UPD pre-release (2)

Author: eboileau

Diff for: CHANGELOG.md

@@ -12,6 +12,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/), and this
 
 ### Changed
 
+- API version management
 - utils
 - Error handling
 - Documentation

Diff for: README.md

@@ -10,6 +10,7 @@ single-base resolution.
 <p align="center">
 <a href="https://dieterich-lab.github.io/scimodom/index.html"><img alt="docs" src="https://github.com/dieterich-lab/scimodom/actions/workflows/static.yml/badge.svg"></a>
 <a href="https://doi.org/10.5281/zenodo.13911907"><img alt="DOI" src="https://zenodo.org/badge/DOI/10.5281/zenodo.13911907.svg"></a>
+<a href="https://img.shields.io/github/v/release/dieterich-lab/scimodom"><img alt="GitHub Release" src="https://img.shields.io/github/v/release/dieterich-lab/scimodom"></a>
 <a href="https://www.gnu.org/licenses/agpl-3.0"><img alt="License: AGPL v3" src="https://img.shields.io/badge/License-AGPL_v3-blue.svg"></a>
 </p>
 

Diff for: client/src/components/compare/CompareStepA.vue

@@ -3,7 +3,7 @@ import { ref, computed } from 'vue'
 import TaxaSelection from '@/components/ui/TaxaSelection.vue'
 import DatasetSelectionMulti from '@/components/ui/DatasetSelectionMulti.vue'
 import { type Dataset, getDatasetsByTaxaId } from '@/services/dataset'
-import { type Taxa } from '@/services/selection'
+import { type Taxa } from '@/services/taxa'
 import { type ResultStepA } from '@/utils/comparison'
 
 const model = defineModel<ResultStepA>()

Diff for: client/src/components/documentation/DocAbout.vue

@@ -115,10 +115,15 @@ import img2 from '@/assets/images/docs/about2.png'
       >.
     </p>
     <p class="indent-4 text-xl leading-relaxed mt-4 mb-2">
-      Consult our development plan for 2024
+      Check out the latest features
       <RouterLink class="pl-2 animate-pulse" :to="{ name: 'roadmap' }">
         <!-- <a class="pl-2 animate-pulse" href="https://www.trr319-rmap.de" target="_blank" rel="noopener noreferrer"> -->
-        <Button icon="pi pi-arrow-right" size="small" label="Learn more" rounded />
+        <Button
+          icon="pi pi-arrow-right"
+          size="small"
+          label="Learn more about our development plan for 2025"
+          rounded
+        />
       </RouterLink>
     </p>
   </div>

Diff for: client/src/components/documentation/DocBrowse.vue

@@ -43,7 +43,7 @@ import img4 from '@/assets/images/docs/browse4.png'
       aggregated site-wise into bedRMod. Each dataset can be downloaded as a
       <a
         class="text-primary-500 hover:text-secondary-500"
-        href="https://dieterich-lab.github.io/scimodom/bedrmod.html"
+        href="https://dieterich-lab.github.io/euf-specs/"
         target="_blank"
         rel="noopener noreferrer"
         >bedRMod</a

Diff for: client/src/components/documentation/DocFAQs.vue

@@ -33,6 +33,30 @@
       </router-link>
       tool. Login is not required. Data is handled securely.
     </p>
+    <p class="indent-4 text-lg underline underline-offset-8 decoration-gb-4/25 font-semibold">
+      Can I get more information about the bedRMod format?
+    </p>
+    <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
+      Yes, the official specifications are available at
+      <a
+        href="https://dieterich-lab.github.io/euf-specs/"
+        class="text-primary-500 hover:text-secondary-500"
+        rel="noopener noreferrer"
+        target="_blank"
+      >
+        EU format specifications </a
+      >. Sci-ModoM imposes a few additional requirements, <span class="italic">e.g.</span>
+      only chromosomes are allowed, and they must be formatted according to the Ensembl short
+      format. For details, consult the
+      <a
+        href="https://dieterich-lab.github.io/scimodom/bedrmod.html"
+        class="text-primary-500 hover:text-secondary-500"
+        rel="noopener noreferrer"
+        target="_blank"
+      >
+        bedRMod format specification (Sci-ModoM) </a
+      >.
+    </p>
     <p class="indent-4 text-lg underline underline-offset-8 decoration-gb-4/25 font-semibold">
       Can I propose new datasets?
     </p>

Diff for: client/src/components/home/HomeFeatures.vue

@@ -21,20 +21,12 @@ import SectionLayout from '@/components/layout/SectionLayout.vue'
             Support and promote the
             <a
               class="text-primary-500 hover:text-secondary-500"
-              href="https://dieterich-lab.github.io/scimodom/bedrmod.html"
+              href="https://dieterich-lab.github.io/euf-specs/"
               target="_blank"
               rel="noopener noreferrer"
               >bedRMod</a
             >
-            format. This format is similar to the
-            <a
-              class="text-primary-500 hover:text-secondary-500"
-              href="https://www.encodeproject.org/data-standards/wgbs/"
-              target="_blank"
-              rel="noopener noreferrer"
-              >ENCODE bedMethyl</a
-            >
-            format (BED9+2).
+            format.
           </span>
         </div>
         <div class="col-12 md:col-4 mb-4 px-5">
@@ -53,7 +45,7 @@ import SectionLayout from '@/components/layout/SectionLayout.vue'
           </span>
           <div class="text-900 text-xl mb-3 font-medium dark:text-white/80">Tools</div>
           <span class="text-700 line-height-3 dark:text-white/80">
-            Search and compare modifications across datasets.
+            Search and compare modifications across datasets. Annotation, interactome.
           </span>
         </div>
         <div class="col-12 md:col-4 mb-4 px-5">
@@ -93,16 +85,16 @@ import SectionLayout from '@/components/layout/SectionLayout.vue'
           <span class="p-3 shadow-2 mb-3 inline-block surface-card" style="border-radius: 10px">
             <i class="pi pi-list text-4xl text-primary-500 dark:text-secondary-500"></i>
           </span>
-          <div class="text-900 text-xl mb-3 font-medium dark:text-white/80">RNA processing</div>
+          <div class="text-900 text-xl mb-3 font-medium dark:text-white/80">More...</div>
           <span class="text-700 line-height-3 dark:text-white/80">
-            Integration of RNA processing and RNA-modification-aware MS data.</span
+            Addition of RNA types (tRNA, rRNA), integration of RNA processing events.</span
           >
         </div>
       </div>
     </div>
     <div class="flex justify-center mt-8 animate-pulse">
       <RouterLink :to="{ name: 'about-docs' }">
-        <Button icon="pi pi-arrow-right" label="Learn more" rounded />
+        <Button icon="pi pi-arrow-right" label="Learn more about Sci-ModoM" rounded />
       </RouterLink>
     </div>
   </SectionLayout>

Diff for: client/src/components/home/HomeIntro.vue

@@ -19,7 +19,7 @@ import SectionLayout from '@/components/layout/SectionLayout.vue'
     </div>
     <div class="flex justify-center mt-4 animate-pulse">
       <a href="https://humanrnomeproject.org" target="_blank" rel="noopener noreferrer">
-        <Button icon="pi pi-arrow-right" label="Learn more" rounded />
+        <Button icon="pi pi-arrow-right" label="Learn more about the RNome project" rounded />
       </a>
     </div>
     <div class="flex justify-center mt-4 py-4">