Merge branch 'develop' into 'master'

[release] Regular merge of develop

See merge request !314

.ci/generateIndex.py

@@ -15,16 +15,19 @@ def build_link(title, href):
     if ('handbook' in href):
         title = re.sub('[0-9.]', '', title).strip()
 
+    # add relative url
+    href = "{{ '" + href + "' | relative_url }}"
+
+    return f'\t\t\t<li><a href="{href}">{title}</a></li>\n'
+
+def root_handbook(href):
     # remove sym link reference in href
     if ('handbook-additional' in href):
         href = href.replace('handbook-additional', 'handbook').strip()
     elif ('handbook-annexes' in href):
         href = href.replace('handbook-annexes', 'handbook').strip()
 
-    # add relative url
-    href = "{{ '" + href + "' | relative_url }}"
-
-    return f'\t\t\t<li><a href="{href}">{title}</a></li>\n'
+    return href
 
 def build_section_start(title, shortcut):
 
@@ -135,7 +138,10 @@ for folder in cardDirs:
                                 print(" > Generating header for: " + fileName)
 
                                 # remove the previous header
-                                remove_header(localroot, root, file, 8)
+                                if "handbook-annexes" in fileName or "handbook-additional" in fileName:
+                                    remove_header(localroot, root, file, 10)
+                                else:
+                                    remove_header(localroot, root, file, 8)
 
                                 # generate a permalink
                                 permalink = "/" + root + "/"
@@ -153,10 +159,16 @@ for folder in cardDirs:
                                 header = "---\n"
                                 header += "layout: page\n"
                                 header += "permalink: " + permalink + "\n"
-                                header += "shortcut: " + shortcut + "\n"
+                                header += "shortcut: " + root_handbook(shortcut) + "\n"
                                 header += "redirect_from:\n"
                                 header += "  - /cards/" + shortcut + "\n"
                                 header += "  - /" + folder + "/cards/" + shortcut + "\n"
+
+                                # special case of handbook
+                                if "handbook-annexes" in permalink or "handbook-additional" in permalink:
+                                    header += "  - /cards/" + root_handbook(shortcut) + "\n"
+                                    header += "  - /" + folder + "/cards/" + root_handbook(shortcut) + "\n"
+
                                 header += "---"
 
                                 # add autogenerated links to whitelist
@@ -164,6 +176,9 @@ for folder in cardDirs:
                                 whiteList += "/?" + shortcut + "\n"
                                 whiteList += "/cards/" +shortcut + "\n"
                                 whiteList += "/" + folder + "/cards/" + shortcut + "\n"
+                                if "handbook-annexes" in permalink or "handbook-additional" in permalink:
+                                    whiteList += "  - /cards/" + root_handbook(shortcut) + "\n"
+                                    whiteList += "  - /" + folder + "/cards/" + root_handbook(shortcut) + "\n"
 
                                 # add the header properly speaking
                                 line_prepender(fileName, header)
@@ -171,7 +186,11 @@ for folder in cardDirs:
                                 # open file and get the title after the header
                                 count = 0
                                 title = ""
-                                bp = 9
+                                if "handbook-annexes" in permalink or "handbook-additional" in permalink:
+                                    bp = 11
+                                else:
+                                    bp = 9
+
                                 with open(fileName, 'r') as f:
                                     for line in f:
                                         count += 1

external/on-offboarding/godparent/godparent.md

@@ -7,7 +7,7 @@ redirect_from:
   - /external/cards/on-offboarding:godparent
 ---
 # Godparents for Newcomers
-Please also consult the [checklist for godparents](https://howto.lcsb.uni.lu/?hr:newcomers:checklistGodparent).
+Please also consult the [checklist for godparents](https://howto.lcsb.uni.lu/?on-offboarding:checklistGodparent).
 
 ### Summary
 In order to help new employees to easily integrate in their new workplace and senior members to better know and understand the new colleague, each new employee will be assigned a "godparent".

external/publication/publishInBiotools/publishInBiotools.md

@@ -15,16 +15,11 @@ First, *bio.tools* serve two main purposes:
 - collecting systematic and reasonable statistics about the available
   software for many purposes, including data science and performance reports
 
-To get your contents in, you need to fill an application and get an account.
-Filling out the application is particularly straightforward.
-
-After you get the account, you can click "Add content" in the "Menu" on the top
-right, then go through around 10 tabs that allow you to fill lots of
+To get your contents in, you need to create an account (sign up). Once logged-in, you can click "Add content" in the "Menu" on the top 
+right, then go through around 10 tabs that allow you to fill lots of 
 interesting information about your tool, and finally submit it, which makes the
 contents immediately visible.
 
-This card collects some reminders about what you should not forget while
-submitting the tool, perhaps useful as a checklist.
 
 ## General tips