WIP: Apply suggestions 1

Co-authored-by: Kabilar Gunalan <[email protected]>

CHANGELOG.md

@@ -3,6 +3,23 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and 
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
-## [0.1.0] - 2021-05-04
-### Added
-+ Added version
+
+## 0.1.1 - 2022-07-05
++ Update - Docker and Compose files
++ Update - Requirements for latest releases of Elements
++ Update - Workflow pipeline, ingestion, and populate scripts
++ Update - Pytests
++ Add - Code of conduct
+
+## 0.1.0 - 2022-04-30
++ Add - Analysis schema and Jupyter notebook for event-aligned calcium activity
++ Add - Data exploration Jupyter notebook
++ Add - Docker and Compose files
++ Update - Pytests
++ Update - README
+
+## 0.1.0a2 - 2021-10-18
++ Update - Change version to reflect release phase
+
+## 0.1.1 - 2021-04-01
++ Add - Version

docker/Dockerfile.test

@@ -1,6 +1,5 @@
 FROM datajoint/djbase:py3.9-debian-8eb1715
 
-ARG GITHUB_USERNAME=datajoint
 USER anaconda:anaconda
 
 COPY ./docker/apt_requirements.txt /tmp/

docker/docker-compose-test.yaml

@@ -8,16 +8,8 @@ services:
     networks:
       miniscope:
     image: datajoint/mysql:5.7
-    # image: mysql:5-debian
-    # platform: linux/amd64
-    # command: --default-authentication-plugin=mysql_native_password
-    # restart: always
     environment:
       MYSQL_ROOT_PASSWORD: simple
-    #   MYSQL_USER: datajoint
-    #   MYSQL_PASSWORD: datajoint
-    # volumes:
-    #   - mysql-miniscope:/var/lib/mysql
     container_name: workflow-miniscope-test-db
 
   workflow:

requirements.txt

@@ -1,8 +1,9 @@
 datajoint>=0.13.0
-element-lab>=0.1.0b0
-element-animal>=0.1.0b0
-element-session>=0.1.0b0
-element-miniscope>=0.1.0
+element-lab>=0.1.1
+element-animal>=0.1.2
+element-session>=0.1.2
+element-event @ git+https://github.com/datajoint/element-event.git
+element-miniscope @ git+https://github.com/datajoint/element-miniscope.git
 element-interface @ git+https://github.com/datajoint/element-interface.git
 djarchive-client @ git+https://github.com/datajoint/djarchive-client.git
 jupytext>=1.13.7

tests/__init__.py

@@ -13,7 +13,6 @@
 import sys
 from element_interface.utils import find_full_path
 
-# from workflow_miniscope.paths import get_miniscope_root_data_dir
 
 # ------------------- SOME CONSTANTS -------------------
 
@@ -89,13 +88,11 @@ def test_data(dj_config):
                 f'\nError: {str(e)}')
 
         import djarchive_client
-        from workflow_miniscope import version
 
         client = djarchive_client.client()
-        workflow_version = version.__version__
 
         client.download('workflow-miniscope-test-set',
-                        workflow_version.replace('.', '_'),
+                        'v1',
                         str(test_data_dir), create_target=False)
     return
 
@@ -178,9 +175,7 @@ def sessions_csv():
 def ingest_sessions(ingest_subjects, sessions_csv):
     from workflow_miniscope.ingest import ingest_sessions
     _, sessions_csv_path = sessions_csv
-    # if not tear_down, skip duplicates
-    skip_duplicates = not _tear_down
-    ingest_sessions(sessions_csv_path, skip_duplicates=skip_duplicates, verbose=verbose)
+    ingest_sessions(sessions_csv_path, verbose=verbose)
     return
 
 

tests/test_ingest.py

@@ -18,6 +18,7 @@ def test_ingest_subjects(pipeline, ingest_subjects):
 
 def test_ingest_sessions(pipeline, sessions_csv, ingest_sessions):
     session = pipeline['session']
+    miniscope = pipeline['miniscope']
     get_miniscope_root_data_dir = pipeline['get_miniscope_root_data_dir']
 
     assert len(session.Session()) == 1

workflow_miniscope/ingest.py

@@ -20,8 +20,7 @@ def ingest_subjects(subject_csv_path='./user_data/subjects.csv',
     ingest_csv_to_table(csvs, tables, skip_duplicates=skip_duplicates, verbose=verbose)
 
 
-def ingest_sessions(session_csv_path='./user_data/sessions.csv', skip_duplicates=False,
-                    verbose=True):
+def ingest_sessions(session_csv_path='./user_data/sessions.csv', verbose=True):
     if verbose:
         print('\n---- Insert new `Session` and `Recording` ----')
     with open(session_csv_path, newline='') as f:
@@ -84,13 +83,13 @@ def ingest_sessions(session_csv_path='./user_data/sessions.csv', skip_duplicates
 
     if verbose:
         print(f'\n---- Insert {len(session_list)} entry(s) into session.Session ----')
-    session.Session.insert(session_list, skip_duplicates=skip_duplicates)
-    session.SessionDirectory.insert(session_dir_list, skip_duplicates=skip_duplicates)
+    session.Session.insert(session_list)
+    session.SessionDirectory.insert(session_dir_list)
 
     if verbose:
         print(f'\n---- Insert {len(recording_list)} entry(s) into '
               + 'miniscope.Recording ----')
-    miniscope.Recording.insert(recording_list, skip_duplicates=skip_duplicates)
+    miniscope.Recording.insert(recording_list)
 
     if verbose:
         print('\n---- Successfully completed ingest_sessions ----')

workflow_miniscope/populate.py

@@ -12,36 +12,25 @@ def populate(display_progress=True, reserve_jobs=False, suppress_errors=False,
                          'suppress_errors': suppress_errors}
 
     if verbose:
-        print('\n---- Populate miniscope.ScanInfo ----')
-    miniscope.ScanInfo.populate(**populate_settings)
+        print("\n---- Populate imported and computed tables ----")
+
+    miniscope.RecordingInfo.populate(**populate_settings)
 
-    if verbose:
-        print('\n---- Populate miniscope.Processing ----')
     miniscope.Processing.populate(**populate_settings)
 
     if verbose:
         print('\n---- Populate miniscope.MotionCorrection ----')
     miniscope.MotionCorrection.populate(**populate_settings)
 
-    if verbose:
-        print('\n---- Populate miniscope.Segmentation ----')
     miniscope.Segmentation.populate(**populate_settings)
 
-    if verbose:
-        print('\n---- Populate miniscope.MaskClassification ----')
-    miniscope.MaskClassification.populate(**populate_settings)
-
-    if verbose:
-        print('\n---- Populate miniscope.Fluorescence ----')
     miniscope.Fluorescence.populate(**populate_settings)
 
-    if verbose:
-        print('\n---- Populate miniscope.Activity ----')
     miniscope.Activity.populate(**populate_settings)
 
     if verbose:
-        print('\n---- Successfully completed workflow_calcium_imaging/populate.py ----')
+        print('\n---- Successfully completed workflow_miniscope/populate.py ----')
 
 
 if __name__ == '__main__':
-    populate()
+    run()