Prepare OpenHCS for image.sc announcement

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,62 @@
+name: Bug report
+description: Report a reproducible OpenHCS failure
+title: "[Bug]: "
+labels:
+  - bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for helping improve OpenHCS. Do not include patient data, credentials, private plate paths, or proprietary images.
+  - type: input
+    id: version
+    attributes:
+      label: OpenHCS version
+      description: Copy the version from About, `python -m openhcs --version`, or package metadata.
+    validations:
+      required: true
+  - type: dropdown
+    id: install
+    attributes:
+      label: Installation route
+      options:
+        - Windows installer
+        - macOS installer
+        - PyPI
+        - Source checkout
+        - Other
+    validations:
+      required: true
+  - type: textarea
+    id: environment
+    attributes:
+      label: Environment
+      description: Operating system, Python version if applicable, CPU/GPU, viewer, and MCP client/surface if involved.
+    validations:
+      required: true
+  - type: textarea
+    id: reproduce
+    attributes:
+      label: Minimal reproduction
+      description: Numbered steps, with a synthetic or redacted example when data is involved.
+    validations:
+      required: true
+  - type: textarea
+    id: expected
+    attributes:
+      label: Expected and actual behavior
+    validations:
+      required: true
+  - type: textarea
+    id: logs
+    attributes:
+      label: Logs or screenshots
+      description: Paste the smallest relevant excerpt and redact sensitive paths or data.
+      render: shell
+  - type: checkboxes
+    id: sensitive
+    attributes:
+      label: Data safety
+      options:
+        - label: I removed credentials, patient data, private paths, and proprietary image content.
+          required: true

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,8 @@
+blank_issues_enabled: true
+contact_links:
+  - name: Security report
+    url: mailto:tristan.simas@mail.mcgill.ca
+    about: Report vulnerabilities privately rather than opening an issue.
+  - name: Documentation
+    url: https://openhcs.readthedocs.io/
+    about: Check installation, architecture, and MCP client guidance.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,16 @@
+## What changed
+
+Describe the user-visible outcome and the declaration or typed owner changed.
+
+## Evidence
+
+- [ ] Added or updated a focused regression
+- [ ] Ran the relevant local tests
+- [ ] Preserved declaration ownership; no mirrored registry or metadata source
+- [ ] Documented platform, GPU, viewer, or installer journeys not run locally
+
+Commands and results:
+
+```text
+
+```

.github/workflows/integration-tests.yml

@@ -533,6 +533,8 @@ jobs:
         run: git config --global core.longpaths true
 
       - uses: actions/checkout@v4
+        with:
+          submodules: ${{ env.OPENHCS_CI_DEP_SOURCE == 'submodules' && 'recursive' || 'false' }}
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v5
@@ -557,6 +559,9 @@ jobs:
           python -m pip install build packaging pytest
           python -m pytest -q -c tests/installer/pytest.ini tests/installer
 
+      - name: Build installer source wheelhouse
+        run: python -m scripts.build_installer_source_wheelhouse --output dist --dependency-source "${{ env.OPENHCS_CI_DEP_SOURCE }}"
+
       - name: Parse Windows PowerShell installer sources
         if: matrix.platform == 'windows'
         shell: pwsh
@@ -574,8 +579,7 @@ jobs:
         shell: pwsh
         timeout-minutes: 30
         run: |
-          python -m build --wheel
-          $releaseVersion = python -c "from pathlib import Path; from packaging.utils import parse_wheel_filename; print(parse_wheel_filename(next(Path('dist').glob('*.whl')).name)[1])"
+          $releaseVersion = python -c "from pathlib import Path; from packaging.utils import parse_wheel_filename; versions=[parse_wheel_filename(path.name)[1] for path in Path('dist').glob('*.whl') if str(parse_wheel_filename(path.name)[0])=='openhcs']; assert len(versions)==1, versions; print(versions[0])"
           $releaseVersion = $releaseVersion.Trim()
           $stage = Join-Path $env:RUNNER_TEMP "OpenHCS-Windows-Smoke"
           $installRoot = Join-Path $env:RUNNER_TEMP "OpenHCS Installed"
@@ -828,8 +832,7 @@ jobs:
       - name: Execute and verify macOS installer
         if: matrix.platform == 'macos'
         run: |
-          python -m build --wheel
-          release_version=$(python -c "from pathlib import Path; from packaging.utils import parse_wheel_filename; print(parse_wheel_filename(next(Path('dist').glob('*.whl')).name)[1])")
+          release_version=$(python -c "from pathlib import Path; from packaging.utils import parse_wheel_filename; versions=[parse_wheel_filename(path.name)[1] for path in Path('dist').glob('*.whl') if str(parse_wheel_filename(path.name)[0])=='openhcs']; assert len(versions)==1, versions; print(versions[0])")
           staged_contract="$RUNNER_TEMP/installer_contract.json"
           installer_app="$RUNNER_TEMP/OpenHCS Release Installer.app"
           smoke_home="$RUNNER_TEMP/openhcs-installer-home"

.gitignore

@@ -180,6 +180,10 @@ benchmark/results/napari_streaming_validator/
 /*.md
 !/README.md
 !/CHANGELOG.md
+!/CITATION.cff
+!/CODE_OF_CONDUCT.md
+!/CONTRIBUTING.md
+!/SECURITY.md
 
 # Chunkhound
 .chunkhound/

CHANGELOG.md

@@ -7,6 +7,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Changed
+
+- Removed the dataset-specific BBBC021 and BBBC038 microscope choices. BBBC
+  datasets now use their declared source bindings, while benchmark dataset IDs
+  remain available as provenance.
+- Renamed Napari component placement from ``slice`` to ``layer`` so display
+  configuration now distinguishes separate viewer layers from genuine image
+  slices; Fiji slice placement is unchanged.
+
 ### Added
 
 #### Auto-Add Output Plate Feature
@@ -41,6 +50,91 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - Added `requests>=2.31.0` dependency for HTTP communication
   - Comprehensive test suite for LLM service and chat panel
 
+## [0.7.11] - 2026-08-01
+
+### Fixed
+
+- Windows multiprocessing now preserves the installed interpreter used to
+  launch OpenHCS instead of resolving to an unrelated Python executable.
+- Desktop monitoring presents the canonical brand and exposes its typed
+  settings without clipped information text.
+
+## [0.7.10] - 2026-08-01
+
+### Fixed
+
+- Execution progress registration now routes through the control authority so
+  UI and agent projections observe the same lifecycle.
+
+## [0.7.9] - 2026-08-01
+
+### Changed
+
+- Configuration layouts now reflow responsively while preserving readable
+  field and help surfaces.
+
+## [0.7.8] - 2026-07-31
+
+### Fixed
+
+- Release builds resolve versions for independently published dependencies
+  from their authoritative package declarations.
+
+## [0.7.7] - 2026-07-31
+
+### Changed
+
+- Native desktop updates and their recovery/presentation lifecycle were
+  hardened across supported platforms.
+
+## [0.7.6] - 2026-07-31
+
+### Fixed
+
+- Dock widgets correctly return to the managed workspace and branding refresh
+  no longer disturbs the native layout.
+
+## [0.7.5] - 2026-07-31
+
+### Changed
+
+- Desktop startup, docked workspace presentation, and CI runner path handling
+  were polished after the initial gallery release.
+
+## [0.7.4] - 2026-07-31
+
+### Added
+
+- A verified workflow media gallery and capture tooling that rejects fabricated
+  UI state.
+- Unit/core CI gates, typed viewer controls, agent-visible viewer authority,
+  UI recovery receipts, and hardened bridge endpoint identity.
+
+### Changed
+
+- The main workspace uses native dock and control theming, preserves geometry,
+  and suppresses consoles for background GUI processes.
+- ObjectState 1.1.1 provides transactional typed configuration and edit-history
+  recovery.
+
+## [0.7.3] - 2026-07-30
+
+### Fixed
+
+- The official logo family is used consistently across release and desktop
+  surfaces.
+
+## [0.7.2] - 2026-07-30
+
+### Added
+
+- Canonical brand assets for the GUI, launcher, installer, website, and package.
+
+### Changed
+
+- Windows GUI launchers suppress the console and the public site describes the
+  current beta without stale patch-level launch claims.
+
 ## [0.7.1] - 2026-07-30
 
 ### Added
@@ -221,4 +315,14 @@ See git history for changes in versions 0.3.14 and earlier.
 
 [0.4.0]: https://github.com/trissim/openhcs/compare/v0.3.15...v0.4.0
 [0.3.15]: https://github.com/trissim/openhcs/releases/tag/v0.3.15
+[0.7.11]: https://github.com/OpenHCSDev/OpenHCS/compare/v0.7.10...v0.7.11
+[0.7.10]: https://github.com/OpenHCSDev/OpenHCS/compare/v0.7.9...v0.7.10
+[0.7.9]: https://github.com/OpenHCSDev/OpenHCS/compare/v0.7.8...v0.7.9
+[0.7.8]: https://github.com/OpenHCSDev/OpenHCS/compare/v0.7.7...v0.7.8
+[0.7.7]: https://github.com/OpenHCSDev/OpenHCS/compare/v0.7.6...v0.7.7
+[0.7.6]: https://github.com/OpenHCSDev/OpenHCS/compare/v0.7.5...v0.7.6
+[0.7.5]: https://github.com/OpenHCSDev/OpenHCS/compare/v0.7.4...v0.7.5
+[0.7.4]: https://github.com/OpenHCSDev/OpenHCS/compare/v0.7.3...v0.7.4
+[0.7.3]: https://github.com/OpenHCSDev/OpenHCS/compare/v0.7.2...v0.7.3
+[0.7.2]: https://github.com/OpenHCSDev/OpenHCS/compare/v0.7.1...v0.7.2
 [0.7.0]: https://github.com/OpenHCSDev/OpenHCS/compare/v0.6.17...v0.7.0

CITATION.cff

@@ -0,0 +1,17 @@
+cff-version: 1.2.0
+message: "If you use OpenHCS, cite the exact release and archive identifier used in your analysis."
+title: "OpenHCS: typed high-content microscopy workflows"
+type: software
+authors:
+  - family-names: Simas
+    given-names: Tristan
+    email: tristan.simas@mail.mcgill.ca
+repository-code: "https://github.com/OpenHCSDev/OpenHCS"
+url: "https://openhcs.readthedocs.io/"
+license: MIT
+keywords:
+  - high-content screening
+  - bioimage analysis
+  - microscopy
+  - image processing
+  - Model Context Protocol

CODE_OF_CONDUCT.md

@@ -0,0 +1,23 @@
+# Code of Conduct
+
+OpenHCS is committed to a welcoming, harassment-free community for scientists,
+software contributors, and users of every background and level of experience.
+
+Be respectful and specific. Critique ideas and evidence rather than people;
+assume good faith while accepting correction; protect private research data;
+and make space for people who are new to bioimage analysis or open-source
+development. Harassment, intimidation, discriminatory language, sexualized
+attention, doxxing, and sustained disruption are not acceptable.
+
+Maintainers may edit or remove contributions and temporarily or permanently
+restrict participation when conduct is unsafe or persistently disruptive.
+Enforcement decisions should be proportionate, documented privately, and avoid
+unnecessary disclosure of the reporter's identity.
+
+Report conduct concerns privately to
+[tristan.simas@mail.mcgill.ca](mailto:tristan.simas@mail.mcgill.ca). Reports
+will be reviewed promptly and handled as confidentially as practical. This
+policy applies in project repositories, documentation, community forums, and
+project-related private communications.
+
+This policy is informed by the Contributor Covenant, version 2.1.

CONTRIBUTING.md

@@ -0,0 +1,69 @@
+# Contributing to OpenHCS
+
+OpenHCS welcomes reproducible bug reports, microscope fixtures, processing
+functions, documentation, and focused code changes.
+
+## Report an issue
+
+Search the issue tracker first, then include the OpenHCS version, installation
+route, operating system, Python version, minimal steps, expected behavior, and
+relevant logs. For microscopy failures, describe the instrument, axes, naming
+pattern, and expected output without uploading sensitive image data.
+
+Security vulnerabilities should be reported privately as described in
+[SECURITY.md](SECURITY.md).
+
+## Development checkout
+
+OpenHCS uses source submodules for its independently published libraries:
+
+```bash
+git clone --depth 1 --recurse-submodules --shallow-submodules \
+  https://github.com/OpenHCSDev/OpenHCS.git
+cd OpenHCS
+python -m venv .venv
+source .venv/bin/activate
+python -m pip install --upgrade pip
+python -m pip install -e "external/python-introspect"
+python -m pip install -e "external/metaclass-registry"
+python -m pip install -e "external/ObjectState"
+python -m pip install -e "external/arraybridge"
+python -m pip install -e "external/pycodify"
+python -m pip install -e "external/PolyStore"
+python -m pip install -e "external/pyqt-reactive"
+python -m pip install -e "external/zmqruntime"
+python -m pip install -e ".[dev,dev-gui,gui,mcp]"
+```
+
+See `docs/development_setup.md` for optional GPU, viewer, Bio-Formats, OMERO,
+and CellProfiler compatibility dependencies.
+
+## Architecture expectations
+
+Read `docs/source/architecture/quick_start.rst`, then
+`system_overview.rst`, `nominal_ownership.rst`, and
+`abstraction_lattices.rst` before a structural change.
+
+- Change the declaration or typed owner of a behavior.
+- Derive schemas, UI projections, registries, and runtime plans from that owner.
+- Do not add mirrored metadata tables, parallel kind registries, sidecars, or
+  compatibility shims when the owning contract can express the rule.
+- Keep compilation deterministic. Workers consume frozen compiled plans rather
+  than reinterpreting mutable authoring objects.
+- Put reusable behavior in the library that owns it; update the OpenHCS
+  submodule pointer only after that library change is independently tested.
+
+## Tests and pull requests
+
+Run the narrowest relevant tests while developing, then the CPU unit gate:
+
+```bash
+OPENHCS_CPU_ONLY=1 python -m pytest tests/unit
+python -m ruff check openhcs tests
+```
+
+GUI tests can use `QT_QPA_PLATFORM=offscreen`. Add a regression that fails for
+the reported behavior and exercises its public or nominal boundary. Keep pull
+requests focused, explain the evidence boundary, and note any platform or GPU
+journey you could not run locally. All contributions must follow
+[CODE_OF_CONDUCT.md](CODE_OF_CONDUCT.md).