Massive update for modernization, layout improvements, and content

.github/workflows/news.yml

@@ -0,0 +1,27 @@
+name: Update news
+
+on:
+  schedule:
+  # Get the feed every day at 1:13 UTC
+    - cron: "13 1 * * *"
+  # allow manual update
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Download File
+      run: |
+        curl https://www.softwareheritage.org/tag/codemeta/feed/ --output ./data/feeds/softwareheritage.xml
+      working-directory: ${{ github.workspace }}
+    - name: Commit and Push Changes
+      run: |
+        git config --global user.name "${{ github.actor }}"
+        git config --global user.email "${{ github.actor }}@users.noreply.github.com"
+
+        git add ./data/feeds/
+        git commit -m 'Update news'
+        git push

config.toml

@@ -1,4 +1,4 @@
-theme = "hugo-material"
+theme = "CodeMeta-Pyramids"
 baseurl = "/"
 relativeurls = true
 title = "The CodeMeta Project"
@@ -7,7 +7,6 @@ disqusShortname = ""
 ignoreFiles = ["\\.Rmd$", "_files$", "_cache$", "\\.csv", "\\.R"]
 publishDir = "../website"
 
-
 [[menu.main]]
     name = "Home"
     url = "/index.html"
@@ -41,24 +40,32 @@ publishDir = "../website"
     url = "/tools"
     weight = 8
 
+[[menu.footer]]
+    name = "Source code on Github"
+    url = "https://github.com/codemeta/"
+    pre = "<i class='bi-github'></i>"
+    weight = 1
+[[menu.footer]]
+    name = "Governance"
+    url = "https://codemeta.github.io/governance/"
+    weight = 2
+[[menu.footer]]
+    name = "Scicodes Consortium"
+    url = "https://scicodes.net/"
+    weight = 3
+
 
 [params]
     name =  "codemeta"
     github =  "codemeta"
-    custom_css = ["glyphicon.css"]
-    #custom_css = ["cboettig.css"]
     repo = "codemeta.github.io"
     background = "img/pyramids.jpg"
+
+    newslimit = 5
 
     date_format = "Mon, Jan 2, 2006"
     description = "A Rosetta Stone for Software Metadata"
 
-    # options for highlight.js (version, additional languages, and theme)
-    highlightjsVersion = "9.10.0"
-    highlightCDN = "//cdn.bootcss.com"
-    highlightjsLang = ["r", "yaml", "json"]
-    highlightjsTheme = "github"
-
     [params.logo]
     url = "logo.png"
     width = 50
@@ -69,3 +76,5 @@ publishDir = "../website"
   [markup.goldmark]
     [markup.goldmark.renderer]
       unsafe = true
+  [markup.highlight]
+    style = 'pygments'

content/_index.md

@@ -1,23 +1,54 @@
 ---
 title: "The CodeMeta Project"
+layout: landing
 ---
 
-## Motivation
+## Introducing CodeMeta
 
-Research relies heavily on scientific software, and a large and growing fraction of researchers are engaged in developing software as part of their own research ([Hannay et al 2009](https://doi.org/10.1109/SECSE.2009.5069155 "How do scientists develop and use scientific software?")). Despite this, _infrastructure to  support the preservation, discovery, reuse, and attribution of software_ lags substantially behind that of other research products such as journal  articles and research data. This lag is driven not so much by a lack of  technology as it is by a lack of unity: existing mechanisms to archive,  document, index, share, discover, and cite software contributions are heterogeneous among both disciplines and archives and rarely meet best practices ([Howison 2015](https://doi.org/10.1002/asi.23538 "Software in the scientific literature: Problems with seeing, finding, and using software mentioned in the biology literature")).  Fortunately, a rapidly growing movement to improve preservation, discovery, reuse and attribution of academic software is now underway: a recent [NIH report](http://softwarediscoveryindex.org), conferences and working groups of [FORCE11](https://www.force11.org/), [WSSSPE](http://wssspe.researchcomputing.org.uk/) & [Software Sustainability Institute](http://www.software.ac.uk/), and the rising adoption of repositories like [GitHub](https://github.com), [Zenodo](https://zenodo.org), [figshare](https://figshare.com) & [DataONE](https://www.dataone.org) by academic software developers. Now is the time to improve how these resources can talk to each other.  
+Software development creates changes, and scientific research requires
+reproducibility. Since software is routinely used in research projects,
+this can cause problems.
 
-## What can software metadata do for you?
+_**CodeMeta acts as a vital bridge between these disciplines.**_
 
-What metadata you want from software is determined by your use case.  If your primary concerns are credit for academic software, then you're most interested in _citation_ metadata.  If you're trying to replicate some analysis, you worry more about versions and dependencies than about authors and titles.  And if you seek to discover software you don't already know about that is suitable for a particular task, well then you are interested more in keywords and descriptions. Frequently, developers of scientific software, repositories that host that software, and users themselves are interested in more than one of these objectives, and others besides.
+[Aiming to solve this problem](/background), CodeMeta was founded in 2016
+by a consortium of researchers. Using existing standards such as Schema.org
+terms and JSON-LD, CodeMeta is now a recognised framework that is employed
+by a worldwide community of developers, researchers, and archivists.
 
-Different software repositories, software languages and scientific domains denote this information in different ways, which makes it difficult or impossible for tools to work across these different sources without losing valuable information along the way.  For instance, a fantastic collaboration between GitHub and figshare provides researchers a way to import software on the former into the persistent archive of the latter, getting a permanent identifier, a DOI in the process.  To assign a DOI, figshare must then pass metadata about the object to DataCite, the central DOI provider for all repositories.  While this makes DataCite a powerful aggregator, the lack of a crosswalk table means that much valuable metadata is currently lost along the way, such as the original software license, platform, and so forth. Any tool or approach working across software repositories faces similar challenges without a crosswalk table to translate between these.
+When used and maintained in code repositories and software distribution
+systems, CodeMeta enables the exact version of a library or application,
+that has been used and cited in scientific and other research, to be
+reliably identified and reused.
 
-For more detail, [visit the project on GitHub](https://github.com/codemeta/codemeta) or check back here soon.
+### Research Software MetaData Guidelines
 
-## Special thanks to our supporters
+CodeMeta is suggested for use by the following 
+[Research Software MetaData Guidelines](https://fair-impact.github.io/RSMD-guidelines/)
+recommendations:
 
-<img width="50px"  src="/img/nsf.jpg"/>
-<img width="50px"  src="/img/datacite.png"/>
-<img width="50px" src="/img/github.png"/>
-<img width="50px"  src="/img/figshare.png"/> 
-<img width="50px"  src="/img/zenodo.jpg"/>
+{{< rsmd >}}
+
+## Use Cases
+
+Credit
+: CodeMeta's _citation_ metadata is useful for ensuring that authors get
+credit for their software, when it is used for published research.
+
+Reproducibility
+: Tracking the software libraries and applications used in research, using
+CodeMeta's _versions_ and _dependencies_ metadata, ensures that important
+findings can be reviewed and verified with greater accuracy.
+
+Discovery
+: Finding software is easier with CodeMeta's _keywords_ and _descriptions_
+metadata. These terms allow everyone to discover relevant software, and use
+or contribute to it.
+
+## Connecting via Crosswalks
+
+Repositories, software languages, and scientific domains often have different
+vocabularies for their metadata. Our Crosswalks exist to provide a reliable
+path to interoperability. By mapping each of these formats to CodeMeta via a
+Crosswalk, CodeMeta acts as a translation layer for data to be converted
+freely, preserving information that would otherwise be lost.

content/background.md

@@ -0,0 +1,16 @@
+---
+title: "The CodeMeta Project"
+layout: sidenav
+---
+
+## Motivation
+
+Research relies heavily on scientific software, and a large and growing fraction of researchers are engaged in developing software as part of their own research ([Hannay et al 2009](https://doi.org/10.1109/SECSE.2009.5069155 "How do scientists develop and use scientific software?")). Despite this, _infrastructure to  support the preservation, discovery, reuse, and attribution of software_ lags substantially behind that of other research products such as journal  articles and research data. This lag is driven not so much by a lack of  technology as it is by a lack of unity: existing mechanisms to archive,  document, index, share, discover, and cite software contributions are heterogeneous among both disciplines and archives and rarely meet best practices ([Howison 2015](https://doi.org/10.1002/asi.23538 "Software in the scientific literature: Problems with seeing, finding, and using software mentioned in the biology literature")).  Fortunately, a rapidly growing movement to improve preservation, discovery, reuse and attribution of academic software is now underway: a recent [NIH report](http://softwarediscoveryindex.org), conferences and working groups of [FORCE11](https://www.force11.org/), [WSSSPE](http://wssspe.researchcomputing.org.uk/) & [Software Sustainability Institute](http://www.software.ac.uk/), and the rising adoption of repositories like [GitHub](https://github.com), [Zenodo](https://zenodo.org), [figshare](https://figshare.com) & [DataONE](https://www.dataone.org) by academic software developers. Now is the time to improve how these resources can talk to each other.  
+
+## What can software metadata do for you?
+
+What metadata you want from software is determined by your use case.  If your primary concerns are credit for academic software, then you're most interested in _citation_ metadata.  If you're trying to replicate some analysis, you worry more about versions and dependencies than about authors and titles.  And if you seek to discover software you don't already know about that is suitable for a particular task, well then you are interested more in keywords and descriptions. Frequently, developers of scientific software, repositories that host that software, and users themselves are interested in more than one of these objectives, and others besides.
+
+Different software repositories, software languages and scientific domains denote this information in different ways, which makes it difficult or impossible for tools to work across these different sources without losing valuable information along the way.  For instance, a fantastic collaboration between GitHub and figshare provides researchers a way to import software on the former into the persistent archive of the latter, getting a permanent identifier, a DOI in the process.  To assign a DOI, figshare must then pass metadata about the object to DataCite, the central DOI provider for all repositories.  While this makes DataCite a powerful aggregator, the lack of a crosswalk table means that much valuable metadata is currently lost along the way, such as the original software license, platform, and so forth. Any tool or approach working across software repositories faces similar challenges without a crosswalk table to translate between these.
+
+For more detail, [visit the project on GitHub](https://github.com/codemeta/codemeta) or check back here soon.

content/create.md

@@ -1,11 +1,60 @@
 ---
 title: "Create a CodeMeta file"
-#layout: login
+layout: wide
 ---
 
-Need to generate a CodeMeta compliant metadata file? Try out the [CodeMeta Generator](https://codemeta.github.io/codemeta-generator), which was created by the folks at [Software Heritage](https://www.softwareheritage.org).
+Need to generate a CodeMeta compliant metadata file? The folks at
+[Software Heritage](https://www.softwareheritage.org) maintain this tool to
+make that easy.
+
+The form below is both a generator and a validator for `codemeta.json` files.
+It can be [accessed directly](https://github.com/codemeta/codemeta-generator).
+
+## Create a new CodeMeta file
+
+Generate a CodeMeta file by filling out the fields in the form below
+according to the [CodeMeta terms](/terms) definitions. The `Name` field in
+the first section is mandatory.
+
+Providing the `Name` of your software will result in a basic `codemeta.json`
+output in the final textarea. Filling out additional fields will build a
+more complete file. The version of CodeMeta can be selected with the
+`Generate codemeta.json v2.0` or `Generate codemeta.json v3.0` buttons above
+the final textarea.
+
+Some fields require specific formatting. The example text in the fields will
+hint the required formatting. Errors will be highlighted by the generator as
+they are encountered.
+
+Your generated file may be copied from the text area, or downloaded with the
+`Download codemeta.json` button above the field.
+
+## Check a CodeMeta file
+
+Pasting the contents of your current `codemeta.json` file into the final
+textarea will allow you to:
+- Validate the syntax with the `Validate codemeta.json` button, and
+- Pre-fill the other form fields with your current values using the
+`Import codemeta.json` button.
 
 {{< rawhtml >}}
+<script type="text/javascript">
+  function iframeResize() {
+      const iFrameID = document.getElementById('generator');
+      if(iFrameID) {
+            iFrameID.height = "";
+            iFrameID.height = (iFrameID.contentWindow.document.body.scrollHeight + 50) + "px";
+      }   
+  }
+window.addEventListener('resize', function() {
+  iframeResize()
+});
+
+</script>
+<iframe id="generator" title="CodeMeta Generator" onload="iframeResize()" src="/codemeta-generator" class="d-inline-block w-100" frameborder="0">
+  If there is no form visible here, you can also access the [CodeMeta Generator](https://codemeta.github.io/codemeta-generator) directly. This may be due to browser security settings.
+</iframe>
+
   <a href="https://www.softwareheritage.org">
-  <img src="/img/swh-logo.png" style="height: 50px;"/> Software Heritage</a>
+  <img alt="" src="/img/swh-logo.png" style="height: 50px;"/> Software Heritage</a>
 {{< /rawhtml >}}

content/developer-guide.md

@@ -1,5 +1,6 @@
 ---
 title: CodeMeta Developer Guide
+layout: sidenav
 ---
 
 This guide is intended for software developers who require detailed information about the CodeMeta project's

content/jsonld.md

@@ -1,5 +1,6 @@
 ---
 title: "The CodeMeta JSON-LD Representation"
+layout: sidenav
 ---
 
 CodeMeta uses JSON-LD to represent and translate between software metadata formats.

content/news.md

@@ -0,0 +1,6 @@
+---
+title: Codemeta News
+layout: single
+---
+
+{{< news >}}

content/terms.md

@@ -1,5 +1,6 @@
 ---
 title: CodeMeta Terms
+layout: sidenav
 ---
 
 ## Terms from Schema.org

content/tools.md

@@ -1,5 +1,6 @@
 ---
 title: Tools
+layout: sidenav
 ---
 
 This page lists some existing tools to help with CodeMeta files.

content/use-cases.md

@@ -1,6 +1,10 @@
+---
+layout: single
+---
+
 Edited Use cases
 CodeMeta meeting in Portland
-Created 20160415 (use cases group pulled from here 230pm 20160516) https://docs.google.com/document/d/1SalOP_tLw7FC6jnoz5hJBB2jA7xBClKqc88wgmJu5Ro/edit
+Created 20160415 (use cases group pulled from here 230pm 20160516) [PDF export of google doc notes](/CodeMeta_Software_Use_Cases-Day2PM_WrkngGrp.pdf)
 
 
 
@@ -296,4 +300,4 @@ datacite/crossref/orcid -- utility providers
 ``Repository'' refers to public software repositories such as GitHub, Netlib, Comprehensive R Archive Network (CRAN), and institutional repositories. \item `
 
 
-``Citation manager`` refers to people and organizations that create scholarly reference management software and websites including Zotero, Mendeley, EndNote, RefWorks, BibDesk, etc., that manage citation information and semi-automatically insert those citations into research products.
+``Citation manager`` refers to people and organizations that create scholarly reference management software and websites including Zotero, Mendeley, EndNote, RefWorks, BibDesk, etc., that manage citation information and semi-automatically insert those citations into research products.

content/user-guide.md

@@ -1,5 +1,6 @@
 ---
 title: User Guide
+layout: sidenav
 ---
 
 ## Generating a CodeMeta file