labnotes 0.0.19__tar.gz → 0.0.20__tar.gz

{labnotes-0.0.19 → labnotes-0.0.20}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: labnotes
-Version: 0.0.19
+Version: 0.0.20
 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>
@@ -14,7 +14,6 @@ Requires-Dist: ipykernel>=7.4.0
 Requires-Dist: jinja2>=3.1.6
 Requires-Dist: jupyter-client>=8.10.0
 Requires-Dist: markdown-it-py>=4.2.0
-Requires-Dist: pyyaml>=6.0.3
 Requires-Dist: rich>=14
 Requires-Dist: starlette>=1.8.0
 Requires-Dist: textual>=8.2.8
@@ -114,29 +113,18 @@ line per event instead.
 - A second `run` of the same experiment fails while the first holds the lock.
 - It exits 1 if any run failed.
 
-`labnotes server` doesn't read `.labnotes.toml` yet. Give it the two folders
-it uses with `--experiments-folder` and `--data-folder`:
-
-- `--experiments-folder` holds one subfolder per experiment, each with a
-  `design.yaml` (with a `study` key) and any number of markdown notes.
-- `--data-folder` holds the run data and a `.dirsql.toml` that declares a
-  `runs` table with a `study` column. An experiment's runs are the rows whose
-  `study` matches its design's.
-
-That serves a local site at http://127.0.0.1:8000: a table of experiments,
-and a page per experiment with its parameters, its notes, progress per cell of
-the design grid, and every run so far. Both folders are watched, so a reload
-shows new runs and edited notes.
-
-`design.yaml` keys the site reads: `study`, `fixed`, `varies` (each key a list
-of values), `runs_per_cell`, and `completed_run`, a SQL condition over the
-`runs` table that marks a run as complete. Anything else shows up as-is.
+`labnotes server` serves a local site at http://127.0.0.1:8000 from the same
+`.labnotes.toml`: a table of experiments, and a page per experiment with its
+params, its markdown files, progress per cell of the params grid, and every
+run so far. A cell is full once it has `repeats` runs that exited 0 and aren't
+excluded, the same count `run` uses. The project is watched, so a reload shows
+new runs and edited notes. Python blocks in a note run with the root as the
+working folder.
 
 `-h`/`--host` and `-p`/`--port` change where it listens; `-h 0.0.0.0` (or a
 Tailscale IP) serves beyond localhost. Every other uvicorn option passes
 through: `--reload`, `--workers`, `--proxy-headers`, `--root-path`, the
-`--ssl-*` set, and the rest. `labnotes server --help` lists them. `LABNOTES_EXPERIMENTS_FOLDER` and
-`LABNOTES_DATA_FOLDER` can stand in for the folder flags.
+`--ssl-*` set, and the rest. `labnotes server --help` lists them.
 
 ## Agent skill
 

{labnotes-0.0.19 → labnotes-0.0.20}/README.md

@@ -91,29 +91,18 @@ line per event instead.
 - A second `run` of the same experiment fails while the first holds the lock.
 - It exits 1 if any run failed.
 
-`labnotes server` doesn't read `.labnotes.toml` yet. Give it the two folders
-it uses with `--experiments-folder` and `--data-folder`:
-
-- `--experiments-folder` holds one subfolder per experiment, each with a
-  `design.yaml` (with a `study` key) and any number of markdown notes.
-- `--data-folder` holds the run data and a `.dirsql.toml` that declares a
-  `runs` table with a `study` column. An experiment's runs are the rows whose
-  `study` matches its design's.
-
-That serves a local site at http://127.0.0.1:8000: a table of experiments,
-and a page per experiment with its parameters, its notes, progress per cell of
-the design grid, and every run so far. Both folders are watched, so a reload
-shows new runs and edited notes.
-
-`design.yaml` keys the site reads: `study`, `fixed`, `varies` (each key a list
-of values), `runs_per_cell`, and `completed_run`, a SQL condition over the
-`runs` table that marks a run as complete. Anything else shows up as-is.
+`labnotes server` serves a local site at http://127.0.0.1:8000 from the same
+`.labnotes.toml`: a table of experiments, and a page per experiment with its
+params, its markdown files, progress per cell of the params grid, and every
+run so far. A cell is full once it has `repeats` runs that exited 0 and aren't
+excluded, the same count `run` uses. The project is watched, so a reload shows
+new runs and edited notes. Python blocks in a note run with the root as the
+working folder.
 
 `-h`/`--host` and `-p`/`--port` change where it listens; `-h 0.0.0.0` (or a
 Tailscale IP) serves beyond localhost. Every other uvicorn option passes
 through: `--reload`, `--workers`, `--proxy-headers`, `--root-path`, the
-`--ssl-*` set, and the rest. `labnotes server --help` lists them. `LABNOTES_EXPERIMENTS_FOLDER` and
-`LABNOTES_DATA_FOLDER` can stand in for the folder flags.
+`--ssl-*` set, and the rest. `labnotes server --help` lists them.
 
 ## Agent skill
 

{labnotes-0.0.19 → labnotes-0.0.20}/pyproject.toml

@@ -19,7 +19,6 @@ dependencies = [
     "jinja2>=3.1.6",
     "jupyter-client>=8.10.0",
     "markdown-it-py>=4.2.0",
-    "pyyaml>=6.0.3",
     "rich>=14",
     "starlette>=1.8.0",
     "textual>=8.2.8",
@@ -38,7 +37,6 @@ dev = [
     "mypy>=2.4.0",
     "pytest>=8.0",
     "ruff==0.8.4",
-    "types-pyyaml>=6.0.12.20260906",
 ]
 
 [tool.hatch.version]

{labnotes-0.0.19 → labnotes-0.0.20}/src/labnotes/context.md

@@ -89,12 +89,4 @@ line per event instead.
 - A second `run` of the same experiment fails while the first holds the lock.
 - It exits 1 if any run failed.
 
-`labnotes server` doesn't read `.labnotes.toml` yet: pass `--experiments-folder` and `--data-folder`, or set `LABNOTES_EXPERIMENTS_FOLDER` and `LABNOTES_DATA_FOLDER`. The experiments folder has one subfolder per experiment, each with a `design.yaml` and markdown notes. The data folder holds run data and a `.dirsql.toml` declaring a `runs` table with a `study` column.
-
-The run data lives in the data folder. Query it with [dirsql](https://dirsql.dev) and the data folder's `.dirsql.toml`, which declares the `runs` table:
-
-```sh
-uvx dirsql -c data/.dirsql.toml "SELECT * FROM runs LIMIT 1" --format json
-```
-
-`uvx labnotes server` serves the experiments and their runs as a local site.
+`uvx labnotes server` serves the experiments, their markdown files and their runs as a local site, read from the same `.labnotes.toml`. A grid cell is full once it has `repeats` runs that exited 0 and aren't excluded.

{labnotes-0.0.19 → labnotes-0.0.20}/src/labnotes/create_app.py

@@ -14,17 +14,17 @@ from starlette.templating import Jinja2Templates
 
 from labnotes.asset_url import asset_url
 from labnotes.drain_watch import drain_watch
+from labnotes.experiment_notes import experiment_notes
 from labnotes.format_value import format_value
 from labnotes.list_experiments import list_experiments
 from labnotes.load_experiment import load_experiment
+from labnotes.models import LabnotesConfig
 from labnotes.notebook_kernel import NotebookKernel
-from labnotes.open_experiments import open_experiments
-from labnotes.open_runs import open_runs
 from labnotes.pivot_cells import pivot_cells
 from labnotes.python_blocks import python_blocks
 from labnotes.saved_outputs import saved_outputs
-from labnotes.sql_quote import quote_string
 from labnotes.stop_idle_kernels import stop_idle_kernels
+from labnotes.tables.open_tables import open_tables
 
 HERE = Path(__file__).parent
 templates = Jinja2Templates(directory=HERE / "templates")
@@ -32,20 +32,15 @@ templates.env.filters["value"] = format_value
 templates.env.globals["asset"] = asset_url
 
 
-def create_app(
-    experiments_folder: Path, data_folder: Path, kernel_idle_minutes: float
-) -> Starlette:
+def create_app(config: LabnotesConfig, kernel_idle_minutes: float) -> Starlette:
     kernels: dict[tuple[str, str], NotebookKernel] = {}
 
     @asynccontextmanager
     async def lifespan(app: Starlette) -> AsyncIterator[None]:
-        app.state.experiments = open_experiments(experiments_folder)
-        app.state.runs = open_runs(data_folder)
-        await app.state.experiments.ready()
-        await app.state.runs.ready()
+        app.state.tables = open_tables(config)
+        await app.state.tables.ready()
         watchers = [
-            asyncio.create_task(drain_watch(app.state.experiments)),
-            asyncio.create_task(drain_watch(app.state.runs)),
+            asyncio.create_task(drain_watch(app.state.tables)),
             asyncio.create_task(stop_idle_kernels(kernels, kernel_idle_minutes)),
         ]
         yield
@@ -55,20 +50,18 @@ def create_app(
             await kernel.stop()
 
     async def index(request: Request) -> Response:
-        state = request.app.state
-        experiments = await list_experiments(state.experiments, state.runs)
+        experiments = await list_experiments(request.app.state.tables)
         return templates.TemplateResponse(
             request,
             "index.html",
-            {"experiments": experiments, "folder": experiments_folder.resolve().name},
+            {"experiments": experiments, "folder": config.root.name},
         )
 
     async def experiment(request: Request) -> Response:
-        state = request.app.state
         name = request.path_params["name"]
         loaded = await load_experiment(
-            state.experiments,
-            state.runs,
+            request.app.state.tables,
+            config.root,
             name,
             request.query_params,
             lambda note, content: saved_outputs(kernels.get((name, note)), content),
@@ -88,14 +81,13 @@ def create_app(
             raise HTTPException(415, "Send JSON")
         name = request.path_params["name"]
         note = request.path_params["note"]
-        found = await request.app.state.experiments.query(
-            "SELECT content FROM notes"
-            f" WHERE experiment = {quote_string(name)} AND name = {quote_string(note)}"
+        found = await experiment_notes(
+            request.app.state.tables, config.root, name, note
         )
         if not found:
             raise HTTPException(404, "No such note")
-        [row] = found
-        return str(row["content"])
+        [note] = found
+        return note["content"]
 
     async def run_block(request: Request) -> Response:
         blocks = python_blocks(await note_content(request))
@@ -104,7 +96,7 @@ def create_app(
         if not isinstance(block, int) or not 0 <= block < len(blocks):
             raise HTTPException(400, "No such block")
         if key not in kernels:
-            kernels[key] = NotebookKernel(data_folder)
+            kernels[key] = NotebookKernel(config.root)
         return HTMLResponse(await kernels[key].run(blocks[block]))
 
     async def restart_kernel(request: Request) -> Response:
@@ -118,9 +110,13 @@ def create_app(
         routes=[
             Route("/", index),
             Route("/experiments/{name}", experiment),
-            Route("/experiments/{name}/notes/{note}/run", run_block, methods=["POST"]),
             Route(
-                "/experiments/{name}/notes/{note}/restart",
+                "/experiments/{name}/notes/{note:path}/run",
+                run_block,
+                methods=["POST"],
+            ),
+            Route(
+                "/experiments/{name}/notes/{note:path}/restart",
                 restart_kernel,
                 methods=["POST"],
             ),

labnotes-0.0.20/src/labnotes/experiment_notes.py

@@ -0,0 +1,23 @@
+from pathlib import Path
+
+from dirsql import DirSQL
+
+from labnotes.sql_quote import quote_string
+
+
+async def experiment_notes(
+    tables: DirSQL, root: Path, experiment: str, note: str | None = None
+) -> list[dict[str, str]]:
+    where = f"experiment = {quote_string(experiment)} AND filename LIKE '%.md'"
+    if note is not None:
+        where += f" AND filename = {quote_string(note)}"
+    rows = await tables.query(
+        f"SELECT filename, path FROM files WHERE {where} ORDER BY filename"
+    )
+    return [
+        {
+            "name": str(row["filename"]),
+            "content": (root / str(row["path"])).read_text(encoding="utf-8"),
+        }
+        for row in rows
+    ]

labnotes-0.0.20/src/labnotes/experiment_progress.py

@@ -0,0 +1,25 @@
+from typing import cast
+
+from dirsql import DirSQL
+
+from labnotes.cell_progress import cell_progress
+from labnotes.count_runs import count_runs
+
+
+async def experiment_progress(
+    tables: DirSQL, source: str, summary: dict[str, object]
+) -> dict[str, object]:
+    varies = cast(dict[str, list[object]], summary["varies"])
+    completed_run = str(summary["completed_run"])
+    runs_per_cell = summary["runs_per_cell"]
+    [totals] = await count_runs(tables, source, completed_run)
+    progress: dict[str, object] = {**totals, "filled": None, "cells": []}
+    if runs_per_cell is None:
+        return progress
+    grouped = await count_runs(tables, source, completed_run, group_by=list(varies))
+    cells = cell_progress(varies, grouped)
+    progress["cells"] = cells
+    progress["filled"] = sum(
+        min(cast(int, cell["completed"]), cast(int, runs_per_cell)) for cell in cells
+    )
+    return progress

labnotes-0.0.20/src/labnotes/experiment_runs.py

@@ -0,0 +1,13 @@
+from labnotes.sql_quote import quote_identifier, quote_string
+
+
+def experiment_runs(experiment: str, params: list[str]) -> str:
+    columns = "".join(
+        f", params ->> {quote_string(f'$.{quote_identifier(key)}')}"
+        f" AS {quote_identifier(key)}"
+        for key in params
+    )
+    return (
+        f"(SELECT *{columns} FROM runs"
+        f" WHERE experiment = {quote_string(experiment)})"
+    )

labnotes-0.0.20/src/labnotes/list_experiments.py

@@ -0,0 +1,26 @@
+import json
+from typing import cast
+
+from dirsql import DirSQL
+
+from labnotes.experiment_progress import experiment_progress
+from labnotes.experiment_runs import experiment_runs
+from labnotes.summarize_config import summarize_config
+
+
+async def list_experiments(tables: DirSQL) -> list[dict[str, object]]:
+    rows = await tables.query(
+        "SELECT name, display_name, config FROM experiments ORDER BY name"
+    )
+    listed = []
+    for row in rows:
+        name = str(row["name"])
+        config = None if row["config"] is None else json.loads(str(row["config"]))
+        summary = summarize_config(config)
+        varies = cast(dict[str, list[object]], summary["varies"])
+        source = experiment_runs(name, list(varies))
+        progress = await experiment_progress(tables, source, summary)
+        listed.append(
+            {"name": name, "display_name": row["display_name"], **summary, **progress}
+        )
+    return listed

{labnotes-0.0.19 → labnotes-0.0.20}/src/labnotes/list_runs.py

@@ -23,7 +23,7 @@ async def list_runs(
     elif view.sort:
         order = f"{quote_identifier(view.sort)} {direction}"
     else:
-        order = "2 DESC"
+        order = "created DESC, id DESC"
     return await runs.query(
         f"SELECT ({completed_run}) AS labnotes_completed, * FROM {source}"
         f"{filtered} ORDER BY {order}"

{labnotes-0.0.19 → labnotes-0.0.20}/src/labnotes/load_experiment.py

@@ -1,19 +1,20 @@
 import json
 from collections.abc import Callable, Mapping, Sequence
+from pathlib import Path
 from typing import cast
 
 from dirsql import DirSQL
 
+from labnotes.experiment_notes import experiment_notes
+from labnotes.experiment_progress import experiment_progress
+from labnotes.experiment_runs import experiment_runs
 from labnotes.list_runs import list_runs
 from labnotes.parse_run_view import parse_run_view
 from labnotes.python_blocks import python_blocks
 from labnotes.render_markdown import render_markdown
-from labnotes.run_columns import run_columns
 from labnotes.sort_href import sort_href
 from labnotes.sql_quote import quote_string
-from labnotes.study_progress import study_progress
-from labnotes.study_runs import study_runs
-from labnotes.summarize_design import summarize_design
+from labnotes.summarize_config import summarize_config
 
 
 def _no_outputs(note: str, content: str) -> Sequence[str]:
@@ -21,53 +22,45 @@ def _no_outputs(note: str, content: str) -> Sequence[str]:
 
 
 async def load_experiment(
-    experiments: DirSQL,
-    runs: DirSQL,
+    tables: DirSQL,
+    root: Path,
     name: str,
     params: Mapping[str, str],
     outputs_for: Callable[[str, str], Sequence[str]] = _no_outputs,
 ) -> dict[str, object] | None:
-    found = await experiments.query(
-        f"SELECT name, study, design FROM experiments WHERE name = {quote_string(name)}"
+    found = await tables.query(
+        "SELECT name, display_name, config FROM experiments"
+        f" WHERE name = {quote_string(name)}"
     )
     if not found:
         return None
     [row] = found
-    notes = await experiments.query(
-        "SELECT name, content FROM notes"
-        f" WHERE experiment = {quote_string(name)} ORDER BY name"
-    )
-    summary = summarize_design(json.loads(str(row["design"])))
+    config = None if row["config"] is None else json.loads(str(row["config"]))
+    summary = summarize_config(config)
     varies = cast(dict[str, list[object]], summary["varies"])
-    study = None if row["study"] is None else str(row["study"])
-    columns = await run_columns(runs)
-    progress = await study_progress(runs, study, summary, columns)
-    shown = columns[:1] + [key for key in varies if key in columns[1:]]
+    source = experiment_runs(name, list(varies))
+    progress = await experiment_progress(tables, source, summary)
+    shown = ["id", *(key for key in varies if key != "id")]
     view = parse_run_view(params, shown)
-    listed = (
-        []
-        if study is None
-        else await list_runs(
-            runs, study_runs(study), str(summary["completed_run"]), view
-        )
-    )
+    notes = await experiment_notes(tables, root, name)
     return {
         "name": row["name"],
-        "study": study,
+        "display_name": row["display_name"],
         **summary,
         **progress,
         "notes": [
             {
                 "name": note["name"],
                 "html": render_markdown(
-                    str(note["content"]),
-                    outputs_for(str(note["name"]), str(note["content"])),
+                    note["content"], outputs_for(note["name"], note["content"])
                 ),
-                "runnable": bool(python_blocks(str(note["content"]))),
+                "runnable": bool(python_blocks(note["content"])),
             }
             for note in notes
         ],
-        "runs_list": listed,
+        "runs_list": await list_runs(
+            tables, source, str(summary["completed_run"]), view
+        ),
         "run_columns": shown,
         "run_view": view,
         "sort_hrefs": {

{labnotes-0.0.19 → labnotes-0.0.20}/src/labnotes/serve_app.py

@@ -4,15 +4,13 @@ from pathlib import Path
 from starlette.applications import Starlette
 
 from labnotes.create_app import create_app
+from labnotes.read_config import read_config
 
-EXPERIMENTS_FOLDER = "LABNOTES_EXPERIMENTS_FOLDER"
-DATA_FOLDER = "LABNOTES_DATA_FOLDER"
+CONFIG = "LABNOTES_CONFIG"
 KERNEL_IDLE_MINUTES = "LABNOTES_KERNEL_IDLE_MINUTES"
 
 
 def serve_app() -> Starlette:
     return create_app(
-        Path(os.environ[EXPERIMENTS_FOLDER]),
-        Path(os.environ[DATA_FOLDER]),
-        int(os.environ[KERNEL_IDLE_MINUTES]),
+        read_config(Path(os.environ[CONFIG])), int(os.environ[KERNEL_IDLE_MINUTES])
     )

{labnotes-0.0.19 → labnotes-0.0.20}/src/labnotes/server.py

@@ -1,29 +1,18 @@
 import os
-from pathlib import Path
 
 import click
 from uvicorn.main import main as uvicorn_main
 
-from labnotes.serve_app import DATA_FOLDER, EXPERIMENTS_FOLDER, KERNEL_IDLE_MINUTES
+from labnotes.load_config import load_config
+from labnotes.read_config import CONFIG_FILE
+from labnotes.serve_app import CONFIG, KERNEL_IDLE_MINUTES
 
 # labnotes owns these; the rest of uvicorn's options pass straight through.
 OWN_OPTIONS = {"app", "factory", "app_dir", "version", "host", "port"}
 
 
-@click.command(help="Serve the experiments and their run data as a local site.")
-@click.option(
-    "--experiments-folder",
-    type=click.Path(path_type=Path),
-    envvar=EXPERIMENTS_FOLDER,
-    required=True,
-    help="One subfolder per experiment, each with a design.yaml and markdown notes.",
-)
-@click.option(
-    "--data-folder",
-    type=click.Path(path_type=Path),
-    envvar=DATA_FOLDER,
-    required=True,
-    help="Run data, with a .dirsql.toml declaring a runs table that has a study column.",
+@click.command(
+    help="Serve the experiments, their notes and their runs as a local site."
 )
 @click.option(
     "--kernel-idle-minutes",
@@ -44,14 +33,16 @@ OWN_OPTIONS = {"app", "factory", "app_dir", "version", "host", "port"}
 @click.pass_context
 def server(
     ctx: click.Context,
-    experiments_folder: Path,
-    data_folder: Path,
     kernel_idle_minutes: int,
     **server_options: object,
 ) -> None:
+    config = load_config(ctx)
+    if config is None:
+        raise click.ClickException(
+            f"No {CONFIG_FILE} here. Run labnotes init, or pass -c PATH."
+        )
     # Through the environment so --reload and --workers child processes see them.
-    os.environ[EXPERIMENTS_FOLDER] = str(experiments_folder.resolve())
-    os.environ[DATA_FOLDER] = str(data_folder.resolve())
+    os.environ[CONFIG] = str(config.path.resolve())
     os.environ[KERNEL_IDLE_MINUTES] = str(kernel_idle_minutes)
     ctx.invoke(
         uvicorn_main,

labnotes-0.0.20/src/labnotes/summarize_config.py

@@ -0,0 +1,26 @@
+from math import prod
+
+# What the runner counts toward repeats.
+COMPLETED_RUN = "exit_code = 0 AND NOT coalesce(excluded, 0)"
+
+
+def summarize_config(config: dict[str, object] | None) -> dict[str, object]:
+    config = config or {}
+    params = config.get("params")
+    varies = {
+        key: values if isinstance(values, list) else [values]
+        for key, values in (params if isinstance(params, dict) else {}).items()
+    }
+    repeats = config.get("repeats", 1) if config else None
+    repeats = repeats if isinstance(repeats, int) else None
+    cells = prod(len(values) for values in varies.values())
+    command = config.get("command")
+    return {
+        "fixed": {},
+        "varies": varies,
+        "cell_count": cells,
+        "runs_per_cell": repeats,
+        "target": cells * repeats if repeats is not None else None,
+        "completed_run": COMPLETED_RUN,
+        "other": {} if command is None else {"command": command},
+    }

{labnotes-0.0.19 → labnotes-0.0.20}/src/labnotes/templates/experiment.html

@@ -1,17 +1,17 @@
 {% extends "base.html" %}
 {% from "macros.html" import meter, percent %}
 {% set e = experiment %}
-{% block title %}{{ e.name }} · labnotes{% endblock %}
-{% block crumbs %}<span class="crumb"><a href="{{ url_for('index') }}">Experiments</a></span><span class="crumb">{{ e.name }}</span>{% endblock %}
+{% block title %}{{ e.display_name }} · labnotes{% endblock %}
+{% block crumbs %}<span class="crumb"><a href="{{ url_for('index') }}">Experiments</a></span><span class="crumb">{{ e.display_name }}</span>{% endblock %}
 {% block main %}
 <section class="intro">
-  <h1>{{ e.name }}</h1>
-  {% if e.study %}<p class="study">{{ e.study }}</p>{% endif %}
+  <h1>{{ e.display_name }}</h1>
+  {% if e.display_name != e.name %}<p class="study">{{ e.name }}</p>{% endif %}
   <nav class="toc">
     <a href="#design">Design</a>
     {% if pivot %}<a href="#progress">Progress</a>{% endif %}
     {% if e.notes %}<a href="#notes">Notes</a>{% endif %}
-    {% if e.study %}<a href="#runs">Runs</a>{% endif %}
+    <a href="#runs">Runs</a>
   </nav>
 </section>
 
@@ -32,7 +32,7 @@
   <div class="figure">
     <div class="figure-label">Cells</div>
     <div class="figure-value">{{ e.cell_count }}</div>
-    <div class="figure-note">{% if e.runs_per_cell %}<span class="num">{{ e.runs_per_cell }}</span> runs each{% else %}no runs_per_cell set{% endif %}</div>
+    <div class="figure-note">{% if e.runs_per_cell %}<span class="num">{{ e.runs_per_cell }}</span> runs each{% else %}no experiment.toml{% endif %}</div>
   </div>
 </section>
 
@@ -68,9 +68,6 @@
     {% endfor %}
     <dt>complete when</dt><dd><code>{{ e.completed_run }}</code></dd>
   </dl>
-  {% if e.missing_columns %}
-  <p class="notice">The runs table has no column for {{ e.missing_columns | join(', ') }}, so progress per cell can't be shown.</p>
-  {% endif %}
 </section>
 
 {% if pivot %}
@@ -120,7 +117,6 @@
 <script src="{{ asset('run-cell.js') }}" defer></script>
 {% endif %}
 
-{% if e.study %}
 <section id="runs" class="block">
   {% set view = e.run_view %}
   {% set narrowed = view.status or view.filters %}
@@ -164,8 +160,7 @@
     {% endfor %}
   </div>
   {% else %}
-  <p class="empty">No runs recorded for <code>{{ e.study }}</code> yet.</p>
+  <p class="empty">No runs recorded yet.</p>
   {% endif %}
 </section>
-{% endif %}
 {% endblock %}

{labnotes-0.0.19 → labnotes-0.0.20}/src/labnotes/templates/index.html

@@ -28,8 +28,8 @@
     {% for experiment in experiments %}
     <tr>
       <td>
-        <a class="title-link" href="{{ url_for('experiment', name=experiment.name) }}">{{ experiment.name }}</a>
-        {% if experiment.study %}<div class="study">{{ experiment.study }}</div>{% endif %}
+        <a class="title-link" href="{{ url_for('experiment', name=experiment.name) }}">{{ experiment.display_name }}</a>
+        {% if experiment.display_name != experiment.name %}<div class="study">{{ experiment.name }}</div>{% endif %}
       </td>
       <td class="design">
         {% for key, values in experiment.varies.items() %}<span class="factor">{{ key }} <b>{{ values | length }}</b>{% if not loop.last or experiment.runs_per_cell %}<span class="times">×</span>{% endif %}</span> {% endfor %}
@@ -52,6 +52,6 @@
 <script src="{{ asset('view-toggle.js') }}" defer></script>
 <script src="{{ asset('row-link.js') }}" defer></script>
 {% else %}
-<p class="empty">No experiments found. Each experiment is a folder holding a <code>design.yaml</code> and its markdown notes.</p>
+<p class="empty">No experiments found. Create one with <code>labnotes experiments new</code>.</p>
 {% endif %}
 {% endblock %}

{labnotes-0.0.19 → labnotes-0.0.20}/uv.lock

@@ -479,7 +479,6 @@ dependencies = [
     { name = "jinja2" },
     { name = "jupyter-client" },
     { name = "markdown-it-py" },
-    { name = "pyyaml" },
     { name = "rich" },
     { name = "starlette" },
     { name = "textual" },
@@ -492,7 +491,6 @@ dev = [
     { name = "mypy" },
     { name = "pytest" },
     { name = "ruff" },
-    { name = "types-pyyaml" },
 ]
 
 [package.metadata]
@@ -505,7 +503,6 @@ requires-dist = [
     { name = "jinja2", specifier = ">=3.1.6" },
     { name = "jupyter-client", specifier = ">=8.10.0" },
     { name = "markdown-it-py", specifier = ">=4.2.0" },
-    { name = "pyyaml", specifier = ">=6.0.3" },
     { name = "rich", specifier = ">=14" },
     { name = "starlette", specifier = ">=1.8.0" },
     { name = "textual", specifier = ">=8.2.8" },
@@ -518,7 +515,6 @@ dev = [
     { name = "mypy", specifier = ">=2.4.0" },
     { name = "pytest", specifier = ">=8.0" },
     { name = "ruff", specifier = "==0.8.4" },
-    { name = "types-pyyaml", specifier = ">=6.0.12.20260906" },
 ]
 
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 version = "27.2.0"
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labnotes-0.0.19/src/labnotes/list_experiments.py

@@ -1,23 +0,0 @@
-import json
-
-from dirsql import DirSQL
-
-from labnotes.run_columns import run_columns
-from labnotes.study_progress import study_progress
-from labnotes.summarize_design import summarize_design
-
-
-async def list_experiments(
-    experiments: DirSQL, runs: DirSQL
-) -> list[dict[str, object]]:
-    rows = await experiments.query(
-        "SELECT name, study, design FROM experiments ORDER BY name"
-    )
-    columns = await run_columns(runs)
-    listed = []
-    for row in rows:
-        summary = summarize_design(json.loads(str(row["design"])))
-        study = None if row["study"] is None else str(row["study"])
-        progress = await study_progress(runs, study, summary, columns)
-        listed.append({"name": row["name"], "study": study, **summary, **progress})
-    return listed

labnotes-0.0.19/src/labnotes/open_experiments.py

@@ -1,26 +0,0 @@
-from pathlib import Path
-
-from dirsql import DirSQL, Table
-
-from labnotes.read_design import read_design
-from labnotes.read_note import read_note
-
-
-def open_experiments(folder: Path) -> DirSQL:
-    return DirSQL(
-        str(folder),
-        tables=[
-            Table(
-                name="experiments",
-                ddl="CREATE TABLE experiments (name TEXT, study TEXT, design TEXT)",
-                glob="*/design.yaml",
-                on_file=read_design,
-            ),
-            Table(
-                name="notes",
-                ddl="CREATE TABLE notes (experiment TEXT, name TEXT, content TEXT)",
-                glob="*/*.md",
-                on_file=read_note,
-            ),
-        ],
-    )

labnotes-0.0.19/src/labnotes/open_runs.py

@@ -1,13 +0,0 @@
-from pathlib import Path
-
-from dirsql import DirSQL
-
-
-def open_runs(folder: Path) -> DirSQL:
-    config = folder / ".dirsql.toml"
-    if not config.is_file():
-        raise FileNotFoundError(
-            f"{config} not found; the data folder needs a dirsql config"
-        )
-    # Run data is usually gitignored (DVC, large outputs), so scan it anyway.
-    return DirSQL(str(folder), config=[str(config)], no_ignore=True)

labnotes-0.0.19/src/labnotes/read_design.py

@@ -1,15 +0,0 @@
-import json
-from pathlib import Path
-
-import yaml
-
-
-def read_design(path: str) -> list[dict[str, object]]:
-    design = yaml.safe_load(Path(path).read_text(encoding="utf-8")) or {}
-    return [
-        {
-            "name": Path(path).parent.name,
-            "study": design.get("study"),
-            "design": json.dumps(design),
-        }
-    ]

labnotes-0.0.19/src/labnotes/read_note.py

@@ -1,12 +0,0 @@
-from pathlib import Path
-
-
-def read_note(path: str) -> list[dict[str, object]]:
-    note = Path(path)
-    return [
-        {
-            "experiment": note.parent.name,
-            "name": note.name,
-            "content": note.read_text(encoding="utf-8"),
-        }
-    ]

labnotes-0.0.19/src/labnotes/run_columns.py

@@ -1,6 +0,0 @@
-from dirsql import DirSQL
-
-
-async def run_columns(runs: DirSQL) -> list[str]:
-    rows = await runs.query("SELECT name FROM pragma_table_info('runs')")
-    return [str(row["name"]) for row in rows]

labnotes-0.0.19/src/labnotes/study_progress.py

@@ -1,38 +0,0 @@
-from typing import cast
-
-from dirsql import DirSQL
-
-from labnotes.cell_progress import cell_progress
-from labnotes.count_runs import count_runs
-from labnotes.study_runs import study_runs
-
-
-async def study_progress(
-    runs: DirSQL, study: str | None, summary: dict[str, object], columns: list[str]
-) -> dict[str, object]:
-    varies = cast(dict[str, list[object]], summary["varies"])
-    completed_run = str(summary["completed_run"])
-    runs_per_cell = summary["runs_per_cell"]
-    missing = [key for key in varies if key not in columns]
-    progress: dict[str, object] = {
-        "runs": 0,
-        "completed": 0,
-        "filled": None,
-        "cells": [],
-        "missing_columns": missing,
-    }
-    if study is None:
-        return progress
-    source = study_runs(study)
-    [totals] = await count_runs(runs, source, completed_run)
-    progress.update(totals)
-    if missing:
-        return progress
-    grouped = await count_runs(runs, source, completed_run, group_by=list(varies))
-    cells = cell_progress(varies, grouped)
-    progress["cells"] = cells
-    if isinstance(runs_per_cell, int):
-        progress["filled"] = sum(
-            min(cast(int, cell["completed"]), runs_per_cell) for cell in cells
-        )
-    return progress

labnotes-0.0.19/src/labnotes/study_runs.py

@@ -1,5 +0,0 @@
-from labnotes.sql_quote import quote_string
-
-
-def study_runs(study: str) -> str:
-    return f"(SELECT * FROM runs WHERE study = {quote_string(study)})"

labnotes-0.0.19/src/labnotes/summarize_design.py

@@ -1,23 +0,0 @@
-from math import prod
-
-
-def summarize_design(design: dict[str, object]) -> dict[str, object]:
-    fixed = design.get("fixed")
-    varies = design.get("varies")
-    fixed = fixed if isinstance(fixed, dict) else {}
-    varies = {
-        key: values if isinstance(values, list) else [values]
-        for key, values in (varies if isinstance(varies, dict) else {}).items()
-    }
-    runs_per_cell = design.get("runs_per_cell")
-    cells = prod(len(values) for values in varies.values())
-    known = {"study", "fixed", "varies", "runs_per_cell", "completed_run"}
-    return {
-        "fixed": fixed,
-        "varies": varies,
-        "cell_count": cells,
-        "runs_per_cell": runs_per_cell,
-        "target": cells * runs_per_cell if isinstance(runs_per_cell, int) else None,
-        "completed_run": str(design.get("completed_run") or "1"),
-        "other": {key: value for key, value in design.items() if key not in known},
-    }