Fix three bugs: file paths, missing Canvas URL scheme, terminal refresh

Bug 1 — FileNotFoundError (wrong output directory):
- All pipeline scripts used PROJECT_DIR (/tmp AppImage mount) for data paths
- Added DATA_DIR = ~/.auto_note/ when frozen, else PROJECT_DIR, to each script
- downloader.py, extract_caption.py, semantic_alignment.py, note_generation.py:
  API key files, config.json, MANIFEST_FILE, course_dirs all use DATA_DIR
- downloader.py base_dir default now uses DATA_DIR instead of PROJECT_DIR
- MANIFEST_FILE in both downloader.py and extract_caption.py now in DATA_DIR

Bug 2 — MissingSchema (no https:// prefix):
- downloader.py loaded CANVAS_URL from PROJECT_DIR/config.json (empty in AppImage)
  causing Canvas("", token) → invalid URL with no scheme
- Fixed: load config from DATA_DIR; auto-prefix https:// if missing

Bug 3 — Terminal only refreshes on page switch:
- Added self._lines.update() + time.sleep(0.02) after page.update() in
  OutputConsole._flush_thread so Flet event loop has time to repaint

Author: nodeeeeee

downloader.py

@@ -36,16 +36,27 @@
 # ── Configuration ──────────────────────────────────────────────────────────────
 
 PROJECT_DIR   = Path(__file__).parent
-MANIFEST_FILE = PROJECT_DIR / "manifest.json"
+MANIFEST_FILE = None   # set after DATA_DIR is resolved below
+
+# When bundled as an AppImage, __file__ resolves to a temp dir deleted on exit.
+# Credentials and config must be read from the persistent ~/.auto_note/ directory.
+if getattr(sys, "frozen", False):
+    DATA_DIR = Path.home() / ".auto_note"
+else:
+    DATA_DIR = PROJECT_DIR
+
+MANIFEST_FILE = DATA_DIR / "manifest.json"
 
 # ── User-configurable connection settings (set via GUI Settings page) ──────────
-_config_file = PROJECT_DIR / "config.json"
+_config_file = DATA_DIR / "config.json"
 _config: dict = json.load(open(_config_file)) if _config_file.exists() else {}
 
-CANVAS_URL   = _config.get("CANVAS_URL",   "")
+CANVAS_URL   = _config.get("CANVAS_URL",   "").strip().rstrip("/")
+if CANVAS_URL and not CANVAS_URL.startswith(("http://", "https://")):
+    CANVAS_URL = "https://" + CANVAS_URL
 PANOPTO_HOST = _config.get("PANOPTO_HOST", "")
 
-_canvas_token_file = PROJECT_DIR / "canvas_token.txt"
+_canvas_token_file = DATA_DIR / "canvas_token.txt"
 CANVAS_TOKEN = (
     _canvas_token_file.read_text().strip()
     if _canvas_token_file.exists() else
@@ -649,7 +660,7 @@ def _classify_with_ai(files: list[dict], course_name: str) -> list[dict]:
     import anthropic
     key = os.environ.get("ANTHROPIC_API_KEY", "")
     if not key:
-        kf = PROJECT_DIR / "anthropic_key.txt"
+        kf = DATA_DIR / "anthropic_key.txt"
         if kf.exists():
             key = kf.read_text().strip()
     client = anthropic.Anthropic(api_key=key)
@@ -975,7 +986,7 @@ def main() -> None:
         parser.print_help()
         sys.exit(0)
 
-    base_dir = Path(args.path) if args.path else PROJECT_DIR
+    base_dir = Path(args.path) if args.path else DATA_DIR
     canvas   = Canvas(CANVAS_URL, CANVAS_TOKEN)
 
     # ── --course-list ──────────────────────────────────────────────────────────

extract_caption.py

@@ -23,7 +23,11 @@
 from pathlib import Path
 
 PROJECT_DIR   = Path(__file__).parent
-MANIFEST_FILE = PROJECT_DIR / "manifest.json"
+if getattr(sys, "frozen", False):
+    DATA_DIR = Path.home() / ".auto_note"
+else:
+    DATA_DIR = PROJECT_DIR
+MANIFEST_FILE = DATA_DIR / "manifest.json"
 
 # ── Tunable constants ─────────────────────────────────────────────────────────
 
@@ -36,7 +40,7 @@
 _API_CHUNK_MINUTES = 60
 
 # OpenAI API key: read from openai_api.txt or OPENAI_API_KEY env var
-_openai_key_file = PROJECT_DIR / "openai_api.txt"
+_openai_key_file = DATA_DIR / "openai_api.txt"
 _OPENAI_API_KEY  = (
     _openai_key_file.read_text().strip()
     if _openai_key_file.exists() else

gui.py

@@ -448,7 +448,9 @@ def _flush_thread() -> None:
                                 no_wrap=False, selectable=True,
                             )
                         )
+                self._lines.update()   # push the ListView itself
                 self.page.update()
+                time.sleep(0.02)       # yield to Flet event loop so repaint fires
 
         def _worker() -> None:
             try:

note_generation.py

@@ -30,6 +30,11 @@
 import alignment_parser
 
 PROJECT_DIR = Path(__file__).parent
+import sys as _sys
+if getattr(_sys, "frozen", False):
+    DATA_DIR = Path.home() / ".auto_note"
+else:
+    DATA_DIR = PROJECT_DIR
 
 # ── Constants ─────────────────────────────────────────────────────────────────
 
@@ -481,7 +486,7 @@ def _make_client(provider: str):
         from openai import OpenAI
         key = os.environ.get("GEMINI_API_KEY", "")
         if not key:
-            kf = PROJECT_DIR / "gemini_api.txt"
+            kf = DATA_DIR / "gemini_api.txt"
             if kf.exists():
                 key = kf.read_text().strip()
         if not key:
@@ -494,7 +499,7 @@ def _make_client(provider: str):
         from anthropic import Anthropic
         key = os.environ.get("ANTHROPIC_API_KEY", "")
         if not key:
-            kf = PROJECT_DIR / "anthropic_key.txt"
+            kf = DATA_DIR / "anthropic_key.txt"
             if kf.exists():
                 key = kf.read_text().strip()
         if not key:
@@ -504,7 +509,7 @@ def _make_client(provider: str):
         from openai import OpenAI
         key = os.environ.get("OPENAI_API_KEY", "")
         if not key:
-            kf = PROJECT_DIR / "openai_api.txt"
+            kf = DATA_DIR / "openai_api.txt"
             if kf.exists():
                 key = kf.read_text().strip()
         if not key:
@@ -1295,7 +1300,7 @@ def main() -> None:
     args = parser.parse_args()
 
     if args.course:
-        course_dir  = PROJECT_DIR / args.course
+        course_dir  = DATA_DIR / args.course
         course_name = args.course_name or f"CS{args.course}"
         lectures    = _discover_lectures(course_dir)
         if args.lectures:

semantic_alignment.py

@@ -39,6 +39,11 @@
 import numpy as np
 
 PROJECT_DIR = Path(__file__).parent
+import sys as _sys
+if getattr(_sys, "frozen", False):
+    DATA_DIR = Path.home() / ".auto_note"
+else:
+    DATA_DIR = PROJECT_DIR
 
 # ── Tunable knobs ─────────────────────────────────────────────────────────────
 
@@ -84,7 +89,7 @@ def _get_openai_key() -> str:
     import os
     key = os.environ.get("OPENAI_API_KEY", "")
     if not key:
-        key_file = PROJECT_DIR / "openai_api.txt"
+        key_file = DATA_DIR / "openai_api.txt"
         if key_file.exists():
             key = key_file.read_text().strip()
     return key
@@ -1082,7 +1087,7 @@ def _content_match_slide_group(
 
 
 def process_course(course_id: int | str) -> None:
-    course_dir = PROJECT_DIR / str(course_id)
+    course_dir = DATA_DIR / str(course_id)
     captions   = sorted((course_dir / "captions").glob("*.json"))
     all_slides = _candidate_slides(course_dir)
     out_dir    = course_dir / "alignment"