align: center
:width: 100%
```
:::

In the update page, users can either replace their files or delete it by checking "clear".

{{% thumbnail "/images/GSoC_2019_images/update_page.png" alt="Update Page" align="center" %}}<p class="text-center">Update Page</p>{{% /thumbnail %}}
:::{card} Update Page
```{image} /_static/images/GSoC_2019_images/update_page.png
:align: center
:width: 100%
```
:::

In addition to these, new features ChemCheck can provide the traceback message instead of only one line error.

{{% thumbnail "/images/GSoC_2019_images/error_page.png" alt="Error Page" align="center" %}}<p class="text-center">Error Page</p>{{% /thumbnail %}}
:::{card} Error Page
```{image} /_static/images/GSoC_2019_images/error_page.png
:align: center
:width: 100%
```
:::

An editing function is also included:

{{% thumbnail "/images/GSoC_2019_images/ace_editor.png" alt="Editor Page" align="center" %}}<p class="text-center">Editor Page</p>{{% /thumbnail %}}
:::{card} Editor Page
```{image} /_static/images/GSoC_2019_images/ace_editor.png
:align: center
:width: 100%
```
:::

## Next Steps

I am working toward catching logging messages to make the error understandable and making the error page look nicer. Also, I will improve editing function (adding download function in editor page, and change highlight settings of ace editor). After that, I will test different
defective mechanism files and providing fix suggestions.
I am working toward catching logging messages to make the error understandable and
making the error page look nicer. Also, I will improve editing function (adding download
function in editor page, and change highlight settings of ace editor). After that, I
will test different defective mechanism files and providing fix suggestions.
10 changes: 4 additions & 6 deletions source/news/cantera-240-released.md
Original file line number Diff line number Diff line change
@@ -32,12 +32,10 @@ contributions from 14 developers: [@speth](https://github.com/speth),
[@vdevgan](https://github.com/vdevgan), [@KyleLinevitchJr](https://github.com/KyleLinevitchJr), and
[@MarcDuQuesne](https://github.com/MarcDuQuesne).

<!-- TEASER_END -->

For installation and compilation instructions for Cantera 2.4.0, please see the directions on the
[Cantera website](https://cantera.org/install/index.html). In addition to Conda packages, Windows
installers, and Ubuntu packages, this release also features the addition of a pre-compiled Matlab
toolbox for macOS users, replacing Homebrew as the prefered method of installing Cantera for Matlab
toolbox for macOS users, replacing Homebrew as the preferred method of installing Cantera for Matlab
on macOS.

Thanks to a small development grant from NumFOCUS (see more about NumFOCUS below),
@@ -52,8 +50,8 @@ everyone.

Cantera is now officially part of NumFOCUS. NumFOCUS is a 501(c)3 nonprofit dedicated to supporting
the open source scientific computing community. If you are interested in learning more about
NumFOCUS, please visit their website at https://numfocus.org, or our website at
https://cantera.org/community.html#donations.
NumFOCUS, please visit their website at <https://numfocus.org>, or our website at
<https://cantera.org/community.html#donations>.

Cantera 2.4.0 is the last release that will be compatible with Python 2.7. Support for Python 2.7
from the Python Software Foundation will [end January 1,
@@ -74,7 +72,7 @@ page](https://github.com/Cantera/cantera/releases/tag/v2.4.0). Major changes are

### Bugs fixed

- Fix inconstencies and bugs in several `ThermoPhase` derived classes, including `PDSS_IdealGas`, `IonsFromNeutralVPSSTP`, `PDSS_IonsFromNeutral`, `PDSS_HKFT`, `LatticePhase`, `PDSS_SSVol`, `ConstDensityThermo`, and `PureFluidPhase`
- Fix inconsistencies and bugs in several `ThermoPhase` derived classes, including `PDSS_IdealGas`, `IonsFromNeutralVPSSTP`, `PDSS_IonsFromNeutral`, `PDSS_HKFT`, `LatticePhase`, `PDSS_SSVol`, `ConstDensityThermo`, and `PureFluidPhase`
- Preserve constant property pair when multiplying `Quantity` objects
- Fix using pure fluids in reactors
- Add temperature dependence of rotational relaxation in transport calculations
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