Merge branch 'main' into dev

.gitlab-ci.yml

@@ -32,15 +32,16 @@ cache:
 
 stages:
  
+
+  - zotero
+  - get-meili-key
+  - build
+  # - build-wiki
   - delete-release
   - build-df-cli
   - lint
-  - get-data
   - deploy-meilisearch
   - update-meilisearch-indexes
-  - get-meili-key
-  - build
-  # - build-wiki
   - deploy
   # - load-website
 
@@ -112,6 +113,7 @@ build:df-wiki-cli:
     #     sleep 1
     #     kubectl -n=${KUBE_NAMESPACE} get po
     #   done
+  when: manual
 
 
 deploy:meilisearch:dev:
@@ -228,14 +230,13 @@ lint:
       --file data/list-systems.json
       --document systems
   allow_failure: false
+  when: manual
 
 
 update-meilisearch-index:dev:
   rules:
     - if: $CI_COMMIT_BRANCH != "main"
   extends: .update-meilisearch-index
-  needs: 
-    - deploy:meilisearch:dev
   variables:
     MEILI_HOST: "https://${MEILI_HOST_DEV}"
 
@@ -244,8 +245,6 @@ update-meilisearch-index:prod:
   rules:
     - if: $CI_COMMIT_BRANCH == "main"
   extends: .update-meilisearch-index
-  needs: 
-    - deploy:meilisearch:prod
   variables:
     MEILI_HOST: "https://${MEILI_HOST_PROD}"
 
@@ -272,8 +271,6 @@ update-meilisearch-index:prod:
 
 set-meili-env:dev:
   extends: .set-meili-env
-  needs: 
-    - deploy:meilisearch:dev
   variables:
     MEILI_HOST: "https://${MEILI_HOST_DEV}"
   rules:
@@ -289,7 +286,7 @@ set-meili-env:prod:
 ##############################
 get-zotero:
   extends: .df-wiki-cli-run
-  stage: get-data
+  stage: zotero
   script:
     - df-wiki-cli articles --key ${ZOTERO_API_KEY} --output content/_data/_articles.json
   artifacts:

components/content/RefseqDb.vue

@@ -104,7 +104,7 @@ const availableTaxo: Ref<string[]> = ref([
 ]);
 
 const scaleTypes = ref<string[]>(['linear', 'sqrt', 'log', 'symlog'])
-const selectedTaxoRank = ref("phylum");
+const selectedTaxoRank = ref("Superkingdom");
 
 const headers = ref([
     { title: "Replicon", key: "replicon" },
@@ -284,7 +284,7 @@ const binPlotOptions = ref({
     grid: true,
     x: { tickRotate: 90, tip: true, label: "Systems" },
     // y: { tickFormat: 's' },
-    color: { scheme: "turbo", legend: true },
+    color: { scheme: "plasma", legend: true },
 })
 
 const binPlotDataOptions = computed(() => {

content/1.help/2.Contributing-Wiki.md

@@ -98,6 +98,16 @@ dataUrls:
 ::
 ```
 
+
+**3. To edit the Experimental validation section**
+
+This part is a bit tricky to edit. Your first option is to create an issue or send us an email and we'll do it on our side. You need to provide the reference, in which bug it was discovered, in which bug it was expressed and against which phages it was effective.
+
+The second option is that you can try within this live editor : https://mermaid.live/
+
+You can copy paste everything that is within `<mermaid></mermaid>` tags in the editor field of the [live editor](https://mermaid.live/), it should reproduce what you site on the website. From there you can try to modify it until you get what you want.
+Here is the documentation about mermaid (the software behind this syntax) : https://mermaid.js.org/intro/
+
 **Custom containers:**
 
 Custom containers can be defined by their types, titles, and contents.

layouts/db.vue

@@ -4,7 +4,7 @@ const { page } = useContent();
 
 </script>
 <template>
-    <LayoutWrapper :title="page?.title" :fluid="true" :toc="false" :edit="false" :nav-drawer="false">
+    <LayoutWrapper :title="page?.title" :fluid="true" :toc="false" :edit="false" :nav-drawer="true">
         <slot />
     </LayoutWrapper>
 </template>