feat(ingest): add NIfTI loader for fd5

.devcontainer/devcontainer.json

@@ -18,6 +18,7 @@
                 "nefrob.vscode-just-syntax"
             ],
             "settings": {
+                "terminal.integrated.defaultProfile.linux": "bash",
                 "python.defaultInterpreterPath": "/root/assets/workspace/.venv/bin/python",
                 "[python]": {
                     "editor.defaultFormatter": "charliermarsh.ruff",

CHANGELOG.md

@@ -9,6 +9,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- **Cross-language conformance test suite** ([#155](https://github.com/vig-os/fd5/issues/155))
+  - 6 canonical fixture generators: minimal, sealed, with-provenance, multiscale, tabular, complex-metadata
+  - 3 invalid fixture generators: missing-id, bad-hash, no-schema
+  - Expected-result JSON files defining the format contract for any language binding
+  - 39 pytest conformance tests covering structure, hash verification, provenance, multiscale, tabular, metadata, schema validation, and negative tests
+  - README documenting how to use the suite and add new cases
+
 - **Preflight feedback and status dashboard for devc-remote** ([#149](https://github.com/vig-os/fd5/issues/149))
   - Each preflight check now prints a success/warning/error status line as it completes
   - New checks: container-already-running, runtime version, compose version, SSH agent forwarding

_typos.toml

@@ -0,0 +1,3 @@
+[default.extend-words]
+OME = "OME"
+tre = "tre"

docs/issues/issue-155.md

@@ -2,17 +2,17 @@
 type: issue
 state: open
 created: 2026-02-26T01:04:00Z
-updated: 2026-02-26T01:04:00Z
+updated: 2026-02-26T10:09:09Z
 author: gerchowl
 author_url: https://github.com/gerchowl
 url: https://github.com/vig-os/fd5/issues/155
-comments: 0
+comments: 3
 labels: priority:high, area:testing, effort:medium, area:core
-assignees: none
+assignees: gerchowl
 milestone: none
 projects: none
 relationship: none
-synced: 2026-02-26T04:15:42.619Z
+synced: 2026-02-27T04:11:40.452Z
 ---
 
 # [Issue 155]: [[TEST] Cross-language conformance test suite for fd5 format](https://github.com/vig-os/fd5/issues/155)
@@ -86,3 +86,115 @@ This is a black-box test — it doesn't test internal APIs, only the format cont
 - Depends on the format spec document (see prerequisite issue) for normative requirements
 - Fixture files should be small (KBs, not MBs) to keep the repo lightweight
 - Inspired by JSON Schema Test Suite: https://github.com/json-schema-org/JSON-Schema-Test-Suite
+---
+
+# [Comment #1]() by [gerchowl]()
+
+_Posted on February 26, 2026 at 09:47 AM_
+
+## Design
+
+### Overview
+
+A Python script (`tests/conformance/generate_fixtures.py`) will use the existing `fd5.create()` API and direct `h5py` calls to generate canonical fixture files and corresponding expected-result JSON files. A pytest-based conformance runner (`tests/conformance/test_conformance.py`) will validate that the Python implementation passes all cases. The suite is designed so any future language binding can load the same fixtures + JSON and assert equivalence.
+
+### Architecture
+
+```
+tests/conformance/
+├── README.md                     # How to use the suite
+├── generate_fixtures.py          # Script that creates all .fd5 + .json files
+├── fixtures/                     # Generated .fd5 files (gitignored, regenerated in CI)
+├── expected/                     # Expected-result JSON files (checked in)
+├── invalid/                      # Invalid .fd5 files + expected-errors.json
+└── test_conformance.py           # Pytest runner that validates fixtures vs expected
+```
+
+### Design Decisions
+
+1. **Fixtures are generated, not checked in.** HDF5 is binary; checking in binaries is fragile and bloats the repo. Instead, `generate_fixtures.py` regenerates them deterministically. The expected JSON files ARE checked in since they define the contract. A conftest fixture runs the generator before tests.
+
+2. **Use a test/conformance product schema.** Register a minimal `ConformanceSchema` via `register_schema()` in the generator and test module. This avoids coupling to imaging-specific schemas (recon) while exercising the full fd5 create/seal pipeline.
+
+3. **Expected JSON format.** Each expected JSON file is a dict with keys matching the test categories from the issue: `root_attrs`, `datasets`, `groups`, `content_hash_prefix`, `verify`, plus fixture-specific keys like `provenance`, `metadata_tree`, etc.
+
+4. **Test categories mapped to fixtures:** minimal.fd5 (structure), with-provenance.fd5 (provenance DAG), multiscale.fd5 (pyramid levels), tabular.fd5 (compound dataset), complex-metadata.fd5 (nested metadata), sealed.fd5 (hash verification).
+
+5. **Invalid fixtures.** Created with direct h5py: missing-id.fd5, bad-hash.fd5, no-schema.fd5, with expected-errors.json.
+
+6. **Multiscale fixture uses ReconSchema.** Only fixture needing a real product schema with pyramid support. All others use the simple conformance schema.
+
+### Testing Strategy
+
+The conformance tests ARE the tests. `test_conformance.py` covers structure, round-trip, hash verification, provenance, schema validation, and negative tests. No separate unit tests for the generator.
+
+### Constraints
+
+- Fixture files stay small (< 10 KB each)
+- No new dependencies
+- Generator uses only public fd5 API where possible, h5py directly for invalid fixtures
+
+---
+
+# [Comment #2]() by [gerchowl]()
+
+_Posted on February 26, 2026 at 09:47 AM_
+
+## Implementation Plan
+
+Issue: #155
+Branch: feature/155-cross-language-conformance-tests
+
+### Tasks
+
+- [ ] Task 1: Create conformance directory structure and README — `tests/conformance/README.md`, `tests/conformance/__init__.py` — verify: files exist
+- [ ] Task 2: Write expected JSON files for valid fixtures — `tests/conformance/expected/minimal.json`, `with-provenance.json`, `multiscale.json`, `tabular.json`, `complex-metadata.json`, `sealed.json` — verify: valid JSON, all test categories covered
+- [ ] Task 3: Write expected-errors JSON for invalid fixtures — `tests/conformance/invalid/expected-errors.json` — verify: valid JSON with error patterns for missing-id, bad-hash, no-schema
+- [ ] Task 4: Write failing conformance tests for structure tests (minimal fixture) — `tests/conformance/test_conformance.py` — verify: `uv run pytest tests/conformance/test_conformance.py -k structure -v` fails (no fixtures yet)
+- [ ] Task 5: Write fixture generator for minimal.fd5 — `tests/conformance/generate_fixtures.py` — verify: `uv run pytest tests/conformance/test_conformance.py -k structure -v` passes
+- [ ] Task 6: Write failing tests for hash verification (sealed fixture) — `tests/conformance/test_conformance.py` — verify: `uv run pytest tests/conformance/test_conformance.py -k hash -v` fails
+- [ ] Task 7: Write fixture generator for sealed.fd5 — `tests/conformance/generate_fixtures.py` — verify: `uv run pytest tests/conformance/test_conformance.py -k hash -v` passes
+- [ ] Task 8: Write failing tests for provenance (with-provenance fixture) — `tests/conformance/test_conformance.py` — verify: `uv run pytest tests/conformance/test_conformance.py -k provenance -v` fails
+- [ ] Task 9: Write fixture generator for with-provenance.fd5 — `tests/conformance/generate_fixtures.py` — verify: `uv run pytest tests/conformance/test_conformance.py -k provenance -v` passes
+- [ ] Task 10: Write failing tests for multiscale fixture — `tests/conformance/test_conformance.py` — verify: `uv run pytest tests/conformance/test_conformance.py -k multiscale -v` fails
+- [ ] Task 11: Write fixture generator for multiscale.fd5 — `tests/conformance/generate_fixtures.py` — verify: `uv run pytest tests/conformance/test_conformance.py -k multiscale -v` passes
+- [ ] Task 12: Write failing tests for tabular and complex-metadata fixtures — `tests/conformance/test_conformance.py` — verify: fails
+- [ ] Task 13: Write fixture generators for tabular.fd5 and complex-metadata.fd5 — `tests/conformance/generate_fixtures.py` — verify: `uv run pytest tests/conformance/test_conformance.py -k "tabular or complex" -v` passes
+- [ ] Task 14: Write failing tests for invalid/negative fixtures — `tests/conformance/test_conformance.py` — verify: fails
+- [ ] Task 15: Write fixture generators for invalid files (missing-id, bad-hash, no-schema) — `tests/conformance/generate_fixtures.py` — verify: `uv run pytest tests/conformance/test_conformance.py -k invalid -v` passes
+- [ ] Task 16: Wire conformance tests into full test suite and add .gitignore for fixtures/ — verify: `just test` passes including conformance
+
+---
+
+# [Comment #3]() by [gerchowl]()
+
+_Posted on February 26, 2026 at 10:09 AM_
+
+## Implementation Complete — PR #157
+
+**PR**: https://github.com/vig-os/fd5/pull/157
+
+### What was implemented
+
+A cross-language conformance test suite for the `fd5` format, comprising:
+
+**Fixture generator** (`tests/conformance/generate_fixtures.py`):
+- Generates 6 valid `.fd5` fixture files: `minimal`, `sealed`, `with-provenance`, `multiscale`, `tabular`, `complex-metadata`
+- Generates 3 invalid fixtures: `invalid-missing-id`, `invalid-bad-hash`, `invalid-no-schema`
+- Uses a dedicated `_ConformanceSchema` to avoid polluting the global schema registry
+
+**Expected results** (`tests/conformance/expected/`):
+- JSON files defining expected structure, metadata, hash verification, and schema validation results for each fixture
+- `invalid/expected-errors.json` for invalid fixture error expectations
+
+**Conformance tests** (`tests/conformance/test_conformance.py`):
+- 40 parameterized pytest tests across 6 categories: structure, metadata, content hash, verification, schema validation, and invalid file handling
+- Session-scoped fixture generation with proper registry cleanup
+
+**Documentation** (`tests/conformance/README.md`):
+- Describes the suite's purpose, fixture inventory, JSON contract format, and how other language implementations can use the fixtures
+
+### CI Note
+
+CI failures are pre-existing across all repo branches (missing optional deps `pydicom`/`nibabel`/`pyarrow` in CI environment). See PR comment for details. All conformance tests pass locally.
+

docs/issues/issue-156.md

@@ -0,0 +1,66 @@
+---
+type: issue
+state: open
+created: 2026-02-26T08:09:28Z
+updated: 2026-02-26T08:09:45Z
+author: gerchowl
+author_url: https://github.com/gerchowl
+url: https://github.com/vig-os/fd5/issues/156
+comments: 0
+labels: bug, area:workflow, effort:small, semver:patch
+assignees: gerchowl
+milestone: none
+projects: none
+relationship: none
+synced: 2026-02-27T04:11:40.009Z
+---
+
+# [Issue 156]: [[BUG] devc-remote.sh compose commands run from repo root instead of .devcontainer/](https://github.com/vig-os/fd5/issues/156)
+
+## Description
+
+`scripts/devc-remote.sh` runs all `podman compose` / `docker compose` commands from `$REMOTE_PATH` (the repo root, e.g. `~/fd5`), but the compose files (`docker-compose.yml`, `docker-compose.project.yaml`, `docker-compose.local.yaml`) live in `$REMOTE_PATH/.devcontainer/`. The standalone `docker-compose` binary (used as podman's external compose provider) fails with "no configuration file provided: not found".
+
+## Steps to Reproduce
+
+1. Run `just devc-remote ksb-meatgrinder:~/fd5`
+2. Pre-flight passes successfully
+3. `remote_compose_up()` executes `cd ~/fd5 && podman compose up -d`
+4. `docker-compose` (external provider) can't find any compose file in `~/fd5`
+
+## Expected Behavior
+
+Compose commands should `cd` into `$REMOTE_PATH/.devcontainer` where the compose files reside, so `podman compose up -d` succeeds.
+
+## Actual Behavior
+
+```
+>>>> Executing external compose provider "/usr/local/bin/docker-compose". <<<<
+no configuration file provided: not found
+Error: executing /usr/local/bin/docker-compose up -d: exit status 1
+```
+
+## Environment
+
+- **OS**: macOS 24.5.0 (host) → Linux (remote: ksb-meatgrinder)
+- **Container Runtime**: Podman 4.9.3 (remote)
+- **Compose**: docker-compose v5.1.0 (standalone, used as podman's external compose provider)
+
+## Additional Context
+
+All compose-related SSH commands in the script use `cd $REMOTE_PATH` instead of `cd $REMOTE_PATH/.devcontainer`:
+- Line 218/220 (preflight container check)
+- Line 351 (`compose_ps_json`)
+- Line 383 (`check_existing_container` down)
+- Line 409 (`remote_compose_up`)
+- Line 411 (error hint message)
+
+## Possible Solution
+
+Change all `cd $REMOTE_PATH` to `cd $REMOTE_PATH/.devcontainer` in compose-related commands.
+
+## Changelog Category
+
+Fixed
+
+- [ ] TDD compliance (see .cursor/rules/tdd.mdc)

docs/issues/issue-158.md

@@ -0,0 +1,58 @@
+---
+type: issue
+state: open
+created: 2026-02-26T10:44:02Z
+updated: 2026-02-26T10:44:28Z
+author: gerchowl
+author_url: https://github.com/gerchowl
+url: https://github.com/vig-os/fd5/issues/158
+comments: 0
+labels: chore, area:workflow, effort:medium
+assignees: gerchowl
+milestone: none
+projects: none
+relationship: none
+synced: 2026-02-27T04:11:39.605Z
+---
+
+# [Issue 158]: [[CHORE] Add opt-in Tailscale SSH to devcontainer](https://github.com/vig-os/fd5/issues/158)
+
+### Chore Type
+
+Configuration change
+
+### Description
+
+Add opt-in Tailscale SSH support to the devcontainer so developers can connect via direct mesh SSH instead of the devcontainer protocol. This is a workaround for Cursor GUI's inability to execute agent shell commands when connected via the devcontainer protocol.
+
+When `TAILSCALE_AUTHKEY` is set (via `docker-compose.local.yaml`), the devcontainer installs Tailscale on first create and connects to the tailnet on every start with SSH enabled. When the env var is unset, the scripts are a no-op — zero impact on normal usage.
+
+### Acceptance Criteria
+
+- [ ] New `setup-tailscale.sh` script with `install` and `start` subcommands
+- [ ] `post-create.sh` calls `setup-tailscale.sh install` (no-op without `TAILSCALE_AUTHKEY`)
+- [ ] `post-start.sh` calls `setup-tailscale.sh start` (no-op without `TAILSCALE_AUTHKEY`)
+- [ ] `.devcontainer/README.md` updated with quick-start instructions
+- [ ] Detailed design doc at `docs/tailscale-devcontainer.md` covering architecture decisions, user setup, known gaps, and upstream considerations
+- [ ] `uv.lock` updated (incidental dependency sync)
+
+### Implementation Notes
+
+Files changed:
+- **New:** `.devcontainer/scripts/setup-tailscale.sh` — single script, two subcommands (`install` / `start`), idempotent, uses userspace networking (`--tun=userspace-networking`)
+- **Modified:** `.devcontainer/scripts/post-create.sh` — hooks `setup-tailscale.sh install`
+- **Modified:** `.devcontainer/scripts/post-start.sh` — adds `SCRIPT_DIR` resolution, hooks `setup-tailscale.sh start`
+- **Modified:** `.devcontainer/README.md` — new "Tailscale SSH" section
+- **New:** `docs/tailscale-devcontainer.md` — full design doc with architecture table, setup guide, known gap (git signing), and upstream notes
+
+### Related Issues
+
+None
+
+### Priority
+
+Medium
+
+### Changelog Category
+
+Added

docs/pull-requests/pr-153.md

@@ -1,9 +1,9 @@
 ---
 type: pull_request
-state: open
+state: closed (merged)
 branch: feature/149-preflight-feedback → dev
 created: 2026-02-26T00:26:40Z
-updated: 2026-02-26T00:26:42Z
+updated: 2026-02-26T08:03:42Z
 author: gerchowl
 author_url: https://github.com/gerchowl
 url: https://github.com/vig-os/fd5/pull/153
@@ -13,7 +13,8 @@ assignees: gerchowl
 milestone: none
 projects: none
 relationship: none
-synced: 2026-02-26T04:16:02.459Z
+merged: 2026-02-26T08:03:42Z
+synced: 2026-02-27T04:11:44.195Z
 ---
 
 # [PR 153](https://github.com/vig-os/fd5/pull/153) feat(devc-remote): add --yes flag, container prompt, and SSH agent improvements (#149)
@@ -92,3 +93,18 @@ This is a follow-up to PR #151 which implemented the initial preflight feedback
 
 Refs: #149
 
+
+
+---
+---
+
+## Commits
+
+### Commit 1: [0521e3f](https://github.com/vig-os/fd5/commit/0521e3fffbd6ca00a30c989d223b6ab04c0a9e46) by [gerchowl](https://github.com/gerchowl) on February 26, 2026 at 12:22 AM
+test: add failing tests for --yes flag, path annotation, container prompt, SSH agent check, 231 files modified (tests/test_devc_remote_preflight.sh)
+
+### Commit 2: [0096477](https://github.com/vig-os/fd5/commit/0096477d415470872789df638c7f537ae6342c26) by [gerchowl](https://github.com/gerchowl) on February 26, 2026 at 12:24 AM
+feat(devc-remote): add --yes flag, path annotations, container prompt, improved SSH agent check, 139 files modified (scripts/devc-remote.sh, tests/test_devc_remote_preflight.sh)
+
+### Commit 3: [7f636ac](https://github.com/vig-os/fd5/commit/7f636ac2e061a5cb4217c8da62dd7a0fbd3178b7) by [gerchowl](https://github.com/gerchowl) on February 26, 2026 at 12:25 AM
+docs: update changelog for preflight feedback improvements, 4 files modified (CHANGELOG.md)