Fix publisher checkout admission and ROI test dependencies for 0.3.1

.github/workflows/publish.yml

@@ -32,7 +32,7 @@ jobs:
       - name: Install build dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install build "twine>=7,<8" ".[dev]"
+          python -m pip install build "twine>=7,<8" -e ".[dev]"
 
       - name: Test release candidate
         run: python -m pytest -q

docs/validation/publisher-admission-031-20261002/COMMANDS.rst

@@ -0,0 +1,38 @@
+Focused qualification command
+=============================
+
+Run from the isolated PolyStore worktree::
+
+  systemd-run --user --scope --quiet \
+    -p MemoryMax=512M -p MemorySwapMax=0 -p CPUQuota=100% \
+    timeout 60s taskset -c 0 env \
+    PYTEST_DISABLE_PLUGIN_AUTOLOAD=1 PYTHONDONTWRITEBYTECODE=1 \
+    OPENBLAS_NUM_THREADS=1 OMP_NUM_THREADS=1 MKL_NUM_THREADS=1 \
+    PYTHONPATH=/home/ts/wt/polystore-publisher-admission-031-20261002/src \
+    /home/ts/wt/openhcs-generated-inputs-installed-parent-20261001/.venv/bin/python -B \
+    /home/ts/wt/openhcs-prior-measurement-role-projection-20261001/docs/validation/selected_plane_stream_materialization_20261001/run_bounded_source.py \
+    /home/ts/wt/openhcs-generated-inputs-installed-parent-20261001/.venv/bin/python -B -m pytest \
+    -o addopts= \
+    --basetemp=docs/validation/publisher-admission-031-20261002/qualified-test-temp \
+    --junitxml=docs/validation/publisher-admission-031-20261002/qualified.xml \
+    tests/test_publisher_admission.py tests/test_basic.py \
+    tests/test_imagej_cache_environment.py tests/test_metadata_namespace.py \
+    tests/test_roi_region_properties.py tests/test_roi.py \
+    tests/test_lazy_package_exports.py -q
+
+The default coverage/report addopts are disabled for this focused resource-bound
+source run, not for the publisher. All selected tests/assertions are unchanged.
+Source fixtures prohibit actual Fiji downloads/JVM execution.
+
+Offline lock attempt (terminal failure)::
+
+  systemd-run --user --scope --quiet \
+    -p MemoryMax=512M -p MemorySwapMax=0 -p CPUQuota=100% \
+    timeout 60s taskset -c 0 uv lock --offline --no-python-downloads
+
+No solution for python_full_version >=3.14 / win32: imglyb not found in cache;
+polystore[all] requires imglyb==2.1.0. No lock file was changed.
+
+Owned disposable output is confined to the three source-test-temp,
+admission-test-temp and qualified-test-temp directories below this receipt root.
+Original log, test XML and qualification notes are durable evidence, not caches.

docs/validation/publisher-admission-031-20261002/RECEIPT.rst

@@ -0,0 +1,73 @@
+PolyStore 0.3.1 publisher admission
+================================
+
+Source base: 84f322e46871de5ed47e7fd20976ad03e533c1c4 (remote main).
+Owner: Dewey, isolated polystore-publisher-admission-031-20261002 worktree.
+Parent owns integration, the sole new 0.3.1 tag, and hosted release acceptance.
+The immutable failed v0.3.0 tag is untouched.
+
+Original failure
+----------------
+
+Run https://github.com/OpenHCSDev/PolyStore/actions/runs/36959840684,
+job 110690882405: 9 failed, 545 passed, 19 skipped in 15.91s.
+Three failures require child processes to import checkout source; the publisher
+installed a regular distribution. Six ROI topology/archive cases fail because
+the existing dev extra omitted roifile. No original test or skip is changed.
+
+The full job log was fetched through the GitHub SDK job-log tool and archived
+as original-job-110690882405.log.gz (lossless gzip), preserving UTF-8 text including
+its original BOM and final newline: 142020 bytes, SHA256
+542d75ef00bcd8677526131a1afe195cea6fa63edca7eca5aa8e0b1b4e4b703c.
+
+Ownership and repair
+--------------------
+
+Replace the existing publisher install with editable .[dev] admission, matching
+the existing ordinary test workflow. The later package build and immutable
+declaration/publish steps are unchanged. Declare roifile in the original dev
+extra, not a workflow-only dependency roster or mandatory runtime requirement.
+Advance the sole project version declaration to 0.3.1; the existing package
+version and release scripts derive it from distribution/project metadata.
+
+Current NRA/refactor-audit skills and packaged pattern catalog were read.
+MEMB-1/MEMB-2: dependency membership remains in the original extras declaration.
+TIME-8: no duplicated version or metadata authority. No Python runtime mechanism
+is introduced, so inheritance/MI would be ornamental here. Independent future
+dev dependencies need only their own extra entry, not publisher consumer edits.
+The real editable-build test reads emitted metadata and the actual source .pth
+from the existing setuptools backend rather than mirroring its implementation.
+
+Open-PR check found only Dependabot PR10, whose publisher-file changes are action
+pins; this patch leaves those pins unchanged. Parent's release worktree is not
+edited. No environment installation, external download, Fiji/native launch,
+science job, tag or release operation was performed.
+
+Focused source qualification
+----------------------------
+
+68 PASS, zero skips: publisher admission/editable metadata, basic package,
+ImageJ cache policy and fresh-process source, namespace handoff, ROI geometry
+and archive roundtrip, and lazy package exports. These include all nine original
+failed cases. The initial original-only run was 63 PASS; new admission controls
+were 2 PASS. Final combined run: 8.43s pytest, 9.089s monitored wall,
+322700 KiB aggregate RSS (315.14 MiB), one CPU, 512 MiB / 60s limits.
+See qualified.xml and qualified-source.txt. The command is in COMMANDS.rst.
+
+Source is explicitly this worktree's src; dependencies/interpreter are readonly
+openhcs-generated-inputs-installed-parent-20261001/.venv/bin/python.
+The two publisher controls exercise the real offline editable build without
+installing its artifact. They verify checkout binding, unfiltered publisher
+pytest invocation, derived version, and dev-only ROI dependency metadata.
+No installed editable-candidate or hosted 0.3.1 acceptance is claimed.
+
+Lock limitation
+---------------
+
+uv lock --offline --no-python-downloads failed because imglyb==2.1.0 is absent
+from the cache for the all/bioformats extras. Original uv.lock already records
+PolyStore 0.2.18 and ZMQRuntime 0.2.21, inconsistent with base declarations.
+The lock is unchanged: no fabricated entries, constrained platforms, dependency
+weakening or downloads. Publisher pip does not consume uv.lock. The existing
+separate distribution CI lock-check remains unqualified until authorized lock
+regeneration; this is not represented as publisher or runtime acceptance.

docs/validation/publisher-admission-031-20261002/admission.xml

@@ -0,0 +1 @@
+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="2" time="1.721" timestamp="2026-10-01T23:43:39.638980-04:00" hostname="desktop"><testcase classname="tests.test_publisher_admission" name="test_publisher_installs_the_dev_candidate_editably" time="0.002" /><testcase classname="tests.test_publisher_admission" name="test_editable_artifact_owns_checkout_path_and_roi_dev_requirement" time="1.594" /></testsuite></testsuites>

docs/validation/publisher-admission-031-20261002/focused-originals.xml

@@ -0,0 +1 @@
+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="63" time="6.262" timestamp="2026-10-01T23:42:07.085949-04:00" hostname="desktop"><testcase classname="tests.test_imagej_cache_environment" name="test_declaration_import_defers_process_configuration" time="0.144" /><testcase classname="tests.test_imagej_cache_environment" name="test_invalid_process_permission_leaves_environment_unchanged" time="0.001" /><testcase classname="tests.test_imagej_cache_environment" name="test_download_policy_decodes_permission_without_copying_retry_defaults[None-True]" time="0.000" /><testcase classname="tests.test_imagej_cache_environment" name="test_download_policy_decodes_permission_without_copying_retry_defaults[true-True]" time="0.000" /><testcase classname="tests.test_imagej_cache_environment" name="test_download_policy_decodes_permission_without_copying_retry_defaults[ FALSE -False]" time="0.000" /><testcase classname="tests.test_imagej_cache_environment" name="test_invalid_download_permission_fails[]" time="0.000" /><testcase classname="tests.test_imagej_cache_environment" name="test_invalid_download_permission_fails[yes]" time="0.000" /><testcase classname="tests.test_imagej_cache_environment" name="test_invalid_download_permission_fails[0]" time="0.000" /><testcase classname="tests.test_imagej_cache_environment" name="test_invalid_download_permission_fails[relative/cache]" time="0.000" /><testcase classname="tests.test_imagej_cache_environment" name="test_forbidden_download_has_no_archive_or_cache_side_effects" time="0.001" /><testcase classname="tests.test_imagej_cache_environment" name="test_unset_bundle_root_retains_distribution_default" time="0.000" /><testcase classname="tests.test_imagej_cache_environment" name="test_invalid_explicit_bundle_root_fails_without_a_fallback[]" time="0.000" /><testcase classname="tests.test_imagej_cache_environment" name="test_invalid_explicit_bundle_root_fails_without_a_fallback[ ]" time="0.000" /><testcase classname="tests.test_imagej_cache_environment" name="test_invalid_explicit_bundle_root_fails_without_a_fallback[relative/cache]" time="0.000" /><testcase classname="tests.test_imagej_cache_environment" name="test_bundle_root_decode_is_independent_of_xdg_cache" time="0.001" /><testcase classname="tests.test_imagej_cache_environment" name="test_fresh_processes_share_one_verified_bundle_not_their_xdg_caches" time="0.369" /><testcase classname="tests.test_metadata_namespace" name="test_namespace_reopen_connection_restore_and_native_handoff[polystore_metadata.json]" time="2.781" /><testcase classname="tests.test_metadata_namespace" name="test_namespace_reopen_connection_restore_and_native_handoff[custom-metadata.json]" time="1.712" /><testcase classname="tests.test_metadata_namespace" name="test_new_namespace_declaration_needs_no_workspace_consumer_edits" time="0.002" /><testcase classname="tests.test_metadata_namespace" name="test_explicit_config_decodes_once_without_mutating_generic_snapshot" time="0.001" /><testcase classname="tests.test_metadata_namespace" name="test_namespace_isolation_has_no_alternate_filename_reader" time="0.001" /><testcase classname="tests.test_metadata_namespace" name="test_connection_retarget_invalidates_mapping_and_namespace" time="0.004" /><testcase classname="tests.test_metadata_namespace" name="test_native_parameter_boundary_uses_constructor_binding" time="0.001" /><testcase classname="tests.test_roi_region_properties" name="test_region_crop_contours_equal_full_canvas_and_archive_reopen[holes-origin0]" time="0.060" /><testcase classname="tests.test_roi_region_properties" name="test_region_crop_contours_equal_full_canvas_and_archive_reopen[holes-origin1]" time="0.006" /><testcase classname="tests.test_roi_region_properties" name="test_region_crop_contours_equal_full_canvas_and_archive_reopen[borders-origin0]" time="0.006" /><testcase classname="tests.test_roi_region_properties" name="test_region_crop_contours_equal_full_canvas_and_archive_reopen[borders-origin1]" time="0.006" /><testcase classname="tests.test_roi_region_properties" name="test_region_crop_contours_equal_full_canvas_and_archive_reopen[topology-origin0]" time="0.007" /><testcase classname="tests.test_roi_region_properties" name="test_region_crop_contours_equal_full_canvas_and_archive_reopen[topology-origin1]" time="0.008" /><testcase classname="tests.test_roi_region_properties" name="test_hole_rings_keep_opposite_orientation" time="0.002" /><testcase classname="tests.test_roi_region_properties" name="test_existing_mask_representation_preserves_exact_topology[holes]" time="0.001" /><testcase classname="tests.test_roi_region_properties" name="test_existing_mask_representation_preserves_exact_topology[borders]" time="0.001" /><testcase classname="tests.test_roi_region_properties" name="test_existing_mask_representation_preserves_exact_topology[topology]" time="0.001" /><testcase classname="tests.test_roi_region_properties" name="test_region_properties_scan_labels_once_and_honor_min_area[holes-True]" time="0.002" /><testcase classname="tests.test_roi_region_properties" name="test_region_properties_scan_labels_once_and_honor_min_area[holes-False]" time="0.001" /><testcase classname="tests.test_roi_region_properties" name="test_region_properties_scan_labels_once_and_honor_min_area[borders-True]" time="0.002" /><testcase classname="tests.test_roi_region_properties" name="test_region_properties_scan_labels_once_and_honor_min_area[borders-False]" time="0.001" /><testcase classname="tests.test_roi_region_properties" name="test_region_properties_scan_labels_once_and_honor_min_area[topology-True]" time="0.001" /><testcase classname="tests.test_roi_region_properties" name="test_region_properties_scan_labels_once_and_honor_min_area[topology-False]" time="0.001" /><testcase classname="tests.test_roi" name="test_napari_roi_converter_projects_ellipse_as_native_bounding_box" time="0.000" /><testcase classname="tests.test_roi" name="test_napari_roi_converter_removes_only_redundant_polygon_vertices" time="0.000" /><testcase classname="tests.test_roi" name="test_napari_polygon_projection_retains_collinear_backtracking_vertex" time="0.000" /><testcase classname="tests.test_roi" name="test_extract_rois_from_labeled_mask_applies_spatial_origin_to_polygons" time="0.001" /><testcase classname="tests.test_roi" name="test_extract_rois_from_labeled_mask_applies_spatial_origin_to_mask_bbox" time="0.001" /><testcase classname="tests.test_roi" name="test_extract_rois_from_labeled_mask_records_source_canvas_shape" time="0.001" /><testcase classname="tests.test_roi" name="test_roi_zip_roundtrip_preserves_source_canvas_shape_metadata" time="0.002" /><testcase classname="tests.test_roi" name="test_load_rois_from_json_decodes_shapes_through_nominal_registry" time="0.001" /><testcase classname="tests.test_roi" name="test_imagej_point_archive_roundtrip" time="0.002" /><testcase classname="tests.test_roi" name="test_external_imagej_point_archive_preserves_every_point" time="0.002" /><testcase classname="tests.test_roi" name="test_imagej_geometry_archive_roundtrip_preserves_native_shape[shape0-FREEHAND]" time="0.002" /><testcase classname="tests.test_roi" name="test_imagej_geometry_archive_roundtrip_preserves_native_shape[shape1-POLYLINE]" time="0.002" /><testcase classname="tests.test_roi" name="test_imagej_geometry_archive_roundtrip_preserves_native_shape[shape2-OVAL]" time="0.002" /><testcase classname="tests.test_roi" name="test_external_integer_imagej_oval_preserves_geometry" time="0.001" /><testcase classname="tests.test_roi" name="test_imagej_archive_rejects_unsupported_native_geometry[NOROI]" time="0.001" /><testcase classname="tests.test_roi" name="test_imagej_archive_rejects_unsupported_native_geometry[RECT]" time="0.001" /><testcase classname="tests.test_roi" name="test_imagej_archive_rejects_unsupported_native_geometry[LINE]" time="0.001" /><testcase classname="tests.test_roi" name="test_imagej_archive_rejects_unsupported_native_geometry[FREELINE]" time="0.001" /><testcase classname="tests.test_roi" name="test_imagej_archive_rejects_unsupported_native_geometry[ANGLE]" time="0.001" /><testcase classname="tests.test_roi" name="test_imagej_archive_rejects_malformed_geometry_and_missing_metadata" time="0.002" /><testcase classname="tests.test_roi" name="test_imagej_archive_rejects_specialized_subtypes_and_masks" time="0.001" /><testcase classname="tests.test_lazy_package_exports" name="test_constants_import_does_not_load_disk_or_array_frameworks" time="0.093" /><testcase classname="tests.test_lazy_package_exports" name="test_root_disk_exports_load_and_cache_the_declared_classes" time="0.262" /><testcase classname="tests.test_lazy_package_exports" name="test_disk_backend_initialization_does_not_load_optional_array_runtimes" time="0.232" /></testsuite></testsuites>

docs/validation/publisher-admission-031-20261002/qualified-source.txt

@@ -0,0 +1,4 @@
+....................................................................     [100%]
+- generated xml file: /home/ts/wt/polystore-publisher-admission-031-20261002/docs/validation/publisher-admission-031-20261002/qualified.xml -
+68 passed in 8.43s
+BOUNDED_SOURCE peak_aggregate_rss_kib=322700 elapsed_seconds=9.089 returncode=0 reason=None