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AllenInstitute · Oct 1, 2024 · 85caa3b · 85caa3b
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,13 +8,31 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 <!-- insertion marker -->
 ## Unreleased
 
-<small>[Compare with latest](https://github.com/AllenInstitute/npc_lims/compare/v0.1.175...HEAD)</small>
+<small>[Compare with latest](https://github.com/AllenInstitute/npc_lims/compare/v0.1.176...HEAD)</small>
+
+### 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).
 
 <!-- insertion marker -->
+## [v0.1.176](https://github.com/AllenInstitute/npc_lims/releases/tag/v0.1.176) - 2024-09-21
+
+<small>[Compare with v0.1.175](https://github.com/AllenInstitute/npc_lims/compare/v0.1.175...v0.1.176)</small>
+
+### 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
 
 <small>[Compare with v0.1.174](https://github.com/AllenInstitute/npc_lims/compare/v0.1.174...v0.1.175)</small>

diff --git a/npc_lims b/npc_lims
diff --git 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 = "[email protected]" },

diff --git 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():