Refactor: centralize matplotlib setup and split job/core.py

Author: imjiaoyuan

.github/copilot-instructions.md

@@ -46,6 +46,16 @@ def parse_gff_attributes(attr_string: str) -> dict[str, str]:
     return attrs
 
 
+def setup_matplotlib():
+    """Configure matplotlib to use Agg backend for headless operation."""
+    import matplotlib
+
+    matplotlib.use("Agg")
+    import matplotlib.pyplot as plt
+
+    return plt
+
+
 def open_text(path: str | Path) -> IO[str]:
     path_str = str(path)
     if path_str.endswith(".gz"):

src/jsrc/core.py

@@ -0,0 +1,54 @@
+"""Job module configuration and path management."""
+
+import os
+from pathlib import Path
+
+
+def config_home() -> Path:
+    """Get XDG config home directory."""
+    xdg = os.getenv("XDG_CONFIG_HOME")
+    if xdg:
+        return Path(xdg).expanduser() / "jsrc"
+    return Path.home() / ".config" / "jsrc"
+
+
+def data_home() -> Path:
+    """Get XDG data home directory."""
+    xdg = os.getenv("XDG_DATA_HOME")
+    if xdg:
+        return Path(xdg).expanduser() / "jsrc"
+    return Path.home() / ".local" / "share" / "jsrc"
+
+
+def history_path() -> Path:
+    """Get job history file path."""
+    override = os.getenv("JSRC_JOBS_FILE", "")
+    if override:
+        return Path(override).expanduser()
+    return config_home() / "job" / "history"
+
+
+def default_log_dir() -> Path:
+    """Get default directory for job log files."""
+    return data_home() / "job-logs"
+
+
+def state_dir() -> Path:
+    """Get directory for job state files."""
+    return data_home() / "job-state"
+
+
+def ensure_dirs() -> None:
+    """Create all required directories if they don't exist."""
+    history_path().parent.mkdir(parents=True, exist_ok=True)
+    default_log_dir().mkdir(parents=True, exist_ok=True)
+    state_dir().mkdir(parents=True, exist_ok=True)
+
+
+def _migrate_old_history() -> None:
+    """Migrate old history file to new location."""
+    old = data_home() / "jobs"
+    new = history_path()
+    if old.exists() and not new.exists():
+        new.parent.mkdir(parents=True, exist_ok=True)
+        old.rename(new)