Ci

.github/workflows/main.yml

@@ -46,10 +46,14 @@ jobs:
           pip install coverage coveralls pyarrow pandas  # for one_cache tests
         env:
           PIP_USE_MIRRORS: true
-
+      - name: Ruff
+        run: |
+          ruff check ./alyx
       - name: Run tests
         run: |
-          sudo touch /var/log/alyx.log; sudo chmod 666 /var/log/alyx.log
+          sudo mkdir /var/log/alyx
+          sudo touch /var/log/alyx/django.log
+          sudo chmod 666 /var/log/alyx/django.log
           cd alyx
           cp ./alyx/environment_template.env ./alyx/.env
           cp ../deploy/docker/settings-deploy.py  alyx/settings.py
@@ -61,37 +65,8 @@ jobs:
           DJANGO_SETTINGS_MODULE: alyx.settings
           PYTHONPATH: $HOME/builds/cortexlab/alyx
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          APACHE_LOG_DIR: /var/log/alyx.log
+          APACHE_LOG_DIR: /var/log/alyx
           POSTGRES_HOST: localhost
-      - name: Flake
-        run: |
-          cd alyx
-          flake8 .
-
-      - name: Generate new requirements_frozen.txt if needed
-        # Only runs when branch pushed to directly OR when a PR is merged
-        if: ${{ github.event_name == 'push' }}
-        run: |
-          pip freeze > requirements_frozen_temp.txt
-          if diff requirements_frozen.txt requirements_frozen_temp.txt > /dev/null; then
-            echo "requirements_frozen.txt unchanged"
-            rm requirements_frozen_temp.txt
-            echo "GIT_PUSH_NEEDED=false" >> "$GITHUB_ENV"
-          else
-            echo "requirements_frozen.txt is different, git push needed"
-            mv requirements_frozen_temp.txt requirements_frozen.txt
-            echo "GIT_PUSH_NEEDED=true" >> "$GITHUB_ENV"
-          fi
-
-      - name: Setup git/commit/push for requirements_frozen.txt if needed
-        # Only runs when requirements_frozen.txt is updated
-        if: env.GIT_PUSH_NEEDED == 'true'
-        run: |
-          git config user.name github-actions
-          git config user.email github-actions@github.com
-          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
       - name: Set Docker conditional value if needed

.gitignore

@@ -12,6 +12,9 @@ alyx/alyx/settings.py
 alyx/static/*/*
 scripts/deployment_examples/docker-apache/settings*
 
+# package if installed
+alyx/alyx.egg-info
+
 # other
 *.pyc
 .DS_Store

.readthedocs.yaml

@@ -7,13 +7,9 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
-    python: "3.9"
-    # You can also specify other tool versions:
-    # nodejs: "16"
-    # rust: "1.55"
-    # golang: "1.17"
+    python: "3.12"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

alyx/actions/admin.py

@@ -1,6 +1,6 @@
 import base64
 import json
-import structlog
+import logging
 
 from django import forms
 from django.conf import settings
@@ -27,7 +27,7 @@
 from experiments.models import ProbeInsertion, FOV
 from jobs.models import Task
 
-logger = structlog.get_logger(__name__)
+logger = logging.getLogger(__name__)
 
 
 # Filters

alyx/actions/models.py

@@ -1,7 +1,7 @@
 from datetime import timedelta
 from math import inf
 
-import structlog
+import logging
 from one.alf.spec import QC
 
 from django.conf import settings
@@ -13,7 +13,7 @@
 from misc.models import Lab, LabLocation, LabMember, Note
 
 
-logger = structlog.get_logger(__name__)
+logger = logging.getLogger(__name__)
 
 
 def _default_water_type():

alyx/actions/notifications.py

@@ -1,12 +1,12 @@
-import structlog
+import logging
 from textwrap import dedent
 
 from django.utils import timezone
 
 from actions.models import create_notification
 
 
-logger = structlog.get_logger(__name__)
+logger = logging.getLogger(__name__)
 
 
 def responsible_user_changed(subject, old_user, new_user):

alyx/actions/tests.py

@@ -219,8 +219,8 @@ def test_notif_water_1(self):
     def test_notif_water_2(self):
         # If the last water admin was on June 3 at 12pm, the notification
         # should be created after June 4 at 11am.
-        l = ((9, False), (10, False), (11, True), (12, True))
-        for (h, r) in l:
+        teupeul = ((9, False), (10, False), (11, True), (12, True))
+        for (h, r) in teupeul:
             date = timezone.datetime(2018, 6, 4, h, 0, 0)
             check_water_administration(self.subject, date=date)
             notif = Notification.objects.last()

alyx/actions/tests_rest.py

@@ -548,15 +548,15 @@ def test_list_retrieve_water_restrictions(self):
     def test_list_retrieve_lab_locations(self):
         # test list
         url = reverse("location-list")
-        l = self.ar(self.client.get(url))
-        self.assertTrue(len(l) > 0)
-        self.assertEqual(set(l[0].keys()), {"name", "json", "lab"})
+        reponse = self.ar(self.client.get(url))
+        self.assertTrue(len(reponse) > 0)
+        self.assertEqual(set(reponse[0].keys()), {"name", "json", "lab"})
         # test detail
-        url = reverse("location-detail", args=[l[0]["name"]])
+        url = reverse("location-detail", args=[reponse[0]["name"]])
         d = self.ar(self.client.get(url))
-        self.assertEqual(d, l[0])
+        self.assertEqual(d, reponse[0])
         # test patch
-        url = reverse("location-detail", args=[l[0]["name"]])
+        url = reverse("location-detail", args=[reponse[0]["name"]])
         json_dict = {
             "string": "look at me! I'm a Json field",
             "integer": 15,

alyx/actions/water_control.py

@@ -4,7 +4,7 @@
 from dateutil.rrule import HOURLY
 import functools
 import io
-import structlog
+import logging
 from operator import attrgetter, itemgetter
 import os.path as op
 
@@ -17,7 +17,7 @@
 import numpy as np
 
 
-logger = structlog.get_logger(__name__)
+logger = logging.getLogger(__name__)
 
 
 PALETTE = {

alyx/alyx/base.py

@@ -1,5 +1,5 @@
 import json
-import structlog
+import logging
 import os
 import os.path as op
 from polymorphic.models import PolymorphicModel
@@ -30,7 +30,7 @@
 from reversion.admin import VersionAdmin
 from alyx import __version__ as version
 
-logger = structlog.get_logger(__name__)
+logger = logging.getLogger(__name__)
 
 DATA_DIR = op.abspath(op.join(op.dirname(__file__), '../../data'))
 DISABLE_MAIL = False  # used for testing
@@ -211,8 +211,8 @@ def __init__(self, *args, **kwargs):
         self.__dict__ = self
 
 
-def flatten(l):
-    return [item for sublist in l for item in sublist]
+def flatten(liste):
+    return [item for sublist in liste for item in sublist]
 
 
 def _show_change(date_time, old, new):

alyx/data/management/commands/files.py

@@ -26,9 +26,9 @@ def _create_missing_file_records_main_globus(dry_run=False, lab=None):
         labs = Lab.objects.filter(name=lab)
     else:
         labs = Lab.objects.all()
-    for l in labs:
-        repos = l.repositories.filter(globus_is_personal=False)
-        dsets = Dataset.objects.filter(session__lab=l)
+    for lab in labs:
+        repos = lab.repositories.filter(globus_is_personal=False)
+        dsets = Dataset.objects.filter(session__lab=lab)
         for r in repos:
             dsr = dsets.annotate(rep_count=Count('file_records',
                                                  filter=Q(file_records__data_repository=r)))

alyx/data/management/commands/transfers_integration.py

@@ -289,7 +289,7 @@ def test_transfers(self):
         ls_local = self.gtc.operation_ls(self.local_endpoint_id,
                                          path=str(Path(exp_files[0]).parent))
         ls_files = [ls['name'] for ls in ls_local['DATA']]
-        assert not Path(exp_files[0]).name in ls_files
+        assert Path(exp_files[0]).name not in ls_files
 
         dsets_to_del = Dataset.objects.filter(session__lab__name=self.lab_name,
                                               name='spikes.times.npy')

alyx/data/models.py

@@ -1,4 +1,4 @@
-import structlog
+import logging
 from one.alf.spec import QC
 
 from django.core.validators import RegexValidator
@@ -11,7 +11,7 @@
 from actions.models import Session
 from alyx.base import BaseModel, modify_fields, BaseManager, CharNullField, BaseQuerySet, ALF_SPEC
 
-logger = structlog.get_logger(__name__)
+logger = logging.getLogger(__name__)
 
 
 def _related_string(field):

alyx/data/transfers.py

@@ -1,5 +1,5 @@
 import json
-import structlog
+import logging
 import os
 import os.path as op
 import re
@@ -18,7 +18,7 @@
 from rest_framework.response import Response
 from actions.models import Session
 
-logger = structlog.get_logger(__name__)
+logger = logging.getLogger(__name__)
 
 # Login
 # ------------------------------------------------------------------------------------------------

alyx/data/views.py

@@ -1,4 +1,4 @@
-import structlog
+import logging
 import re
 
 from django.contrib.auth import get_user_model
@@ -37,7 +37,7 @@
                         _create_dataset_file_records, bulk_sync, _check_dataset_protected,
                         _get_name_collection_revision)
 
-logger = structlog.get_logger(__name__)
+logger = logging.getLogger(__name__)
 
 # DataRepositoryType
 # ------------------------------------------------------------------------------------------------

alyx/experiments/models.py

@@ -1,4 +1,4 @@
-import structlog
+import logging
 import uuid
 
 from django.db import models
@@ -13,7 +13,7 @@
 from alyx.base import BaseModel, BaseManager
 from actions.models import ChronicRecording
 
-logger = structlog.get_logger(__name__)
+logger = logging.getLogger(__name__)
 
 X_HELP_TEXT = ("brain surface medio-lateral coordinate (um) of"
                "the insertion, right +, relative to Bregma")

alyx/misc/management/commands/download_gsheets.py

@@ -42,8 +42,8 @@ def pad(s):
     return re.sub(r'\_([0-9]+)$', lambda m: '_%04d' % int(m.group(1)), s)
 
 
-def flatten(l):
-    return [item for sublist in l for item in sublist]
+def flatten(line):
+    return [item for sublist in line for item in sublist]
 
 
 def get_username(initials):
@@ -72,8 +72,8 @@ def parse(date_str, time=False):
         return ''
     try:
         ret = parse_(date_str)
-    except:
-        logger.warn("Could not parse date %s.", date_str)
+    except Exception:
+        logger.warning("Could not parse date %s.", date_str)
         return ''
     if not time:
         return ret.strftime("%Y-%m-%d")
@@ -120,11 +120,11 @@ def sheet_to_table(wks, header_line=0, first_line=2):
     table = []
     headers = rows[header_line]
     for row in rows[first_line:]:
-        l = {headers[i].strip(): row[i].strip() for i in range(len(headers))}
+        line = {headers[i].strip(): row[i].strip() for i in range(len(headers))}
         # Empty line = end of table.
-        if all(_ == '' for _ in l.values()):
+        if all(_ == '' for _ in line.values()):
             break
-        table.append(Bunch(l))
+        table.append(Bunch(line))
     return table
 
 
@@ -366,9 +366,9 @@ def _get_subjects(self, line_tables):
     def _get_line(self, line):
         out = self.lines.get(line, None)
         if not out:
-            for l in self.lines.values():
-                if l.auto_name == line:
-                    return l
+            for line in self.lines.values():
+                if line.auto_name == line:
+                    return line
         return out
 
     def _get_litters(self, subjects):

alyx/misc/management/commands/report.py

@@ -18,28 +18,28 @@
 logger = logging.getLogger(__name__)
 
 
-def _repr_log_entry(l):
-    if l.is_addition():
+def _repr_log_entry(log):
+    if log.is_addition():
         action = 'Added'
-    elif l.is_change():
+    elif log.is_change():
         action = 'Changed'
-    elif l.is_deletion():
+    elif log.is_deletion():
         action = 'Deleted'
-    changed = json.loads(l.change_message or '[]')
+    changed = json.loads(log.change_message or '[]')
     if changed and changed[0].get('changed', {}):
         changed = ('(%s)' %
                    (', '.join(changed[0].get('changed', {}).get('fields', {}))))
     else:
         changed = ''
     s = '%02d:%02d - %s <%s> %s' % (
-        l.action_time.hour,
-        l.action_time.minute,
+        log.action_time.hour,
+        log.action_time.minute,
         action,
         # l.content_type,
 
         # NOTE: use this when debugging repr (the repr string is directly saved in the LogEntry)
         # str(l.get_edited_object()),
-        l.object_repr,
+        log.object_repr,
 
         changed,
     )
@@ -206,7 +206,7 @@ def make_past_changes(self, user):
         logs = LogEntry.objects.filter(user=user,
                                        action_time__date=yesterday,
                                        ).order_by('action_time')
-        return 'Your actions yesterday:\n\n' + '\n'.join('* ' + _repr_log_entry(l) for l in logs)
+        return 'Your actions yesterday:\n\n' + '\n'.join('* ' + _repr_log_entry(log) for log in logs)
 
     def make_training(self, user):
         """Send training report to the specified user."""