geniekit 0.0.1__tar.gz

geniekit-0.0.1/CHANGELOG.md

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+# Changelog
+
+All notable changes to geniekit are recorded here. The format follows
+Keep a Changelog, and the project follows semantic versioning.
+
+## [Unreleased]
+
+## [0.0.1] - 2026-10-17
+
+First public release: the foundation modules.
+
+### Added
+- `geniekit.releases`: registry of the six public GENIE BPC releases (NSCLC
+  v2.0, CRC v2.0, BrCa v1.0, PANC v1.0, Prostate v1.0, BLADDER v1.0) with the
+  Synapse id of every clinical, genomic, cBioPortal and documentation file,
+  generated from the public Synapse entity tree.
+- `geniekit.dictionary`: the six Variable Synopsis workbooks compiled into one
+  data dictionary, with presence matrices and cross-cohort comparison of
+  types, labels and permitted values.
+- `geniekit` command line interface with `releases` and `dictionary`
+  subcommands.
+- Build scripts in `data-raw/` that regenerate the packaged metadata.
+- `geniekit.io`: `CohortData` container, `load_release` for release folders on
+  disk (Synapse layout, geniekit download layout, flat folders, gzip), and a
+  Synapse client (`SynapseSession`, `download_release`) with token
+  resolution, access-status reporting and MD5-verified downloads.
+- `geniekit.synthetic`: dictionary-driven synthetic cohorts for all six
+  public releases, with coherent patient histories, regimens, imaging and
+  oncologist assessments, sequencing samples and genomic tables.
+- CLI commands `access`, `download` and `inspect`.
+- Test fixture `tests/fixtures/nsclc_sim` derived from the simulated data
+  shipped with the R package genieBPC (MIT).

geniekit-0.0.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Muntaser Syed
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

geniekit-0.0.1/MANIFEST.in

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+include README.md CHANGELOG.md NOTICE.md LICENSE MANIFEST.in
+recursive-include src/geniekit/resources *.json *.csv.gz
+recursive-include tests *.py *.md *.gz
+recursive-include data-raw *.py *.md
+recursive-include scripts *.py
+recursive-include examples *.py
+prune data-raw/cache

geniekit-0.0.1/NOTICE.md

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+# Notice
+
+geniekit is an independent, community-developed tool. It is not produced,
+endorsed or maintained by the American Association for Cancer Research (AACR),
+AACR Project GENIE, Sage Bionetworks or any GENIE-participating institution.
+
+## Data
+
+geniekit ships no patient-level data. All GENIE and GENIE BPC data are
+obtained by the user from Synapse (https://www.synapse.org) under the GENIE
+access requirement and the terms of use that accompany each release. Users are
+responsible for complying with those terms, including restrictions on
+redistribution and on attempts to re-identify individuals.
+
+## Packaged metadata and its sources
+
+The files in `src/geniekit/resources/` are derived from public materials:
+
+- `releases.json` is generated from the public entity tree of the GENIE BPC
+  "Data Releases" folder on Synapse (syn27056700) through the Synapse REST API,
+  plus cohort facts published on the AACR Project GENIE website
+  (https://aacrprojectgenie.org/data/).
+- `dictionary.csv.gz` is compiled from the Variable Synopsis workbooks that
+  AACR publishes with each public BPC release. The workbooks are linked from
+  the cohort pages on https://aacrprojectgenie.org/data/ and are the
+  authoritative description of each release; geniekit reproduces variable
+  names, field labels, data types and permitted values so that software can
+  reason about them. Consult the Analytic Data Guide of each release for the
+  full definitions.
+
+## Test fixture
+
+`tests/fixtures/nsclc_sim/` is derived from the `nsclc_test_data` object of
+the R package genieBPC (https://github.com/GENIE-BPC/genieBPC, MIT licence,
+copyright 2022 genieBPC authors), which its authors describe as simulated fake
+data for examples and tests. It contains no real patient records. See
+`tests/fixtures/README.md`.
+
+AACR Project GENIE and GENIE BPC are trademarks of their respective owners.
+
+## Citing the data
+
+Users of GENIE data are asked by AACR to cite:
+
+AACR Project GENIE Consortium. AACR Project GENIE: Powering Precision Medicine
+through an International Consortium. Cancer Discovery 2017;7(8):818-831.
+https://doi.org/10.1158/2159-8290.CD-17-0151
+
+and, for BPC cohorts, the cohort-specific publication listed on the cohort's
+page at https://aacrprojectgenie.org/data/.

geniekit-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: geniekit
+Version: 0.0.1
+Summary: Harmonise the AACR Project GENIE BPC cohorts, compute lines of therapy, and run aggregate-only analyses.
+Author-email: Muntaser Syed <jemsbhai@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/jemsbhai/geniekit
+Project-URL: Issues, https://github.com/jemsbhai/geniekit/issues
+Project-URL: AACR Project GENIE, https://aacrprojectgenie.org/
+Keywords: AACR,GENIE,BPC,oncology,clinicogenomic,line of therapy,harmonization,Synapse
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE.md
+Requires-Dist: pandas<4,>=2.2
+Requires-Dist: numpy<3,>=1.26
+Requires-Dist: requests<3,>=2.32
+Requires-Dist: pyyaml<7,>=6.0
+Provides-Extra: synapse
+Requires-Dist: synapseclient<5,>=4.4; extra == "synapse"
+Provides-Extra: survival
+Requires-Dist: lifelines<1,>=0.29; extra == "survival"
+Provides-Extra: notebook
+Requires-Dist: jupyter<2,>=1.1; extra == "notebook"
+Requires-Dist: matplotlib<4,>=3.9; extra == "notebook"
+Provides-Extra: dev
+Requires-Dist: pytest<9,>=8.3; extra == "dev"
+Requires-Dist: pytest-cov<8,>=6.0; extra == "dev"
+Requires-Dist: ruff<1,>=0.9; extra == "dev"
+Requires-Dist: openpyxl<4,>=3.1; extra == "dev"
+Requires-Dist: build<2,>=1.2; extra == "dev"
+Requires-Dist: twine<7,>=6.0; extra == "dev"
+Dynamic: license-file
+
+# geniekit
+
+Python tools for the AACR Project GENIE Biopharma Collaborative (BPC)
+clinicogenomic cohorts.
+
+- **Harmonise** the six public BPC cohorts (NSCLC, CRC, BrCa, PANC, Prostate,
+  BLADDER) to one schema so that cross-cohort analyses do not have to deal
+  with per-cohort variable names, types and code lists.
+- **Lines of therapy**: derive first and subsequent lines from the regimen
+  data relative to an index event that the user chooses (diagnosis,
+  metastatic diagnosis, first progression, first systemic therapy, or any
+  custom event), with explicit, configurable rules.
+- **Aggregate-only analytic layer**: produce cohort-level summaries with
+  disclosure control (minimum cell sizes, suppression, no row-level output)
+  for users who may not access patient-level records.
+
+geniekit ships metadata only. The data themselves come from Synapse under the
+GENIE access requirement (see [Data access](#data-access)).
+
+## Status
+
+Version 0.0.1 is the first public release and contains the foundation: the
+release registry, the data dictionary, data loading and download, and the
+synthetic cohorts. The harmonisation, line-of-therapy and aggregate layers
+follow in the next minor releases.
+
+| Module | Purpose | State |
+|---|---|---|
+| `geniekit.releases` | Registry of the six public BPC releases with the Synapse id of every clinical, genomic, cBioPortal and documentation file | done |
+| `geniekit.dictionary` | The six Variable Synopsis workbooks compiled into one data dictionary, with cross-cohort comparison helpers | done |
+| `geniekit.io` | Download from Synapse (personal access token, access-status check, MD5 verification) and load release folders from disk into one `CohortData` object | done |
+| `geniekit.synthetic` | Dictionary-driven synthetic cohorts: every declared column, cohort-specific naming, coherent simulated histories | done |
+| `geniekit.harmonize` | Crosswalk-driven normalisation of the six cohorts | planned |
+| `geniekit.lot` | Line-of-therapy derivation with user-defined index events | planned |
+| `geniekit.aggregate` | Aggregate-only analyses with disclosure control | planned |
+
+## Installation
+
+```powershell
+pip install geniekit
+```
+
+Optional extras: `geniekit[synapse]` (official Synapse client), `geniekit[survival]`
+(Kaplan-Meier summaries), `geniekit[notebook]` (Jupyter and plotting),
+`geniekit[dev]` (tests and linting).
+
+From a clone:
+
+```powershell
+pip install -e ".[dev]"
+pytest tests/ -v --cov=geniekit --cov-report=term
+```
+
+## Quick start
+
+```python
+from geniekit import releases, dictionary
+
+# What is available, and where on Synapse
+for r in releases.list_releases():
+    print(r.label, r.n_patients, r.release_folder, sorted(r.clinical))
+
+# How the cohorts differ before any harmonisation
+dd = dictionary.load()
+print(dd.compare("ca_cigarette", table="cancer").summary())
+print(dd.differences(table="patient").head())
+```
+
+Loading data (after approval, see [Data access](#data-access)):
+
+```python
+from geniekit import io
+
+# download one release with a personal access token in SYNAPSE_AUTH_TOKEN
+folder = io.download_release("CRC", dest="data/genie_bpc")       # data/genie_bpc/CRC_v2.0-public
+crc = io.load_release(folder)                                     # CohortData with 12 tables
+crc["regimen"].head()
+
+# or point at a folder you downloaded through the Synapse website
+nsclc = io.load_release("downloads/NSCLC_2.0-public")
+```
+
+Working without the data:
+
+```python
+from geniekit import synthetic
+
+fake = synthetic.generate("BLADDER", n_patients=300, seed=0)     # same tables and columns as the real release
+fake["cancer_index"][["record_id", "stage_dx", "dist_mets_liver", "tt_os_dx_days"]].head()
+```
+
+Synthetic cohorts carry the exact column set of the corresponding release
+(checked against the dictionary in the test suite) and mutually consistent
+identifiers, intervals and outcomes, but their values are invented. They
+exist so that code can be written and tested before access is granted; never
+report numbers computed from them.
+
+Command line:
+
+```powershell
+geniekit releases --files
+geniekit dictionary lookup naaccr_seer_sum_stage --table cancer --values
+geniekit dictionary diff --table cancer --kind dtype --kind value_set
+geniekit dictionary presence --table patient --only-partial
+geniekit access                                   # token and GENIE approval status
+geniekit download CRC --dest data/genie_bpc       # after approval
+geniekit inspect data/genie_bpc/CRC_v2.0-public   # table summary and column check
+```
+
+## The six public releases
+
+| Cohort | Version | Patients | Institutions | Synapse | Schema generation |
+|---|---|---|---|---|---|
+| NSCLC | v2.0-public | 1846 | DFCI, MSK, UHN, VICC | syn27056697 | 1 |
+| CRC | v2.0-public | 1485 | DFCI, MSK, VICC | syn30991637 | 1 |
+| BrCa | v1.0-public | 1130 | DFCI, MSK, VICC | syn71825332 | 2 |
+| PANC | v1.0-public | 1109 | DFCI, MSK, UHN, VICC | syn72666404 | 2 |
+| Prostate | v1.0-public | 1116 | DFCI, MSK, UHN, VICC | syn73719283 | 2 |
+| BLADDER | v1.0-public | 716 | DFCI, MSK, UHN, VICC | syn75201334 | 2 |
+
+"Schema generation" is a geniekit label, not a GENIE term. The two 2022
+releases (NSCLC, CRC) and the four 2025 to 2026 releases share most of their
+variables, but the later releases renamed or recoded a measurable subset. Of
+the 1105 distinct (table, variable) pairs declared across the six Variable
+Synopses, 505 are declared in all six cohorts. Examples of what differs:
+
+- smoking history is `ca_lung_cigarette` in generation 1 and `ca_cigarette` in generation 2;
+- distant metastasis sites are `dmets_*` / `dx_to_dmets_*` (9 sites) in generation 1 and `dist_mets_*` / `dx_to_dist_mets_*` (17 sites) in generation 2;
+- `naaccr_seer_sum_stage` is free text in generation 1 and a coded numeric field in generation 2;
+- `cpt_seq_date` is character in generation 1 and numeric in generation 2;
+- `ca_grade`, `pfs_cohort`, `ca_heme_type`, `ca_clin_t_stage` and others have different permitted value sets;
+- tumor-marker tables exist only for CRC, BrCa, PANC and Prostate; radiation-therapy tables only for PANC, Prostate and BLADDER;
+- structural variants are `data_fusions.txt` in generation 1 and `data_sv.txt` in generation 2;
+- UHN contributes to NSCLC, PANC, Prostate and BLADDER but not to CRC or BrCa.
+
+`geniekit dictionary diff` lists every such difference.
+
+## Data access
+
+1. Create a Synapse account and request access to the GENIE BPC data: open
+   https://www.synapse.org/Synapse:syn27056700 and click "Request Access".
+   One access requirement (id 9606645) covers both the BPC cohorts and the
+   main GENIE registry.
+2. Complete the Sage Bionetworks Access and Compliance Team (ACT) form linked
+   from that dialog, using your Synapse username. Both steps are required.
+3. After approval, create a personal access token (Synapse profile, Settings,
+   Personal Access Tokens) with "view" and "download" scope and expose it as
+   `SYNAPSE_AUTH_TOKEN` (see `.env.example`). Never commit the token.
+   `geniekit access` reports whether the token works and whether the access
+   request is approved, pending or missing.
+
+The per-cohort Analytic Data Guides and Variable Synopses are public and are
+linked from https://aacrprojectgenie.org/data/.
+
+## Relationship to the R package genieBPC
+
+The R package [genieBPC](https://github.com/GENIE-BPC/genieBPC) by the MSK
+Biostatistics team downloads BPC releases and builds analytic cohorts one
+cohort at a time. geniekit uses the same logical table names where they exist
+(`releases.GENIEBPC_TABLE_NAMES` maps between the two) so that workflows can
+move between the languages, and adds the cross-cohort harmonisation, line-of-
+therapy and aggregate-only layers.
+
+## Development
+
+```powershell
+git clone https://github.com/jemsbhai/geniekit.git
+cd geniekit
+python -m venv .venv
+.\.venv\Scripts\Activate.ps1
+pip install -e ".[dev]"
+pytest tests/ -v --cov=geniekit --cov-report=term
+ruff check src tests data-raw
+python scripts/check_vocabulary.py
+```
+
+Regenerating the packaged metadata (requires network access, no Synapse login):
+
+```powershell
+python data-raw/build_releases.py
+python data-raw/build_dictionary.py
+```
+
+## License
+
+MIT. See `LICENSE`. See `NOTICE.md` for the provenance of the packaged
+metadata and for how to cite the data.

geniekit-0.0.1/README.md

@@ -0,0 +1,187 @@
+# geniekit
+
+Python tools for the AACR Project GENIE Biopharma Collaborative (BPC)
+clinicogenomic cohorts.
+
+- **Harmonise** the six public BPC cohorts (NSCLC, CRC, BrCa, PANC, Prostate,
+  BLADDER) to one schema so that cross-cohort analyses do not have to deal
+  with per-cohort variable names, types and code lists.
+- **Lines of therapy**: derive first and subsequent lines from the regimen
+  data relative to an index event that the user chooses (diagnosis,
+  metastatic diagnosis, first progression, first systemic therapy, or any
+  custom event), with explicit, configurable rules.
+- **Aggregate-only analytic layer**: produce cohort-level summaries with
+  disclosure control (minimum cell sizes, suppression, no row-level output)
+  for users who may not access patient-level records.
+
+geniekit ships metadata only. The data themselves come from Synapse under the
+GENIE access requirement (see [Data access](#data-access)).
+
+## Status
+
+Version 0.0.1 is the first public release and contains the foundation: the
+release registry, the data dictionary, data loading and download, and the
+synthetic cohorts. The harmonisation, line-of-therapy and aggregate layers
+follow in the next minor releases.
+
+| Module | Purpose | State |
+|---|---|---|
+| `geniekit.releases` | Registry of the six public BPC releases with the Synapse id of every clinical, genomic, cBioPortal and documentation file | done |
+| `geniekit.dictionary` | The six Variable Synopsis workbooks compiled into one data dictionary, with cross-cohort comparison helpers | done |
+| `geniekit.io` | Download from Synapse (personal access token, access-status check, MD5 verification) and load release folders from disk into one `CohortData` object | done |
+| `geniekit.synthetic` | Dictionary-driven synthetic cohorts: every declared column, cohort-specific naming, coherent simulated histories | done |
+| `geniekit.harmonize` | Crosswalk-driven normalisation of the six cohorts | planned |
+| `geniekit.lot` | Line-of-therapy derivation with user-defined index events | planned |
+| `geniekit.aggregate` | Aggregate-only analyses with disclosure control | planned |
+
+## Installation
+
+```powershell
+pip install geniekit
+```
+
+Optional extras: `geniekit[synapse]` (official Synapse client), `geniekit[survival]`
+(Kaplan-Meier summaries), `geniekit[notebook]` (Jupyter and plotting),
+`geniekit[dev]` (tests and linting).
+
+From a clone:
+
+```powershell
+pip install -e ".[dev]"
+pytest tests/ -v --cov=geniekit --cov-report=term
+```
+
+## Quick start
+
+```python
+from geniekit import releases, dictionary
+
+# What is available, and where on Synapse
+for r in releases.list_releases():
+    print(r.label, r.n_patients, r.release_folder, sorted(r.clinical))
+
+# How the cohorts differ before any harmonisation
+dd = dictionary.load()
+print(dd.compare("ca_cigarette", table="cancer").summary())
+print(dd.differences(table="patient").head())
+```
+
+Loading data (after approval, see [Data access](#data-access)):
+
+```python
+from geniekit import io
+
+# download one release with a personal access token in SYNAPSE_AUTH_TOKEN
+folder = io.download_release("CRC", dest="data/genie_bpc")       # data/genie_bpc/CRC_v2.0-public
+crc = io.load_release(folder)                                     # CohortData with 12 tables
+crc["regimen"].head()
+
+# or point at a folder you downloaded through the Synapse website
+nsclc = io.load_release("downloads/NSCLC_2.0-public")
+```
+
+Working without the data:
+
+```python
+from geniekit import synthetic
+
+fake = synthetic.generate("BLADDER", n_patients=300, seed=0)     # same tables and columns as the real release
+fake["cancer_index"][["record_id", "stage_dx", "dist_mets_liver", "tt_os_dx_days"]].head()
+```
+
+Synthetic cohorts carry the exact column set of the corresponding release
+(checked against the dictionary in the test suite) and mutually consistent
+identifiers, intervals and outcomes, but their values are invented. They
+exist so that code can be written and tested before access is granted; never
+report numbers computed from them.
+
+Command line:
+
+```powershell
+geniekit releases --files
+geniekit dictionary lookup naaccr_seer_sum_stage --table cancer --values
+geniekit dictionary diff --table cancer --kind dtype --kind value_set
+geniekit dictionary presence --table patient --only-partial
+geniekit access                                   # token and GENIE approval status
+geniekit download CRC --dest data/genie_bpc       # after approval
+geniekit inspect data/genie_bpc/CRC_v2.0-public   # table summary and column check
+```
+
+## The six public releases
+
+| Cohort | Version | Patients | Institutions | Synapse | Schema generation |
+|---|---|---|---|---|---|
+| NSCLC | v2.0-public | 1846 | DFCI, MSK, UHN, VICC | syn27056697 | 1 |
+| CRC | v2.0-public | 1485 | DFCI, MSK, VICC | syn30991637 | 1 |
+| BrCa | v1.0-public | 1130 | DFCI, MSK, VICC | syn71825332 | 2 |
+| PANC | v1.0-public | 1109 | DFCI, MSK, UHN, VICC | syn72666404 | 2 |
+| Prostate | v1.0-public | 1116 | DFCI, MSK, UHN, VICC | syn73719283 | 2 |
+| BLADDER | v1.0-public | 716 | DFCI, MSK, UHN, VICC | syn75201334 | 2 |
+
+"Schema generation" is a geniekit label, not a GENIE term. The two 2022
+releases (NSCLC, CRC) and the four 2025 to 2026 releases share most of their
+variables, but the later releases renamed or recoded a measurable subset. Of
+the 1105 distinct (table, variable) pairs declared across the six Variable
+Synopses, 505 are declared in all six cohorts. Examples of what differs:
+
+- smoking history is `ca_lung_cigarette` in generation 1 and `ca_cigarette` in generation 2;
+- distant metastasis sites are `dmets_*` / `dx_to_dmets_*` (9 sites) in generation 1 and `dist_mets_*` / `dx_to_dist_mets_*` (17 sites) in generation 2;
+- `naaccr_seer_sum_stage` is free text in generation 1 and a coded numeric field in generation 2;
+- `cpt_seq_date` is character in generation 1 and numeric in generation 2;
+- `ca_grade`, `pfs_cohort`, `ca_heme_type`, `ca_clin_t_stage` and others have different permitted value sets;
+- tumor-marker tables exist only for CRC, BrCa, PANC and Prostate; radiation-therapy tables only for PANC, Prostate and BLADDER;
+- structural variants are `data_fusions.txt` in generation 1 and `data_sv.txt` in generation 2;
+- UHN contributes to NSCLC, PANC, Prostate and BLADDER but not to CRC or BrCa.
+
+`geniekit dictionary diff` lists every such difference.
+
+## Data access
+
+1. Create a Synapse account and request access to the GENIE BPC data: open
+   https://www.synapse.org/Synapse:syn27056700 and click "Request Access".
+   One access requirement (id 9606645) covers both the BPC cohorts and the
+   main GENIE registry.
+2. Complete the Sage Bionetworks Access and Compliance Team (ACT) form linked
+   from that dialog, using your Synapse username. Both steps are required.
+3. After approval, create a personal access token (Synapse profile, Settings,
+   Personal Access Tokens) with "view" and "download" scope and expose it as
+   `SYNAPSE_AUTH_TOKEN` (see `.env.example`). Never commit the token.
+   `geniekit access` reports whether the token works and whether the access
+   request is approved, pending or missing.
+
+The per-cohort Analytic Data Guides and Variable Synopses are public and are
+linked from https://aacrprojectgenie.org/data/.
+
+## Relationship to the R package genieBPC
+
+The R package [genieBPC](https://github.com/GENIE-BPC/genieBPC) by the MSK
+Biostatistics team downloads BPC releases and builds analytic cohorts one
+cohort at a time. geniekit uses the same logical table names where they exist
+(`releases.GENIEBPC_TABLE_NAMES` maps between the two) so that workflows can
+move between the languages, and adds the cross-cohort harmonisation, line-of-
+therapy and aggregate-only layers.
+
+## Development
+
+```powershell
+git clone https://github.com/jemsbhai/geniekit.git
+cd geniekit
+python -m venv .venv
+.\.venv\Scripts\Activate.ps1
+pip install -e ".[dev]"
+pytest tests/ -v --cov=geniekit --cov-report=term
+ruff check src tests data-raw
+python scripts/check_vocabulary.py
+```
+
+Regenerating the packaged metadata (requires network access, no Synapse login):
+
+```powershell
+python data-raw/build_releases.py
+python data-raw/build_dictionary.py
+```
+
+## License
+
+MIT. See `LICENSE`. See `NOTICE.md` for the provenance of the packaged
+metadata and for how to cite the data.

geniekit-0.0.1/data-raw/README.md

@@ -0,0 +1,21 @@
+# data-raw
+
+Scripts that regenerate the packaged metadata in `src/geniekit/resources/`.
+They need network access but no Synapse login; everything they read is public.
+
+| Script | Output | Source |
+|---|---|---|
+| `build_releases.py` | `releases.json` | Synapse REST API: entity tree of the BPC "Data Releases" folder (syn27056700); cohort facts from aacrprojectgenie.org |
+| `build_dictionary.py` | `dictionary.csv.gz`, `dictionary.meta.json` | The six Variable Synopsis workbooks linked from aacrprojectgenie.org (downloaded into `cache/`, which is gitignored) |
+
+Run from the repository root, in this order:
+
+```powershell
+python data-raw/build_releases.py
+python data-raw/build_dictionary.py
+pytest tests/ -q
+```
+
+Commit the regenerated resources together with the script change that
+produced them; the diff of `releases.json` is the review artefact when a new
+public release appears.