Merge branch 'main' of https://github.com/datajoint/element-deeplabcut

sidhulyalkar · Jan 5, 2024 · 50f0d43 · 50f0d43
2 parents b4a6ae0 + 499d85e
commit 50f0d43
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,9 +3,13 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and 
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
-## [0.2.11] - 2023-11-28
+## [0.2.11] - 2023-01-04
 
-+ Fix - Modify training to update init_weights path in pose_cfg.yaml
++ Fix - docstring typo
++ Fix - `dj.config()` setup moved to `tutorial_pipeline.py` instead of `__init__.py`
++ Bugfix - Resolved AttributeError from the latest update of the YAML dependency
++ Update - Flowchart images to increase consistency with other DataJoint Elements
++ Update - Elements installed directly from GitHub instead of PyPI
 
 ## [0.2.10] - 2023-11-20
 

diff --git a/docs/src/.overrides/assets/stylesheets/extra.css b/docs/src/.overrides/assets/stylesheets/extra.css
@@ -92,7 +92,6 @@ html a[title="YouTube"].md-social__link svg {
     /* --md-footer-fg-color: var(--dj-white); */
 }
 
-[data-md-color-scheme="slate"] td,
-th {
+[data-md-color-scheme="slate"] .jupyter-wrapper .Table Td {
     color: var(--dj-black)
 }
diff --git a/element_deeplabcut/__init__.py b/element_deeplabcut/__init__.py
@@ -1,21 +1 @@
-import os
-import datajoint as dj
 
-if "custom" not in dj.config:
-    dj.config["custom"] = {}
-
-# overwrite dj.config['custom'] values with environment variables if available
-
-dj.config["custom"]["database.prefix"] = os.getenv(
-    "DATABASE_PREFIX", dj.config["custom"].get("database.prefix", "")
-)
-
-dj.config["custom"]["dlc_root_data_dir"] = os.getenv(
-    "DLC_ROOT_DATA_DIR", dj.config["custom"].get("dlc_root_data_dir", "")
-)
-
-dj.config["custom"]["dlc_processed_data_dir"] = os.getenv(
-    "DLC_PROCESSED_DATA_DIR", dj.config["custom"].get("dlc_processed_data_dir", "")
-)
-
-db_prefix = dj.config["custom"].get("database.prefix", "")
diff --git a/element_deeplabcut/model.py b/element_deeplabcut/model.py
@@ -308,7 +308,7 @@ class Model(dj.Manual):
         config_template (longblob): Dictionary of the config for analyze_videos().
         project_path ( varchar(255) ): DLC's project_path in config relative to root.
         model_prefix ( varchar(32) ): Optional. Prefix for model files.
-        model_description ( varchar(1000) ): Optional. User-entered description.
+        model_description ( varchar(300) ): Optional. User-entered description.
         TrainingParamSet (foreign key): Optional. Training parameters primary key.
 
     Note:

diff --git a/images/flowchart.drawio b/images/flowchart.drawio
diff --git a/images/flowchart.svg b/images/flowchart.svg
diff --git a/notebooks/tutorial.ipynb b/notebooks/tutorial.ipynb
diff --git a/notebooks/tutorial_pipeline.py b/notebooks/tutorial_pipeline.py
@@ -1,3 +1,4 @@
+import os
 import datajoint as dj
 from collections import abc
 from element_lab import lab
@@ -8,22 +9,31 @@
 from element_animal.subject import Subject
 from element_lab.lab import Source, Lab, Protocol, User, Project
 
-__all__ = [
-    "Subject",
-    "Source",
-    "Lab",
-    "Protocol",
-    "User",
-    "Project",
-    "Session",
-]
+
+if "custom" not in dj.config:
+    dj.config["custom"] = {}
+
+# overwrite dj.config['custom'] values with environment variables if available
+
+dj.config["custom"]["database.prefix"] = os.getenv(
+    "DATABASE_PREFIX", dj.config["custom"].get("database.prefix", "")
+)
+
+dj.config["custom"]["dlc_root_data_dir"] = os.getenv(
+    "DLC_ROOT_DATA_DIR", dj.config["custom"].get("dlc_root_data_dir", "")
+)
+
+dj.config["custom"]["dlc_processed_data_dir"] = os.getenv(
+    "DLC_PROCESSED_DATA_DIR", dj.config["custom"].get("dlc_processed_data_dir", "")
+)
 
 if "custom" not in dj.config:
     dj.config["custom"] = {}
 
 db_prefix = dj.config["custom"].get("database.prefix", "")
 
 
+# Declare functions for retrieving data
 def get_dlc_root_data_dir() -> list:
     """Returns a list of root directories for Element DeepLabCut"""
     dlc_root_dirs = dj.config.get("custom", {}).get("dlc_root_data_dir")
@@ -46,18 +56,24 @@ def get_dlc_processed_data_dir() -> str:
         return None
 
 
-# Activate "lab", "subject", "session" schema -------------
+__all__ = [
+    "Subject",
+    "Source",
+    "Lab",
+    "Protocol",
+    "User",
+    "Project",
+    "Session",
+]
+
+# Activate schemas -------------
 
 lab.activate(db_prefix + "lab")
-
 subject.activate(db_prefix + "subject", linking_module=__name__)
-
 Experimenter = lab.User
 Session = session.Session
 session.activate(db_prefix + "session", linking_module=__name__)
 
-# Activate equipment table ------------------------------------
-
 
 @lab.schema
 class Device(dj.Lookup):

diff --git a/setup.py b/setup.py
@@ -24,7 +24,7 @@
     packages=find_packages(exclude=["contrib", "docs", "tests*"]),
     scripts=[],
     install_requires=[
-        "datajoint>=0.13",
+        "datajoint>=0.13.0",
         "graphviz",
         "pydot",
         "ipykernel",
@@ -40,10 +40,10 @@
         ],
         "dlc_gui": ["deeplabcut[gui]"],
         "elements": [
-            "element-lab>=0.3.0",
-            "element-animal>=0.1.8",
-            "element-session>=0.1.5",
-            "element-interface>=0.6.0",
+            "element-lab @ git+https://github.com/datajoint/element-lab.git",
+            "element-animal @ git+https://github.com/datajoint/element-animal.git",
+            "element-session @ git+https://github.com/datajoint/element-session.git",
+            "element-interface @ git+https://github.com/datajoint/element-interface.git",
         ],
     },
 )