nttk to 3.9.4. Test with mockups by Priya. Contributors in reame.md

README.md

@@ -361,6 +361,9 @@ Try SOMEF in Binder with our sample notebook: [![Binder](https://mybinder.org/ba
 
 If you want to contribute with a pull request, please do so by submitting it to the `dev` branch.
 
+## Contributors:
+Priyanka O.
+
 ## Next features:
 
 To see upcoming features, please have a look at our [open issues](https://github.com/KnowledgeCaptureAndDiscovery/somef/issues) and [milestones](https://github.com/KnowledgeCaptureAndDiscovery/somef/milestones)

src/somef/process_repository.py

@@ -51,10 +51,16 @@ def rate_limit_get(*args, backoff_rate=2, initial_backoff=1, size_limit_mb=const
     parsed = urlparse(url)
     is_api_request = "api.github.com" in parsed.netloc
     content_length = None
-    # just verify size if NOT is a request to api.github.com
+    # Check file size before downloading the full body (skip for GitHub API requests,
+    # which are always small JSON payloads).
     if not is_api_request:
         try:
-            head_response = requests.get(url, stream=True, allow_redirects=True, **kwargs)
+            # head_response = requests.get(url, stream=True, allow_redirects=True, **kwargs)
+            # Use a proper HEAD request to read only the response headers.
+
+            head_response = requests.head(url, allow_redirects=True,
+                                           timeout=constants.DOWNLOAD_TIMEOUT_SECONDS, **kwargs)
+            head_response.close()  # release the connection back to the pool immediately
             content_length = head_response.headers.get("Content-Length")
             if content_length is not None:
                 size_bytes = int(content_length)
@@ -789,59 +795,153 @@ def download_repository_files(owner, repo_name, default_branch, repo_type, targe
         return None
 
 
+# def download_github_files(directory, owner, repo_name, repo_ref, authorization):
+#     """
+#     Download all repository files from a GitHub repository
+#     Parameters
+#     ----------
+#     repo_ref: link to branch of the repo
+#     repo_name: name of the repo
+#     owner: GitHub owner
+#     directory: directory where to extract all downloaded files
+#     authorization: GitHub authorization token
+
+#     Returns
+#     -------
+#     path to the folder where all files have been downloaded
+#     """
+#     # download the repo at the selected branch with the link
+#     repo_archive_url = f"https://github.com/{owner}/{repo_name}/archive/{repo_ref}.zip"
+#     logging.info(f"Downloading {repo_archive_url}")
+
+#     repo_download, date = rate_limit_get(repo_archive_url, headers=header_template(authorization))
+
+#     if repo_download is None:
+#         logging.warning(f"Repository archive skipped due to size limit: {constants.SIZE_DOWNLOAD_LIMIT_MB} MB or not content lenght.")
+#         return None
+
+#     if repo_download.status_code == 300:
+#         logging.warning(f"Ambiguous ref detected for {repo_ref}, trying tags/heads resolution")
+
+#         for ref_type in ["tags", "heads"]:
+#             repo_archive_url = f"https://github.com/{owner}/{repo_name}/archive/refs/{ref_type}/{repo_ref}.zip"
+#             logging.info(f"Trying to download {repo_archive_url}")
+
+#             repo_download, date = rate_limit_get(repo_archive_url, headers=header_template(authorization))
+
+#             if repo_download is None:
+#                     logging.warning(f"Repository archive skipped due to size limit: {constants.SIZE_DOWNLOAD_LIMIT_MB} MB or not content length.")
+#                     return None
+
+#             if repo_download.status_code == 200:
+#                 break
+
+#     if repo_download.status_code == 404:
+#         logging.error(f"Error: Archive request failed with HTTP {repo_download.status_code}")
+#         repo_archive_url = f"https://github.com/{owner}/{repo_name}/archive/main.zip"
+#         logging.info(f"Trying to download {repo_archive_url}")
+#         repo_download, date = rate_limit_get(repo_archive_url, headers=header_template(authorization))
+#         if repo_download is None:
+#             logging.warning(f"Repository archive skipped due to size limit: {constants.SIZE_DOWNLOAD_LIMIT_MB} MB or not content lenght.")
+#             return None
+
+#     if repo_download.status_code != 200:
+#         logging.error(f"Error: Archive request failed with HTTP {repo_download.status_code}")
+#         return None
+
+#     repo_zip = repo_download.content
+
+#     repo_name_full = owner + "_" + repo_name
+#     repo_zip_file = os.path.join(directory, repo_name_full + ".zip")
+#     repo_extract_dir = os.path.join(directory, repo_name_full)
+
+#     with open(repo_zip_file, "wb") as f:
+#         f.write(repo_zip)
+
+#     try:
+#         with zipfile.ZipFile(repo_zip_file, "r") as zip_ref: 
+#             zip_ref.extractall(repo_extract_dir) 
+#     except zipfile.BadZipFile: 
+#         logging.error("Downloaded archive is not a valid zip (repo may be empty)") 
+#         return None
+
+#     repo_folders = os.listdir(repo_extract_dir)
+#     if not repo_folders: 
+#         logging.warning("Repository archive is empty") 
+#         return None
+
+#     repo_dir = os.path.join(repo_extract_dir, repo_folders[0])
+#     return repo_dir
+
 def download_github_files(directory, owner, repo_name, repo_ref, authorization):
     """
-    Download all repository files from a GitHub repository
+    Download all repository files from a GitHub repository.
+
+    GitHub's short-form archive URL ``/archive/{ref}.zip`` returns HTTP 300 (Multiple
+    Choices) when the ref name is **ambiguous** — i.e. a branch and a tag share the
+    same name (e.g. a repo whose default branch is ``v2.0`` and also has a tag called
+    ``v2.0``).  In that case we must use the fully-qualified ref URLs:
+      - ``/archive/refs/heads/{ref}.zip``  (explicit branch)
+      - ``/archive/refs/tags/{ref}.zip``   (explicit tag)
+
+    We also keep the legacy ``main.zip`` fallback for repositories that renamed their
+    default branch to ``main`` after being created with ``master`` (or vice-versa) so
+    that the GitHub API default_branch value is momentarily stale.
+
+    Fallback order tried in sequence until one returns HTTP 200:
+      1. ``/archive/{ref}.zip``              — short form, works for unambiguous refs
+      2. ``/archive/refs/heads/{ref}.zip``   — unambiguous branch (fixes HTTP 300)
+      3. ``/archive/refs/tags/{ref}.zip``    — unambiguous tag  (fixes HTTP 300)
+      4. ``/archive/main.zip``               — legacy branch-rename fallback
+
     Parameters
     ----------
-    repo_ref: link to branch of the repo
+    repo_ref: default branch (or tag) returned by the GitHub API
     repo_name: name of the repo
     owner: GitHub owner
     directory: directory where to extract all downloaded files
     authorization: GitHub authorization token
 
     Returns
     -------
-    path to the folder where all files have been downloaded
+    Path to the folder where all files have been downloaded, or None on failure.
     """
-    # download the repo at the selected branch with the link
-    repo_archive_url = f"https://github.com/{owner}/{repo_name}/archive/{repo_ref}.zip"
-    logging.info(f"Downloading {repo_archive_url}")
-
-    repo_download, date = rate_limit_get(repo_archive_url, headers=header_template(authorization))
 
-    if repo_download is None:
-        logging.warning(f"Repository archive skipped due to size limit: {constants.SIZE_DOWNLOAD_LIMIT_MB} MB or not content lenght.")
-        return None
-
-    if repo_download.status_code == 300:
-        logging.warning(f"Ambiguous ref detected for {repo_ref}, trying tags/heads resolution")
-
-        for ref_type in ["tags", "heads"]:
-            repo_archive_url = f"https://github.com/{owner}/{repo_name}/archive/refs/{ref_type}/{repo_ref}.zip"
-            logging.info(f"Trying to download {repo_archive_url}")
-
-            repo_download, date = rate_limit_get(repo_archive_url, headers=header_template(authorization))
-
-            if repo_download is None:
-                    logging.warning(f"Repository archive skipped due to size limit: {constants.SIZE_DOWNLOAD_LIMIT_MB} MB or not content length.")
-                    return None
-
-            if repo_download.status_code == 200:
-                break
-
-    if repo_download.status_code == 404:
-        logging.error(f"Error: Archive request failed with HTTP {repo_download.status_code}")
-        repo_archive_url = f"https://github.com/{owner}/{repo_name}/archive/main.zip"
-        logging.info(f"Trying to download {repo_archive_url}")
+    # Candidate archive URLs tried in order.  We start with the short form because it
+    # works for the vast majority of repos and avoids an extra HTTP round-trip.  When
+    # that returns 300 (ambiguous ref) or 404 (ref not found), we escalate to the
+    # fully-qualified refs/heads/ and refs/tags/ forms before falling back to main.
+    candidate_urls = [
+        f"https://github.com/{owner}/{repo_name}/archive/{repo_ref}.zip",
+        f"https://github.com/{owner}/{repo_name}/archive/refs/heads/{repo_ref}.zip",
+        f"https://github.com/{owner}/{repo_name}/archive/refs/tags/{repo_ref}.zip",
+        f"https://github.com/{owner}/{repo_name}/archive/main.zip",
+    ]
+    repo_download = None
+    repo_archive_url = None
+    for repo_archive_url in candidate_urls:
+        logging.info(f"Downloading {repo_archive_url}")
         repo_download, date = rate_limit_get(repo_archive_url, headers=header_template(authorization))
         if repo_download is None:
-            logging.warning(f"Repository archive skipped due to size limit: {constants.SIZE_DOWNLOAD_LIMIT_MB} MB or not content lenght.")
+            # Size limit exceeded or streaming error — no point trying other URLs
+            logging.warning(
+                f"Repository archive skipped due to size limit: "
+                f"{constants.SIZE_DOWNLOAD_LIMIT_MB} MB or no content-length."
+            )
             return None
 
-    if repo_download.status_code != 200:
-        logging.error(f"Error: Archive request failed with HTTP {repo_download.status_code}")
-        return None
+        if repo_download.status_code == 200:
+            break
+        logging.warning(
+            f"Archive URL {repo_archive_url} returned HTTP {repo_download.status_code}, "
+            f"trying next fallback..."
+        )
+    if repo_download is None or repo_download.status_code != 200:
+            logging.error(
+                f"All archive download attempts failed for {owner}/{repo_name} "
+                f"(last status: {getattr(repo_download, 'status_code', 'N/A')})"
+            )
+            return None
 
     repo_zip = repo_download.content