Source code

[fred-atherden]

Description

Source code associated with the whole article. Covers a wide variety of file types.

User Stories

• (1) As an author, I want to be able to see any source code files associated with my article so that I can make sure none are missing.
• (2) As an author, I want to be able to download any source code files associated with my articles so that I can check the files themselves are correct.
• (3) As an author, I want to be able to update a source code file so that I can fix errors in the file originally supplied.
• (4) As an author, I want to be able to edit the title and caption of a source code file, so that I can correct any errors.
• (5) As an author, I want to be able to add reference or asset citations to my source code title and legend so that I can cite other articles and assets in this context.
• (6) As an author, I want to be able to adjust the type and placement of source code files so that I can ensure that they display correctly within the manuscript. [E.g. change a source code file to source data, or to change it to source code for a figure]

Production staff

• (7) As production staff, I want to be able to add source code files so that I can include any missing assets.
• (8) As production staff, I want to be able to remove source code files, so that I eliminate anything that has been incorrectly supplied.
• (9) As production staff, I want to know why an author has changed a source code file so that I am aware of the reason for the change.
• (10) As production staff, I want to provide an explanation for why I am replacing a source code file so that I can record the reason for the change.

But what if . . . ?

Considerations

• The eLife labelling scheme for these files is
  • Source code 1
  • Source code 2
• Labels will vary from publisher to publisher.
• This is a variant of a supplementary file (outlined in this ticket), with a different labelling convention.

XML requirements

Captured as a supplementary-material in back/sec[@sec-type="supplementary-material"] element. The value of the label is 'Source code X.'

<back>
     ...
     <sec sec-type="supplementary-material">
          <title>Additional files</title>
          ...
          <supplementary-material id="scode1">
               <label>Source code 1.</label>
               <caption>
                    <title>R codes used for Bayesian statistical analysis.</title>
               </caption>
               <media mime-subtype="zip" mimetype="application" xlink:href="elife-31549-code1-v1.zip"/>
          </supplementary-material>
          <supplementary-material id="scode2">
               <label>Source code 2.</label>
               <caption>
                    <title>SAS code used for estimation of gametocyte half-life for gametocytes.</title>
               </caption>
               <media mime-subtype="docx" mimetype="application" xlink:href="elife-31549-code2-v1.docx"/>
          </supplementary-material>
          ...
     </sec>
     ...
<back>

Mock ups

Proposal