aadr-subset 0.1.0__tar.gz

aadr_subset-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Carsten Erickson
+
+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.

aadr_subset-0.1.0/PKG-INFO

@@ -0,0 +1,291 @@
+Metadata-Version: 2.4
+Name: aadr-subset
+Version: 0.1.0
+Summary: Declarative AADR panel subsetting from YAML selectors; the missing first-class tool for cohort definitions in ancient-DNA / population-genetics workflows.
+Author-email: Carsten Erickson <carstene@mailbox.org>
+License: MIT
+Project-URL: Homepage, https://github.com/carstenerickson/aadr-subset
+Project-URL: Issues, https://github.com/carstenerickson/aadr-subset/issues
+Project-URL: Changelog, https://github.com/carstenerickson/aadr-subset/blob/main/CHANGELOG.md
+Keywords: bioinformatics,genetics,aadr,ancient-dna,admixtools,population-genetics
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: MacOS :: MacOS X
+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: Typing :: Typed
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: aadr-resolve<0.3,>=0.2.0
+Requires-Dist: pandas<3,>=2.2
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: ruamel.yaml>=0.18
+Requires-Dist: jsonschema>=4.20
+Requires-Dist: click<9,>=8.1
+Requires-Dist: rfc8785>=0.1
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0; extra == "dev"
+Requires-Dist: pytest-cov>=5.0; extra == "dev"
+Requires-Dist: ruff>=0.6; extra == "dev"
+Requires-Dist: mypy>=1.11; extra == "dev"
+Requires-Dist: types-jsonschema>=4.0; extra == "dev"
+Requires-Dist: types-PyYAML>=6.0; extra == "dev"
+Requires-Dist: pandas-stubs>=2.2; extra == "dev"
+Requires-Dist: build>=1.2; extra == "dev"
+Requires-Dist: twine>=5.0; extra == "dev"
+Dynamic: license-file
+
+# aadr-subset
+
+Declarative AADR panel subsetting from YAML selectors. Replaces ad-hoc
+`awk` pipelines and one-off scripts with version-stable,
+PR-reviewable cohort definitions. Built on top of
+[aadr-resolve](https://github.com/carstenerickson/aadr-resolve) for
+cross-AADR-version sample-ID mapping.
+
+```yaml
+# britain_iron_age.yaml
+populations: [England_IA, England_IA.AG, England_IA.SG]
+date: {min_calbp: 1900, max_calbp: 2400}
+min_coverage: 0.3
+exclude:
+  individual_ids: [I12345]   # known contaminated sample
+```
+
+```bash
+$ aadr-subset select britain_iron_age.yaml v66.HO.aadr.PUB.anno -o cohort.ids
+Selector: britain_iron_age.yaml (sha256:1a2b3c4...d5e6f7g)
+.anno:    v66.HO.aadr.PUB.anno (v66.0, class E)
+
+Matched 45 samples across 1 populations.
+
+Per-population: England_IA=45
+
+Wrote cohort.ids (45 lines)
+Done in 0.18s (parse 0.16s, eval 0.02s, write 0.00s).
+
+$ plink2 --pfile aadr_v66 --keep cohort.ids --make-pgen --out britain_iron_age
+```
+
+## Why it exists
+
+Ancient-DNA workflows live and die on cohort definitions — *which samples
+go into this analysis*. Today that's typically a hand-curated set of
+Group_ID literals in someone's shell script, prone to: silent breakage
+when AADR releases a new version with renamed labels; no version pinning
+in commit history; no way to share the exact cohort between collaborators
+short of swapping `.ind` files.
+
+`aadr-subset` makes the cohort itself a first-class artifact:
+
+- **Selector YAMLs are version-stable.** They cite AADR releases via
+  `tested_against:` metadata; the `selector_signature` (RFC 8785 JCS
+  SHA-256 over the canonical form) gives you a hash that survives
+  YAML formatting churn.
+- **Reviewable in PRs.** The grammar is flat (top-level AND with
+  one-level `any:` OR and one-level `exclude:` NOT). What you see is
+  what runs.
+- **Cross-version via `aadr-resolve`.** `resolve_to_version:` lifts
+  Individual_IDs from an older release to the newer one through the
+  GID-stable bridge + MID-rename map.
+- **Five subcommands** cover the full lifecycle: `validate`, `select`,
+  `inspect`, `report`, `template`.
+
+## Install
+
+```bash
+pip install aadr-subset            # once PyPI'd; currently:
+pip install git+https://github.com/carstenerickson/aadr-subset.git
+```
+
+Python 3.11+. The only external dependency is `aadr-resolve` (also
+installed via git URL until both ship to PyPI).
+
+For development:
+
+```bash
+git clone https://github.com/carstenerickson/aadr-subset.git
+cd aadr-subset
+pip install -e ".[dev]"
+pytest
+```
+
+## The five subcommands
+
+### `validate SELECTOR.yaml`
+
+JSON-schema + semantic-constraint check on a selector. No `.anno`
+required. Useful as a CI gate.
+
+```bash
+$ aadr-subset validate britain_iron_age.yaml
+# exit 0 on valid; exit 4 on schema or semantic violation
+# Errors carry precise file:line:col + JSON pointer:
+$ aadr-subset validate broken.yaml
+broken.yaml:7:5: at /populations/2: 42 is not of type 'string'
+broken.yaml:12:3: at /any/0/min_coverage: -0.5 is less than the minimum of 0
+```
+
+### `select SELECTOR.yaml ANNO.anno [-o PATH] [--format ids|tsv|json]`
+
+The main case: materialize a selector against a target `.anno` and
+write matched sample IDs / TSV / JSON.
+
+```bash
+aadr-subset select britain_iron_age.yaml v66.HO.aadr.PUB.anno -o cohort.ids
+aadr-subset select britain_iron_age.yaml v66.HO.aadr.PUB.anno --format tsv -o cohort.tsv
+aadr-subset select britain_iron_age.yaml v66.HO.aadr.PUB.anno --format json -o cohort.json
+```
+
+Cross-version flow (selector defined against an older release than the
+materialized one):
+
+```yaml
+# britain_v62_lift.yaml
+individual_ids: [I12345, I12346]
+source_version: v62.0
+resolve_to_version: v66.0
+```
+
+```bash
+aadr-subset select britain_v62_lift.yaml v66.HO.aadr.PUB.anno \
+    --source-anno v62.0_HO_public.anno \
+    -o lifted.ids
+```
+
+v62.0 inputs (class D — no native coverage column) need a derived proxy
+for `min_coverage:` filters:
+
+```bash
+aadr-subset select britain_iron_age.yaml v62.0_HO_public.anno \
+    --coverage-derive snps_hit_1240k -o cohort.ids
+```
+
+### `inspect SELECTOR.yaml ANNO.anno`
+
+Dry-run: shows what a selector matches without writing any file.
+Always exits 0 — meant for debugging selector logic.
+
+```
+$ aadr-subset inspect britain_iron_age.yaml v66.HO.aadr.PUB.anno
+Selector: britain_iron_age.yaml
+.anno:    v66.HO.aadr.PUB.anno (v66.0, class E, 27,755 samples)
+
+Matched: 45 samples across 1 population
+
+Per-population breakdown:
+  England_IA  45
+
+Branch contributions:
+  top_level  45
+
+Date range of matched: 1934 - 2398 calBP (median 2103)
+Coverage range:        0.34 - 4.81x (median 1.28)
+
+Selector signature: sha256:1a2b3c4d5e6f7g8h9i0j1k2l3m4n5o6p7q8r9s0t1u2v3w4x5y6z7a8b9c0d1e
+```
+
+### `report SELECTOR.yaml ANNO.anno [-o PATH] [--format tsv|json]`
+
+Per-population aggregates: how many samples each Group_ID contributed,
+with date range and coverage stats.
+
+```
+$ aadr-subset report britain_iron_age.yaml v66.HO.aadr.PUB.anno
+group_id    n_matched   n_in_anno   pct_matched   date_min_calbp   date_max_calbp   coverage_median
+England_IA  45          51          88.2          1934             2398             1.28
+```
+
+`--include-empty-groups` adds rows for `.anno` groups that matched
+zero samples (useful for population-survey workflows).
+
+### `template [NAME] [-o PATH]`
+
+Ships starter selectors for common cohorts. No-arg form lists
+shipped templates; arg form emits the verbatim YAML (comments + metadata
+block preserved) to stdout or `--out PATH`.
+
+```
+$ aadr-subset template
+bronze_age_europe
+iron_age_britain
+modern_european
+neolithic_anatolia
+viking_period_scandinavian
+wsh_steppe_pool
+
+$ aadr-subset template iron_age_britain -o britain.yaml
+# britain.yaml now contains a working starting point — edit + extend.
+```
+
+All shipped templates are verified against AADR **v62.0** and **v66.0** —
+each template's `tested_against:` metadata reflects the releases it
+resolves to non-zero matches against.
+
+## Exit codes
+
+| Code | Meaning |
+|---|---|
+| 0 | Success |
+| 1 | Soft validation failure (e.g. zero-match without `--allow-empty`, `--strict-resolve` missing IIDs) |
+| 2 | I/O failure (file not found, `.anno` schema unrecognized, etc.) |
+| 4 | Usage error (schema violation, flag misuse, unknown template) |
+| 70 | Internal error (please file an issue) |
+
+## Selector grammar (overview)
+
+Flat — one level of nesting maximum. Top-level keys AND-combine.
+
+```yaml
+# Top-level AND
+populations: [Western_HG, Eastern_HG]   # match against group_id
+individual_ids: [Loschbour, KO1]         # match against individual_id
+individual_ids_source: ids.txt           # newline-delimited file
+modern_only: true                        # shorthand: date_calbp <= 70
+min_coverage: 0.3
+coverage_column: snps_hit_1240k          # override; selector-side wins over --coverage-derive
+date:
+  min_calbp: 1900
+  max_calbp: 2400
+source_version: v62.0                    # cross-version lift
+resolve_to_version: v66.0
+
+# One-level OR (matches any branch)
+any:
+  - populations: [Western_HG]
+    min_coverage: 1.0
+  - populations: [Eastern_HG]
+    min_coverage: 0.5
+
+# One-level NOT-of-OR (drops matches)
+exclude:
+  group_ids: [English.SG]
+  individual_ids: [I12345]
+```
+
+Full spec: [aadr-subset HLD](https://github.com/carstenerickson/aadr-subset/blob/main/docs/hld.md).
+
+## Composing with `plink2`
+
+```bash
+# Materialize a cohort
+aadr-subset select britain_iron_age.yaml v66.HO.aadr.PUB.anno -o cohort.ids
+
+# Use it as a plink2 keep set
+plink2 --pfile aadr_v66 \
+       --keep cohort.ids \
+       --make-pgen --out britain_iron_age_subset
+```
+
+`select --format json` produces a structured artifact suitable for
+pipeline metadata logging (records the selector signature, AADR version,
+schema class, and effective coverage column).
+
+## License
+
+MIT. See [LICENSE](LICENSE).

aadr_subset-0.1.0/README.md

@@ -0,0 +1,249 @@
+# aadr-subset
+
+Declarative AADR panel subsetting from YAML selectors. Replaces ad-hoc
+`awk` pipelines and one-off scripts with version-stable,
+PR-reviewable cohort definitions. Built on top of
+[aadr-resolve](https://github.com/carstenerickson/aadr-resolve) for
+cross-AADR-version sample-ID mapping.
+
+```yaml
+# britain_iron_age.yaml
+populations: [England_IA, England_IA.AG, England_IA.SG]
+date: {min_calbp: 1900, max_calbp: 2400}
+min_coverage: 0.3
+exclude:
+  individual_ids: [I12345]   # known contaminated sample
+```
+
+```bash
+$ aadr-subset select britain_iron_age.yaml v66.HO.aadr.PUB.anno -o cohort.ids
+Selector: britain_iron_age.yaml (sha256:1a2b3c4...d5e6f7g)
+.anno:    v66.HO.aadr.PUB.anno (v66.0, class E)
+
+Matched 45 samples across 1 populations.
+
+Per-population: England_IA=45
+
+Wrote cohort.ids (45 lines)
+Done in 0.18s (parse 0.16s, eval 0.02s, write 0.00s).
+
+$ plink2 --pfile aadr_v66 --keep cohort.ids --make-pgen --out britain_iron_age
+```
+
+## Why it exists
+
+Ancient-DNA workflows live and die on cohort definitions — *which samples
+go into this analysis*. Today that's typically a hand-curated set of
+Group_ID literals in someone's shell script, prone to: silent breakage
+when AADR releases a new version with renamed labels; no version pinning
+in commit history; no way to share the exact cohort between collaborators
+short of swapping `.ind` files.
+
+`aadr-subset` makes the cohort itself a first-class artifact:
+
+- **Selector YAMLs are version-stable.** They cite AADR releases via
+  `tested_against:` metadata; the `selector_signature` (RFC 8785 JCS
+  SHA-256 over the canonical form) gives you a hash that survives
+  YAML formatting churn.
+- **Reviewable in PRs.** The grammar is flat (top-level AND with
+  one-level `any:` OR and one-level `exclude:` NOT). What you see is
+  what runs.
+- **Cross-version via `aadr-resolve`.** `resolve_to_version:` lifts
+  Individual_IDs from an older release to the newer one through the
+  GID-stable bridge + MID-rename map.
+- **Five subcommands** cover the full lifecycle: `validate`, `select`,
+  `inspect`, `report`, `template`.
+
+## Install
+
+```bash
+pip install aadr-subset            # once PyPI'd; currently:
+pip install git+https://github.com/carstenerickson/aadr-subset.git
+```
+
+Python 3.11+. The only external dependency is `aadr-resolve` (also
+installed via git URL until both ship to PyPI).
+
+For development:
+
+```bash
+git clone https://github.com/carstenerickson/aadr-subset.git
+cd aadr-subset
+pip install -e ".[dev]"
+pytest
+```
+
+## The five subcommands
+
+### `validate SELECTOR.yaml`
+
+JSON-schema + semantic-constraint check on a selector. No `.anno`
+required. Useful as a CI gate.
+
+```bash
+$ aadr-subset validate britain_iron_age.yaml
+# exit 0 on valid; exit 4 on schema or semantic violation
+# Errors carry precise file:line:col + JSON pointer:
+$ aadr-subset validate broken.yaml
+broken.yaml:7:5: at /populations/2: 42 is not of type 'string'
+broken.yaml:12:3: at /any/0/min_coverage: -0.5 is less than the minimum of 0
+```
+
+### `select SELECTOR.yaml ANNO.anno [-o PATH] [--format ids|tsv|json]`
+
+The main case: materialize a selector against a target `.anno` and
+write matched sample IDs / TSV / JSON.
+
+```bash
+aadr-subset select britain_iron_age.yaml v66.HO.aadr.PUB.anno -o cohort.ids
+aadr-subset select britain_iron_age.yaml v66.HO.aadr.PUB.anno --format tsv -o cohort.tsv
+aadr-subset select britain_iron_age.yaml v66.HO.aadr.PUB.anno --format json -o cohort.json
+```
+
+Cross-version flow (selector defined against an older release than the
+materialized one):
+
+```yaml
+# britain_v62_lift.yaml
+individual_ids: [I12345, I12346]
+source_version: v62.0
+resolve_to_version: v66.0
+```
+
+```bash
+aadr-subset select britain_v62_lift.yaml v66.HO.aadr.PUB.anno \
+    --source-anno v62.0_HO_public.anno \
+    -o lifted.ids
+```
+
+v62.0 inputs (class D — no native coverage column) need a derived proxy
+for `min_coverage:` filters:
+
+```bash
+aadr-subset select britain_iron_age.yaml v62.0_HO_public.anno \
+    --coverage-derive snps_hit_1240k -o cohort.ids
+```
+
+### `inspect SELECTOR.yaml ANNO.anno`
+
+Dry-run: shows what a selector matches without writing any file.
+Always exits 0 — meant for debugging selector logic.
+
+```
+$ aadr-subset inspect britain_iron_age.yaml v66.HO.aadr.PUB.anno
+Selector: britain_iron_age.yaml
+.anno:    v66.HO.aadr.PUB.anno (v66.0, class E, 27,755 samples)
+
+Matched: 45 samples across 1 population
+
+Per-population breakdown:
+  England_IA  45
+
+Branch contributions:
+  top_level  45
+
+Date range of matched: 1934 - 2398 calBP (median 2103)
+Coverage range:        0.34 - 4.81x (median 1.28)
+
+Selector signature: sha256:1a2b3c4d5e6f7g8h9i0j1k2l3m4n5o6p7q8r9s0t1u2v3w4x5y6z7a8b9c0d1e
+```
+
+### `report SELECTOR.yaml ANNO.anno [-o PATH] [--format tsv|json]`
+
+Per-population aggregates: how many samples each Group_ID contributed,
+with date range and coverage stats.
+
+```
+$ aadr-subset report britain_iron_age.yaml v66.HO.aadr.PUB.anno
+group_id    n_matched   n_in_anno   pct_matched   date_min_calbp   date_max_calbp   coverage_median
+England_IA  45          51          88.2          1934             2398             1.28
+```
+
+`--include-empty-groups` adds rows for `.anno` groups that matched
+zero samples (useful for population-survey workflows).
+
+### `template [NAME] [-o PATH]`
+
+Ships starter selectors for common cohorts. No-arg form lists
+shipped templates; arg form emits the verbatim YAML (comments + metadata
+block preserved) to stdout or `--out PATH`.
+
+```
+$ aadr-subset template
+bronze_age_europe
+iron_age_britain
+modern_european
+neolithic_anatolia
+viking_period_scandinavian
+wsh_steppe_pool
+
+$ aadr-subset template iron_age_britain -o britain.yaml
+# britain.yaml now contains a working starting point — edit + extend.
+```
+
+All shipped templates are verified against AADR **v62.0** and **v66.0** —
+each template's `tested_against:` metadata reflects the releases it
+resolves to non-zero matches against.
+
+## Exit codes
+
+| Code | Meaning |
+|---|---|
+| 0 | Success |
+| 1 | Soft validation failure (e.g. zero-match without `--allow-empty`, `--strict-resolve` missing IIDs) |
+| 2 | I/O failure (file not found, `.anno` schema unrecognized, etc.) |
+| 4 | Usage error (schema violation, flag misuse, unknown template) |
+| 70 | Internal error (please file an issue) |
+
+## Selector grammar (overview)
+
+Flat — one level of nesting maximum. Top-level keys AND-combine.
+
+```yaml
+# Top-level AND
+populations: [Western_HG, Eastern_HG]   # match against group_id
+individual_ids: [Loschbour, KO1]         # match against individual_id
+individual_ids_source: ids.txt           # newline-delimited file
+modern_only: true                        # shorthand: date_calbp <= 70
+min_coverage: 0.3
+coverage_column: snps_hit_1240k          # override; selector-side wins over --coverage-derive
+date:
+  min_calbp: 1900
+  max_calbp: 2400
+source_version: v62.0                    # cross-version lift
+resolve_to_version: v66.0
+
+# One-level OR (matches any branch)
+any:
+  - populations: [Western_HG]
+    min_coverage: 1.0
+  - populations: [Eastern_HG]
+    min_coverage: 0.5
+
+# One-level NOT-of-OR (drops matches)
+exclude:
+  group_ids: [English.SG]
+  individual_ids: [I12345]
+```
+
+Full spec: [aadr-subset HLD](https://github.com/carstenerickson/aadr-subset/blob/main/docs/hld.md).
+
+## Composing with `plink2`
+
+```bash
+# Materialize a cohort
+aadr-subset select britain_iron_age.yaml v66.HO.aadr.PUB.anno -o cohort.ids
+
+# Use it as a plink2 keep set
+plink2 --pfile aadr_v66 \
+       --keep cohort.ids \
+       --make-pgen --out britain_iron_age_subset
+```
+
+`select --format json` produces a structured artifact suitable for
+pipeline metadata logging (records the selector signature, AADR version,
+schema class, and effective coverage column).
+
+## License
+
+MIT. See [LICENSE](LICENSE).

aadr_subset-0.1.0/pyproject.toml

@@ -0,0 +1,109 @@
+[build-system]
+requires = ["setuptools>=68", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "aadr-subset"
+version = "0.1.0"
+description = "Declarative AADR panel subsetting from YAML selectors; the missing first-class tool for cohort definitions in ancient-DNA / population-genetics workflows."
+readme = "README.md"
+license = { text = "MIT" }
+requires-python = ">=3.11"
+authors = [
+    { name = "Carsten Erickson", email = "carstene@mailbox.org" },
+]
+keywords = ["bioinformatics", "genetics", "aadr", "ancient-dna", "admixtools", "population-genetics"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: MacOS :: MacOS X",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Typing :: Typed",
+]
+dependencies = [
+    # aadr-resolve is the hard library dependency per HLD §aadr-resolve as a
+    # library dependency. Tracking the 0.2.x line: 0.2.0 ships the
+    # `MissingNativeFieldError`, `AnnoFrame.path`, and `resolve_master_ids`
+    # APIs that aadr-subset relies on.
+    "aadr-resolve>=0.2.0,<0.3",
+    "pandas>=2.2,<3",
+    "pyyaml>=6.0",
+    "ruamel.yaml>=0.18",
+    "jsonschema>=4.20",
+    "click>=8.1,<9",
+    "rfc8785>=0.1",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=8.0",
+    "pytest-cov>=5.0",
+    "ruff>=0.6",
+    "mypy>=1.11",
+    "types-jsonschema>=4.0",
+    "types-PyYAML>=6.0",
+    "pandas-stubs>=2.2",
+    "build>=1.2",
+    "twine>=5.0",
+]
+
+[project.scripts]
+aadr-subset = "aadr_subset.cli:main"
+
+[project.urls]
+Homepage = "https://github.com/carstenerickson/aadr-subset"
+Issues = "https://github.com/carstenerickson/aadr-subset/issues"
+Changelog = "https://github.com/carstenerickson/aadr-subset/blob/main/CHANGELOG.md"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+aadr_subset = ["py.typed", "schemas/*.json", "templates/*.yaml"]
+
+[tool.ruff]
+line-length = 100
+target-version = "py311"
+
+[tool.ruff.lint]
+select = ["E", "F", "W", "I", "UP", "B", "RUF"]
+# RUF003: ambiguous-unicode-in-comment. We intentionally use ∪ / × etc. for
+# set-theory and matrix notation in test/code comments — these are clearer
+# than the ASCII equivalents and don't affect runtime behavior.
+ignore = ["RUF003"]
+
+[tool.mypy]
+python_version = "3.11"
+strict = true
+
+[tool.pytest.ini_options]
+markers = [
+    "slow: tests that take more than a few seconds",
+    "integration: end-to-end tests requiring committed fixtures",
+    "external_tool: tests requiring plink2 or pgen-samplebind on PATH",
+]
+
+[tool.coverage.run]
+source = ["src/aadr_subset"]
+omit = [
+    # Orchestration shells (per LLD §1.5). Exercised by integration tests
+    # via subprocess, where coverage in this process isn't measured.
+    "src/aadr_subset/__main__.py",
+    "src/aadr_subset/cli.py",
+    "src/aadr_subset/commands/*",
+]
+
+[tool.coverage.report]
+fail_under = 90
+exclude_also = [
+    # Defensive branches; not exercised by happy paths.
+    "raise InvariantViolation",
+    "except Exception",
+    # Forward-compat fallbacks in _locate_node etc.
+    "except.*:  # ?defensive",
+]

aadr_subset-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

aadr_subset-0.1.0/src/aadr_subset/__init__.py

@@ -0,0 +1,5 @@
+"""aadr-subset: declarative AADR panel subsetting from YAML selectors."""
+
+__version__ = "0.1.0"
+
+__all__ = ["__version__"]

aadr_subset-0.1.0/src/aadr_subset/__main__.py

@@ -0,0 +1,6 @@
+"""Enable `python -m aadr_subset` invocation."""
+
+from aadr_subset.cli import main
+
+if __name__ == "__main__":
+    main()