feat: initial (slop) commit

README.md

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+# `units`: A Quarto Extension for Standardized Scientific Unit Notation
+
+
+This extension provides a centralized, extensible mechanism for the consistent rendering of physical quantities across Quarto-based scientific websites and publications.
+It is designed principally for use in computational chemistry, biochemistry, and computer-aided drug design (CADD), disciplines in which a single document routinely reports energies, distances, timescales, concentrations, electrostatic potentials, and temperatures spanning many orders of magnitude and multiple unit systems.
+
+## Motivation
+
+The correct typographic and semantic treatment of physical quantities is governed by well-established conventions.
+Most notably those of the International Bureau of Weights and Measures (BIPM) as codified in the SI Brochure, and their discipline-specific elaborations in the IUPAC *Quantities, Units and Symbols in Physical Chemistry* ("Green Book") and NIST Special Publication 811.
+These conventions specify, among other things: upright (non-italic) typesetting of unit symbols; a non-breaking space between a numerical value and its associated unit; the use of negative exponents rather than stacked solidi for compound units; and unambiguous conversion factors between coherent and non-coherent units within a given physical dimension.
+
+In practice, manuscripts and websites authored under time constraints tend to depart from these conventions inconsistently: for example, a bond length may be rendered as `1.54 Å` in one section and `1.54Å` (with an ordinary, breakable space) in another or an energy value may be transcribed from kJ·mol⁻¹ to kcal·mol⁻¹ by hand.
+
+## Installation
+
+You can install this Quarto extension with the following command:
+
+
+```bash
+quarto add https://git.scient.ing/infra/units-quarto-extension/archive/main.zip
+```
+
+Following installation, confirm the presence of the extension within the project:
+
+```text
+_extensions/
+└── units/
+    ├── _extension.yml
+    └── units.lua
+```
+
+A minimal document using the extension should render without error:
+
+```markdown
+---
+title: "Installation Check"
+---
+
+The bond length is {{< distance 1.54 angstrom >}}.
+```
+
+## Reference: Shortcodes
+
+| Shortcode | Signature | Description |
+|---|---|---|
+| `unit` | `{{< unit <unit-key> >}}` | Renders the typeset symbol for a single unit, with no numerical value or conversion. |
+| `sci` | `{{< sci <value> >}}` | Renders a bare numerical value in scientific notation, independent of any unit. |
+| `energy` | `{{< energy <value> <unit> [<target-unit>] >}}` | Bulk (non-molar) energy: J, kJ, cal, kcal. |
+| `molarenergy` | `{{< molarenergy <value> <unit> [<target-unit>] >}}` | Molar energy: J/mol, kJ/mol, cal/mol, kcal/mol, eV, hartree, cm⁻¹. |
+| `distance` | `{{< distance <value> <unit> [<target-unit>] >}}` | Distance: angstrom, nanometer, picometer, bohr, meter. |
+| `time` | `{{< time <value> <unit> [<target-unit>] >}}` | Time: second and its SI-prefixed subdivisions, plus minute, hour, day. |
+| `concentration` | `{{< concentration <value> <unit> [<target-unit>] >}}` | Molar concentration: M, mM, μM, nM, pM, fM. |
+| `voltage` | `{{< voltage <value> <unit> [<target-unit>] >}}` | Electrical potential: kV, V, mV, μV. |
+| `temperature` | `{{< temperature <value> <unit> [<target-unit>] >}}` | Temperature: kelvin, celsius, fahrenheit (affine conversion). |
+| `massconc` | `{{< massconc <value> <mass-unit> <molar-mass> <target-unit> >}}` | Mass-per-volume concentration converted to molar concentration given an explicit molar mass. |
+
+Each quantity shortcode accepts an optional keyword argument, `notation=sci` or `notation=plain`, which overrides the automatic determination of numerical formatting described in Section 6.
+
+## Supported Unit Categories
+
+### Bulk Energy (base unit: joule)
+
+| Unit key | Symbol | Notes |
+|---|---|---|
+| `J` | J | SI base representation |
+| `kJ` | kJ | |
+| `cal` | cal | Thermochemical calorie (1 cal = 4.184 J) |
+| `kcal` | kcal | |
+
+### Molar Energy (base unit: kJ·mol⁻¹)
+
+| Unit key | Symbol | Notes |
+|---|---|---|
+| `J/mol` | J·mol⁻¹ | |
+| `kJ/mol` | kJ·mol⁻¹ | |
+| `cal/mol` | cal·mol⁻¹ | |
+| `kcal/mol` | kcal·mol⁻¹ | |
+| `eV` | eV | 1 eV = 96.485 kJ·mol⁻¹ |
+| `hartree` | *E*ₕ | Atomic unit of energy; 1 hartree = 2625.5 kJ·mol⁻¹ |
+| `cm-1` | cm⁻¹ | Wavenumber, as conventionally reported in vibrational spectroscopy |
+
+### Distance (base unit: ångström)
+
+| Unit key | Symbol | Notes |
+|---|---|---|
+| `angstrom` | Å | Rendered using U+00C5, the canonical (NFKC-normalized) form |
+| `nanometer` | nm | |
+| `picometer` | pm | |
+| `bohr` | *a*₀ | Atomic unit of length |
+| `meter` | m | |
+
+### Time (base unit: second)
+
+| Unit key | Symbol |
+|---|---|
+| `second` | s |
+| `millisecond` | ms |
+| `microsecond` | μs |
+| `nanosecond` | ns |
+| `picosecond` | ps |
+| `femtosecond` | fs |
+| `minute` | min |
+| `hour` | h |
+| `day` | d |
+
+### Molar Concentration (base unit: molar)
+
+| Unit key | Symbol |
+|---|---|
+| `molar` | M |
+| `millimolar` | mM |
+| `micromolar` | μM |
+| `nanomolar` | nM |
+| `picomolar` | pM |
+| `femtomolar` | fM |
+
+### Mass Concentration (base unit: mg·mL⁻¹)
+
+| Unit key | Symbol |
+|---|---|
+| `mg/mL` | mg·mL⁻¹ |
+| `μg/mL` | μg·mL⁻¹ |
+| `ng/mL` | ng·mL⁻¹ |
+
+This category is consumed exclusively by the `massconc` shortcode, which additionally requires a molar mass argument to compute the corresponding molar concentration.
+
+### Voltage (base unit: volt)
+
+| Unit key | Symbol |
+|---|---|
+| `kilovolt` | kV |
+| `volt` | V |
+| `millivolt` | mV |
+| `microvolt` | μV |
+
+### Temperature
+
+| Unit key | Symbol | Conversion basis |
+|---|---|---|
+| `kelvin` | K | Identity (SI base unit; no degree sign, per convention) |
+| `celsius` | °C | *T*(K) = *T*(°C) + 273.15 |
+| `fahrenheit` | °F | *T*(K) = [*T*(°F) + 459.67] × 5/9 |
+
+## Numerical Formatting
+
+The rendered representation of a numerical value is determined automatically unless overridden by the `notation` keyword argument.
+
+By default, a value is formatted to three significant figures using fixed decimal notation.
+Should this formatting internally require exponential notation, the extension instead renders the value in explicit scientific notation, with the mantissa and a true superscript exponent joined by a non-breaking multiplication sign:
+
+```markdown
+{{< sci 6.02214076e23 >}}
+```
+
+renders as 6.022 × 10²³, rather than the unprocessed string `6.02e+23`.
+
+## Worked Examples
+
+### Distance
+
+```markdown
+The O–H bond length is {{< distance 0.96 angstrom >}}.
+Converted to nanometers: {{< distance 1.54 angstrom nanometer >}}.
+```
+> The O–H bond length is 0.96 Å.
+> Converted to nanometers: 1.54 Å (0.154 nm).
+
+### Bulk Energy
+
+```markdown
+Combustion releases {{< energy 4.18 J >}} of heat under these conditions.
+```
+> Combustion releases 4.18 J of heat under these conditions.
+
+### Molar Energy
+
+```markdown
+The activation barrier was {{< molarenergy 45.2 kJ/mol kcal/mol >}}.
+A single-point DFT energy of {{< molarenergy 0.0421 hartree kcal/mol >}} was obtained.
+```
+> The activation barrier was 45.2 kJ·mol⁻¹ (10.8 kcal·mol⁻¹).
+> A single-point DFT energy of 0.0421 *E*ₕ (110 kcal·mol⁻¹) was obtained.
+
+### Time
+
+```markdown
+The production molecular dynamics simulation was extended to
+{{< time 500 nanosecond microsecond >}}, using an integration timestep of
+{{< time 2e-15 second femtosecond >}}.
+```
+> The production molecular dynamics simulation was extended to 500 ns
+> (0.5 μs), using an integration timestep of 2 × 10⁻¹⁵ s (2 fs).
+
+### Molar Concentration
+
+```markdown
+The compound exhibited a Kᵢ of {{< concentration 12 nanomolar >}}
+against the target enzyme.
+```
+> The compound exhibited a Kᵢ of 12 nM against the target enzyme.
+
+### Voltage
+
+```markdown
+Resting membrane potential was recorded at {{< voltage -70 millivolt >}}.
+```
+> Resting membrane potential was recorded at -70 mV.
+
+### Temperature
+
+```markdown
+Assays were conducted at {{< temperature 25 celsius kelvin >}}, approximating
+physiological temperature of {{< temperature 310.15 kelvin celsius >}}.
+```
+> Assays were conducted at 25 °C (298 K), approximating physiological
+> temperature of 310.15 K (37 °C).
+
+### Scientific Notation and Rate Constants
+
+```markdown
+The observed second-order rate constant was
+{{< concentration 2.1e6 molar notation=sci >}}⁻¹·{{< unit second >}}⁻¹.
+```
+> The observed second-order rate constant was 2.1 × 10⁶ M⁻¹·s⁻¹.
+
+### Mass-to-Molar Concentration Conversion
+
+```markdown
+A stock solution prepared at {{< massconc 0.5 mg/mL 350.4 micromolar >}}
+was used for the binding assay.
+```
+> A stock solution prepared at 0.5 mg·mL⁻¹ (1.43 μM, MW 350.4 g/mol) was
+> used for the binding assay.
+

_extensions/units/_extension.yml

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+
+title: Units
+author: Alex Maldonado
+version: 0.1.0
+quarto-required: ">=1.2.0"
+contributes:
+  shortcodes:
+    - units.lua

_extensions/units/units.lua

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+local NBSP = "\u{00A0}"
+local function nbsp() return pandoc.Str(NBSP) end
+
+-- render a value already known to be in scientific-notation range
+-- returns a list of inlines: mantissa <NBSP> × <NBSP> 10^exp^
+local function formatSci(value)
+  local s = string.format("%.3e", value) -- e.g. "6.020e+23" or "1.500e-06"
+  local mantissa, sign, exp = s:match("^(-?%d+%.?%d*)e([+-])(%d+)$")
+  if not mantissa then
+    -- fallback, shouldn't happen with %.3e, but never crash on bad input
+    return { pandoc.Str(s) }
+  end
+  -- trim trailing zeros (and a trailing bare decimal point) from mantissa
+  mantissa = mantissa:gsub("0+$", ""):gsub("%.$", "")
+  local expNum = tonumber(sign .. exp) -- keeps sign, drops leading zeros (e.g. "+23" -> 23, "-06" -> -6)
+
+  local out = { pandoc.Str(mantissa) }
+  if expNum ~= 0 then
+    table.insert(out, nbsp())
+    table.insert(out, pandoc.Str("×"))
+    table.insert(out, nbsp())
+    table.insert(out, pandoc.Str("10"))
+    table.insert(out, pandoc.Superscript({ pandoc.Str(tostring(expNum)) }))
+  end
+  return out
+end
+
+-- render a value in plain decimal notation, 3 significant figures.
+-- IMPORTANT: C's %g spec has its own internal rule for switching to
+-- exponential form ("use %e if exponent < -4 or exponent >= precision").
+-- With precision 3, that means %.3g silently flips to "1e+03"-style
+-- output for anything >= 1000 -- BEFORE any magnitude threshold of ours
+-- gets a say. Rather than duplicating that rule with a second threshold
+-- we let %g decide, then intercept its exponential output and re-render it through
+-- formatSci() instead of ever emitting the raw "1e+03" string.
+local function formatPlain(value)
+  local s = string.format("%.3g", value)
+  if s:find("[eE]") then
+    return formatSci(value)
+  end
+  return { pandoc.Str(s) }
+end
+
+-- decide plain vs. scientific, unless overridden.
+-- mode: nil/"auto" (let %g decide, see formatPlain), "sci", or "plain"
+local function formatNumber(value, mode)
+  if value == 0 then return { pandoc.Str("0") } end
+  if mode == "sci" then return formatSci(value) end
+  return formatPlain(value) -- handles both "auto" and explicit "plain"
+end
+
+local function appendAll(dst, list)
+  for _, inl in ipairs(list) do table.insert(dst, inl) end
+end
+
+local ENERGY_UNITS = {
+  ["J"]    = { md = "J",    per_base = 1 },
+  ["kJ"]   = { md = "kJ",   per_base = 1e-3 },
+  ["cal"]  = { md = "cal",  per_base = 1 / 4.184 },
+  ["kcal"] = { md = "kcal", per_base = 1 / 4184 },
+}
+
+local MOLAR_ENERGY_UNITS = {
+  ["J/mol"]    = { md = "J·mol^-1^",    per_base = 1000 },
+  ["kJ/mol"]   = { md = "kJ·mol^-1^",   per_base = 1 },
+  ["cal/mol"]  = { md = "cal·mol^-1^",  per_base = 1000 / 4.184 },
+  ["kcal/mol"] = { md = "kcal·mol^-1^", per_base = 1 / 4.184 },
+  ["eV"]       = { md = "eV",           per_base = 1 / 96.485 },
+  ["hartree"]  = { md = "*E*~h~",       per_base = 1 / 2625.5 },
+  ["cm-1"]     = { md = "cm^-1^",       per_base = 1 / 0.0119627 },
+}
+
+local DISTANCE_UNITS = {
+  ["angstrom"]  = { md = "Å",      per_base = 1 },
+  ["nanometer"] = { md = "nm",     per_base = 0.1 },
+  ["picometer"] = { md = "pm",     per_base = 100 },
+  ["bohr"]      = { md = "*a*~0~", per_base = 1.8897259886 },
+  ["meter"]     = { md = "m",      per_base = 1e-10 },
+}
+
+local TIME_UNITS = {
+  ["second"]      = { md = "s",   per_base = 1 },
+  ["millisecond"] = { md = "ms",  per_base = 1e3 },
+  ["microsecond"] = { md = "μs",  per_base = 1e6 },
+  ["nanosecond"]  = { md = "ns",  per_base = 1e9 },
+  ["picosecond"]  = { md = "ps",  per_base = 1e12 },
+  ["femtosecond"] = { md = "fs",  per_base = 1e15 },
+  ["minute"]      = { md = "min", per_base = 1 / 60 },
+  ["hour"]        = { md = "h",   per_base = 1 / 3600 },
+  ["day"]         = { md = "d",   per_base = 1 / 86400 },
+}
+
+local CONCENTRATION_UNITS = {
+  ["molar"]      = { md = "M",  per_base = 1 },
+  ["millimolar"] = { md = "mM", per_base = 1e3 },
+  ["micromolar"] = { md = "μM", per_base = 1e6 },
+  ["nanomolar"]  = { md = "nM", per_base = 1e9 },
+  ["picomolar"]  = { md = "pM", per_base = 1e12 },
+  ["femtomolar"] = { md = "fM", per_base = 1e15 },
+}
+
+local VOLTAGE_UNITS = {
+  ["kilovolt"]  = { md = "kV", per_base = 1e-3 },
+  ["volt"]      = { md = "V",  per_base = 1 },
+  ["millivolt"] = { md = "mV", per_base = 1e3 },
+  ["microvolt"] = { md = "μV", per_base = 1e6 },
+}
+
+local TEMPERATURE_UNITS = {
+  ["kelvin"]     = {
+    md = "K",
+    toKelvin   = function(v) return v end,
+    fromKelvin = function(k) return k end,
+  },
+  ["celsius"]    = {
+    md = "°C",
+    toKelvin   = function(v) return v + 273.15 end,
+    fromKelvin = function(k) return k - 273.15 end,
+  },
+  ["fahrenheit"] = {
+    md = "°F",
+    toKelvin   = function(v) return (v + 459.67) * 5 / 9 end,
+    fromKelvin = function(k) return k * 9 / 5 - 459.67 end,
+  },
+}
+
+local MASS_CONC_UNITS = {
+  ["mg/mL"] = { md = "mg·mL^-1^", per_base = 1 },
+  ["μg/mL"] = { md = "μg·mL^-1^", per_base = 1e3 },
+  ["ng/mL"] = { md = "ng·mL^-1^", per_base = 1e6 },
+}
+
+local SYMBOLS = {}
+for _, tbl in ipairs({
+  ENERGY_UNITS, MOLAR_ENERGY_UNITS, DISTANCE_UNITS,
+  TIME_UNITS, CONCENTRATION_UNITS, VOLTAGE_UNITS, TEMPERATURE_UNITS,
+}) do
+  for k, v in pairs(tbl) do SYMBOLS[k] = v end
+end
+
+local function md_to_inlines(md)
+  return pandoc.read(md, "markdown").blocks[1].content
+end
+
+-- {{< unit nanomolar >}}  ->  just the formatted symbol, any category
+local function unit(args)
+  local key = pandoc.utils.stringify(args[1])
+  local u = SYMBOLS[key]
+  if not u then
+    io.stderr:write("[units] unknown unit '" .. key .. "'\n")
+    return pandoc.Str(key)
+  end
+  return md_to_inlines(u.md)
+end
+
+-- {{< sci 6.02e23 >}}  ->  6.02 × 10²³   (always scientific, no unit)
+local function sci(args)
+  local value = tonumber(pandoc.utils.stringify(args[1]))
+  if not value then
+    io.stderr:write("[units] bad sci() arg: '" .. pandoc.utils.stringify(args[1]) .. "'\n")
+    return pandoc.Str("[sci error]")
+  end
+  return formatSci(value)
+end
+
+-- generic converter, parameterized by which table to use.
+-- optional kwargs.notation = "sci" | "plain" forces that format
+-- for both the source value and (if present) the converted value.
+local function makeQuantityShortcode(TABLE, label)
+  return function(args, kwargs)
+    local value   = tonumber(pandoc.utils.stringify(args[1]))
+    local fromKey = pandoc.utils.stringify(args[2])
+    local toKey   = args[3] and pandoc.utils.stringify(args[3]) or nil
+    local from    = TABLE[fromKey]
+    local mode    = kwargs and kwargs["notation"] and pandoc.utils.stringify(kwargs["notation"]) or nil
+
+    if not value or not from then
+      io.stderr:write("[units] bad " .. label .. "() args, unit='" ..
+        tostring(fromKey) .. "'\n")
+      return pandoc.Str("[" .. label .. " error]")
+    end
+
+    local out = {}
+    appendAll(out, formatNumber(value, mode))
+    table.insert(out, nbsp())
+    appendAll(out, md_to_inlines(from.md))
+
+    if toKey then
+      local to = TABLE[toKey]
+      if to then
+        local baseVal   = value / from.per_base
+        local converted = baseVal * to.per_base
+        table.insert(out, nbsp())
+        table.insert(out, pandoc.Str("("))
+        appendAll(out, formatNumber(converted, mode))
+        table.insert(out, nbsp())
+        appendAll(out, md_to_inlines(to.md))
+        table.insert(out, pandoc.Str(")"))
+      else
+        io.stderr:write("[units] unknown target unit '" .. toKey .. "' for " .. label .. "\n")
+      end
+    end
+    return out
+  end
+end
+
+-- {{< temperature 25 celsius kelvin >}}
+-- Uses toKelvin/fromKelvin round-trip instead of a per_base ratio,
+-- since C/F/K aren't related by a pure multiplicative factor.
+local function temperature(args, kwargs)
+  local value   = tonumber(pandoc.utils.stringify(args[1]))
+  local fromKey = pandoc.utils.stringify(args[2])
+  local toKey   = args[3] and pandoc.utils.stringify(args[3]) or nil
+  local from    = TEMPERATURE_UNITS[fromKey]
+  local mode    = kwargs and kwargs["notation"] and pandoc.utils.stringify(kwargs["notation"]) or nil
+
+  if not value or not from then
+    io.stderr:write("[units] bad temperature() args, unit='" .. tostring(fromKey) .. "'\n")
+    return pandoc.Str("[temperature error]")
+  end
+
+  local kelvin = from.toKelvin(value)
+  if kelvin < 0 then
+    io.stderr:write("[units] warning: temperature() computed " ..
+      string.format("%.2f", kelvin) .. " K, below absolute zero -- check input\n")
+  end
+
+  local out = {}
+  appendAll(out, formatNumber(value, mode))
+  table.insert(out, nbsp())
+  appendAll(out, md_to_inlines(from.md))
+
+  if toKey then
+    local to = TEMPERATURE_UNITS[toKey]
+    if to then
+      local converted = to.fromKelvin(kelvin)
+      table.insert(out, nbsp())
+      table.insert(out, pandoc.Str("("))
+      appendAll(out, formatNumber(converted, mode))
+      table.insert(out, nbsp())
+      appendAll(out, md_to_inlines(to.md))
+      table.insert(out, pandoc.Str(")"))
+    else
+      io.stderr:write("[units] unknown target unit '" .. toKey .. "' for temperature\n")
+    end
+  end
+  return out
+end
+
+-- {{< massconc 0.5 mg/mL 350.4 micromolar >}}
+local function massconc(args, kwargs)
+  local value   = tonumber(pandoc.utils.stringify(args[1]))
+  local fromKey = pandoc.utils.stringify(args[2])
+  local mw      = tonumber(pandoc.utils.stringify(args[3]))
+  local toKey   = pandoc.utils.stringify(args[4])
+  local from    = MASS_CONC_UNITS[fromKey]
+  local to      = CONCENTRATION_UNITS[toKey]
+  local mode    = kwargs and kwargs["notation"] and pandoc.utils.stringify(kwargs["notation"]) or nil
+
+  if not (value and from and mw and to) then
+    io.stderr:write("[units] bad massconc() args\n")
+    return pandoc.Str("[massconc error]")
+  end
+
+  local gPerL     = value / from.per_base
+  local molPerL   = gPerL / mw
+  local converted = molPerL * to.per_base
+
+  local out = {}
+  appendAll(out, formatNumber(value, mode))
+  table.insert(out, nbsp())
+  appendAll(out, md_to_inlines(from.md))
+  table.insert(out, nbsp())
+  table.insert(out, pandoc.Str("("))
+  appendAll(out, formatNumber(converted, mode))
+  table.insert(out, nbsp())
+  appendAll(out, md_to_inlines(to.md))
+  table.insert(out, pandoc.Str(", MW " .. tostring(mw) .. NBSP .. "g/mol)"))
+  return out
+end
+
+return {
+  ["unit"]          = unit,
+  ["sci"]           = sci,
+  ["energy"]        = makeQuantityShortcode(ENERGY_UNITS, "energy"),
+  ["molarenergy"]   = makeQuantityShortcode(MOLAR_ENERGY_UNITS, "molarenergy"),
+  ["distance"]      = makeQuantityShortcode(DISTANCE_UNITS, "distance"),
+  ["time"]          = makeQuantityShortcode(TIME_UNITS, "time"),
+  ["concentration"] = makeQuantityShortcode(CONCENTRATION_UNITS, "concentration"),
+  ["voltage"]       = makeQuantityShortcode(VOLTAGE_UNITS, "voltage"),
+  ["temperature"]   = temperature,
+  ["massconc"]      = massconc,
+}