labnotes 0.0.101__tar.gz → 0.0.102__tar.gz

{labnotes-0.0.101 → labnotes-0.0.102}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: labnotes
-Version: 0.0.101
+Version: 0.0.102
 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>
@@ -51,7 +51,9 @@ labnotes reads the file from the working folder, or from the path given with
 
 When `experiment.toml` sits next to `.labnotes.toml`, the root is the one
 experiment, named after its folder. Paths then drop `{experiment}`: files
-default to `files/` and runs to `runs/{run}`.
+default to `files/` and runs to `runs/{run}`. An `[experiment]` table in
+`.labnotes.toml` takes the same keys as `experiment.toml` and is the base
+that `experiment.toml` layers over.
 
 `labnotes experiments` reads three tables from those paths:
 

{labnotes-0.0.101 → labnotes-0.0.102}/README.md

@@ -27,7 +27,9 @@ labnotes reads the file from the working folder, or from the path given with
 
 When `experiment.toml` sits next to `.labnotes.toml`, the root is the one
 experiment, named after its folder. Paths then drop `{experiment}`: files
-default to `files/` and runs to `runs/{run}`.
+default to `files/` and runs to `runs/{run}`. An `[experiment]` table in
+`.labnotes.toml` takes the same keys as `experiment.toml` and is the base
+that `experiment.toml` layers over.
 
 `labnotes experiments` reads three tables from those paths:
 

labnotes-0.0.102/src/labnotes/compose_experiment.py

@@ -0,0 +1,8 @@
+def compose_experiment(
+    base: dict[str, object], layer: dict[str, object]
+) -> dict[str, object]:
+    composed = {**base, **layer}
+    base_params, layer_params = base.get("params"), layer.get("params")
+    if isinstance(base_params, dict) and isinstance(layer_params, dict):
+        composed["params"] = {**base_params, **layer_params}
+    return composed

{labnotes-0.0.101 → labnotes-0.0.102}/src/labnotes/context.md

@@ -15,7 +15,7 @@ path = "{experiment}/runs/{run}" # one folder per run
 
 Paths are relative to the root. `{experiment}` and `{run}` stand for folder names; the experiments and files paths use `{experiment}`, the runs path both. A project laid out differently keeps its folders and changes the paths: look at where its experiments, notes and runs live, then write the templates that match.
 
-When `experiment.toml` sits next to `.labnotes.toml`, the root is the one experiment, named after its folder. Paths then drop `{experiment}`: files default to `files/`, runs to `runs/{run}`, and `[experiments] path` is rejected.
+When `experiment.toml` sits next to `.labnotes.toml`, the root is the one experiment, named after its folder. Paths then drop `{experiment}`: files default to `files/`, runs to `runs/{run}`, and `[experiments] path` is rejected. An `[experiment]` table in `.labnotes.toml` holds the same keys as `experiment.toml` and is the base each `experiment.toml` layers over (top-level keys replace, `params` merge by name). With no `[experiments] path`, it also makes the root the one experiment.
 
 `labnotes experiments` reads three tables from those paths:
 

{labnotes-0.0.101 → labnotes-0.0.102}/src/labnotes/models.py

@@ -49,6 +49,8 @@ class LabnotesConfig:
     concurrency: int = 1
     # Set when the config's folder is itself the one experiment.
     experiment: str | None = None
+    # [experiment] in .labnotes.toml, under each experiment.toml.
+    defaults: dict[str, object] = field(default_factory=dict)
 
 
 @dataclass(frozen=True)

{labnotes-0.0.101 → labnotes-0.0.102}/src/labnotes/read_config.py

@@ -4,6 +4,7 @@ from pathlib import Path
 from labnotes.models import LabnotesConfig
 from labnotes.is_positive_int import is_positive_int
 from labnotes.modes import DEFAULT_MODE, MODES
+from labnotes.runner.read_experiment_config import SETTINGS
 from labnotes.read_path import DEFAULT_PATHS, read_path
 
 CONFIG_FILE = ".labnotes.toml"
@@ -15,16 +16,27 @@ def read_config(path: Path) -> LabnotesConfig:
             values = tomllib.load(file)
     except tomllib.TOMLDecodeError as error:
         raise ValueError(f"{path}: {error}") from error
-    unknown = sorted(values.keys() - DEFAULT_PATHS.keys())
+    unknown = sorted(values.keys() - {*DEFAULT_PATHS, "experiment"})
     if unknown:
         raise ValueError(f"{path}: unknown tables {', '.join(unknown)}")
+    experiments = values.get("experiments", {})
+    defaults = values.get("experiment", {})
+    if not isinstance(defaults, dict):
+        raise ValueError(f"{path}: experiment must be a table, like [experiment]")
+    unknown = sorted(defaults.keys() - SETTINGS)
+    if unknown:
+        raise ValueError(f"{path}: unknown keys in [experiment]: {', '.join(unknown)}")
     root = path.resolve().parent
-    single = (root / "experiment.toml").is_file()
+    # An [experiments] path means many experiments, each taking [experiment] as
+    # its defaults; without one, [experiment] makes the root the experiment.
+    single = (root / "experiment.toml").is_file() or (
+        "experiment" in values
+        and not (isinstance(experiments, dict) and "path" in experiments)
+    )
     paths = {
         table: read_path(path, table, values.get(table, {}), single=single)
         for table in DEFAULT_PATHS
     }
-    experiments = values.get("experiments", {})
     mode = experiments.get("mode", DEFAULT_MODE)
     if mode not in MODES:
         raise ValueError(f"{path}: [experiments] mode must be matrix or adhoc")
@@ -40,4 +52,5 @@ def read_config(path: Path) -> LabnotesConfig:
         mode=mode,
         concurrency=concurrency,
         experiment=root.name if single else None,
+        defaults=defaults,
     )

{labnotes-0.0.101 → labnotes-0.0.102}/src/labnotes/runner/prepare_experiment.py

@@ -19,9 +19,13 @@ async def prepare_experiment(
         folder = config.experiments.replace("{experiment}", name)
         experiment_config = config.root / folder / "experiment.toml"
     source = await file_text(config.root, experiment_config)
-    if source is None:
+    if source is None and not config.defaults:
         raise ValueError(f"No experiment.toml for {name} at {experiment_config}.")
     experiment = read_experiment_config(
-        experiment_config, source, config.mode, config.concurrency
+        config.path if source is None else experiment_config,
+        source or "",
+        config.mode,
+        config.concurrency,
+        config.defaults,
     )
     return experiment, experiment.concurrency if concurrency is None else concurrency

{labnotes-0.0.101 → labnotes-0.0.102}/src/labnotes/runner/read_experiment_config.py

@@ -1,7 +1,9 @@
 import json
 import tomllib
 from pathlib import Path
+from typing import Any
 
+from labnotes.compose_experiment import compose_experiment
 from labnotes.default_counts import DEFAULT_COUNTS
 from labnotes.models import ExperimentConfig
 from labnotes.is_positive_int import is_positive_int
@@ -11,12 +13,17 @@ SETTINGS = {"name", "command", "repeats", "params", "counts", "mode", "concurren
 
 
 def read_experiment_config(
-    path: Path, source: str, mode: str, concurrency: int
+    path: Path,
+    source: str,
+    mode: str,
+    concurrency: int,
+    defaults: dict[str, object] | None = None,
 ) -> ExperimentConfig:
     try:
-        values = tomllib.loads(source)
+        layer = tomllib.loads(source)
     except tomllib.TOMLDecodeError as error:
         raise ValueError(f"{path}: {error}") from error
+    values: dict[str, Any] = compose_experiment(defaults or {}, layer)
     unknown = sorted(values.keys() - SETTINGS)
     if unknown:
         raise ValueError(f"{path}: unknown keys {', '.join(unknown)}")

labnotes-0.0.102/src/labnotes/tables/experiments_ddl.py

@@ -0,0 +1,34 @@
+import json
+
+from labnotes.models import LabnotesConfig
+from labnotes.sql_quote import quote_string
+
+# experiments is a view, so files and runs can't declare a foreign key to it.
+EXPERIMENTS = """
+CREATE TABLE experiment_configs (
+  experiment TEXT PRIMARY KEY, config TEXT, source TEXT
+);
+CREATE VIEW experiments AS
+  SELECT name, coalesce(config ->> 'name', name) AS display_name, config, source
+  FROM (
+    SELECT
+      names.name,
+      coalesce(experiment_configs.config, {defaults}) AS config,
+      experiment_configs.source
+    FROM (
+      SELECT experiment AS name FROM experiment_configs
+      UNION SELECT experiment FROM files
+      UNION SELECT experiment FROM runs{one}
+    ) AS names
+    LEFT JOIN experiment_configs ON experiment_configs.experiment = names.name
+  );
+"""
+
+
+def experiments_ddl(config: LabnotesConfig) -> str:
+    defaults = json.dumps(config.defaults, default=str) if config.defaults else None
+    one = config.experiment
+    return EXPERIMENTS.format(
+        defaults="NULL" if defaults is None else quote_string(defaults),
+        one="" if one is None else f"\n      UNION SELECT {quote_string(one)}",
+    )

{labnotes-0.0.101 → labnotes-0.0.102}/src/labnotes/tables/open_tables.py

@@ -4,6 +4,7 @@ from dirsql import DirSQL, Table
 
 from labnotes.models import LabnotesConfig
 from labnotes.tables.experiment_toml import experiment_toml
+from labnotes.tables.experiments_ddl import experiments_ddl
 from labnotes.tables.path_glob import path_glob
 from labnotes.tables.read_blocks import read_blocks
 from labnotes.tables.read_experiment import read_experiment
@@ -11,24 +12,6 @@ from labnotes.tables.read_file import read_file
 from labnotes.tables.read_log import read_log
 from labnotes.tables.read_run import read_run
 
-# experiments is a view, so files and runs can't declare a foreign key to it.
-EXPERIMENTS = """
-CREATE TABLE experiment_configs (
-  experiment TEXT PRIMARY KEY, config TEXT, source TEXT
-);
-CREATE VIEW experiments AS
-  SELECT
-    names.name,
-    coalesce(experiment_configs.config ->> 'name', names.name) AS display_name,
-    experiment_configs.config,
-    experiment_configs.source
-  FROM (
-    SELECT experiment AS name FROM experiment_configs
-    UNION SELECT experiment FROM files
-    UNION SELECT experiment FROM runs
-  ) AS names
-  LEFT JOIN experiment_configs ON experiment_configs.experiment = names.name;
-"""
 FILES = """
 CREATE TABLE files (
   experiment TEXT, filename TEXT, path TEXT PRIMARY KEY, ctime TEXT, mtime TEXT,
@@ -97,13 +80,14 @@ def open_tables(config: LabnotesConfig) -> DirSQL:
             ),
             Table(
                 name="experiment_configs",
-                ddl=EXPERIMENTS,
+                ddl=experiments_ddl(config),
                 glob=path_glob(experiment_toml(config.experiments)),
                 on_file=partial(
                     read_experiment,
                     root,
                     config.experiments,
                     experiment=config.experiment,
+                    defaults=config.defaults,
                 ),
             ),
         ],

{labnotes-0.0.101 → labnotes-0.0.102}/src/labnotes/tables/read_experiment.py

@@ -2,19 +2,24 @@ import json
 import tomllib
 from pathlib import Path
 
+from labnotes.compose_experiment import compose_experiment
 from labnotes.tables.experiment_toml import experiment_toml
 from labnotes.tables.path_pattern import path_pattern
 
 
 def read_experiment(
-    root: Path, template: str, path: str, experiment: str | None = None
+    root: Path,
+    template: str,
+    path: str,
+    experiment: str | None = None,
+    defaults: dict[str, object] | None = None,
 ) -> list[dict[str, object]]:
     relative = Path(path).relative_to(root).as_posix()
     found = path_pattern(experiment_toml(template)).fullmatch(relative)
     if found is None:
         return []
     source = Path(path).read_text(encoding="utf-8")
-    config = tomllib.loads(source)
+    config = compose_experiment(defaults or {}, tomllib.loads(source))
     return [
         {
             "experiment": experiment or found["experiment"],