Merge pull request #103 from MilagrosMarin/main

Update setup dependencies + fix YAML bug + fix diagram + fix typo in docstring + tutorial setup

CHANGELOG.md

@@ -3,6 +3,14 @@
 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] - 2023-01-04
+
++ 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
 
 + Fix - Revert fixing of networkx version in setup 

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", "")

element_deeplabcut/model.py

@@ -7,7 +7,7 @@
 import os
 import cv2
 import csv
-import yaml
+from ruamel.yaml import YAML
 import inspect
 import importlib
 import numpy as np
@@ -239,8 +239,9 @@ def extract_new_body_parts(cls, dlc_config: dict, verbose: bool = True):
                 ".yaml",
             ), f"dlc_config is neither dict nor filepath\n Check: {dlc_config_fp}"
             if dlc_config_fp.suffix in (".yml", ".yaml"):
+                yaml = YAML(typ="safe", pure=True)
                 with open(dlc_config_fp, "rb") as f:
-                    dlc_config = yaml.safe_load(f)
+                    dlc_config = yaml.load(f)
         # -- Check and insert new BodyPart --
         assert "bodyparts" in dlc_config, f"Found no bodyparts section in {dlc_config}"
         tracked_body_parts = cls.fetch("body_part")
@@ -307,7 +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:
@@ -381,8 +382,9 @@ def insert_new_model(
             "dlc_config is not a filepath" + f"\n Check: {dlc_config_fp}"
         )
         if dlc_config_fp.suffix in (".yml", ".yaml"):
+            yaml = YAML(typ="safe", pure=True)
             with open(dlc_config_fp, "rb") as f:
-                dlc_config = yaml.safe_load(f)
+                dlc_config = yaml.load(f)
         if isinstance(params, dict):
             dlc_config.update(params)
 

element_deeplabcut/readers/dlc_reader.py

@@ -4,7 +4,7 @@
 import pandas as pd
 from pathlib import Path
 import pickle
-import ruamel.yaml as yaml
+from ruamel.yaml import YAML
 from element_interface.utils import find_root_directory, dict_to_uuid
 from .. import model
 from ..model import get_dlc_root_data_dir
@@ -145,7 +145,8 @@ def yml(self):
         """json-structured config.yaml file contents"""
         if self._yml is None:
             with open(self.yml_path, "rb") as f:
-                self._yml = yaml.safe_load(f)
+                yaml = YAML(typ="safe", pure=True)
+                self._yml = yaml.load(f)
         return self._yml
 
     @property

element_deeplabcut/version.py

@@ -1,4 +1,4 @@
 """
 Package metadata
 """
-__version__ = "0.2.10"
+__version__ = "0.2.11"

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):

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",
         ],
     },
 )