zarrmony-phenix 0.2.0__tar.gz

zarrmony_phenix-0.2.0/.github/workflows/ci.yml

@@ -0,0 +1,35 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    name: Test (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: "3.13"
+
+      - name: Install zarrmony-phenix and dev tools
+        run: uv pip install -e ".[dev]"
+
+      - name: Lint
+        run: .venv/bin/ruff check
+
+      - name: Format check
+        run: .venv/bin/ruff format --check
+
+      - name: Test
+        run: .venv/bin/pytest

zarrmony_phenix-0.2.0/.github/workflows/release.yml

@@ -0,0 +1,26 @@
+name: Release
+
+on:
+  push:
+    tags: ['v*']
+
+jobs:
+  build-and-publish:
+    name: Build and publish to PyPI
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write   # OIDC for PyPI trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: "3.13"
+
+      - name: Build sdist and wheel
+        run: uv build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

zarrmony_phenix-0.2.0/.gitignore

@@ -0,0 +1,31 @@
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+*.egg-info/
+*.egg
+build/
+dist/
+pip-wheel-metadata/
+
+# Virtual envs
+.venv/
+venv/
+env/
+
+# uv
+uv.lock
+
+# Test / lint caches
+.pytest_cache/
+.ruff_cache/
+.coverage
+htmlcov/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+.DS_Store

zarrmony_phenix-0.2.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format follows [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).
+
+## [0.2.0] — 2026-05-11
+
+### Changed (BREAKING)
+
+- `PhenixReader.scenes` now contains vendor-native field labels (`F001`,
+  `F002`, ...) instead of the v0.1.0 `<row-letter><col>-f<field>` encoding
+  (`B04-f02`). Plate coordinates live on the new `plate_layout` attribute.
+  Code that keys `--per-scene-metadata` (or any other lookup) by the old
+  scene-name format must be re-keyed to the new `F\d{3}` shape.
+
+### Added
+
+- `PhenixReader.plate_layout` is now a populated `PlateLayout`, so
+  `zarrmony convert` with `--layout auto` (or `--layout plate`) writes a
+  single OME-NGFF 0.5 plate store.
+
+### Changed
+
+- Bumped `zarrmony>=0.3.0` (the plate writer was added there).
+- Multi-acquisition Phenix experiments emit a `LayoutDowngradeWarning`
+  and only the first acquisition's fields are exported.
+
+## [0.1.0] — 2026-05-08
+
+### Added
+
+- Initial release. `PhenixReader` adapter wraps `pyphenix.OperaPhenixReader`
+  and satisfies zarrmony's `ReaderProtocol`. Registers as `zarrmony-phenix`
+  via the `zarrmony.readers` entry point.
+- Scenes flatten `(well, field)` pairs into names like `B04-f02` so plate
+  coordinates remain recoverable from flat output (zarrmony ADR-0002).
+- `layout_hint = "plate"` set from day one; zarrmony 0.2.x ignores the hint
+  and emits per-scene flat output until HCS-Plate writer support lands.
+- Detects both Phenix on-disk shapes: export (`Images/Index.xml`) and archive
+  (`index/*.xml`).

zarrmony_phenix-0.2.0/CLAUDE.md

@@ -0,0 +1,15 @@
+# zarrmony-phenix
+
+## Agent skills
+
+### Issue tracker
+
+Issues live in the `ferrinm/zarrmony-phenix` GitHub repo, managed via the `gh` CLI. See `docs/agents/issue-tracker.md`.
+
+### Triage labels
+
+Canonical names (`needs-triage`, `needs-info`, `ready-for-agent`, `ready-for-human`, `wontfix`). See `docs/agents/triage-labels.md`.
+
+### Domain docs
+
+Single-context: one `CONTEXT.md` + `docs/adr/` at the repo root. See `docs/agents/domain.md`.

zarrmony_phenix-0.2.0/LICENSE

@@ -0,0 +1,201 @@
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zarrmony_phenix-0.2.0/PKG-INFO

@@ -0,0 +1,112 @@
+Metadata-Version: 2.4
+Name: zarrmony-phenix
+Version: 0.2.0
+Summary: Opera Phenix reader plugin for zarrmony — wraps pyphenix.OperaPhenixReader.
+Project-URL: Homepage, https://github.com/ferrinm/zarrmony-phenix
+Project-URL: Issues, https://github.com/ferrinm/zarrmony-phenix/issues
+Project-URL: Changelog, https://github.com/ferrinm/zarrmony-phenix/blob/main/CHANGELOG.md
+Author-email: Max Ferrin <ferrin@calicolabs.com>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Requires-Python: >=3.13
+Requires-Dist: dask>=2026.3.0
+Requires-Dist: numpy>=2
+Requires-Dist: pyphenix>=0.3.3
+Requires-Dist: xarray>=2025.9.0
+Requires-Dist: zarrmony>=0.3.0
+Provides-Extra: dev
+Requires-Dist: pytest-cov>=7; extra == 'dev'
+Requires-Dist: pytest>=8; extra == 'dev'
+Requires-Dist: ruff>=0.14; extra == 'dev'
+Requires-Dist: tifffile>=2024.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# zarrmony-phenix
+
+Opera Phenix reader plugin for [zarrmony](https://github.com/ferrinm/zarrmony).
+Wraps [`pyphenix.OperaPhenixReader`](https://github.com/ferrinm/pyphenix) so
+that `zarrmony convert /path/to/PhenixExperiment` Just Works.
+
+## Install
+
+```bash
+pip install zarrmony-phenix
+```
+
+This pulls `zarrmony` and `pyphenix` from PyPI as transitive dependencies.
+
+## Verify the plugin registered
+
+```python
+from zarrmony.readers.plugin import list_plugins
+print([p.name for p in list_plugins()])
+# -> [..., 'zarrmony-phenix']
+```
+
+## Use
+
+```bash
+zarrmony inspect /path/to/PhenixExperiment   # lists fields per well
+zarrmony convert /path/to/PhenixExperiment ./out
+```
+
+`zarrmony convert` defaults to `--layout auto`, which dispatches to the HCS
+plate writer for plate-shaped readers. The output at `./out` is a single
+OME-NGFF 0.5 plate store: well groups at `<row>/<column>/` (e.g. `B/04/`)
+each containing one image per imaged field. Pass `--layout plate` to make
+the choice explicit, or `--layout per-scene` to produce one
+`<scene>.ome.zarr` per FOV instead.
+
+Scenes are named with the vendor's native field labels (`F001`, `F002`, …);
+plate coordinates live on the `plate_layout` attribute that zarrmony's plate
+writer consumes (see the
+[reader-plugin authoring guide §9](https://github.com/ferrinm/zarrmony/blob/main/docs/writing-a-reader-plugin.md#9-writing-a-plate-shaped-reader)
+and zarrmony [ADR-0004](https://github.com/ferrinm/zarrmony/blob/main/docs/adr/0004-plate-output-design.md)).
+Multi-acquisition Phenix experiments emit a `LayoutDowngradeWarning` and
+only the first acquisition's fields are exported; pass `--layout per-scene`
+to get all acquisitions in one pass.
+
+### Migrating from v0.1.0
+
+- Scene names changed from `<row-letter><col>-f<field>` (e.g. `B04-f02`)
+  to vendor-native field labels (`F001`, `F002`, …). Code that keys
+  `--per-scene-metadata` (or anything else) by the old name must be
+  re-keyed; plate coordinates now live on `reader.plate_layout`, not in
+  the scene name.
+- Default output is now a single plate store, not one
+  `.ome.zarr` per FOV. Pass `--layout per-scene` to keep the v0.1.0 shape.
+- `zarrmony>=0.3.0` is now required (the plate writer ships there).
+
+## Supported Phenix exports
+
+- **Export format**: directory with `Images/Index.xml` and TIFFs under
+  `Images/`.
+- **Archive format**: directory with `index/<something>.xml` and TIFFs under
+  `images/`.
+
+Detection is by the presence of either marker; both are scored equally.
+
+## Limitations
+
+- **Flat-field correction is disabled.** zarrmony streams data into Zarr
+  chunk-by-chunk and pyphenix's FFC pipeline requires loading whole stacks
+  eagerly. If you need FFC-corrected output, run pyphenix's own loader and
+  feed the corrected NumPy arrays into a custom writer.
+- **Multi-acquisition Phenix experiments degrade gracefully.** Zarrmony's
+  v1 plate writer is single-acquisition; if more than one `AcquisitionID`
+  is detected in `Index.xml`, the adapter emits a `LayoutDowngradeWarning`
+  and exports only the first acquisition's fields. Pass
+  `--layout per-scene` to capture every acquisition as its own store.
+
+## Why a separate package?
+
+Phenix carries real domain logic (FFC math, plate-coordinate parsing, mosaic
+stitching) and dependencies (PIL, custom XML parsing) that don't belong in
+zarrmony's import graph. See zarrmony [ADR-0003](https://github.com/ferrinm/zarrmony/blob/main/docs/adr/0003-external-adapter-package-for-non-bioio-readers.md)
+for the full rationale and the
+[reader-plugin authoring guide](https://github.com/ferrinm/zarrmony/blob/main/docs/writing-a-reader-plugin.md)
+for how to build your own.
+
+## License
+
+Apache-2.0.

zarrmony_phenix-0.2.0/README.md

@@ -0,0 +1,89 @@
+# zarrmony-phenix
+
+Opera Phenix reader plugin for [zarrmony](https://github.com/ferrinm/zarrmony).
+Wraps [`pyphenix.OperaPhenixReader`](https://github.com/ferrinm/pyphenix) so
+that `zarrmony convert /path/to/PhenixExperiment` Just Works.
+
+## Install
+
+```bash
+pip install zarrmony-phenix
+```
+
+This pulls `zarrmony` and `pyphenix` from PyPI as transitive dependencies.
+
+## Verify the plugin registered
+
+```python
+from zarrmony.readers.plugin import list_plugins
+print([p.name for p in list_plugins()])
+# -> [..., 'zarrmony-phenix']
+```
+
+## Use
+
+```bash
+zarrmony inspect /path/to/PhenixExperiment   # lists fields per well
+zarrmony convert /path/to/PhenixExperiment ./out
+```
+
+`zarrmony convert` defaults to `--layout auto`, which dispatches to the HCS
+plate writer for plate-shaped readers. The output at `./out` is a single
+OME-NGFF 0.5 plate store: well groups at `<row>/<column>/` (e.g. `B/04/`)
+each containing one image per imaged field. Pass `--layout plate` to make
+the choice explicit, or `--layout per-scene` to produce one
+`<scene>.ome.zarr` per FOV instead.
+
+Scenes are named with the vendor's native field labels (`F001`, `F002`, …);
+plate coordinates live on the `plate_layout` attribute that zarrmony's plate
+writer consumes (see the
+[reader-plugin authoring guide §9](https://github.com/ferrinm/zarrmony/blob/main/docs/writing-a-reader-plugin.md#9-writing-a-plate-shaped-reader)
+and zarrmony [ADR-0004](https://github.com/ferrinm/zarrmony/blob/main/docs/adr/0004-plate-output-design.md)).
+Multi-acquisition Phenix experiments emit a `LayoutDowngradeWarning` and
+only the first acquisition's fields are exported; pass `--layout per-scene`
+to get all acquisitions in one pass.
+
+### Migrating from v0.1.0
+
+- Scene names changed from `<row-letter><col>-f<field>` (e.g. `B04-f02`)
+  to vendor-native field labels (`F001`, `F002`, …). Code that keys
+  `--per-scene-metadata` (or anything else) by the old name must be
+  re-keyed; plate coordinates now live on `reader.plate_layout`, not in
+  the scene name.
+- Default output is now a single plate store, not one
+  `.ome.zarr` per FOV. Pass `--layout per-scene` to keep the v0.1.0 shape.
+- `zarrmony>=0.3.0` is now required (the plate writer ships there).
+
+## Supported Phenix exports
+
+- **Export format**: directory with `Images/Index.xml` and TIFFs under
+  `Images/`.
+- **Archive format**: directory with `index/<something>.xml` and TIFFs under
+  `images/`.
+
+Detection is by the presence of either marker; both are scored equally.
+
+## Limitations
+
+- **Flat-field correction is disabled.** zarrmony streams data into Zarr
+  chunk-by-chunk and pyphenix's FFC pipeline requires loading whole stacks
+  eagerly. If you need FFC-corrected output, run pyphenix's own loader and
+  feed the corrected NumPy arrays into a custom writer.
+- **Multi-acquisition Phenix experiments degrade gracefully.** Zarrmony's
+  v1 plate writer is single-acquisition; if more than one `AcquisitionID`
+  is detected in `Index.xml`, the adapter emits a `LayoutDowngradeWarning`
+  and exports only the first acquisition's fields. Pass
+  `--layout per-scene` to capture every acquisition as its own store.
+
+## Why a separate package?
+
+Phenix carries real domain logic (FFC math, plate-coordinate parsing, mosaic
+stitching) and dependencies (PIL, custom XML parsing) that don't belong in
+zarrmony's import graph. See zarrmony [ADR-0003](https://github.com/ferrinm/zarrmony/blob/main/docs/adr/0003-external-adapter-package-for-non-bioio-readers.md)
+for the full rationale and the
+[reader-plugin authoring guide](https://github.com/ferrinm/zarrmony/blob/main/docs/writing-a-reader-plugin.md)
+for how to build your own.
+
+## License
+
+Apache-2.0.

zarrmony_phenix-0.2.0/docs/agents/domain.md

@@ -0,0 +1,38 @@
+# Domain Docs
+
+How the engineering skills should consume this repo's domain documentation when exploring the codebase.
+
+## Before exploring, read these
+
+- **`CONTEXT.md`** at the repo root, or
+- **`CONTEXT-MAP.md`** at the repo root if it exists — it points at one `CONTEXT.md` per context. Read each one relevant to the topic.
+- **`docs/adr/`** — read ADRs that touch the area you're about to work in. In multi-context repos, also check `src/<context>/docs/adr/` for context-scoped decisions.
+
+If any of these files don't exist, **proceed silently**. Don't flag their absence; don't suggest creating them upfront. The producer skill (`/grill-with-docs`) creates them lazily when terms or decisions actually get resolved.
+
+## File structure
+
+This repo is **single-context**:
+
+```
+/
+├── CONTEXT.md
+├── docs/adr/
+│   ├── 0001-example-decision.md
+│   └── 0002-another-decision.md
+└── src/
+```
+
+For reference, a multi-context layout (not used here) would have `CONTEXT-MAP.md` at the root pointing to per-context `CONTEXT.md` files under `src/<context>/`.
+
+## Use the glossary's vocabulary
+
+When your output names a domain concept (in an issue title, a refactor proposal, a hypothesis, a test name), use the term as defined in `CONTEXT.md`. Don't drift to synonyms the glossary explicitly avoids.
+
+If the concept you need isn't in the glossary yet, that's a signal — either you're inventing language the project doesn't use (reconsider) or there's a real gap (note it for `/grill-with-docs`).
+
+## Flag ADR conflicts
+
+If your output contradicts an existing ADR, surface it explicitly rather than silently overriding:
+
+> _Contradicts ADR-0007 (event-sourced orders) — but worth reopening because…_

zarrmony_phenix-0.2.0/docs/agents/issue-tracker.md

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+# Issue tracker: GitHub
+
+Issues and PRDs for this repo live as GitHub issues. Use the `gh` CLI for all operations.
+
+## Conventions
+
+- **Create an issue**: `gh issue create --title "..." --body "..."`. Use a heredoc for multi-line bodies.
+- **Read an issue**: `gh issue view <number> --comments`, filtering comments by `jq` and also fetching labels.
+- **List issues**: `gh issue list --state open --json number,title,body,labels,comments --jq '[.[] | {number, title, body, labels: [.labels[].name], comments: [.comments[].body]}]'` with appropriate `--label` and `--state` filters.
+- **Comment on an issue**: `gh issue comment <number> --body "..."`
+- **Apply / remove labels**: `gh issue edit <number> --add-label "..."` / `--remove-label "..."`
+- **Close**: `gh issue close <number> --comment "..."`
+
+Infer the repo from `git remote -v` — `gh` does this automatically when run inside a clone.
+
+## When a skill says "publish to the issue tracker"
+
+Create a GitHub issue.
+
+## When a skill says "fetch the relevant ticket"
+
+Run `gh issue view <number> --comments`.

zarrmony_phenix-0.2.0/docs/agents/triage-labels.md

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+# Triage Labels
+
+The skills speak in terms of five canonical triage roles. This file maps those roles to the actual label strings used in this repo's issue tracker.
+
+| Label in mattpocock/skills | Label in our tracker | Meaning                                  |
+| -------------------------- | -------------------- | ---------------------------------------- |
+| `needs-triage`             | `needs-triage`       | Maintainer needs to evaluate this issue  |
+| `needs-info`               | `needs-info`         | Waiting on reporter for more information |
+| `ready-for-agent`          | `ready-for-agent`    | Fully specified, ready for an AFK agent  |
+| `ready-for-human`          | `ready-for-human`    | Requires human implementation            |
+| `wontfix`                  | `wontfix`            | Will not be actioned                     |
+
+When a skill mentions a role (e.g. "apply the AFK-ready triage label"), use the corresponding label string from this table.
+
+Edit the right-hand column to match whatever vocabulary you actually use.
+
+## Note on label creation
+
+Only `wontfix` exists in the repo today. The other four will need to be created the first time a triage skill applies them — `gh label create <name>` will do this. Creating them lazily is fine; the skill will surface a clear error if the label is missing.