Update documentation links

README.md

@@ -5,9 +5,9 @@ SigProfilerPlotting provides a standard tool for displaying all types of mutatio
 
 **INTRODUCTION**
 
-The purpose of this document is to provide a guide for using the SigProfilerPlotting framework and associated functions/tools to visualize the output from SigProfilerExtraction and SigProfilerSimulator. The primary documentation is now maintained in this repository under `docs/`, and the legacy OSF wiki source is at https://osf.io/2aj6t/wiki/home.
+The purpose of this document is to provide a guide for using the SigProfilerPlotting framework and associated functions/tools to visualize the output from SigProfilerExtraction and SigProfilerSimulator. The primary documentation is available at https://sigprofilersuite.github.io/SigProfilerPlotting/.
 
-For users that prefer working in an R environment, a wrapper package is provided and can be found and installed from: https://github.com/AlexandrovLab/SigProfilerPlottingR
+For users that prefer working in an R environment, a wrapper package is provided and can be found and installed from: https://github.com/SigProfilerSuite/SigProfilerPlottingR
 
 ![schematic](schematic.png)
 

docs/assets/osf/manifest.json

@@ -1,15 +1,30 @@
 {
   "https://files.osf.io/v1/resources/2aj6t/providers/osfstorage/5c5de3d676653c0018270138?mode=render": "assets/osf/5c5de3d676653c0018270138.png",
   "https://files.osf.io/v1/resources/2aj6t/providers/osfstorage/5c73d34f8d5d98001a393840?mode=render": "assets/osf/5c73d34f8d5d98001a393840.png",
+  "https://osf.io/2he54/": "assets/osf/2he54.png",
   "https://osf.io/2wh7g/": "assets/osf/2wh7g.zip",
   "https://osf.io/2ydqt/": "assets/osf/2ydqt.bin",
   "https://osf.io/3rm96/": "assets/osf/3rm96.bin",
   "https://osf.io/43e76/": "assets/osf/43e76.bin",
+  "https://osf.io/78htw/": "assets/osf/78htw.png",
   "https://osf.io/8ubjp/": "assets/osf/8ubjp.bin",
+  "https://osf.io/b7m2t/": "assets/osf/b7m2t.png",
+  "https://osf.io/cmv6d/": "assets/osf/cmv6d.png",
   "https://osf.io/d3e6f/": "assets/osf/d3e6f.bin",
+  "https://osf.io/egk7c/": "assets/osf/egk7c.png",
+  "https://osf.io/fgc8z/": "assets/osf/fgc8z.png",
   "https://osf.io/gmcyp/": "assets/osf/gmcyp.bin",
+  "https://osf.io/hfqr2/": "assets/osf/hfqr2.png",
+  "https://osf.io/jcemf/": "assets/osf/jcemf.png",
+  "https://osf.io/kmd2f/": "assets/osf/kmd2f.png",
+  "https://osf.io/kw8py/": "assets/osf/kw8py.png",
+  "https://osf.io/kwd3y/": "assets/osf/kwd3y.png",
   "https://osf.io/p2fxv/": "assets/osf/p2fxv.bin",
   "https://osf.io/p3yzs/": "assets/osf/p3yzs.bin",
+  "https://osf.io/s7wuj/": "assets/osf/s7wuj.png",
+  "https://osf.io/sc9qj/": "assets/osf/sc9qj.png",
   "https://osf.io/synw4/": "assets/osf/synw4.bin",
+  "https://osf.io/uabr5/": "assets/osf/uabr5.png",
+  "https://osf.io/uxyfv/": "assets/osf/uxyfv.png",
   "https://osf.io/xd9ym/": "assets/osf/xd9ym.bin"
 }

mkdocs_hooks.py

@@ -9,13 +9,18 @@
 _OSF_IMAGE_SIZE_SUFFIX_RE = re.compile(r"(!\[[^\]]*\]\([^\s)]+)\s+=\d+(?:%x|x)(\))")
 _OSF_URL_IN_MD_IMAGE_RE = re.compile(r"(!\[[^\]]*\]\()([^) \t\r\n]+)(\))")
 _OSF_URL_IN_HTML_IMG_RE = re.compile(r'(<img\b[^>]*\bsrc=")([^"]+)(")', re.IGNORECASE)
-_OSF_EMBED_RE = re.compile(r"@\[(osf)\]\(([^)]+)\)", re.IGNORECASE)
+_OSF_EMBED_RE = re.compile(r"@\[\s*osf\s*\]\(([^)]+)\)", re.IGNORECASE)
 _OSF_WIKI_URL_RE = re.compile(r"https://osf\.io/([^/]+)/wiki/([^\s)\"]+)", re.IGNORECASE)
 _OSF_MANIFEST_CACHE = None
 _OSF_MANIFEST_LOADED = False
 _OSF_MISSING_CACHE = None
 _OSF_MISSING_LOADED = False
 _OSF_PLACEHOLDER = "assets/osf/osf_asset_unavailable.svg"
+_IMAGE_EXTS = {".png", ".jpg", ".jpeg", ".gif", ".svg", ".webp", ".bmp"}
+_URL_REWRITES = {
+    "https://github.com/AlexandrovLab/SigProfilerPlotting": "https://github.com/SigProfilerSuite/SigProfilerPlotting",
+    "https://github.com/AlexandrovLab/SigProfilerPlottingR": "https://github.com/SigProfilerSuite/SigProfilerPlottingR",
+}
 
 # Map OSF wiki page names (decoded from URL) to local docs filenames.
 _OSF_WIKI_PAGE_TO_DOC = {
@@ -47,27 +52,29 @@ def on_page_markdown(markdown: str, page, config, files):
         line for line in lines if not _TOC_MARKER_LINE_RE.match(line.strip("\n"))
     ]
     cleaned = "".join(filtered_lines)
+    for old, new in _URL_REWRITES.items():
+        cleaned = cleaned.replace(old, new)
 
     # OSF Wiki sometimes appends non-standard size hints like " =50%x" inside
     # Markdown image links, which breaks rendering in MkDocs/Markdown.
     cleaned = _OSF_IMAGE_SIZE_SUFFIX_RE.sub(r"\1\2", cleaned)
 
-    # Convert OSF embed markers (e.g. "@[osf](abcde)") into plain links.
-    cleaned = _OSF_EMBED_RE.sub(r"[OSF](https://osf.io/\2/)", cleaned)
-
     prefix = _page_relative_prefix(page)
+    manifest = _load_osf_manifest(config) or {}
+    missing = _load_osf_missing(config) or set()
+
+    # Replace OSF embed markers with local assets if available.
+    cleaned = _replace_osf_embeds(cleaned, manifest=manifest, missing=missing, prefix=prefix)
 
     # Rewrite OSF wiki links to local pages (prevents navigation to downloaded HTML stubs).
     cleaned = _rewrite_osf_wiki_links(cleaned, prefix=prefix)
 
-    manifest = _load_osf_manifest(config)
     if manifest:
         for url, rel_path in manifest.items():
             if _is_osf_wiki_url(url):
                 continue
             cleaned = cleaned.replace(url, prefix + rel_path)
 
-    missing = _load_osf_missing(config)
     if missing:
         cleaned = _replace_blocked_osf_images(cleaned, missing, prefix=prefix)
 
@@ -165,6 +172,27 @@ def html_repl(m):
     return out
 
 
+def _replace_osf_embeds(markdown: str, *, manifest: dict, missing: set, prefix: str) -> str:
+    def repl(m):
+        raw_id = m.group(1).strip().strip("/")
+        if not raw_id:
+            return f"![OSF asset unavailable]({prefix + _OSF_PLACEHOLDER})"
+
+        short_url = f"https://osf.io/{raw_id}/"
+        rel_path = manifest.get(short_url) if manifest else None
+        if rel_path:
+            target = prefix + rel_path
+            if Path(rel_path).suffix.lower() in _IMAGE_EXTS:
+                return f"![{raw_id}]({target})"
+            return f"[Download asset]({target})"
+
+        if short_url in missing:
+            return f"![OSF asset unavailable]({prefix + _OSF_PLACEHOLDER})"
+        return f"![OSF asset unavailable]({prefix + _OSF_PLACEHOLDER})"
+
+    return _OSF_EMBED_RE.sub(repl, markdown)
+
+
 def _rewrite_osf_wiki_links(markdown: str, *, prefix: str) -> str:
     """
     Rewrite links like:

tools/mirror_osf_wiki.py

@@ -13,6 +13,7 @@
 _OSF_API = "https://api.osf.io/v2"
 _OSF_FILES_RE = re.compile(r"https://files\.osf\.io/[^\s)\"']+")
 _OSF_SHORT_RE = re.compile(r"https://osf\.io/[^\s)\"']+")
+_OSF_EMBED_RE = re.compile(r"@\[\s*osf\s*\]\(([^)]+)\)", re.IGNORECASE)
 _OSF_IMAGE_SIZE_SUFFIX_RE = re.compile(
     r"(https://files\.osf\.io/[^\s)\"']+)\s+=\d+(?:%x|x)$"
 )
@@ -280,6 +281,11 @@ def _resolve_osf_file_download_url(
 
 def _extract_osf_file_urls(markdown: str) -> list[str]:
     urls = []
+    for embed_id in _OSF_EMBED_RE.findall(markdown):
+        asset_id = embed_id.strip().strip("/")
+        if asset_id:
+            urls.append(f"https://osf.io/{asset_id}/")
+
     for raw in _OSF_FILES_RE.findall(markdown) + _OSF_SHORT_RE.findall(markdown):
         url = raw.rstrip(").,")
         url = _OSF_IMAGE_SIZE_SUFFIX_RE.sub(r"\1", url)