Dev

.github/workflows/main.yml

@@ -86,7 +86,8 @@ jobs:
         run: |
           git config user.name github-actions
           git config user.email [email protected]
-          git commit -m "GitHub Actions generated requirements_frozen.txt" -a
+          git add requirements_frozen.txt
+          git commit -m "GitHub Actions generated requirements_frozen.txt"
           git push
 
       # Docker steps only run when master branch pushed to directly OR when a PR is merged

alyx/actions/views.py

@@ -457,7 +457,10 @@ def get(self, request, format=None, nickname=None):
         end_date = request.query_params.get('end_date', None)
         subject = Subject.objects.get(nickname=nickname)
         records = subject.water_control.to_jsonable(start_date=start_date, end_date=end_date)
-        data = {'subject': nickname, 'implant_weight': subject.implant_weight, 'records': records}
+        data = {'subject': nickname, 'implant_weight': subject.implant_weight,
+                'reference_weight_pct': subject.water_control.reference_weight_pct,
+                'zscore_weight_pct': subject.water_control.zscore_weight_pct,
+                'records': records}
         return Response(data)
 
 

alyx/actions/water_control.py

@@ -8,6 +8,7 @@
 from operator import attrgetter, itemgetter
 import os.path as op
 
+from django.conf import settings
 from django.urls import reverse
 from django.utils.html import format_html
 from django.http import HttpResponse
@@ -563,7 +564,9 @@ def water_control(subject):
         implant_weight=subject.implant_weight
     )
     wc.add_threshold(percentage=rw_pct + zw_pct, bgcolor=PALETTE['orange'], fgcolor='#FFC28E')
-    wc.add_threshold(percentage=.7, bgcolor=PALETTE['red'], fgcolor='#F08699', line_style='--')
+    if absolute_min := settings.WEIGHT_THRESHOLD:
+        wc.add_threshold(
+            percentage=absolute_min, bgcolor=PALETTE['red'], fgcolor='#F08699', line_style='--')
     # Water restrictions.
     wrs = sorted(list(subject.actions_waterrestrictions.all()), key=attrgetter('start_time'))
     # Reference weight.

alyx/alyx/settings_lab_template.py

@@ -10,7 +10,7 @@
 DEFAULT_PROTOCOL = '1'
 SUPERUSERS = ('root',)
 STOCK_MANAGERS = ('root',)
-WEIGHT_THRESHOLD = 0.75
+WEIGHT_THRESHOLD = 0.8  # Absolute minimum weight threshold (red line in plots)
 DEFAULT_LAB_NAME = 'defaultlab'
 WATER_RESTRICTIONS_EDITABLE = False  # if set to True, all users can edit water restrictions
 DEFAULT_LAB_PK = '4027da48-7be3-43ec-a222-f75dffe36872'

alyx/experiments/serializers.py

@@ -46,15 +46,6 @@ class TrajectoryEstimateSerializer(serializers.ModelSerializer):
         queryset=CoordinateSystem.objects.all(),
     )
 
-    def to_internal_value(self, data):
-        if data.get('chronic_insertion', None) is None:
-            data['chronic_insertion'] = None
-
-        if data.get('probe_insertion', None) is None:
-            data['probe_insertion'] = None
-
-        return super(TrajectoryEstimateSerializer, self).to_internal_value(data)
-
     class Meta:
         model = TrajectoryEstimate
         fields = '__all__'

alyx/experiments/tests_rest.py

@@ -185,6 +185,7 @@ def test_create_list_delete_trajectory(self):
         # create a trajectory
         url = reverse('trajectoryestimate-list')
         tdict = {'probe_insertion': alyx_insertion['id'],
+                 'chronic_insertion': None,
                  'x': -4521.2,
                  'y': 2415.0,
                  'z': 0,
@@ -216,6 +217,7 @@ def test_create_list_delete_channels(self):
         # create the probe insertion
         pi = self.ar(self.post(reverse('probeinsertion-list'), self.dict_insertion), 201)
         tdict = {'probe_insertion': pi['id'],
+                 'chronic_insertion': None,
                  'x': -4521.2,
                  'y': 2415.0,
                  'z': 0,
@@ -273,6 +275,7 @@ def test_chronic_insertion(self):
 
         # create a trajectory and attach it to the chronic insertion
         traj_dict = {'chronic_insertion': ci['id'],
+                     'probe_insertion': None,
                      'x': -4521.2,
                      'y': 2415.0,
                      'z': 0,

alyx/subjects/serializers.py

@@ -28,10 +28,18 @@ def get_reference_weight(self, obj):
     def get_last_water_restriction(self, obj):
         return obj.water_control.water_restriction_at()
 
+    def get_reference_weight_pct(self, obj):
+        return obj.water_control.reference_weight_pct
+
+    def get_zscore_weight_pct(self, obj):
+        return obj.water_control.zscore_weight_pct
+
     expected_water = serializers.SerializerMethodField()
     remaining_water = serializers.SerializerMethodField()
     reference_weight = serializers.SerializerMethodField()
     last_water_restriction = serializers.SerializerMethodField()
+    reference_weight_pct = serializers.SerializerMethodField()
+    zscore_weight_pct = serializers.SerializerMethodField()
 
 
 class WaterRestrictedSubjectListSerializer(_WaterRestrictionBaseSerializer):
@@ -42,6 +50,8 @@ class Meta:
                   'remaining_water',
                   'reference_weight',
                   'last_water_restriction',
+                  'reference_weight_pct',
+                  'zscore_weight_pct'
                   )
 
         lookup_field = 'nickname'

requirements.txt

@@ -28,4 +28,4 @@ python-magic
 pytz
 structlog>=21.5.0
 webdavclient3
-ONE-api~=2.7rc0
+ONE-api>=2.7

requirements_frozen.txt

@@ -1,7 +1,7 @@
 asgiref==3.8.1
 backports.zoneinfo==0.2.1
-boto3==1.34.70
-botocore==1.34.70
+boto3==1.34.84
+botocore==1.34.84
 certifi==2024.2.2
 cffi==1.16.0
 charset-normalizer==3.3.2
@@ -16,11 +16,11 @@ cryptography==42.0.5
 cycler==0.12.1
 Django==4.2.11
 django-admin-list-filter-dropdown==1.0.3
-django-admin-rangefilter==0.12.1
+django-admin-rangefilter==0.12.4
 django-autocomplete-light==3.11.0
 django-cleanup==8.1.0
-django-filter==24.1
-django-ipware==6.0.4
+django-filter==24.2
+django-ipware==6.0.5
 django-js-asset==2.2.0
 django-mptt==0.14.0
 django-polymorphic==3.1.0
@@ -33,9 +33,9 @@ docopt==0.6.2
 docutils==0.20.1
 drfdocs==0.0.11
 flake8==7.0.0
-fonttools==4.50.0
-globus-cli==3.26.0
-globus-sdk==3.37.0
+fonttools==4.51.0
+globus-cli==3.27.0
+globus-sdk==3.39.0
 iblutil==1.8.0
 idna==3.7
 importlib_metadata==7.1.0
@@ -45,7 +45,7 @@ Jinja2==3.1.3
 jmespath==1.0.1
 kiwisolver==1.4.5
 llvmlite==0.41.1
-lxml==5.1.0
+lxml==5.2.1
 Markdown==3.6
 MarkupSafe==2.1.5
 matplotlib==3.7.5
@@ -59,22 +59,22 @@ pillow==10.3.0
 psycopg2-binary==2.9.9
 pyarrow==15.0.2
 pycodestyle==2.11.1
-pycparser==2.21
+pycparser==2.22
 pyflakes==3.2.0
 PyJWT==2.8.0
 pyparsing==3.1.2
 python-dateutil==2.9.0.post0
-python-ipware==2.0.2
+python-ipware==2.0.3
 python-magic==0.4.27
 pytz==2024.1
 PyYAML==6.0.1
 requests==2.31.0
 s3transfer==0.10.1
 six==1.16.0
-sqlparse==0.4.4
+sqlparse==0.5.0
 structlog==24.1.0
 tqdm==4.66.2
-typing_extensions==4.10.0
+typing_extensions==4.11.0
 tzdata==2024.1
 uritemplate==4.1.1
 urllib3==1.26.18

scripts/sync_ucl/prune_cortexlab.py

@@ -45,8 +45,7 @@
 
 # the sessions should also have the cortexlab lab field properly labeled before import
 if Lab.objects.using('cortexlab').filter(name='cortexlab').count() == 0:
-    lab_dict = {'pk': CORTEX_LAB_PK,
-                'name': 'cortexlab'}
+    lab_dict = {'pk': CORTEX_LAB_PK, 'name': 'cortexlab'}
     lab = Lab.objects.using('cortexlab').create(**lab_dict)
     lab.save()
 else: