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Use when code uses clifpy.","sajor2000\u002Fmethodsmith","sajor2000","https:\u002F\u002Favatars.githubusercontent.com\u002Fu\u002F126191042?v=4","01M71QG4M3561SH49E3S7J3GKT","JC Rojas ","01M71QG4N56X2P61YTJSRP95VD",6,"MIT","https:\u002F\u002Fgithub.com\u002Fsajor2000\u002Fmethodsmith\u002Fblob\u002Fmain\u002Fplugins\u002Fmethodsmith\u002Fskills\u002Fmethod-clifpy\u002FSKILL.md",[18],{"categoryNo":19,"categoryName":20,"taxonomyType":21,"taxonomyTypeDesc":22},"01JBSEEDCAT000000000000030","开发工程师","PROFESSION","适用职业",[24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41],"method clifpy","file","helpers","verified","name","timezone rules","python code","task","api","code","version","when","Rules","use","calls","python","timezone","reviews","2026-11-10 13:02:02",false,"---\nname: method-clifpy\ndescription: \"Writes and reviews CLIF Python code that calls clifpy correctly: verified API, version and timezone rules, no reimplemented helpers. Use when code uses clifpy.\"\nargument-hint: \"[task, file, or clifpy function name]\"\n---\n\n# clifpy Usage\n\n## Skill Value\n\n- **Problem it solves:** CLIF projects hand-roll SOFA, outlier handling, unit conversion, stitching, and wide datasets that `clifpy` already provides, and call `clifpy` from memory with wrong arguments, wrong version vocabularies, and silent timezone shifts.\n- **Use when:** Writing, fixing, upgrading, or reviewing Python that loads CLIF tables or calls any `clifpy` function, class, or utility.\n- **Output:** Working `clifpy` code that uses the verified API, the selected CLIF version, explicit timezone handling, post-call assertions, and output paths that keep row-level artifacts out of shared folders.\n- **Ask only if:** The CLIF version family or the site timezone is unknown and the code depends on it. Exception: the output-path approval gate in workflow step 6 always applies; ask for any output, DuckDB temp, or log path that lacks approval before running on real data.\n- **Do not do:** Do not write `clifpy` calls from memory, copy examples from the upstream README or validation guide without checking them, or reimplement a capability `clifpy` already ships.\n- **Interaction:** Check repo\u002Fconfig\u002Fchat evidence first. Ask one decision-changing question at a time; use the current harness's blocking question UI when available, otherwise present numbered choices and wait.\n\nThe references were verified against `clifpy` GitHub commit `c4a1eeb` (2026-10-14),\ndiffed against the published 2.1.0 package, and checked against the\npublic docs at `https:\u002F\u002Fcommon-longitudinal-icu-data-format.github.io\u002Fclifpy\u002F`.\n`https:\u002F\u002Fclif-icu.com\u002F` remains authoritative for the data dictionary and mCIDE.\n\n## Workflow\n\n1. **Anchor CLIF context.** Consume `__CE_CLIF__` when present; otherwise load\n   the `method-clif` skill. Take `version=` (2.1.0 or 3.0.0) from it and never\n   infer a family from table names. CLIF 2.1.0 is the current release; 3.0.0 is\n   pre-release on clif-icu.com.\n2. **Establish the installed version.** Read `uv.lock` (or `requirements*.txt`,\n   `pyproject.toml`) and, when an environment exists, run\n   `python -c \"import clifpy; print(clifpy.__version__)\"`. If the project pins a\n   version older than the references, verify each call against that version's\n   source with `inspect.signature` before using it; old pins (0.2-0.5) lack\n   SOFA-2, `run_full_dqa`, the 3.0 crosswalk, and the polars helpers. Use\n   Python 3.10 or newer: the package declares 3.9, but dose conversion and\n   SOFA-2 fail to import on 3.9. Add or upgrade with `uv add clifpy` and keep the\n   lockfile; never add an unpinned `pip install` to project code.\n3. **Reuse before writing.** Map the task to the capability table below. If\n   `clifpy` covers it, call `clifpy`. Write custom code only for a documented gap\n   (see the table) or when a project must reproduce a frozen earlier method, and\n   say so in a comment that names the gap.\n4. **Write the call from the references.** Read `references\u002Fapi-reference.md`\n   or `references\u002Futilities-reference.md` for the signature and\n   `references\u002Frecipes.md` for the workflow. Apply the\n   version, timezone, and mutation rules in `references\u002Fpitfalls.md` before\n   finishing.\n5. **Assert after every high-risk call.** Required checks, aggregate only:\n   - every loaded table has `schema is not None` (a typo in `clif_version` silently disables validation);\n   - the expected `hospitalization_id` count survives `create_wide_dataset` and `convert_wide_to_hourly` (failed batches are dropped silently);\n   - `_convert_status == \"success\"` share after dose conversion, with failures filtered or reported;\n   - every category literal in filters exists in the selected family's vocabulary (2.1 `IMV` versus 3.0 `imv`);\n   - datetime columns carry the expected zone after each step that can strip it.\n6. **Keep outputs in the boundary.** Set `output_directory`, DuckDB\n   `temp_directory`, and log locations to an approved restricted location;\n   gitignore is an extra safeguard, not a substitute for approval. If these\n   paths are not already declared approved (project config, the saved\n   sensitive-data boundary, or the user), stop and ask the user to supply or\n   confirm them before running anything on real data; never default to a\n   repo-relative, `\u002Ftmp`, or merely gitignored path. Done when every one of the\n   three paths is recorded in the run manifest as user- or config-approved. Treat `clifpy` logs, validation CSVs,\n   DQA JSON\u002FPDF, ECDF and summary files, and DuckDB spill files as restricted\n   until reviewed; several contain row-level values or sample IDs. Shared\n   results still go only to `output\u002Ffinal_no_phi\u002F` under the CLIF small-cell rule\n   in `method-clif`.\n7. **Record provenance.** Write the `clifpy` version, CLIF version, site\n   timezone, and key parameters (stitch window, SOFA config, preferred units) to\n   the run manifest or log, not just the README.\n\n## Capability map\n\n| Need | Use | Not |\n| --- | --- | --- |\n| Load and filter tables | `ClifOrchestrator.initialize(tables, columns, filters)` or `Table.from_file(filters=, columns=)` | Raw `pd.read_parquet` of CLIF tables without tz handling |\n| Validate schema, DQA report | `validate_all()`; `run_full_dqa` + `generate_text_report` | Custom dtype or category checks that duplicate the schema |\n| Outlier handling | `apply_outlier_handling(table_obj)` before the waterfall | Forked threshold files, capping instead of nulling |\n| Respiratory support fill | `RespiratorySupport.waterfall()` | Hand forward-fill of device or mode |\n| Medication units | `convert_dose_units_for_continuous_meds` \u002F `_intermittent_meds` | Row-wise conversion or pivots across mixed units |\n| Encounter linkage | `ClifOrchestrator(stitch_encounter=True, stitch_time_interval=...)` or `stitch_encounters` | `shift()`-based gap logic |\n| Wide and hourly frames | `create_wide_dataset` then `convert_wide_to_hourly` | Per-table `pivot_table` and hand hourly grids |\n| SOFA | `calculate_sofa2` \u002F `calculate_sofa2_daily` (new work); legacy `compute_sofa_scores` or `compute_sofa_polars` only to replicate SOFA-1 | Vendored SOFA forks |\n| Adult sepsis event | `clifpy.utils.ase.compute_ase` | Reimplemented CDC ASE logic |\n| Comorbidity | `calculate_cci`, `calculate_elix` | Hand ICD maps |\n| MDRO | `calculate_mdro_flags` (pseudomonas only today) | Custom resistance rules for that organism |\n| 2.1 to 3.0 values | `crosswalk_table_2_1_to_3_0`, `CrosswalkMigrationRunner` | Bulk lowercasing |\n| Demo data | `clifpy.data.load_demo_clif` | Real data for development |\n\nDocumented gaps where project code is acceptable: norepinephrine-equivalent\ndose outside SOFA-2, CRRT episode fill, encounter-block keys for `compute_ase`,\n`compute_sofa_polars`, and `calculate_cci` (map IDs before and after), CRRT and\n3.0-only analytics, and MAR action de-duplication\n(`resolve_mar_action_duplicates()` is an empty stub).\n\n## Version rule for analytics\n\n`clif_version` changes only the validation schema. Legacy SOFA, `compute_sofa_polars`,\nSOFA-2's respiratory rules, and the waterfall heuristics still compare against\nCLIF 2.1 spellings. On 3.0 data, ventilated patients can silently miss\nrespiratory SOFA points and room-air or HFNC rules never fire. For a 3.0 project,\neither confirm the installed version fixed this or map the affected\n`device_category` values to the 2.1 spellings for the analytic call only, record\nthe mapping, and never write the mapped values back as CLIF data. In-memory\nmapping works for functions that take a frame (legacy `compute_sofa`, the\nwaterfall). SOFA-2 and `compute_sofa_polars` read tables from files, so give\nthem a mapped copy of `respiratory_support` in a temporary dataset directory in\nthe approved restricted area, with its own config pointing there. Create and\ndelete it in one `try`\u002F`finally` block so a failed or cancelled run still\nremoves it, and confirm the directory no longer exists before reporting the\nrun complete. On the published 2.1.0 package, validate 3.0 data with table\nclasses (`Table.from_file(..., clif_version=\"3.0\")`); `ClifOrchestrator` has no\n`clif_version` argument there.\n\n## Reviewing existing clifpy code\n\nWhen asked to review rather than write, check the capability map, every pitfall\nin `references\u002Fpitfalls.md`, and the installed version, and report each finding\nwith `file:line`, the failure it causes, and the corrected call. For a whole\nrepository audit, route to `method-clif-audit`.\n\n## References\n\n- `references\u002Fapi-reference.md` — package facts, config keys, and verified signatures for `ClifOrchestrator` and the table classes. Read before writing any orchestrator or table call.\n- `references\u002Futilities-reference.md` — verified signatures for io, wide\u002Fhourly, units, outliers, stitching, waterfall, SOFA, ASE, comorbidity, MDRO, crosswalk, DQA, logging, and demo loaders. Read before calling any utility.\n- `references\u002Frecipes.md` — end-to-end recipes for loading, timezones, wide\u002Fhourly, waterfall, units, SOFA-2, legacy SOFA, ASE, stitching, comorbidity, MDRO, DQA, migration, and demo data.\n- `references\u002Fpitfalls.md` — version, mutation, timezone, performance, logging, PHI-surface, and upstream-doc defects. Read before finishing any change.\n","# clifpy Usage\n\n## Skill Value\n\n- **Problem it solves:** CLIF projects hand-roll SOFA, outlier handling, unit conversion, stitching, and wide datasets that `clifpy` already provides, and call `clifpy` from memory with wrong arguments, wrong version vocabularies, and silent timezone shifts.\n- **Use when:** Writing, fixing, upgrading, or reviewing Python that loads CLIF tables or calls any `clifpy` function, class, or utility.\n- **Output:** Working `clifpy` code that uses the verified API, the selected CLIF version, explicit timezone handling, post-call assertions, and output paths that keep row-level artifacts out of shared folders.\n- **Ask only if:** The CLIF version family or the site timezone is unknown and the code depends on it. Exception: the output-path approval gate in workflow step 6 always applies; ask for any output, DuckDB temp, or log path that lacks approval before running on real data.\n- **Do not do:** Do not write `clifpy` calls from memory, copy examples from the upstream README or validation guide without checking them, or reimplement a capability `clifpy` already ships.\n- **Interaction:** Check repo\u002Fconfig\u002Fchat evidence first. Ask one decision-changing question at a time; use the current harness's blocking question UI when available, otherwise present numbered choices and wait.\n\nThe references were verified against `clifpy` GitHub commit `c4a1eeb` (2026-10-14),\ndiffed against the published 2.1.0 package, and checked against the\npublic docs at `https:\u002F\u002Fcommon-longitudinal-icu-data-format.github.io\u002Fclifpy\u002F`.\n`https:\u002F\u002Fclif-icu.com\u002F` remains authoritative for the data dictionary and mCIDE.\n\n## Workflow\n\n1. **Anchor CLIF context.** Consume `__CE_CLIF__` when present; otherwise load\n   the `method-clif` skill. Take `version=` (2.1.0 or 3.0.0) from it and never\n   infer a family from table names. CLIF 2.1.0 is the current release; 3.0.0 is\n   pre-release on clif-icu.com.\n2. **Establish the installed version.** Read `uv.lock` (or `requirements*.txt`,\n   `pyproject.toml`) and, when an environment exists, run\n   `python -c \"import clifpy; print(clifpy.__version__)\"`. If the project pins a\n   version older than the references, verify each call against that version's\n   source with `inspect.signature` before using it; old pins (0.2-0.5) lack\n   SOFA-2, `run_full_dqa`, the 3.0 crosswalk, and the polars helpers. Use\n   Python 3.10 or newer: the package declares 3.9, but dose conversion and\n   SOFA-2 fail to import on 3.9. Add or upgrade with `uv add clifpy` and keep the\n   lockfile; never add an unpinned `pip install` to project code.\n3. **Reuse before writing.** Map the task to the capability table below. If\n   `clifpy` covers it, call `clifpy`. Write custom code only for a documented gap\n   (see the table) or when a project must reproduce a frozen earlier method, and\n   say so in a comment that names the gap.\n4. **Write the call from the references.** Read `references\u002Fapi-reference.md`\n   or `references\u002Futilities-reference.md` for the signature and\n   `references\u002Frecipes.md` for the workflow. Apply the\n   version, timezone, and mutation rules in `references\u002Fpitfalls.md` before\n   finishing.\n5. **Assert after every high-risk call.** Required checks, aggregate only:\n   - every loaded table has `schema is not None` (a typo in `clif_version` silently disables validation);\n   - the expected `hospitalization_id` count survives `create_wide_dataset` and `convert_wide_to_hourly` (failed batches are dropped silently);\n   - `_convert_status == \"success\"` share after dose conversion, with failures filtered or reported;\n   - every category literal in filters exists in the selected family's vocabulary (2.1 `IMV` versus 3.0 `imv`);\n   - datetime columns carry the expected zone after each step that can strip it.\n6. **Keep outputs in the boundary.** Set `output_directory`, DuckDB\n   `temp_directory`, and log locations to an approved restricted location;\n   gitignore is an extra safeguard, not a substitute for approval. If these\n   paths are not already declared approved (project config, the saved\n   sensitive-data boundary, or the user), stop and ask the user to supply or\n   confirm them before running anything on real data; never default to a\n   repo-relative, `\u002Ftmp`, or merely gitignored path. Done when every one of the\n   three paths is recorded in the run manifest as user- or config-approved. Treat `clifpy` logs, validation CSVs,\n   DQA JSON\u002FPDF, ECDF and summary files, and DuckDB spill files as restricted\n   until reviewed; several contain row-level values or sample IDs. Shared\n   results still go only to `output\u002Ffinal_no_phi\u002F` under the CLIF small-cell rule\n   in `method-clif`.\n7. **Record provenance.** Write the `clifpy` version, CLIF version, site\n   timezone, and key parameters (stitch window, SOFA config, preferred units) to\n   the run manifest or log, not just the README.\n\n## Capability map\n\n| Need | Use | Not |\n| --- | --- | --- |\n| Load and filter tables | `ClifOrchestrator.initialize(tables, columns, filters)` or `Table.from_file(filters=, columns=)` | Raw `pd.read_parquet` of CLIF tables without tz handling |\n| Validate schema, DQA report | `validate_all()`; `run_full_dqa` + `generate_text_report` | Custom dtype or category checks that duplicate the schema |\n| Outlier handling | `apply_outlier_handling(table_obj)` before the waterfall | Forked threshold files, capping instead of nulling |\n| Respiratory support fill | `RespiratorySupport.waterfall()` | Hand forward-fill of device or mode |\n| Medication units | `convert_dose_units_for_continuous_meds` \u002F `_intermittent_meds` | Row-wise conversion or pivots across mixed units |\n| Encounter linkage | `ClifOrchestrator(stitch_encounter=True, stitch_time_interval=...)` or `stitch_encounters` | `shift()`-based gap logic |\n| Wide and hourly frames | `create_wide_dataset` then `convert_wide_to_hourly` | Per-table `pivot_table` and hand hourly grids |\n| SOFA | `calculate_sofa2` \u002F `calculate_sofa2_daily` (new work); legacy `compute_sofa_scores` or `compute_sofa_polars` only to replicate SOFA-1 | Vendored SOFA forks |\n| Adult sepsis event | `clifpy.utils.ase.compute_ase` | Reimplemented CDC ASE logic |\n| Comorbidity | `calculate_cci`, `calculate_elix` | Hand ICD maps |\n| MDRO | `calculate_mdro_flags` (pseudomonas only today) | Custom resistance rules for that organism |\n| 2.1 to 3.0 values | `crosswalk_table_2_1_to_3_0`, `CrosswalkMigrationRunner` | Bulk lowercasing |\n| Demo data | `clifpy.data.load_demo_clif` | Real data for development |\n\nDocumented gaps where project code is acceptable: norepinephrine-equivalent\ndose outside SOFA-2, CRRT episode fill, encounter-block keys for `compute_ase`,\n`compute_sofa_polars`, and `calculate_cci` (map IDs before and after), CRRT and\n3.0-only analytics, and MAR action de-duplication\n(`resolve_mar_action_duplicates()` is an empty stub).\n\n## Version rule for analytics\n\n`clif_version` changes only the validation schema. Legacy SOFA, `compute_sofa_polars`,\nSOFA-2's respiratory rules, and the waterfall heuristics still compare against\nCLIF 2.1 spellings. On 3.0 data, ventilated patients can silently miss\nrespiratory SOFA points and room-air or HFNC rules never fire. For a 3.0 project,\neither confirm the installed version fixed this or map the affected\n`device_category` values to the 2.1 spellings for the analytic call only, record\nthe mapping, and never write the mapped values back as CLIF data. In-memory\nmapping works for functions that take a frame (legacy `compute_sofa`, the\nwaterfall). SOFA-2 and `compute_sofa_polars` read tables from files, so give\nthem a mapped copy of `respiratory_support` in a temporary dataset directory in\nthe approved restricted area, with its own config pointing there. Create and\ndelete it in one `try`\u002F`finally` block so a failed or cancelled run still\nremoves it, and confirm the directory no longer exists before reporting the\nrun complete. On the published 2.1.0 package, validate 3.0 data with table\nclasses (`Table.from_file(..., clif_version=\"3.0\")`); `ClifOrchestrator` has no\n`clif_version` argument there.\n\n## Reviewing existing clifpy code\n\nWhen asked to review rather than write, check the capability map, every pitfall\nin `references\u002Fpitfalls.md`, and the installed version, and report each finding\nwith `file:line`, the failure it causes, and the corrected call. For a whole\nrepository audit, route to `method-clif-audit`.\n\n## References\n\n- `references\u002Fapi-reference.md` — package facts, config keys, and verified signatures for `ClifOrchestrator` and the table classes. Read before writing any orchestrator or table call.\n- `references\u002Futilities-reference.md` — verified signatures for io, wide\u002Fhourly, units, outliers, stitching, waterfall, SOFA, ASE, comorbidity, MDRO, crosswalk, DQA, logging, and demo loaders. Read before calling any utility.\n- `references\u002Frecipes.md` — end-to-end recipes for loading, timezones, wide\u002Fhourly, waterfall, units, SOFA-2, legacy SOFA, ASE, stitching, comorbidity, MDRO, DQA, migration, and demo data.\n- `references\u002Fpitfalls.md` — version, mutation, timezone, performance, logging, PHI-surface, and upstream-doc defects. 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