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AndrewSazonovCopilot
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Copilot
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Extract refln into a dedicated experiment category (#163)
* Add powder Refln category plan * Record powder Refln category decisions * Add plan workflow instructions * Add powder Refln category Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * Wire powder Refln into Bragg experiments Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * Extract Cryspy powder reflection records Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * Populate powder Refln during calculation Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * Use powder Refln for Bragg ticks Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * Document powder Refln Bragg ticks Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * Update powder Refln implementation plan Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * Fix powder Refln CWL tick units Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * Fix powder Refln d-spacing ticks Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * Scale Bragg panel height with the number of phases * Add powder Refln verification tests Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * Verify powder Refln implementation Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * Finalize powder Refln plan Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * Remove completed powder plot plans Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * Reverse Bragg tick row order Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * Fix powder refln lifecycle and Bragg scaling Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * Extract refln into a dedicated experiment categor * Fix linting, formatting and tests * Fix refln category extraction * Remove completed plan * Restore refln compatibility entry points * Keep refln API break and fix Plotly height * Restore default Plotly composite height --------- Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
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‎.github/copilot-instructions.md‎

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## Workflow
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### Planning Workflow
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- When asked to create a plan, first gather enough repository context to
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make the plan concrete. Ask all ambiguous, potentially ambiguous, or
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unclear questions in one concise batch, and record unresolved
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questions in the plan if the user wants the plan saved before
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answering them.
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- Save plans as Markdown files in `docs/dev` with the filename pattern
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`plan_<feature-name>.md`. The `<feature-name>` part uses lowercase
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words separated by dashes, for example
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`docs/dev/plan_background-refactor.md`.
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- Use the same `<feature-name>` to create the implementation branch,
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normally `feature/<feature-name>`. Do not push the branch unless the
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user explicitly asks.
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- Each plan must include a status checklist with `[ ]` items. Mark each
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item as `[x]` as it is completed during implementation.
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- Plans for non-trivial work must separate the work into two phases:
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- **Phase 1 — Implementation:** the agent works independently through
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all implementation steps, updating the plan checklist as it goes. Do
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not create tests or run tests in this phase unless the user
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explicitly asks. When Phase 1 is complete, stop and ask the user to
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review the implementation.
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- **Phase 2 — Verification:** after user approval, add/update tests,
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run formatting, linting, unit tests, integration tests, and script
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or notebook checks requested by the plan.
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- Every completed implementation step must end with a local commit.
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Stage only the files modified for that step, using explicit paths
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where practical. Do not include data files, project files, CIF files,
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or other generated artifacts created by integration tests, script
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tests, or notebook execution unless the user explicitly asked to
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update those artifacts.
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- Keep commits atomic, single-purpose, and aligned with plan steps. Use
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imperative commit messages, no type prefix, and keep the subject line
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at or below 72 characters.
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- Before each commit, inspect the worktree and avoid staging unrelated
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user changes. If unrelated dirty files exist, leave them untouched and
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mention them only when relevant.
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- The plan should be easy to maintain while working: include concrete
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files likely to change, decisions already made, open questions,
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verification commands for Phase 2, and a short suggested commit
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message or branch name when useful.
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### General Workflow
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- Two-phase workflow for non-trivial changes:
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- **Phase 1 — Implementation:** code, docs, architecture updates. Do
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not create new tests or run existing tests. Present for review and

‎docs/architecture/package-structure-full.md‎

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│ ├── 📁 calculators
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│ │ ├── 📄 __init__.py
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│ │ ├── 📄 base.py
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│ │ │ ├── 🏷️ class PowderReflnRecord
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│ │ │ └── 🏷️ class CalculatorBase
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│ │ ├── 📄 crysfml.py
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│ │ │ └── 🏷️ class CrysfmlCalculator
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│ │ │ │ │ ├── 🏷️ class PdDataBase
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│ │ │ │ │ ├── 🏷️ class PdCwlData
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│ │ │ │ │ └── 🏷️ class PdTofData
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│ │ │ │ ├── 📄 bragg_sc.py
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│ │ │ │ │ ├── 🏷️ class Refln
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│ │ │ │ │ └── 🏷️ class ReflnData
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│ │ │ │ ├── 📄 factory.py
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│ │ │ │ │ └── 🏷️ class DataFactory
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│ │ │ │ └── 📄 total_pd.py
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│ │ │ │ │ └── 🏷️ class TotalGaussianDampedSinc
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│ │ │ │ └── 📄 total_mixins.py
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│ │ │ │ └── 🏷️ class TotalBroadeningMixin
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│ │ │ ├── 📁 refln
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│ │ │ │ ├── 📄 __init__.py
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│ │ │ │ ├── 📄 bragg_pd.py
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│ │ │ │ │ ├── 🏷️ class PowderReflnBase
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│ │ │ │ │ ├── 🏷️ class PowderCwlRefln
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│ │ │ │ │ ├── 🏷️ class PowderTofRefln
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│ │ │ │ │ ├── 🏷️ class PowderReflnDataBase
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│ │ │ │ │ ├── 🏷️ class PowderCwlReflnData
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│ │ │ │ │ └── 🏷️ class PowderTofReflnData
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│ │ │ │ ├── 📄 bragg_sc.py
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│ │ │ │ │ ├── 🏷️ class Refln
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│ │ │ │ │ └── 🏷️ class ReflnData
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│ │ │ │ └── 📄 factory.py
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│ │ │ │ └── 🏷️ class ReflnFactory
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│ │ │ └── 📄 __init__.py
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│ │ ├── 📁 item
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│ │ │ ├── 📄 __init__.py

‎docs/architecture/package-structure-short.md‎

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│ │ │ ├── 📁 data
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│ │ │ │ ├── 📄 __init__.py
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│ │ │ │ ├── 📄 bragg_pd.py
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│ │ │ │ ├── 📄 bragg_sc.py
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│ │ │ │ ├── 📄 factory.py
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│ │ │ │ └── 📄 total_pd.py
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│ │ │ ├── 📁 diffrn
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│ │ │ │ ├── 📄 tof_mixins.py
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│ │ │ │ ├── 📄 total.py
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│ │ │ │ └── 📄 total_mixins.py
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│ │ │ ├── 📁 refln
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│ │ │ │ ├── 📄 __init__.py
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│ │ │ │ ├── 📄 bragg_pd.py
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│ │ │ │ ├── 📄 bragg_sc.py
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│ │ │ │ └── 📄 factory.py
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│ │ │ └── 📄 __init__.py
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│ │ ├── 📁 item
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│ │ │ ├── 📄 __init__.py

‎docs/architecture/plan-threePanelPowderPlot.prompt.md‎

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