labnotes 0.2.32__tar.gz → 0.2.34__tar.gz

{labnotes-0.2.32 → labnotes-0.2.34}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: labnotes
-Version: 0.2.32
+Version: 0.2.34
 Summary: Browse experiment designs, notes, and run data from a folder.
 Project-URL: Repository, https://github.com/thekevinscott/labnotes
 Author-email: Kevin Scott <me@thekevinscott.com>

labnotes-0.2.34/src/labnotes/runner/finalize_lost_runs.py

@@ -0,0 +1,32 @@
+import json
+import os
+from labnotes.list_runs import UNFINISHED
+from labnotes.models import LabnotesConfig
+from labnotes.runner.claim_run import LOCK_FILE, claim_run
+from labnotes.runner.mark_lost import mark_lost
+from labnotes.tables.open_tables import open_tables
+from labnotes.utils.process_alive import process_alive
+
+
+async def finalize_lost_runs(config: LabnotesConfig) -> None:
+    rows = await open_tables(config).query(
+        f"SELECT folder, run FROM runs WHERE {UNFINISHED}"
+    )
+    for row in rows:
+        folder = config.root / str(row["folder"])
+        if (folder / LOCK_FILE).exists():
+            lock = claim_run(folder)
+            if lock is None:
+                continue
+            try:
+                mark_lost(folder)
+            finally:
+                os.close(lock)
+        else:
+            run = json.loads(str(row["run"]))
+            pid, created = run.get("pid"), run.get("pid_created")
+            if isinstance(pid, int) and process_alive(
+                pid, created if isinstance(created, int | float) else None
+            ):
+                continue
+            mark_lost(folder)

labnotes-0.2.34/src/labnotes/runner/mark_lost.py

@@ -0,0 +1,24 @@
+import json
+import time
+from pathlib import Path
+
+from labnotes.runner.write_run_json import write_run_json
+from labnotes.tables.iso_time import iso_time
+
+
+def mark_lost(folder: Path) -> None:
+    try:
+        run = json.loads((folder / "run.json").read_text(encoding="utf-8"))
+    except (OSError, ValueError):
+        return
+    if (
+        not isinstance(run, dict)
+        or run.get("ended") is not None
+        or run.get("exit_code") is not None
+    ):
+        return
+    lost = {"ended": iso_time(time.time()), "ended_by": "lost"}
+    run |= lost
+    if invocations := run.get("invocations"):
+        invocations[-1] |= lost
+    write_run_json(folder, run)

{labnotes-0.2.32 → labnotes-0.2.34}/src/labnotes/runner/read_experiment_config.py

@@ -1,4 +1,5 @@
 import json
+import re
 import tomllib
 from pathlib import Path
 from typing import Any
@@ -13,6 +14,7 @@ from labnotes.is_positive_int import is_positive_int
 from labnotes.config_migration import MISSING_CONTINUES, REMOVED_MODE
 from labnotes.retries import RETRY_SECONDS
 
+SHELL_IDENTIFIER = re.compile(r"[A-Za-z_][A-Za-z0-9_]*\Z")
 SETTINGS = {
     "name",
     "command",
@@ -103,6 +105,11 @@ def read_experiment_config(
     for key, value in env.items():
         if key.startswith("LABNOTES_"):
             raise ValueError(f"{path}: env.{key} is reserved for labnotes")
+        if not SHELL_IDENTIFIER.match(key):
+            raise ValueError(
+                f"{path}: env.{key} must be a shell identifier"
+                " (letters, digits, underscore; not starting with a digit)"
+            )
         if not isinstance(value, str):
             raise ValueError(f"{path}: env.{key} must be a string")
     if "continues" not in values:

{labnotes-0.2.32 → labnotes-0.2.34}/src/labnotes/runner/write_run_json.py

@@ -1,8 +1,9 @@
 import json
+import os
 from pathlib import Path
 
 
 def write_run_json(folder: Path, run: dict[str, object]) -> None:
-    partial = folder / "run.json.tmp"
+    partial = folder / f"run.json.{os.getpid()}.tmp"
     partial.write_text(json.dumps(run, indent=2) + "\n", encoding="utf-8")
     partial.replace(folder / "run.json")

labnotes-0.2.32/src/labnotes/runner/finalize_lost_runs.py

@@ -1,33 +0,0 @@
-import json
-import time
-
-from labnotes.list_runs import UNFINISHED
-from labnotes.models import LabnotesConfig
-from labnotes.runner.claim_run import LOCK_FILE
-from labnotes.runner.run_locked import run_locked
-from labnotes.runner.write_run_json import write_run_json
-from labnotes.tables.iso_time import iso_time
-from labnotes.tables.open_tables import open_tables
-from labnotes.utils.process_alive import process_alive
-
-
-async def finalize_lost_runs(config: LabnotesConfig) -> None:
-    rows = await open_tables(config).query(
-        f"SELECT folder, run FROM runs WHERE {UNFINISHED}"
-    )
-    for row in rows:
-        run = json.loads(str(row["run"]))
-        folder = config.root / str(row["folder"])
-        pid, created = run.get("pid"), run.get("pid_created")
-        if (folder / LOCK_FILE).exists():
-            if run_locked(folder):
-                continue
-        elif isinstance(pid, int) and process_alive(
-            pid, created if isinstance(created, int | float) else None
-        ):
-            continue
-        lost = {"ended": iso_time(time.time()), "ended_by": "lost"}
-        run |= lost
-        if invocations := run.get("invocations"):
-            invocations[-1] |= lost
-        write_run_json(folder, run)