Fix Sphinx documentation warnings - #515

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Fix Sphinx documentation warnings#515
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@munechika-koyomunechika-koyo commented Aug 25, 2026

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Summary

  • improve Sphinx and reStructuredText formatting across API docstrings and model documentation
  • correct mathematical notation, units, cross-references, and code examples
  • fix several documentation typos and clarify parameter descriptions
  • use explicit function evaluation for the laser polarization profile

Example changes

m^3 -> m\\:sup:`3`
:math:`n_e` -> :math:`n_\mathrm{e}`
:math:`exp()` -> :math:`\exp\left( \right)`

- Updated parameter descriptions in `build_constant_slab_plasma` to use proper formatting for units.
- Changed class definitions in `pipelines.py` to remove unnecessary parentheses and improved unit formatting in comments.
- Modified documentation in `custom_models.rst` to reference the correct class path for `InhomogeneousVolumeEmitter`.
- Enhanced mathematical notation in `charge_exchange_calculation.rst` for better readability and consistency.
- Corrected unit formatting across various documentation files to use LaTeX-style notation for clarity.
@jacklovell

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I think \\ :sup:`-3` is significantly less readable than ^-3 in docstrings. It might look better in the HTML documentation, but when working with the source code or when in a python REPL calling help() it hurts readability.

Since most cases of :sup: are for raising to an integral power, why not instead use unicode?

^2 --> ² (U+00B2)
^3 --> ³ (U+00B3)
^- --> ⁻ (U+207B)

(U+207<n>) give superscript digits from 4 to 9 as well as + and - so should cater for most cases. Similarly, (U+208<n>) give subscript digits and (U+209) subscript letters to cover most use cases.

I actually think readability of docstrings/comments in source code is more important than strict typographical correctness, as long as the HTML renders "well enough." For RST in the ./docs folder that will realistically only ever be viewed as HTML it is good to stick to semantic correctness, but not elsewhere in the code at the expense of readability. For a similar reason, I would prefer \exp() in a docstring instead of \exp\left( \right) unless the resulting HTML looks terrible. And while n_\mathrm{e} is technically more correct than n_e, the latter is definitely easier to read in raw format (though better still may be nₑ using U+2091).

One thing which would help is by converting docstrings with LaTeX expressions to raw strings r""" to avoid having a load of double backslashes.

@jacklovell

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I also wonder whether some of the more equation-heavy docstrings would be better split up: have sections in the relevant rst file in ./docs which contain all the maths and make the docstring itself focus more on the API with perhaps a reference to the appropriate bit of the documentation. Realistically, how many people are going to be able to parse this when looking at it in a REPL or a text editor?

n(x, y, z) = \frac{R}{2\pi v_0 \sigma_x\sigma_y} \exp\left(-\frac{1}{2}\left(\frac{x^2}{\sigma_x^2}+\frac{y^2}{\sigma_y^2}\right)\right)\exp\left(-\int_{0}^{z}\frac{S(z')}{v_0}dz'\right),
\sigma_x = \sqrt{\sigma^2 + (ztg(\alpha_x))^2},\quad\sigma_y = \sqrt{\sigma^2 + (ztg(\alpha_y))^2},

@munechika-koyo can you create an issue where we can discuss this further before revisiting this PR, if there isn't one already?

@munechika-koyo

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Using a Unicode suffix/superscript looks much better if available.
I will try to use them as much as possible.

I also wonder whether some of the more equation-heavy docstrings would be better split up...

I agree with you.
I think what is important when reading the docstrings is understanding how to use the API.
Some APIs have docstrings that include equations (like numpy.gradient), but they are written at the bottom of the docstrings as a Note section.

@munechika-koyo can you create an issue where we can discuss this further before revisiting this PR, if there isn't one already?

Sure, I will.

@munechika-koyo

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Created #516 to discuss the docstring/documentation split and formatting guidelines before revisiting this PR.

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
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Fix Sphinx documentation warnings - #515

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munechika-koyo:fix/sphinx-warnings
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Fix Sphinx documentation warnings#515
munechika-koyo wants to merge 1 commit into
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munechika-koyo:fix/sphinx-warnings

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@munechika-koyo

@munechika-koyomunechika-koyo commented Aug 25, 2026

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Summary

  • improve Sphinx and reStructuredText formatting across API docstrings and model documentation
  • correct mathematical notation, units, cross-references, and code examples
  • fix several documentation typos and clarify parameter descriptions
  • use explicit function evaluation for the laser polarization profile

Example changes

m^3 -> m\\:sup:`3`
:math:`n_e` -> :math:`n_\mathrm{e}`
:math:`exp()` -> :math:`\exp\left( \right)`

- Updated parameter descriptions in `build_constant_slab_plasma` to use proper formatting for units.
- Changed class definitions in `pipelines.py` to remove unnecessary parentheses and improved unit formatting in comments.
- Modified documentation in `custom_models.rst` to reference the correct class path for `InhomogeneousVolumeEmitter`.
- Enhanced mathematical notation in `charge_exchange_calculation.rst` for better readability and consistency.
- Corrected unit formatting across various documentation files to use LaTeX-style notation for clarity.
@jacklovell

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I think \\ :sup:`-3` is significantly less readable than ^-3 in docstrings. It might look better in the HTML documentation, but when working with the source code or when in a python REPL calling help() it hurts readability.

Since most cases of :sup: are for raising to an integral power, why not instead use unicode?

^2 --> ² (U+00B2)
^3 --> ³ (U+00B3)
^- --> ⁻ (U+207B)

(U+207<n>) give superscript digits from 4 to 9 as well as + and - so should cater for most cases. Similarly, (U+208<n>) give subscript digits and (U+209) subscript letters to cover most use cases.

I actually think readability of docstrings/comments in source code is more important than strict typographical correctness, as long as the HTML renders "well enough." For RST in the ./docs folder that will realistically only ever be viewed as HTML it is good to stick to semantic correctness, but not elsewhere in the code at the expense of readability. For a similar reason, I would prefer \exp() in a docstring instead of \exp\left( \right) unless the resulting HTML looks terrible. And while n_\mathrm{e} is technically more correct than n_e, the latter is definitely easier to read in raw format (though better still may be nₑ using U+2091).

One thing which would help is by converting docstrings with LaTeX expressions to raw strings r""" to avoid having a load of double backslashes.

@jacklovell

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I also wonder whether some of the more equation-heavy docstrings would be better split up: have sections in the relevant rst file in ./docs which contain all the maths and make the docstring itself focus more on the API with perhaps a reference to the appropriate bit of the documentation. Realistically, how many people are going to be able to parse this when looking at it in a REPL or a text editor?

n(x, y, z) = \frac{R}{2\pi v_0 \sigma_x\sigma_y} \exp\left(-\frac{1}{2}\left(\frac{x^2}{\sigma_x^2}+\frac{y^2}{\sigma_y^2}\right)\right)\exp\left(-\int_{0}^{z}\frac{S(z')}{v_0}dz'\right),
\sigma_x = \sqrt{\sigma^2 + (ztg(\alpha_x))^2},\quad\sigma_y = \sqrt{\sigma^2 + (ztg(\alpha_y))^2},

@munechika-koyo can you create an issue where we can discuss this further before revisiting this PR, if there isn't one already?

@munechika-koyo

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Using a Unicode suffix/superscript looks much better if available.
I will try to use them as much as possible.

I also wonder whether some of the more equation-heavy docstrings would be better split up...

I agree with you.
I think what is important when reading the docstrings is understanding how to use the API.
Some APIs have docstrings that include equations (like numpy.gradient), but they are written at the bottom of the docstrings as a Note section.

@munechika-koyo can you create an issue where we can discuss this further before revisiting this PR, if there isn't one already?

Sure, I will.

@munechika-koyo

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Created #516 to discuss the docstring/documentation split and formatting guidelines before revisiting this PR.

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2 participants

@munechika-koyo@jacklovell
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix"); } } catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
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Fix Sphinx documentation warnings - #515

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Fix Sphinx documentation warnings#515
munechika-koyo wants to merge 1 commit into
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@munechika-koyo

@munechika-koyomunechika-koyo commented Aug 25, 2026

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Summary

  • improve Sphinx and reStructuredText formatting across API docstrings and model documentation
  • correct mathematical notation, units, cross-references, and code examples
  • fix several documentation typos and clarify parameter descriptions
  • use explicit function evaluation for the laser polarization profile

Example changes

m^3 -> m\\:sup:`3`
:math:`n_e` -> :math:`n_\mathrm{e}`
:math:`exp()` -> :math:`\exp\left( \right)`

- Updated parameter descriptions in `build_constant_slab_plasma` to use proper formatting for units.
- Changed class definitions in `pipelines.py` to remove unnecessary parentheses and improved unit formatting in comments.
- Modified documentation in `custom_models.rst` to reference the correct class path for `InhomogeneousVolumeEmitter`.
- Enhanced mathematical notation in `charge_exchange_calculation.rst` for better readability and consistency.
- Corrected unit formatting across various documentation files to use LaTeX-style notation for clarity.
@jacklovell

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I think \\ :sup:`-3` is significantly less readable than ^-3 in docstrings. It might look better in the HTML documentation, but when working with the source code or when in a python REPL calling help() it hurts readability.

Since most cases of :sup: are for raising to an integral power, why not instead use unicode?

^2 --> ² (U+00B2)
^3 --> ³ (U+00B3)
^- --> ⁻ (U+207B)

(U+207<n>) give superscript digits from 4 to 9 as well as + and - so should cater for most cases. Similarly, (U+208<n>) give subscript digits and (U+209) subscript letters to cover most use cases.

I actually think readability of docstrings/comments in source code is more important than strict typographical correctness, as long as the HTML renders "well enough." For RST in the ./docs folder that will realistically only ever be viewed as HTML it is good to stick to semantic correctness, but not elsewhere in the code at the expense of readability. For a similar reason, I would prefer \exp() in a docstring instead of \exp\left( \right) unless the resulting HTML looks terrible. And while n_\mathrm{e} is technically more correct than n_e, the latter is definitely easier to read in raw format (though better still may be nₑ using U+2091).

One thing which would help is by converting docstrings with LaTeX expressions to raw strings r""" to avoid having a load of double backslashes.

@jacklovell

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I also wonder whether some of the more equation-heavy docstrings would be better split up: have sections in the relevant rst file in ./docs which contain all the maths and make the docstring itself focus more on the API with perhaps a reference to the appropriate bit of the documentation. Realistically, how many people are going to be able to parse this when looking at it in a REPL or a text editor?

n(x, y, z) = \frac{R}{2\pi v_0 \sigma_x\sigma_y} \exp\left(-\frac{1}{2}\left(\frac{x^2}{\sigma_x^2}+\frac{y^2}{\sigma_y^2}\right)\right)\exp\left(-\int_{0}^{z}\frac{S(z')}{v_0}dz'\right),
\sigma_x = \sqrt{\sigma^2 + (ztg(\alpha_x))^2},\quad\sigma_y = \sqrt{\sigma^2 + (ztg(\alpha_y))^2},

@munechika-koyo can you create an issue where we can discuss this further before revisiting this PR, if there isn't one already?

@munechika-koyo

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Using a Unicode suffix/superscript looks much better if available.
I will try to use them as much as possible.

I also wonder whether some of the more equation-heavy docstrings would be better split up...

I agree with you.
I think what is important when reading the docstrings is understanding how to use the API.
Some APIs have docstrings that include equations (like numpy.gradient), but they are written at the bottom of the docstrings as a Note section.

@munechika-koyo can you create an issue where we can discuss this further before revisiting this PR, if there isn't one already?

Sure, I will.

@munechika-koyo

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Created #516 to discuss the docstring/documentation split and formatting guidelines before revisiting this PR.

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@munechika-koyo@jacklovell
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms"); } } catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
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Fix Sphinx documentation warnings - #515

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Fix Sphinx documentation warnings#515
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@munechika-koyo

@munechika-koyomunechika-koyo commented Aug 25, 2026

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Summary

  • improve Sphinx and reStructuredText formatting across API docstrings and model documentation
  • correct mathematical notation, units, cross-references, and code examples
  • fix several documentation typos and clarify parameter descriptions
  • use explicit function evaluation for the laser polarization profile

Example changes

m^3 -> m\\:sup:`3`
:math:`n_e` -> :math:`n_\mathrm{e}`
:math:`exp()` -> :math:`\exp\left( \right)`

- Updated parameter descriptions in `build_constant_slab_plasma` to use proper formatting for units.
- Changed class definitions in `pipelines.py` to remove unnecessary parentheses and improved unit formatting in comments.
- Modified documentation in `custom_models.rst` to reference the correct class path for `InhomogeneousVolumeEmitter`.
- Enhanced mathematical notation in `charge_exchange_calculation.rst` for better readability and consistency.
- Corrected unit formatting across various documentation files to use LaTeX-style notation for clarity.
@jacklovell

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I think \\ :sup:`-3` is significantly less readable than ^-3 in docstrings. It might look better in the HTML documentation, but when working with the source code or when in a python REPL calling help() it hurts readability.

Since most cases of :sup: are for raising to an integral power, why not instead use unicode?

^2 --> ² (U+00B2)
^3 --> ³ (U+00B3)
^- --> ⁻ (U+207B)

(U+207<n>) give superscript digits from 4 to 9 as well as + and - so should cater for most cases. Similarly, (U+208<n>) give subscript digits and (U+209) subscript letters to cover most use cases.

I actually think readability of docstrings/comments in source code is more important than strict typographical correctness, as long as the HTML renders "well enough." For RST in the ./docs folder that will realistically only ever be viewed as HTML it is good to stick to semantic correctness, but not elsewhere in the code at the expense of readability. For a similar reason, I would prefer \exp() in a docstring instead of \exp\left( \right) unless the resulting HTML looks terrible. And while n_\mathrm{e} is technically more correct than n_e, the latter is definitely easier to read in raw format (though better still may be nₑ using U+2091).

One thing which would help is by converting docstrings with LaTeX expressions to raw strings r""" to avoid having a load of double backslashes.

@jacklovell

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I also wonder whether some of the more equation-heavy docstrings would be better split up: have sections in the relevant rst file in ./docs which contain all the maths and make the docstring itself focus more on the API with perhaps a reference to the appropriate bit of the documentation. Realistically, how many people are going to be able to parse this when looking at it in a REPL or a text editor?

n(x, y, z) = \frac{R}{2\pi v_0 \sigma_x\sigma_y} \exp\left(-\frac{1}{2}\left(\frac{x^2}{\sigma_x^2}+\frac{y^2}{\sigma_y^2}\right)\right)\exp\left(-\int_{0}^{z}\frac{S(z')}{v_0}dz'\right),
\sigma_x = \sqrt{\sigma^2 + (ztg(\alpha_x))^2},\quad\sigma_y = \sqrt{\sigma^2 + (ztg(\alpha_y))^2},

@munechika-koyo can you create an issue where we can discuss this further before revisiting this PR, if there isn't one already?

@munechika-koyo

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MemberAuthor

Using a Unicode suffix/superscript looks much better if available.
I will try to use them as much as possible.

I also wonder whether some of the more equation-heavy docstrings would be better split up...

I agree with you.
I think what is important when reading the docstrings is understanding how to use the API.
Some APIs have docstrings that include equations (like numpy.gradient), but they are written at the bottom of the docstrings as a Note section.

@munechika-koyo can you create an issue where we can discuss this further before revisiting this PR, if there isn't one already?

Sure, I will.

@munechika-koyo

Copy link
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MemberAuthor

Created #516 to discuss the docstring/documentation split and formatting guidelines before revisiting this PR.

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2 participants

@munechika-koyo@jacklovell
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links"); } } catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); } })(); (function(){ try { var __m = "youtube.com"; var __re = new RegExp('^' + "youtube\\.com" + '
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Fix Sphinx documentation warnings - #515

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Fix Sphinx documentation warnings#515
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@munechika-koyomunechika-koyo commented Aug 25, 2026

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Summary

  • improve Sphinx and reStructuredText formatting across API docstrings and model documentation
  • correct mathematical notation, units, cross-references, and code examples
  • fix several documentation typos and clarify parameter descriptions
  • use explicit function evaluation for the laser polarization profile

Example changes

m^3 -> m\\:sup:`3`
:math:`n_e` -> :math:`n_\mathrm{e}`
:math:`exp()` -> :math:`\exp\left( \right)`

- Updated parameter descriptions in `build_constant_slab_plasma` to use proper formatting for units.
- Changed class definitions in `pipelines.py` to remove unnecessary parentheses and improved unit formatting in comments.
- Modified documentation in `custom_models.rst` to reference the correct class path for `InhomogeneousVolumeEmitter`.
- Enhanced mathematical notation in `charge_exchange_calculation.rst` for better readability and consistency.
- Corrected unit formatting across various documentation files to use LaTeX-style notation for clarity.
@jacklovell

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I think \\ :sup:`-3` is significantly less readable than ^-3 in docstrings. It might look better in the HTML documentation, but when working with the source code or when in a python REPL calling help() it hurts readability.

Since most cases of :sup: are for raising to an integral power, why not instead use unicode?

^2 --> ² (U+00B2)
^3 --> ³ (U+00B3)
^- --> ⁻ (U+207B)

(U+207<n>) give superscript digits from 4 to 9 as well as + and - so should cater for most cases. Similarly, (U+208<n>) give subscript digits and (U+209) subscript letters to cover most use cases.

I actually think readability of docstrings/comments in source code is more important than strict typographical correctness, as long as the HTML renders "well enough." For RST in the ./docs folder that will realistically only ever be viewed as HTML it is good to stick to semantic correctness, but not elsewhere in the code at the expense of readability. For a similar reason, I would prefer \exp() in a docstring instead of \exp\left( \right) unless the resulting HTML looks terrible. And while n_\mathrm{e} is technically more correct than n_e, the latter is definitely easier to read in raw format (though better still may be nₑ using U+2091).

One thing which would help is by converting docstrings with LaTeX expressions to raw strings r""" to avoid having a load of double backslashes.

@jacklovell

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I also wonder whether some of the more equation-heavy docstrings would be better split up: have sections in the relevant rst file in ./docs which contain all the maths and make the docstring itself focus more on the API with perhaps a reference to the appropriate bit of the documentation. Realistically, how many people are going to be able to parse this when looking at it in a REPL or a text editor?

n(x, y, z) = \frac{R}{2\pi v_0 \sigma_x\sigma_y} \exp\left(-\frac{1}{2}\left(\frac{x^2}{\sigma_x^2}+\frac{y^2}{\sigma_y^2}\right)\right)\exp\left(-\int_{0}^{z}\frac{S(z')}{v_0}dz'\right),
\sigma_x = \sqrt{\sigma^2 + (ztg(\alpha_x))^2},\quad\sigma_y = \sqrt{\sigma^2 + (ztg(\alpha_y))^2},

@munechika-koyo can you create an issue where we can discuss this further before revisiting this PR, if there isn't one already?

@munechika-koyo

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Using a Unicode suffix/superscript looks much better if available.
I will try to use them as much as possible.

I also wonder whether some of the more equation-heavy docstrings would be better split up...

I agree with you.
I think what is important when reading the docstrings is understanding how to use the API.
Some APIs have docstrings that include equations (like numpy.gradient), but they are written at the bottom of the docstrings as a Note section.

@munechika-koyo can you create an issue where we can discuss this further before revisiting this PR, if there isn't one already?

Sure, I will.

@munechika-koyo

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Created #516 to discuss the docstring/documentation split and formatting guidelines before revisiting this PR.

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default"); } } catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
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Fix Sphinx documentation warnings - #515

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Fix Sphinx documentation warnings#515
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@munechika-koyomunechika-koyo commented Aug 25, 2026

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Summary

  • improve Sphinx and reStructuredText formatting across API docstrings and model documentation
  • correct mathematical notation, units, cross-references, and code examples
  • fix several documentation typos and clarify parameter descriptions
  • use explicit function evaluation for the laser polarization profile

Example changes

m^3 -> m\\:sup:`3`
:math:`n_e` -> :math:`n_\mathrm{e}`
:math:`exp()` -> :math:`\exp\left( \right)`

- Updated parameter descriptions in `build_constant_slab_plasma` to use proper formatting for units.
- Changed class definitions in `pipelines.py` to remove unnecessary parentheses and improved unit formatting in comments.
- Modified documentation in `custom_models.rst` to reference the correct class path for `InhomogeneousVolumeEmitter`.
- Enhanced mathematical notation in `charge_exchange_calculation.rst` for better readability and consistency.
- Corrected unit formatting across various documentation files to use LaTeX-style notation for clarity.
@jacklovell

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I think \\ :sup:`-3` is significantly less readable than ^-3 in docstrings. It might look better in the HTML documentation, but when working with the source code or when in a python REPL calling help() it hurts readability.

Since most cases of :sup: are for raising to an integral power, why not instead use unicode?

^2 --> ² (U+00B2)
^3 --> ³ (U+00B3)
^- --> ⁻ (U+207B)

(U+207<n>) give superscript digits from 4 to 9 as well as + and - so should cater for most cases. Similarly, (U+208<n>) give subscript digits and (U+209) subscript letters to cover most use cases.

I actually think readability of docstrings/comments in source code is more important than strict typographical correctness, as long as the HTML renders "well enough." For RST in the ./docs folder that will realistically only ever be viewed as HTML it is good to stick to semantic correctness, but not elsewhere in the code at the expense of readability. For a similar reason, I would prefer \exp() in a docstring instead of \exp\left( \right) unless the resulting HTML looks terrible. And while n_\mathrm{e} is technically more correct than n_e, the latter is definitely easier to read in raw format (though better still may be nₑ using U+2091).

One thing which would help is by converting docstrings with LaTeX expressions to raw strings r""" to avoid having a load of double backslashes.

@jacklovell

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I also wonder whether some of the more equation-heavy docstrings would be better split up: have sections in the relevant rst file in ./docs which contain all the maths and make the docstring itself focus more on the API with perhaps a reference to the appropriate bit of the documentation. Realistically, how many people are going to be able to parse this when looking at it in a REPL or a text editor?

n(x, y, z) = \frac{R}{2\pi v_0 \sigma_x\sigma_y} \exp\left(-\frac{1}{2}\left(\frac{x^2}{\sigma_x^2}+\frac{y^2}{\sigma_y^2}\right)\right)\exp\left(-\int_{0}^{z}\frac{S(z')}{v_0}dz'\right),
\sigma_x = \sqrt{\sigma^2 + (ztg(\alpha_x))^2},\quad\sigma_y = \sqrt{\sigma^2 + (ztg(\alpha_y))^2},

@munechika-koyo can you create an issue where we can discuss this further before revisiting this PR, if there isn't one already?

@munechika-koyo

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Using a Unicode suffix/superscript looks much better if available.
I will try to use them as much as possible.

I also wonder whether some of the more equation-heavy docstrings would be better split up...

I agree with you.
I think what is important when reading the docstrings is understanding how to use the API.
Some APIs have docstrings that include equations (like numpy.gradient), but they are written at the bottom of the docstrings as a Note section.

@munechika-koyo can you create an issue where we can discuss this further before revisiting this PR, if there isn't one already?

Sure, I will.

@munechika-koyo

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Created #516 to discuss the docstring/documentation split and formatting guidelines before revisiting this PR.

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers"); } } catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
Skip to content

Fix Sphinx documentation warnings - #515

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Fix Sphinx documentation warnings#515
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@munechika-koyo

@munechika-koyomunechika-koyo commented Aug 25, 2026

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Summary

  • improve Sphinx and reStructuredText formatting across API docstrings and model documentation
  • correct mathematical notation, units, cross-references, and code examples
  • fix several documentation typos and clarify parameter descriptions
  • use explicit function evaluation for the laser polarization profile

Example changes

m^3 -> m\\:sup:`3`
:math:`n_e` -> :math:`n_\mathrm{e}`
:math:`exp()` -> :math:`\exp\left( \right)`

- Updated parameter descriptions in `build_constant_slab_plasma` to use proper formatting for units.
- Changed class definitions in `pipelines.py` to remove unnecessary parentheses and improved unit formatting in comments.
- Modified documentation in `custom_models.rst` to reference the correct class path for `InhomogeneousVolumeEmitter`.
- Enhanced mathematical notation in `charge_exchange_calculation.rst` for better readability and consistency.
- Corrected unit formatting across various documentation files to use LaTeX-style notation for clarity.
@jacklovell

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I think \\ :sup:`-3` is significantly less readable than ^-3 in docstrings. It might look better in the HTML documentation, but when working with the source code or when in a python REPL calling help() it hurts readability.

Since most cases of :sup: are for raising to an integral power, why not instead use unicode?

^2 --> ² (U+00B2)
^3 --> ³ (U+00B3)
^- --> ⁻ (U+207B)

(U+207<n>) give superscript digits from 4 to 9 as well as + and - so should cater for most cases. Similarly, (U+208<n>) give subscript digits and (U+209) subscript letters to cover most use cases.

I actually think readability of docstrings/comments in source code is more important than strict typographical correctness, as long as the HTML renders "well enough." For RST in the ./docs folder that will realistically only ever be viewed as HTML it is good to stick to semantic correctness, but not elsewhere in the code at the expense of readability. For a similar reason, I would prefer \exp() in a docstring instead of \exp\left( \right) unless the resulting HTML looks terrible. And while n_\mathrm{e} is technically more correct than n_e, the latter is definitely easier to read in raw format (though better still may be nₑ using U+2091).

One thing which would help is by converting docstrings with LaTeX expressions to raw strings r""" to avoid having a load of double backslashes.

@jacklovell

Copy link
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Member

I also wonder whether some of the more equation-heavy docstrings would be better split up: have sections in the relevant rst file in ./docs which contain all the maths and make the docstring itself focus more on the API with perhaps a reference to the appropriate bit of the documentation. Realistically, how many people are going to be able to parse this when looking at it in a REPL or a text editor?

n(x, y, z) = \frac{R}{2\pi v_0 \sigma_x\sigma_y} \exp\left(-\frac{1}{2}\left(\frac{x^2}{\sigma_x^2}+\frac{y^2}{\sigma_y^2}\right)\right)\exp\left(-\int_{0}^{z}\frac{S(z')}{v_0}dz'\right),
\sigma_x = \sqrt{\sigma^2 + (ztg(\alpha_x))^2},\quad\sigma_y = \sqrt{\sigma^2 + (ztg(\alpha_y))^2},

@munechika-koyo can you create an issue where we can discuss this further before revisiting this PR, if there isn't one already?

@munechika-koyo

Copy link
Copy Markdown
MemberAuthor

Using a Unicode suffix/superscript looks much better if available.
I will try to use them as much as possible.

I also wonder whether some of the more equation-heavy docstrings would be better split up...

I agree with you.
I think what is important when reading the docstrings is understanding how to use the API.
Some APIs have docstrings that include equations (like numpy.gradient), but they are written at the bottom of the docstrings as a Note section.

@munechika-koyo can you create an issue where we can discuss this further before revisiting this PR, if there isn't one already?

Sure, I will.

@munechika-koyo

Copy link
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MemberAuthor

Created #516 to discuss the docstring/documentation split and formatting guidelines before revisiting this PR.

Sign up for freeto join this conversation on GitHub. Already have an account? Sign in to comment

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Successfully merging this pull request may close these issues.

2 participants

@munechika-koyo@jacklovell
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode"); } } catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); } })(); })();
Skip to content

Fix Sphinx documentation warnings - #515

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munechika-koyo wants to merge 1 commit into
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Fix Sphinx documentation warnings#515
munechika-koyo wants to merge 1 commit into
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@munechika-koyo

@munechika-koyomunechika-koyo commented Aug 25, 2026

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Summary

  • improve Sphinx and reStructuredText formatting across API docstrings and model documentation
  • correct mathematical notation, units, cross-references, and code examples
  • fix several documentation typos and clarify parameter descriptions
  • use explicit function evaluation for the laser polarization profile

Example changes

m^3 -> m\\:sup:`3`
:math:`n_e` -> :math:`n_\mathrm{e}`
:math:`exp()` -> :math:`\exp\left( \right)`

- Updated parameter descriptions in `build_constant_slab_plasma` to use proper formatting for units.
- Changed class definitions in `pipelines.py` to remove unnecessary parentheses and improved unit formatting in comments.
- Modified documentation in `custom_models.rst` to reference the correct class path for `InhomogeneousVolumeEmitter`.
- Enhanced mathematical notation in `charge_exchange_calculation.rst` for better readability and consistency.
- Corrected unit formatting across various documentation files to use LaTeX-style notation for clarity.
@jacklovell

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I think \\ :sup:`-3` is significantly less readable than ^-3 in docstrings. It might look better in the HTML documentation, but when working with the source code or when in a python REPL calling help() it hurts readability.

Since most cases of :sup: are for raising to an integral power, why not instead use unicode?

^2 --> ² (U+00B2)
^3 --> ³ (U+00B3)
^- --> ⁻ (U+207B)

(U+207<n>) give superscript digits from 4 to 9 as well as + and - so should cater for most cases. Similarly, (U+208<n>) give subscript digits and (U+209) subscript letters to cover most use cases.

I actually think readability of docstrings/comments in source code is more important than strict typographical correctness, as long as the HTML renders "well enough." For RST in the ./docs folder that will realistically only ever be viewed as HTML it is good to stick to semantic correctness, but not elsewhere in the code at the expense of readability. For a similar reason, I would prefer \exp() in a docstring instead of \exp\left( \right) unless the resulting HTML looks terrible. And while n_\mathrm{e} is technically more correct than n_e, the latter is definitely easier to read in raw format (though better still may be nₑ using U+2091).

One thing which would help is by converting docstrings with LaTeX expressions to raw strings r""" to avoid having a load of double backslashes.

@jacklovell

Copy link
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Member

I also wonder whether some of the more equation-heavy docstrings would be better split up: have sections in the relevant rst file in ./docs which contain all the maths and make the docstring itself focus more on the API with perhaps a reference to the appropriate bit of the documentation. Realistically, how many people are going to be able to parse this when looking at it in a REPL or a text editor?

n(x, y, z) = \frac{R}{2\pi v_0 \sigma_x\sigma_y} \exp\left(-\frac{1}{2}\left(\frac{x^2}{\sigma_x^2}+\frac{y^2}{\sigma_y^2}\right)\right)\exp\left(-\int_{0}^{z}\frac{S(z')}{v_0}dz'\right),
\sigma_x = \sqrt{\sigma^2 + (ztg(\alpha_x))^2},\quad\sigma_y = \sqrt{\sigma^2 + (ztg(\alpha_y))^2},

@munechika-koyo can you create an issue where we can discuss this further before revisiting this PR, if there isn't one already?

@munechika-koyo

Copy link
Copy Markdown
MemberAuthor

Using a Unicode suffix/superscript looks much better if available.
I will try to use them as much as possible.

I also wonder whether some of the more equation-heavy docstrings would be better split up...

I agree with you.
I think what is important when reading the docstrings is understanding how to use the API.
Some APIs have docstrings that include equations (like numpy.gradient), but they are written at the bottom of the docstrings as a Note section.

@munechika-koyo can you create an issue where we can discuss this further before revisiting this PR, if there isn't one already?

Sure, I will.

@munechika-koyo

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MemberAuthor

Created #516 to discuss the docstring/documentation split and formatting guidelines before revisiting this PR.

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2 participants

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