3.6.2

.github/workflows/release.yml

@@ -52,14 +52,24 @@ jobs:
       - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.workflow_run.head_sha }}
+          fetch-depth: 0
 
       - name: Create tag and GitHub release
         run: |
           git config user.name "github-actions[bot]"
           git config user.email "github-actions[bot]@users.noreply.github.com"
           git tag -a "$VERSION" -m "Release $VERSION"
           git push origin "$VERSION"
-          gh release create "$VERSION" --title "$VERSION" --generate-notes
+
+          PREV_TAG=$(git describe --tags --abbrev=0 --match '[0-9]*.[0-9]*.[0-9]*' "$VERSION^" 2>/dev/null || true)
+          if [[ -n "$PREV_TAG" && "$(git rev-list --count "$PREV_TAG..$VERSION")" == "1" ]]; then
+            # Single squash commit since the last release: use its message verbatim
+            # instead of --generate-notes, which would just restate the same one commit.
+            NOTES="$(git log -1 --format=%B "$VERSION")"
+            gh release create "$VERSION" --title "$VERSION" --notes "$NOTES"
+          else
+            gh release create "$VERSION" --title "$VERSION" --generate-notes
+          fi
 
       # A tag pushed by GITHUB_TOKEN does not trigger build-image.yml's push-tags event
       # (GitHub suppresses it to avoid recursion), so dispatch the build explicitly.

CHANGELOG.md

@@ -5,6 +5,25 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [3.6.2]
+
+### Fixed
+
+- Scoped delete_zygosity_rule post delete hook, improving performance on delete
+
+### Changed
+
+- Removed unused dj_database_url dependency
+- Omit WSGI from CI code coverage
+- Changed default docker project name
+- Use commit message for release description on squash commits to master
+- Pin ruff and remove flake8
+
+### Added
+
+- DOI badge in README
+- Release steps to README
+
 ## [3.6.1]
 
 ### Fixed
@@ -14,7 +33,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
-- Worklfow tests now run in parallel and asserts no new migrations
+- Workflow tests now run in parallel and asserts no new migrations
 
 ## [3.6.0]
 

README.md

@@ -2,6 +2,7 @@
 
 [![Github Actions](https://github.com/cortex-lab/alyx/actions/workflows/main.yml/badge.svg)](https://github.com/cortex-lab/alyx/actions/)
 [![Coverage Status](https://coveralls.io/repos/github/cortex-lab/alyx/badge.svg?branch=github_action)](https://coveralls.io/github/cortex-lab/alyx?branch=master)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.21513696.svg)](https://doi.org/10.5281/zenodo.21513696)
 
 Database for experimental neuroscience laboratories
 
@@ -34,12 +35,18 @@ Contribution checklist:
 - [ ] update version number in `./alyx/alyx/__init__.py`
 - [ ] update `CHANGELOG.md`
 
+Release process:
+1. Open a PR from your feature branch into dev
+2. On dev, bump the Alyx version and update the changelog
+3. Open a PR from dev to master
+4. When CI passes, make a squash commit into master using the version as the commit title, and changelog section as the message
+5. Actions will automatically create a new release, deploy containers, and assign a DOI
 
 ### Running tests
 
 Continuous integration is set up. But before submitting a PR or commit,the tests can run locally. First install the test dependencies with `pip install -r requirements_test.txt`.
     - `./manage.py test -n --parallel` parallel test without migrations (fastest)
-    - `./manage.py test` test with migrations (recommended if model changes)
+    - `./manage.py test` test with migrations (recommended if models change)
 
 ### Documentation contribution guide
 

alyx/alyx/__init__.py

@@ -1 +1 @@
-VERSION = __version__ = '3.6.1'
+VERSION = __version__ = '3.6.2'

alyx/subjects/models.py

@@ -892,10 +892,9 @@ def genotype_from_litter(self, subject, force=False):
             self._create_zygosity(subject, allele, z, force=force)
 
 
-@receiver(post_delete)
+@receiver(post_delete, sender=ZygosityRule)
 def delete_zygosity_rule(sender, instance, **kwargs):
-    if isinstance(instance, ZygosityRule):
-        _update_zygosities(instance.line, instance.sequence0)
+    _update_zygosities(instance.line, instance.sequence0)
 
 
 class AlleleManager(models.Manager):

deploy/app/docker/settings-deploy.py

@@ -10,7 +10,6 @@
 
 import os
 import json
-import dj_database_url
 import logging
 import dotenv
 import urllib.parse
@@ -31,16 +30,17 @@
 
 # %% Databases
 SECRET_KEY = os.getenv('DJANGO_SECRET_KEY')
-# Build the connection URL
-POSTGRES_USER = urllib.parse.quote(os.getenv('POSTGRES_USER', ''))
-POSTGRES_PASSWORD = urllib.parse.quote(os.getenv('POSTGRES_PASSWORD', ''))
-POSTGRES_HOST = urllib.parse.quote(os.getenv('POSTGRES_HOST', ''))
-POSTGRES_PORT = urllib.parse.quote(os.getenv('POSTGRES_PORT', '5432'))  # Default PostgreSQL port
-POSTGRES_DB = urllib.parse.quote(os.getenv('POSTGRES_DB', ''))
-# the database details are provided in the form of an URL. The URL looks like:
-# "postgres://USER:PASSWORD@HOST:PORT/DB_NAME"
-database_url = f"postgres://{POSTGRES_USER}:{POSTGRES_PASSWORD}@{POSTGRES_HOST}:{POSTGRES_PORT}/{POSTGRES_DB}"
-DATABASES = {"default": dj_database_url.parse(database_url)}
+DATABASES = {
+    "default": {
+        "ENGINE": "django.db.backends.postgresql",
+        "USER": urllib.parse.quote(os.getenv('POSTGRES_USER', '')),
+        "PASSWORD": urllib.parse.quote(os.getenv('POSTGRES_PASSWORD', '')),
+        "HOST": urllib.parse.quote(os.getenv('POSTGRES_HOST', '')),
+        "NAME": urllib.parse.quote(os.getenv('POSTGRES_DB', '')),
+        # Default PostgreSQL port
+        "PORT": urllib.parse.quote(os.getenv('POSTGRES_PORT', '5432'))
+    }
+}
 # %% S3 access to write cache tables
 # the s3 access details are provided in the form of a JSON string. The variable looks like:
 # S3_ACCESS={"access_key":"xxxxx", "secret_key":"xxxxx", "region":"us-east-1"}

deploy/app/template.env

@@ -13,6 +13,7 @@ GLOBUS_CLIENT_ID=525cc543-8ccb-4d11-8036-af332da5eafd
 TZ=UTC  # Alyx datetime timezone. See https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
 DJANGO_MEDIA_ROOT=~/uploaded
 DJANGO_TABLES_ROOT=~/tables
+COMPOSE_PROJECT_NAME=alyx-deploy
 # DJANGO_MEDIA_ROOT=~/scratch/uploaded  # add if local storage
 # DJANGO_TABLES_ROOT=~/scratch/uploaded # add if local storage
 # DJANGO_MEDIA_S3=https://alyx-uploaded.s3.eu-west-2.amazonaws.com/uploaded/  # add if s3 (overrides local media)

requirements.txt

@@ -13,12 +13,10 @@ django-storages
 django-structlog
 django-test-without-migrations
 djangorestframework
-dj_database_url
 drf-spectacular
 docutils
 dotenv
 drfdocs
-flake8
 fonttools>=4.61.0
 globus-cli>=3.41.0
 globus-sdk>=4.3.0

requirements_test.txt

@@ -1,6 +1,10 @@
 # for code coverage
 coverage
 coveralls
+# pin ruff explicitly -- it's otherwise pulled in transitively and unpinned via ONE-api,
+# so a new ruff release can silently start failing CI with no code change at all (see
+# cortex-lab/alyx#1027: ruff 0.16.0 added new default rules, 821 new findings overnight)
+ruff==0.15.22
 # for ONE cache table generation tests
 pyarrow
 pandas

setup.cfg

@@ -7,6 +7,8 @@ source = alyx
 concurrency = multiprocessing
 parallel = True
 omit =
+    */wsgi.py
+    */gunicorn_wsgi.py
 
 [coverage:report]
 exclude_lines =