Update parkour2 latest

CLAUDE.md

@@ -52,7 +52,7 @@ To update a component version: change `BUILD_<name>` and `BUILD_<name>_SRCURL` i
 ```
 nginx (reverse proxy, SSL termination, static files)
   └─> gunicorn (WSGI unix socket)
-        └─> Django/parkour2 backend (wui.settings.prod)
+        └─> Django/parkour2 backend (config.settings.prod)
 frontend/dist/  (Vue3/Vite built by npm run build, served as static by nginx)
 postgresql      (unix socket in $DEVSHM)
 ```
@@ -107,7 +107,7 @@ sqlite → python → uv → node → postgresql → nginx
 
 ### Build
 
-`nginx.build.sh` compiles nginx (`--with-http_ssl_module`, `--with-http_v2_module`, most optional modules disabled, `--with-debug`, all temp/pid/lock paths under `$DEVSHM`). It applies `nginx.chicken.patch` before `./configure` (`patch ... --forward || true`, so it's idempotent — a stale nginx source tree that already has the patch is fine); the patch is a bit of build-identity fun (`--build=bwakbwakbwak`, `nginx.h` version-string hunk) and its hunk context is nginx-version-specific, so bumping `BUILD_nginx` can require re-fitting the patch (done for 1.31.3 in `cc59d00`, 1.31.4 in `b067910`). If `NGINX_SSL_DHPARAM` is set, the build also generates that 2048-bit dhparam file once if missing.
+`nginx.build.sh` compiles nginx (`--with-http_ssl_module`, `--with-http_v2_module`, most optional modules disabled, `--with-debug`, all temp/pid/lock paths under `$DEVSHM`). It applies `nginx.chicken.patch` before `./configure` (`patch ... --forward || true`, so it's idempotent — a stale nginx source tree that already has the patch is fine); the patch is a bit of build-identity fun (`--build=bwakbwakbwak`, `nginx.h` version-string hunk) and its hunk context is nginx-version-specific, so **every** `BUILD_nginx` bump requires re-fitting the `nginx.h` hunk's `-` context lines to the new real version. Because of the `|| true`, a stale hunk fails *silently* (1.31.4 shipped reporting `nginx/1.31.4` instead of `chicken/1.32.2`), so dry-run it first: `patch -p1 --dry-run --forward --input=nginx.chicken.patch` in the extracted source. If `NGINX_SSL_DHPARAM` is set, the build also generates that 2048-bit dhparam file once if missing.
 
 ### Routing
 

build.profile

@@ -1,4 +1,4 @@
-BUILD_TAG=26.08.31
+BUILD_TAG=26.10.05
 
 BUILD_parkour2=parkour2-develop
 
@@ -37,23 +37,23 @@ PGDATABASE=parkour2
 BUILD_sqlite=sqlite-3.53.4
 BUILD_sqlite_SRCURL="https://beehive.molgen.mpg.de/ee54db5a5b04e77d4883ce0c051a1eba/sqlite-autoconf-3530400.tar.gz"
 
-# md5repo.sh "https://www.python.org/ftp/python/3.13.15/Python-3.13.15.tgz"
-BUILD_python=Python-3.13.15
-BUILD_python_SRCURL="https://beehive.molgen.mpg.de/7d2f36334007c01c034ad37c965ff535/${BUILD_python}.tgz"
+# md5repo.sh "https://www.python.org/ftp/python/3.13.16/Python-3.13.16.tgz"
+BUILD_python=Python-3.13.16
+BUILD_python_SRCURL="https://beehive.molgen.mpg.de/1c314524d94004d7e51148a4a819d191/${BUILD_python}.tgz"
 
 # https://github.com/astral-sh/uv/releases
-# wget "https://github.com/astral-sh/uv/releases/download/0.12.8/uv-x86_64-unknown-linux-gnu.tar.gz"
-BUILD_uv=uv-0.12.8
-BUILD_uv_SRCURL="https://beehive.molgen.mpg.de/e84aacc82a3b7e2cd99fbaa0cb796b55/uv-x86_64-unknown-linux-gnu.tar.gz"
+# wget "https://github.com/astral-sh/uv/releases/download/0.12.23/uv-x86_64-unknown-linux-gnu.tar.gz"
+BUILD_uv=uv-0.12.23
+BUILD_uv_SRCURL="https://beehive.molgen.mpg.de/48de2ba157b7aacb58edda6ff2872898/uv-x86_64-unknown-linux-gnu.tar.gz"
 
-# wget "https://nodejs.org/download/release/v24.20.0/node-v24.20.0.tar.gz"
-BUILD_node=node-24.20.0
-BUILD_node_SRCURL="https://beehive.molgen.mpg.de/6d782834cb05d397ec78d98f59ef716e/${BUILD_node/-/-v}.tar.gz"
+# wget "https://nodejs.org/download/release/v24.21.0/node-v24.21.0.tar.gz"
+BUILD_node=node-24.21.0
+BUILD_node_SRCURL="https://beehive.molgen.mpg.de/a0d4131e52d9055f8428439542018d44/${BUILD_node/-/-v}.tar.gz"
 
 # wget "https://ftp.postgresql.org/pub/source/v16.15/postgresql-16.15.tar.gz"
 BUILD_postgresql=postgresql-16.15
 BUILD_postgresql_SRCURL="https://beehive.molgen.mpg.de/ac0e604676bda7a306f704b916a4e194/${BUILD_postgresql}.tar.gz"
 
-# wget "https://nginx.org/download/nginx-1.31.4.tar.gz"
-BUILD_nginx=nginx-1.31.4
-BUILD_nginx_SRCURL="https://beehive.molgen.mpg.de/f73114f560071ae341e57ed123322f4c/${BUILD_nginx}.tar.gz"
+# wget "https://nginx.org/download/nginx-1.31.6.tar.gz"
+BUILD_nginx=nginx-1.31.6
+BUILD_nginx_SRCURL="https://beehive.molgen.mpg.de/6d59f919382fae46812c44ffbc87498a/${BUILD_nginx}.tar.gz"

buildall.sh

@@ -126,7 +126,7 @@ build() {
             touch "$_tag"
         else
             echo "${_pkg}.build.sh failed exit code $r"
-            exit
+            exit $r
         fi
     fi
 }
@@ -145,3 +145,7 @@ done
 echo "built target ${PROJECT} done."
 
 } 2>&1 | tee "${LOGS}/${logfile}"
+# The tee would otherwise mask any failure inside the braces as success.
+r=${PIPESTATUS[0]}
+[[ $r == 0 ]] || echo "# build FAILED (exit $r), see ${LOGS}/${logfile}" >&2
+exit $r

nginx.chicken.patch

@@ -63,8 +63,8 @@ index f4ccc61..8ff917c 100644
  #define _NGINX_H_INCLUDED_
 
 
--#define nginx_version      1031003
--#define NGINX_VERSION      "1.31.3"
+-#define nginx_version      1031006
+-#define NGINX_VERSION      "1.31.6"
 -#define NGINX_VER          "nginx/" NGINX_VERSION
 +#define nginx_version      1032002
 +#define NGINX_VERSION      "1.32.2"

parkour2.build.sh

@@ -109,7 +109,7 @@ fi
 cat <<_EOC_
 # generated by $0 in $PWD
 
-DJANGO_SETTINGS_MODULE=wui.settings.prod
+DJANGO_SETTINGS_MODULE=config.settings.prod
 
 SECRET_KEY=${PARKOUR2_SECRET_KEY}
 

profile.build.sh

@@ -39,7 +39,7 @@ PGDATABASE=${PGDATABASE}
 DB_USERNAME=${DB_USERNAME}
 DB_PASSWORD=${DB_PASSWORD}
 
-DJANGO_SETTINGS_MODULE=wui.settings.prod
+DJANGO_SETTINGS_MODULE=config.settings.prod
 DATABASE_URL=postgres://${DB_USERNAME}:${DB_PASSWORD}@/${PGDATABASE}?host=${PGHOST}
 
 PARKOUR2_BIND_ADDR=${PARKOUR2_BIND_ADDR}

startstop.build.sh

@@ -92,7 +92,7 @@ if not User.objects.filter(email='${PARKOUR2_ADMIN_EMAIL}').exists():
         --pid "${DEVSHM}/gunicorn.pid"
         --access-logfile "${LOGDIR}/gunicorn-access.log"
         --error-logfile "${LOGDIR}/gunicorn-error.log"
-        wui.wsgi:application
+        config.wsgi:application
     )
 
     gunicorn "\${_opts[@]}"

test-parkour2.sh

@@ -0,0 +1,41 @@
+#!/bin/bash
+# Run this repo's parkour2 regression tests (tests/parkour2/<app>/test_*.py)
+# against the built parkour2 checkout in ${PROJECT}/${BUILD_parkour2}.
+#
+# Each test file is copied into the matching backend app for the run and
+# removed afterwards, so the checkout stays clean for `git pull`. Postgres
+# must be running (`./startstop.sh start postgresql`); Django creates and
+# drops its own test_* database, the real one is not touched.
+#
+#   ./test-parkour2.sh            # all tests
+#   ./test-parkour2.sh -v 2       # extra args go to `manage.py test`
+
+. build.profile
+
+set -u
+set -e
+
+BACKEND=${PROJECT}/${BUILD_parkour2}/backend
+SRC=$(pwd)/tests/parkour2
+
+copied=()
+cleanup() { rm -f "${copied[@]}"; }
+trap cleanup EXIT
+
+labels=()
+for f in "${SRC}"/*/test_*.py; do
+    rel=${f#${SRC}/}
+    dst=${BACKEND}/${rel}
+    if [ -e "${dst}" ]; then
+        echo "# ${dst} already exists in checkout, refusing to overwrite" >&2
+        exit 1
+    fi
+    cp "${f}" "${dst}"
+    copied+=("${dst}")
+    rel=${rel%.py}
+    labels+=("${rel//\//.}")
+done
+
+. ${PROJECT}/profile
+cd "${BACKEND}"
+python manage.py test --noinput "$@" "${labels[@]}"

tests/parkour2/library_sample_shared/test_indexpair_orphan.py

@@ -0,0 +1,52 @@
+"""Regression test: IndexPair whose IndexType was deleted.
+
+IndexPair.index_type is ForeignKey(on_delete=SET_NULL), so deleting an
+IndexType leaves its pairs behind with index_type=None. IndexPair.__str__
+then dereferences self.index_type.is_dual and raises AttributeError, which
+makes /admin/library_sample_shared/indexpair/ return HTTP 500 for everyone
+(seen on parkour-dev 2026-10-02 after a plate IndexType with pairs was
+deleted and re-created).
+
+Either upstream fix is accepted: a None-safe __str__ (pair survives as an
+orphan) or on_delete=CASCADE (pair is deleted along with its type).
+"""
+
+from common.tests import BaseTestCase
+from django.urls import reverse
+
+from .models import IndexI7, IndexPair, IndexType
+
+
+class OrphanedIndexPairTest(BaseTestCase):
+    def setUp(self):
+        index_type = IndexType.objects.create(
+            name="ONT Native Barcoding 96", format="plate"
+        )
+        index1 = IndexI7.objects.create(prefix="NB", number="01", index="ACGT")
+        index_type.indices_i7.add(index1)
+        IndexPair.objects.create(
+            index_type=index_type, index1=index1, char_coord="A", num_coord=1
+        )
+
+        # Same sequence as in the admin: delete the index, then the type.
+        index1.delete()
+        index_type.delete()
+
+        self.pair = IndexPair.objects.first()
+
+    def test_str_without_index_type(self):
+        if self.pair is None:
+            self.skipTest("pair was cascade-deleted with its IndexType")
+        self.assertIsNone(self.pair.index_type)
+        self.assertEqual(str(self.pair), "")
+
+    def test_admin_changelist_with_orphaned_pair(self):
+        user = self.create_user(email="admin@test.io")
+        user.is_superuser = True
+        user.save()
+        self.client.force_login(user)
+
+        response = self.client.get(
+            reverse("admin:library_sample_shared_indexpair_changelist")
+        )
+        self.assertEqual(response.status_code, 200)