fix: Add equation id and alttext for MathML in JATS

src/codecs/jats/__file_snapshots__/elife-43154-v2.yaml

@@ -2044,6 +2044,7 @@ content:
           width="thinmathspace"/><mml:mn>0.24</mml:mn><mml:mo>,</mml:mo></mml:mrow></mml:mstyle></mml:math>
       - ' then by the law of total probability:'
   - type: MathBlock
+    id: equ1
     mathLanguage: mathml
     text: >-
       <mml:math id="m1"><mml:mstyle displaystyle="true"

src/codecs/jats/__file_snapshots__/elife-52882-v2.yaml

@@ -5883,6 +5883,7 @@ content:
           id="inf187"><mml:msub><mml:mi>p</mml:mi><mml:mrow><mml:mi>t</mml:mi><mml:mo>⁢</mml:mo><mml:mi>u</mml:mi><mml:mo>⁢</mml:mo><mml:mi>r</mml:mi><mml:mo>⁢</mml:mo><mml:mi>n</mml:mi></mml:mrow></mml:msub></mml:math>
       - ' in the form:'
   - type: MathBlock
+    id: equ1
     mathLanguage: mathml
     text: >-
       <mml:math
@@ -5893,6 +5894,7 @@ content:
     content:
       - using
   - type: MathBlock
+    id: equ2
     mathLanguage: mathml
     text: >-
       <mml:math
@@ -5907,6 +5909,7 @@ content:
     content:
       - and
   - type: MathBlock
+    id: equ3
     mathLanguage: mathml
     text: >-
       <mml:math
@@ -5915,6 +5918,7 @@ content:
     content:
       - with
   - type: MathBlock
+    id: equ4
     mathLanguage: mathml
     text: >-
       <mml:math

src/codecs/jats/__file_snapshots__/plosone-0178565.yaml

@@ -2355,6 +2355,7 @@ content:
         where both the proteins are absent. The modified formula of Hamming
         distance is:
   - type: MathBlock
+    id: pone.0178565.e001
     mathLanguage: mathml
     text: >-
       <mml:math display="block"

src/codecs/jats/index.ts

@@ -2126,10 +2126,17 @@ function decodeMath(
     return inline ? image : [stencila.paragraph({ content: image })]
   }
 
+  const id = attrOrUndefined(formula, 'id')
+
+  const altText = attrOrUndefined(mathml, 'alttext')
+  const meta = altText !== undefined ? { altText } : undefined
+
   // Wrapper is needed to dump the entire math element
   const text = xml.dump(elem('wrapper', mathml))
   return [
     (inline ? stencila.mathFragment : stencila.mathBlock)({
+      id,
+      meta,
       mathLanguage: 'mathml',
       text,
     }),

src/codecs/plos/__file_snapshots__/pcbi-1007273.yaml

@@ -2466,6 +2466,7 @@ content:
       - |2
          as:
   - type: MathBlock
+    id: pcbi.1007273.e001
     mathLanguage: mathml
     text: >-
       <mml:math display="block" id="M1"><mml:mtable
@@ -2615,6 +2616,7 @@ content:
         to the proximity of two contigs on the chromosome, we use the graph
         topology to establish this relationship. Let 
       - type: MathFragment
+        id: pcbi.1007273.e002
         mathLanguage: mathml
         text: >-
           <mml:math display="inline" id="M2"><mml:mover
@@ -2673,20 +2675,23 @@ content:
           - v
       - '), '
       - type: MathFragment
+        id: pcbi.1007273.e003
         mathLanguage: mathml
         text: >-
           <mml:math display="inline"
           id="M3"><mml:mrow><mml:mi>σ</mml:mi><mml:mo>(</mml:mo><mml:mi>u</mml:mi><mml:mo>,</mml:mo><mml:mover
           accent="true"><mml:mi>v</mml:mi><mml:mo>¯</mml:mo></mml:mover><mml:mo>)</mml:mo></mml:mrow></mml:math>
       - ', '
       - type: MathFragment
+        id: pcbi.1007273.e004
         mathLanguage: mathml
         text: >-
           <mml:math display="inline"
           id="M4"><mml:mrow><mml:mi>σ</mml:mi><mml:mo>(</mml:mo><mml:mover
           accent="true"><mml:mi>u</mml:mi><mml:mo>¯</mml:mo></mml:mover><mml:mo>,</mml:mo><mml:mi>v</mml:mi><mml:mo>)</mml:mo></mml:mrow></mml:math>
       - ' and '
       - type: MathFragment
+        id: pcbi.1007273.e005
         mathLanguage: mathml
         text: >-
           <mml:math display="inline"
@@ -2696,6 +2701,7 @@ content:
       - |
         . With this, the score for a pair of contigs is defined as follows:
   - type: MathBlock
+    id: pcbi.1007273.e006
     mathLanguage: mathml
     text: >-
       <mml:math display="block" id="M6"><mml:mtable

src/codecs/plos/__file_snapshots__/pmed-1002858.yaml

@@ -3296,6 +3296,7 @@ content:
     content:
       - 'Patient data are denoted '
       - type: MathFragment
+        id: pmed.1002858.e001
         mathLanguage: mathml
         text: >-
           <mml:math display="inline"
@@ -3442,6 +3443,7 @@ content:
     content:
       - 'This model fit estimates the set of parameters '
       - type: MathFragment
+        id: pmed.1002858.e002
         mathLanguage: mathml
         text: >-
           <mml:math display="inline" id="M2"><mml:mrow><mml:msub><mml:mover
@@ -3457,6 +3459,7 @@ content:
     content:
       - 'In a second stage, the sets of parameters '
       - type: MathFragment
+        id: pmed.1002858.e003
         mathLanguage: mathml
         text: >-
           <mml:math display="inline"
@@ -3470,6 +3473,7 @@ content:
           - '30'
       - ']) and obtain a global estimate '
       - type: MathFragment
+        id: pmed.1002858.e004
         mathLanguage: mathml
         text: >-
           <mml:math display="inline" id="M4"><mml:mover accent="true"><mml:mi
@@ -3479,6 +3483,7 @@ content:
     content:
       - 'The global estimate '
       - type: MathFragment
+        id: pmed.1002858.e005
         mathLanguage: mathml
         text: >-
           <mml:math display="inline" id="M5"><mml:mover accent="true"><mml:mi