v1.3.3 (#303)

Closes #298 Closes #301 Closes #302 - adds support for multiple blog post authors - improves citation error logging - adds status badges to first time setup workflow to add it to user readmes New template version checklist: - [x] I have updated CITATION and CHANGELOG as appropriate. - [x] I have updated lab-website-template-docs as appropriate. - [x] I have checked the testbed as appropriate.
greenelab · Jan 27, 2025 · 4fafdf0 · 4fafdf0
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diff --git a/.github/workflows/first-time-setup.yaml b/.github/workflows/first-time-setup.yaml
@@ -76,11 +76,15 @@ jobs:
       - name: Personalize readme for user
         run: |
           printf "
-          # ${{ env.USER }}'s Website
+            ![on-push](../../actions/workflows/on-push.yaml/badge.svg)
+            ![on-pull-request](../../actions/workflows/on-pull-request.yaml/badge.svg)
+            ![on-schedule](../../actions/workflows/on-schedule.yaml/badge.svg)
 
-          Visit **[website url](#)** 🚀
+            # ${{ env.USER }}'s Website
 
-          _Built with [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs)_
+            Visit **[website url](#)** 🚀
+
+            _Built with [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs)_
           " > README.md
 
       - name: Personalize Jekyll config for user

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,17 @@
 
 Reference: common-changelog.org
 
+## 1.3.3 - 2025-01-25
+
+### Changed
+
+- Citation process logging enhancements.
+
+### Added
+
+- Add support for multiple authors in blog posts.
+- Add GitHub Actions workflow status badges to readme.
+
 ## 1.3.2 - 2025-01-06
 
 ### Changed

diff --git a/CITATION.cff b/CITATION.cff
@@ -1,8 +1,8 @@
 # citation metadata for the template itself
 
 title: "Lab Website Template"
-version: 1.3.2
-date-released: 2025-01-06
+version: 1.3.3
+date-released: 2025-01-25
 url: "https://github.com/greenelab/lab-website-template"
 authors:
   - family-names: "Rubinetti"

diff --git a/_cite/cite.py b/_cite/cite.py
@@ -13,8 +13,9 @@
 load_dotenv()
 
 
-# error flag
-error = False
+# save errors/warnings for reporting at end
+errors = []
+warnings = []
 
 # output citations file
 output_file = "_data/citations.yaml"
@@ -41,46 +42,46 @@
     files = Path.cwd().glob(f"_data/{plugin.stem}*.*")
     files = list(filter(lambda p: p.suffix in [".yaml", ".yml", ".json"], files))
 
-    log(f"Found {len(files)} {plugin.stem}* data file(s)", 1)
+    log(f"Found {len(files)} {plugin.stem}* data file(s)", indent=1)
 
     # loop through data files
     for file in files:
-        log(f"Processing data file {file.name}", 1)
+        log(f"Processing data file {file.name}", indent=1)
 
         # load data from file
         try:
             data = load_data(file)
             # check if file in correct format
             if not list_of_dicts(data):
-                raise Exception("File not a list of dicts")
+                raise Exception(f"{file.name} data file not a list of dicts")
         except Exception as e:
-            log(e, 2, "ERROR")
-            error = True
+            log(e, indent=2, level="ERROR")
+            errors.append(e)
             continue
 
         # loop through data entries
         for index, entry in enumerate(data):
-            log(f"Processing entry {index + 1} of {len(data)}, {label(entry)}", 2)
+            log(f"Processing entry {index + 1} of {len(data)}, {label(entry)}", level=2)
 
             # run plugin on data entry to expand into multiple sources
             try:
                 expanded = import_module(f"plugins.{plugin.stem}").main(entry)
                 # check that plugin returned correct format
                 if not list_of_dicts(expanded):
-                    raise Exception("Plugin didn't return list of dicts")
+                    raise Exception(f"{plugin.stem} plugin didn't return list of dicts")
             # catch any plugin error
             except Exception as e:
                 # log detailed pre-formatted/colored trace
                 print(traceback.format_exc())
                 # log high-level error
-                log(e, 3, "ERROR")
-                error = True
+                log(e, indent=3, level="ERROR")
+                errors.append(e)
                 continue
 
             # loop through sources
             for source in expanded:
                 if plugin.stem != "sources":
-                    log(label(source), 3)
+                    log(label(source), level=3)
 
                 # include meta info about source
                 source["plugin"] = plugin.name
@@ -90,7 +91,7 @@
                 sources.append(source)
 
             if plugin.stem != "sources":
-                log(f"{len(expanded)} source(s)", 3)
+                log(f"{len(expanded)} source(s)", indent=3)
 
 
 log("Merging sources by id")
@@ -103,7 +104,7 @@
     for b in range(a + 1, len(sources)):
         b_id = get_safe(sources, f"{b}.id", "")
         if b_id == a_id:
-            log(f"Found duplicate {b_id}", 2)
+            log(f"Found duplicate {b_id}", indent=2)
             sources[a].update(sources[b])
             sources[b] = {}
 sources = [entry for entry in sources if entry]
@@ -136,21 +137,26 @@
 
     # Manubot doesn't work without an id
     if _id:
-        log("Using Manubot to generate citation", 1)
+        log("Using Manubot to generate citation", indent=1)
 
         try:
             # run Manubot and set citation
             citation = cite_with_manubot(_id)
 
         # if Manubot cannot cite source
         except Exception as e:
+            plugin = get_safe(source, "plugin", "")
+            file = get_safe(source, "file", "")
             # if regular source (id entered by user), throw error
-            if get_safe(source, "plugin", "") == "sources.py":
-                log(e, 3, "ERROR")
-                error = True
+            if plugin == "sources.py":
+                log(e, indent=3, level="ERROR")
+                errors.append(f"Manubot could not generate citation for source {_id}")
             # otherwise, if from metasource (id retrieved from some third-party API), just warn
             else:
-                log(e, 3, "WARNING")
+                log(e, indent=3, level="WARNING")
+                warnings.append(
+                    f"Manubot could not generate citation for source {_id} (from {file} with {plugin})"
+                )
                 # discard source from citations
                 continue
 
@@ -175,14 +181,26 @@
     save_data(output_file, citations)
 except Exception as e:
     log(e, level="ERROR")
-    error = True
+    errors.append(e)
 
 
-# exit at end, so user can see all errors in one run
-if error:
-    log("Error(s) occurred above", level="ERROR")
+log()
+
+
+# exit at end, so user can see all errors/warnings in one run
+if len(warnings):
+    log(f"{len(warnings)} warning(s) occurred above", level="WARNING")
+    for warning in warnings:
+        log(warning, indent=1, level="WARNING")
+
+if len(errors):
+    log(f"{len(errors)} error(s) occurred above", level="ERROR")
+    for error in errors:
+        log(error, indent=1, level="ERROR")
+    log()
     exit(1)
+
 else:
     log("All done!", level="SUCCESS")
 
-log("\n")
+log()
diff --git a/_cite/util.py b/_cite/util.py
@@ -39,20 +39,25 @@ def log(message="\n--------------------\n", indent=0, level="", newline=True):
     log to terminal, color determined by indent and level
     """
 
-    palette = {
+    colors = {
         0: "[orange1]",
         1: "[salmon1]",
         2: "[violet]",
         3: "[sky_blue1]",
-        "ERROR": "[white on #F43F5E]",
-        "WARNING": "[black on #EAB308]",
-        "SUCCESS": "[black on #10B981]",
+        "ERROR": "[#F43F5E]",
+        "WARNING": "[#EAB308]",
+        "SUCCESS": "[#10B981]",
         "INFO": "[grey70]",
     }
-    color = get_safe(palette, level, "") or get_safe(palette, indent, "") or "[white]"
+    prefixes = {
+        "ERROR": "🚫 ERROR: ",
+        "WARNING": "⚠️ WARNING: ",
+    }
+    color = get_safe(colors, level, "") or get_safe(colors, indent, "") or "[white]"
+    prefix = get_safe(prefixes, level, "")
     if newline:
         print()
-    print(indent * "    " + color + str(message) + "[/]", end="", flush=True)
+    print(indent * "    " + color + prefix + str(message) + "[/]", end="", flush=True)
 
 
 def label(entry):
@@ -179,7 +184,7 @@ def cite_with_manubot(_id):
         commands = ["manubot", "cite", _id, "--log-level=WARNING"]
         output = subprocess.Popen(commands, stdout=subprocess.PIPE).communicate()
     except Exception as e:
-        log(e, 3)
+        log(e, indent=3)
         raise Exception("Manubot could not generate citation")
 
     # parse results as json

diff --git a/_includes/post-info.html b/_includes/post-info.html
@@ -1,17 +1,25 @@
 <div class="post-info">
   {% if include.author %}
-    {% assign member = site.members
-      | where_exp: "member", "member.slug == include.author"
-      | first
+    {% assign authors = include.author
+      | join: ","
+      | downcase
+      | split: ","
+      | array_filter
     %}
-    {% if member %}
-      {% include portrait.html lookup=include.author style="tiny" %}
-    {% else %}
-      <span data-tooltip="Author">
-        {% include icon.html icon="fa-solid fa-feather-pointed" %}
-        <span>{{ include.author }}</span>
-      </span>
-    {% endif %}
+    {% for author in authors %}
+      {% assign member = site.members
+        | where_exp: "member", "member.slug == author"
+        | first
+      %}
+      {% if member %}
+        {% include portrait.html lookup=author style="tiny" %}
+      {% else %}
+        <span data-tooltip="Author">
+          {% include icon.html icon="fa-solid fa-feather-pointed" %}
+          <span>{{ author }}</span>
+        </span>
+      {% endif %}
+    {% endfor %}
   {% endif %}
 
   {% assign published = include.published | date: "%B %d, %Y" %}