diff --git a/CHANGELOG.md b/CHANGELOG.md
index 39db160..6256f03 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,13 +8,31 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
## Unreleased
-[Compare with latest](https://github.com/AllenInstitute/npc_lims/compare/v0.1.175...HEAD)
+[Compare with latest](https://github.com/AllenInstitute/npc_lims/compare/v0.1.176...HEAD)
+
+### Added
+
+- Add sessions from notebook ([cd40392](https://github.com/AllenInstitute/npc_lims/commit/cd40392c77a6ca66c12c2111e893d4f04b884e08) by bjhardcastle).
### Fixed
-- Fix previous ([f12d318](https://github.com/AllenInstitute/npc_lims/commit/f12d3184042d16e98918a4f64b62fefbe24ea77c) by bjhardcastle).
+- Fix type ([11aaf3b](https://github.com/AllenInstitute/npc_lims/commit/11aaf3b36b4e396127748b535d57f0e4897c90a0) by bjhardcastle).
+- Fix getting `is_templeton` from tracked_sessions.yaml ([05e9d84](https://github.com/AllenInstitute/npc_lims/commit/05e9d848d998154b9da7ac545a28f19169200ced) by bjhardcastle).
+
+### Removed
+
+- Remove duplicate sessions ([c90c4d0](https://github.com/AllenInstitute/npc_lims/commit/c90c4d0c78f3de5999cec9d86dfbc3b95e5d2091) by bjhardcastle).
+- Remove hard-coded sorted data asset for session ([95dec71](https://github.com/AllenInstitute/npc_lims/commit/95dec71033c9bda9064f818060fb0d01a61f368c) by bjhardcastle).
+## [v0.1.176](https://github.com/AllenInstitute/npc_lims/releases/tag/v0.1.176) - 2024-09-21
+
+[Compare with v0.1.175](https://github.com/AllenInstitute/npc_lims/compare/v0.1.175...v0.1.176)
+
+### Fixed
+
+- Fix previous ([f12d318](https://github.com/AllenInstitute/npc_lims/commit/f12d3184042d16e98918a4f64b62fefbe24ea77c) by bjhardcastle).
+
## [v0.1.175](https://github.com/AllenInstitute/npc_lims/releases/tag/v0.1.175) - 2024-09-18
[Compare with v0.1.174](https://github.com/AllenInstitute/npc_lims/compare/v0.1.174...v0.1.175)
diff --git a/npc_lims b/npc_lims
index f12d318..11aaf3b 160000
--- a/npc_lims
+++ b/npc_lims
@@ -1 +1 @@
-Subproject commit f12d3184042d16e98918a4f64b62fefbe24ea77c
+Subproject commit 11aaf3b36b4e396127748b535d57f0e4897c90a0
diff --git a/pyproject.toml b/pyproject.toml
index 2733456..339edeb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
[project]
name = "npc_lims"
-version = "0.1.176"
+version = "0.1.177"
description = "Tools to fetch and update paths, metadata and state for Mindscope Neuropixels sessions, in the cloud."
authors = [
{ name = "Arjun Sridhar", email = "arjun.sridhar@alleninstitute.org" },
diff --git a/src/npc_lims/status/tracked_sessions.py b/src/npc_lims/status/tracked_sessions.py
index a19a5db..56d19d6 100644
--- a/src/npc_lims/status/tracked_sessions.py
+++ b/src/npc_lims/status/tracked_sessions.py
@@ -590,14 +590,14 @@ def _get_session_info_from_file(ttl_hash: int | None = None) -> tuple[SessionInf
f"Add loader for {_TRACKED_SESSIONS_FILE.suffix}"
) # pragma: no cover
+
def _add_session_to_file(
- platform: Literal['ephys', 'behavior', 'behavior_with_sync'],
- project: Literal['DynamicRouting', 'TempletonPilotSession'],
- k: str, v: dict[str, Any],
+ platform: Literal["ephys", "behavior", "behavior_with_sync"],
+ project: Literal["DynamicRouting", "TempletonPilotSession"],
+ k: str,
+ v: dict[str, Any],
) -> None:
- f = yaml.load(
- _TRACKED_SESSIONS_FILE.read_bytes(), Loader=yaml.FullLoader
- )
+ f = yaml.load(_TRACKED_SESSIONS_FILE.read_bytes(), Loader=yaml.FullLoader)
if any(k in entry for entry in f[platform][project]):
print(f"Session {k} already exists in {_TRACKED_SESSIONS_FILE} - skipping")
return
@@ -614,47 +614,60 @@ def _add_session_to_file(
new[platform][project].append({k: v})
new_path.write_text(yaml.dump(new))
+
def add_tracked_ephys_sessions_from_spreadsheet(
- csv_path: str | upath.UPath = "C:/Users/ben.hardcastle/OneDrive - Allen Institute/Shared Documents - Dynamic Routing/Mouse and experiment tracking/Ephys Experiment Tracking.csv"
+ csv_path: (
+ str | upath.UPath
+ ) = "C:/Users/ben.hardcastle/OneDrive - Allen Institute/Shared Documents - Dynamic Routing/Mouse and experiment tracking/Ephys Experiment Tracking.csv",
) -> None:
try:
import polars as pl
except ImportError:
- raise ImportError("Optional dependencies are required to use this function: reinstall with `pip install npc_lims[polars]`")
- df = (
- pl.read_csv(csv_path, infer_schema_length=1000)
- .with_columns(
- pl.col('Date').cum_count().over('Mouse').alias("day"),
+ raise ImportError(
+ "Optional dependencies are required to use this function: reinstall with `pip install npc_lims[polars]`"
)
+ df = pl.read_csv(csv_path, infer_schema_length=1000).with_columns(
+ pl.col("Date").cum_count().over("Mouse").alias("day"),
)
upath.UPath("new_sessions.yaml").unlink(missing_ok=True)
- project = 'DynamicRouting'
- platform = 'ephys'
+ project = "DynamicRouting"
+ platform = "ephys"
for row in df.iter_rows(named=True):
info = {}
session_kwargs = {}
- dc = row['Date'].split('/')
- date: str = f"{dc[2]}{'0' if len(dc[0])<2 else ''}{dc[0]}{'0' if len(dc[1]) < 2 else ''}{dc[1]}"
+ dc = row["Date"].split("/")
+ date: str = (
+ f"{dc[2]}{'0' if len(dc[0])<2 else ''}{dc[0]}{'0' if len(dc[1]) < 2 else ''}{dc[1]}"
+ )
session_id = f"{row['Mouse']}_{date}"
- k: str = f'//allen/programs/mindscope/workgroups/dynamicrouting/PilotEphys/Task 2 pilot/DRpilot_{row["Mouse"]}_{date}'
- probes = ''.join(npc_session.extract_probe_letter(v) or '' for v in row['Probes in brain'])
+ k: str = (
+ f'//allen/programs/mindscope/workgroups/dynamicrouting/PilotEphys/Task 2 pilot/DRpilot_{row["Mouse"]}_{date}'
+ )
+ probes = "".join(
+ npc_session.extract_probe_letter(v) or "" for v in row["Probes in brain"]
+ )
if not probes:
print(f"Skipping {session_id} - no probes")
continue
- session_kwargs['probe_letters_to_skip'] = ''.join(letter for letter in 'ABCDEF' if letter not in probes)
- if (x := row.get('Injection substance', '')) or row.get('is perturbation experiment', None) is not None:
+ session_kwargs["probe_letters_to_skip"] = "".join(
+ letter for letter in "ABCDEF" if letter not in probes
+ )
+ if (x := row.get("Injection substance", "")) or row.get(
+ "is perturbation experiment", None
+ ) is not None:
if x:
- if 'control' in x.lower() or 'acsf' in x.lower():
- session_kwargs['is_injection_control'] = True # type: ignore [assignment]
+ if "control" in x.lower() or "acsf" in x.lower():
+ session_kwargs["is_injection_control"] = True # type: ignore [assignment]
else:
- session_kwargs['is_injection_perturbation'] = True # type: ignore [assignment]
+ session_kwargs["is_injection_perturbation"] = True # type: ignore [assignment]
else:
- session_kwargs['is_perturbation'] = 'unknown_type'
-
- info['day'] = row['day']
- info['session_kwargs'] = session_kwargs
- _add_session_to_file(platform, project, k, info) # type: ignore [arg-type]
-
+ session_kwargs["is_perturbation"] = "unknown_type"
+
+ info["day"] = row["day"]
+ info["session_kwargs"] = session_kwargs
+ _add_session_to_file(platform, project, k, info) # type: ignore [arg-type]
+
+
def _session_info_from_file_contents(contents: FileContents) -> tuple[SessionInfo, ...]:
sessions: MutableSequence[SessionInfo] = []
for session_type, projects in contents.items():