From 27ac862e11f15564f5bdb412348a1d6e61c6f884 Mon Sep 17 00:00:00 2001 From: Conrad Date: Thu, 29 Oct 2026 14:19:27 -0400 Subject: [PATCH 1/7] docs: Describe the package, its installs and its commands The two installs, in the tense that is true: nothing is published yet, and the pileup extra resolves with uv and not yet with pip until its git-pinned dependency ships to PyPI. The reason for that pin has one home, the comment on the uv sources table, which this points at rather than restates. A development section carries the sync, test, format and lint commands, which otherwise live only in the test workflow -- not where a contributor looks for them. It also states where the version comes from, because nothing in the tree says: a tag names a release, a commit between tags reports that release plus the commit it is, and a build from an unpacked distribution reports the version that distribution was built with. --- README.md | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..4d2cd7b --- /dev/null +++ b/README.md @@ -0,0 +1,41 @@ +# quadrat + +Sequence-to-function training data, straight from BAM. + +A quadrat is the fixed-size frame a field ecologist drops on the ground to tally everything inside it, moved across a landscape by a sampling design chosen separately from the frame. This package is that: a fixed-length window, placed at loci by a sampling scheme, tallying the cut sites that fall inside. + +Everything between a set of alignments and a batch of `(sequence, signal)` pairs is independent of the model that consumes them. `quadrat` implements that span — the pileup, the window cache, the sampler and the loader — so any sequence-to-function architecture can be trained without reimplementing it. + +## Status + +Under construction. The data path is being extracted from [cherimoya](https://github.com/conradbzura/cherimoya); see [#1](https://github.com/abdenlab/quadrat/issues/1) for the specification and the slices it lands in. + +## Install + +Nothing is published yet. Once the data path lands, the two installs will be: + +```bash +pip install quadrat # stream windows over cut-site tables +pip install "quadrat[pileup]" # also build those tables from alignments +``` + +The `pileup` extra adds the engine that builds those tables: [polars-bio](https://github.com/biodatageeks/polars-bio) and [giql](https://github.com/abdenlab/giql) among its dependencies. The base install is enough for a caller who already has cut-site tables; `quadrat`'s package docstring states the import guarantee that makes it so. + +The extra resolves with `uv` and not yet with pip, because one of its dependencies is pinned to a git revision that only `uv` reads — the comment on `[tool.uv.sources]` in `pyproject.toml` says why and when that changes. + +## Development + +```bash +uv sync --locked --all-extras # install, pileup engine included +uv run pytest -q # run the suite +uv run ruff format --check src tests build-hooks # check formatting +uv run ruff check src tests build-hooks # lint +``` + +The version is the repository's rather than a literal in the tree: a `vMAJOR.MINOR.PATCH` tag names a release, and a commit between tags reports the last release plus the commit it is, so releasing is pushing a tag and nothing in the tree changes for one. A build from a tree that is not a checkout — an unpacked source distribution — reports the version that distribution was built with. + +`uv sync --locked --no-dev` installs what `pip install quadrat` will, which is the base install the import guarantee above is about; CI runs it as a job of its own. + +## License + +MIT. From c3887146191179f269a83da8f747719a87712cd7 Mon Sep 17 00:00:00 2001 From: Conrad Date: Thu, 29 Oct 2026 14:19:27 -0400 Subject: [PATCH 2/7] build: Stand up the installable package and pin its dependencies Somewhere for the ported data path to land, with no logic yet, so a later failure is attributable to the port rather than to the scaffolding it lands on. Follow abdenlab/giql, the nearest sibling and quadrat's own dependency: src layout, hatchling, ruff at line-length 89, four-space indentation, PEP 735 dependency groups. The Python floor is 3.11 rather than cherimoya's 3.10, because polars-bio, polars and giql are all gated there and the pileup is not an optional part of what this package is for. Runtime dependencies shear from cherimoya's sixteen to six, with the pileup engine behind a pileup extra. Every one of those imports is already lazy inside a function body upstream, so a caller that streams windows over tables it already has never pays for them. The package docstring states that guarantee over the relationship rather than over the members, so the extra stays the single enumeration and adding a fifth dependency does not falsify it. Two defects in cherimoya's manifest are corrected rather than carried: pyfaidx is imported by production code but declared only in a dev group, and cherimoya.workers is missing from the explicit package list, so it never ships in a built distribution. Hatchling's src discovery makes the second unrepeatable. The ruff select is pinned rather than left to the default. Ruff enables UP, SIM, FURB and RUF by default, and UP032 alone fires on the str.format style used throughout the code this repository is about to receive, so the default would demand a style migration inside the change that moves the code. I is in anyway, because import order is mechanical even in ported code and is the one style defect a reviewer reliably misses. giql resolves from the public commit at the tip of its cherimoya-mvp branch. The datafusion-bio target is not on PyPI and cherimoya pins a path outside its own tree, which a published package cannot inherit. That commit's library code is identical to what cherimoya builds against; the only delta is benchmark material outside src. That pin is also why the pileup extra resolves with uv and not yet with pip. The licence is declared once, as a PEP 639 expression with no accompanying classifier, since PyPI rejects a distribution carrying both. The sdist contents are named under the sdist target, where hatchling reads them: it does not read MANIFEST.in, which is a setuptools file, so a graft expressed there would be inert. Both sides of the notebook-checkpoint exclusion carry a double star, because the pattern is gitignore-style and a single one spans a single path segment. Pytest runs with --strict-markers, so a misspelt marker is a collection error rather than a test silently neither selected nor deselected. The .sdlc directory holds local review roles, authoring guides and accumulated review documents, untracked here as in the sibling projects: that history is versioned by its own repository under .sdlc, and the guides are config rather than a project artifact. The version is derived from the repository rather than read from a literal. A vMAJOR.MINOR.PATCH tag names a release and every commit between tags reports that release plus the commit it is, so releasing is pushing a tag and nothing in the tree changes for one. There are no pre-release or development segments, because there is no release branch for one to describe. The hook shells out to git rather than taking a library, so the build requires nothing beyond the backend and an offline build cannot fail for want of a wheel to resolve. It ships inside the source distribution and falls back to the version PKG-INFO carries, because the backend re-runs the metadata hook when it builds a wheel from an sdist, where there is no history to read. It also requires the repository root to be the project root, since git searches upward and an sdist unpacked inside an unrelated checkout would otherwise take that project's tags. The package attribute reads the installed distribution's metadata, so the version travels from the repository to the artifact to the attribute rather than from a literal outward. It is a plain assignment rather than a guarded one, because the marker convention the suite enforces only reads a top-level declaration, and a src layout means an uninstalled import fails before it could reach a fallback. --- .gitignore | 39 + build-hooks/__init__.py | 0 build-hooks/_git.py | 113 ++ build-hooks/metadata.py | 25 + pyproject.toml | 147 ++ src/quadrat/__init__.py | 45 + uv.lock | 3067 +++++++++++++++++++++++++++++++++++++++ 7 files changed, 3436 insertions(+) create mode 100644 .gitignore create mode 100644 build-hooks/__init__.py create mode 100644 build-hooks/_git.py create mode 100644 build-hooks/metadata.py create mode 100644 pyproject.toml create mode 100644 src/quadrat/__init__.py create mode 100644 uv.lock diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..d75dc6d --- /dev/null +++ b/.gitignore @@ -0,0 +1,39 @@ +# macOS +.DS_Store + +# Python +__pycache__/ +*.py[cod] +*$py.class +*.so +build/ +dist/ +sdist/ +wheels/ +*.egg-info/ +*.egg +.eggs/ + +# Environments +.venv/ +venv/ + +# Tooling +.pytest_cache/ +.ruff_cache/ +.hypothesis/ +.coverage +coverage.xml +htmlcov/ + +# Docs +docs/_build/ + +# Jupyter +.ipynb_checkpoints/ + +# SDLC working state: local review roles, guides and accumulated review +# documents. Untracked here as it is in the sibling projects -- the +# review history is versioned by its own repo under .sdlc, and the +# guides are local working config rather than a project artifact. +.sdlc/ diff --git a/build-hooks/__init__.py b/build-hooks/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/build-hooks/_git.py b/build-hooks/_git.py new file mode 100644 index 0000000..5689b72 --- /dev/null +++ b/build-hooks/_git.py @@ -0,0 +1,113 @@ +"""Derive the distribution's version from the repository's tag history. + +A release is named by a ``vMAJOR.MINOR.PATCH`` tag and nothing else is +a release. A commit carrying no tag takes the last tagged release plus +a local identifier naming the commit it is, so every build is +traceable to one without inventing a release number for it. There are +no pre-release or development segments, because there is no release +branch for one to describe. + +.. rubric:: Implementation notes + +``git`` is invoked as a subprocess rather than through a library, so +the build requires nothing beyond the backend itself and an offline +build cannot fail for want of a wheel to resolve. +""" + +import pathlib +import re +import subprocess + +# The only tags that name a release. Anything else in the tag +# namespace -- a moved pointer, a `latest`, something pushed by hand -- +# is ignored rather than guessed at. +RELEASE_TAG = "v[0-9]*.[0-9]*.[0-9]*" + +# `git describe` renders a tagged commit as the tag alone and any other +# as `--g`. The distance is discarded, because a +# count of commits since a release is not a release. +DESCRIBED = re.compile(r"^v(?P\d+\.\d+\.\d+)(?:-\d+-g(?P[0-9a-f]+))?$") + +# What a version falls back to before the first release tag exists, and +# what an unversionable tree reports. +INITIAL_RELEASE = "0.0.0" + + +def _git(root, *arguments): + """Return the stdout of a git command in ``root``, or ``None``.""" + + try: + completed = subprocess.run( + ("git", "-C", str(root)) + arguments, + capture_output=True, + text=True, + check=True, + ) + except (OSError, subprocess.CalledProcessError): + return None + return completed.stdout.strip() + + +def _is_own_repository(root): + """Return whether ``root`` is itself the root of a git repository.""" + + # `git -C` searches upward, so an unpacked sdist sitting inside an + # unrelated checkout would otherwise take that repository's tags. + # The project root and the repository root are the same directory + # here, so requiring them to match rules that out. + toplevel = _git(root, "rev-parse", "--show-toplevel") + if toplevel is None: + return False + return pathlib.Path(toplevel).resolve() == pathlib.Path(root).resolve() + + +def _packaged_version(root): + """Return the version an unpacked sdist already carries, or ``None``.""" + + # An sdist has no history to read, but the build that produced it + # wrote the version it resolved into PKG-INFO, so a wheel built + # from one reports the version of the tree it came from rather than + # failing for want of a repository. + try: + metadata = (pathlib.Path(root) / "PKG-INFO").read_text() + except OSError: + return None + match = re.search(r"^Version: *(.+)$", metadata, re.MULTILINE) + return match.group(1).strip() if match else None + + +def version(root): + """Return the PEP 440 version of the tree at ``root``. + + A tagged, clean commit is exactly its release. Any other commit in + a repository is the last release plus a local identifier, i.e. the + abbreviated commit and ``dirty`` where the tree has uncommitted or + untracked content. A tree that is not a repository falls back to + the version an sdist carries, and failing that to the initial + release. + """ + + if not _is_own_repository(root): + return _packaged_version(root) or INITIAL_RELEASE + + described = _git(root, "describe", "--tags", "--abbrev=7", "--match", RELEASE_TAG) + match = DESCRIBED.match(described) if described else None + if match: + release, commit = match.group("release"), match.group("commit") + else: + # No release tag is reachable, so the commit is all there is to + # name the build by. + release = INITIAL_RELEASE + commit = _git(root, "rev-parse", "--short=7", "HEAD") + + local = [commit] if commit else [] + # Untracked files count as well as modified ones, because the + # default include is broad enough that one can reach the artifact. + if _git(root, "status", "--porcelain"): + local.append("dirty") + + # A period, not the hyphen git uses: PEP 440 separates local + # segments with periods and normalises anything else to one, so + # emitting the canonical form keeps the string the build reports + # identical to the string a resolver compares. + return "{}+{}".format(release, ".".join(local)) if local else release diff --git a/build-hooks/metadata.py b/build-hooks/metadata.py new file mode 100644 index 0000000..0560c91 --- /dev/null +++ b/build-hooks/metadata.py @@ -0,0 +1,25 @@ +"""Supply the ``version`` that ``project.dynamic`` leaves to the build.""" + +import os +import sys + +sys.path.insert(0, os.path.dirname(__file__)) + +import _git +from hatchling.metadata.plugin.interface import MetadataHookInterface + + +class QuadratMetadataHook(MetadataHookInterface): + """Resolve the version from the repository rather than from a literal. + + .. rubric:: Implementation notes + + The hook's directory is prepended to ``sys.path`` because hatchling + executes this file directly rather than importing it as part of a + package, so a sibling module is not otherwise reachable. + """ + + PLUGIN_NAME = "quadrat-metadata" + + def update(self, metadata): + metadata["version"] = _git.version(self.root) diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..619bfd0 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,147 @@ +[build-system] +build-backend = "hatchling.build" +requires = ["hatchling"] + +[project] +authors = [ + { name = "Nezar Abdennur", email = "nabdennur@gmail.com" }, + { name = "Conrad Bzura", email = "conradbzura@gmail.com" }, +] +# No licence classifier: PEP 639 deprecates them and directs tools not +# to combine one with `License-Expression`, which `license = "MIT"` +# below produces. PyPI rejects a distribution carrying both. +classifiers = [ + "Intended Audience :: Science/Research", + "Programming Language :: Python :: 3", + "Topic :: Scientific/Engineering :: Bio-Informatics", +] +description = "Sequence-to-function training data, straight from BAM." +dynamic = ["version"] +license = "MIT" +maintainers = [ + { name = "Nezar Abdennur", email = "nabdennur@gmail.com" }, + { name = "Conrad Bzura", email = "conradbzura@gmail.com" }, +] +name = "quadrat" +readme = "README.md" +requires-python = ">=3.11" + +# Floors, not tested ceilings. 3.11 rather than 3.10 because the pileup +# engine -- polars-bio, polars, giql -- is gated there, and the pileup is +# not an optional part of what this package is for. +dependencies = [ + "numpy>=1.14.2", + "pandas>=1.3.3", + "torch>=2.9.0", + "tqdm>=4.64.1", + "joblib>=1.0.0", + "tangermeme>=1.5.0", +] + +# `pyfaidx` belongs in this extra rather than in a dev group: the +# pileup imports it at runtime, so it is a runtime dependency of the +# extra rather than a test one. The lazy-import guarantee that makes +# the base install sufficient is stated in the package docstring. +[project.optional-dependencies] +pileup = [ + "polars-bio>=0.35.1", + "polars>=1.30", + "giql>=0.7", + "pyfaidx>=0.9", +] + +[dependency-groups] +dev = [ + "pytest>=9.1.1", + "pytest-mock>=3.14", + "hypothesis>=6.0.0", + "pysam", + "ruff>=0.1.0", +] +docs = [ + "sphinx>=7.0", + "sphinx-autobuild>=2024.0", + "sphinx-book-theme>=1.1", + "sphinx-design>=0.6", +] + +# BRANCH-ONLY. The datafusion-bio GIQL target is not on PyPI and lives on +# a proof-of-concept branch, so this pins the public commit at that +# branch's tip. Its library code is identical to what cherimoya builds +# against; the only delta is benchmark material outside `src`. Replace +# with a version specifier once the target reaches `main` and ships. +[tool.uv.sources] +giql = { git = "https://github.com/abdenlab/giql", rev = "59c74276e07cc4680cb24303a9192c3a71c11d59" } + +# The version is the repository's, not a literal anyone has to +# remember to bump: a `vMAJOR.MINOR.PATCH` tag names a release and every +# commit between tags reports the last release plus the commit it is. +# Releasing is therefore pushing a tag, and nothing in the tree has to +# change for one. +[tool.hatch.metadata.hooks.custom] +path = "build-hooks/metadata.py" + +[tool.hatch.build.targets.wheel] +packages = ["src/quadrat"] + +# The whole test tree ships, so the suite runs from an sdist exactly as +# it does from the repository -- without conftest.py it would run +# against a different cache directory than the one the suite assumes. +# +# Stated here rather than in a MANIFEST.in, which hatchling does not +# read: a MANIFEST.in's directives are inert under this backend, and an +# sdist built with or without the file is byte-identical. +[tool.hatch.build.targets.sdist] +include = [ + "src", + "tests", + "build-hooks", + "README.md", + "LICENSE", +] + +# `**` on both sides, because this is a gitignore-style pattern: one +# containing a slash is anchored at the project root and a single `*` +# spans one path segment, so `*/.ipynb_checkpoints/*` excludes a +# checkpoint directory one level down and ships every deeper one. +exclude = ["**/.ipynb_checkpoints/**"] + +[tool.ruff] +line-length = 89 + +# Stated explicitly rather than left to the default, which has widened +# over ruff releases and would otherwise change what passes when the +# pin moves. Pyflakes plus the pycodestyle errors that are errors: +# undefined names, unused imports, broken syntax. +# +# Deliberately absent are the style-migration families -- UP, SIM, FURB, +# RUF. The code ported from cherimoya uses `str.format` throughout and +# `class X(object)` by convention. Flagging either would mean rewriting +# thousands of lines in the same change that moves them, which is the +# one thing that makes a port unreviewable. +# +# `I` is in despite that argument, because import order is mechanical in +# ported code too, `--fix` for it is safe and localised, and getting it +# wrong is the one style defect a reviewer reliably misses. +[tool.ruff.lint] +select = ["E4", "E7", "E9", "F", "I"] + +[tool.ruff.format] +docstring-code-format = true + +# `--strict-markers` turns a misspelt marker into an error rather than a +# test that is silently neither selected nor deselected. +[tool.pytest.ini_options] +addopts = ["--strict-markers"] +testpaths = ["tests"] +markers = [ + "packaging: spawns a fresh interpreter or a real build to observe import-time or artifact state", +] + +# Scoped rather than blanket: a deprecation raised inside `quadrat` is a +# stale API this suite should fail on, while pysam deprecates ahead of +# removals on a schedule this project does not set. +filterwarnings = [ + "error::DeprecationWarning:quadrat.*", + "ignore::DeprecationWarning:pysam.*", +] diff --git a/src/quadrat/__init__.py b/src/quadrat/__init__.py new file mode 100644 index 0000000..2c86304 --- /dev/null +++ b/src/quadrat/__init__.py @@ -0,0 +1,45 @@ +"""Training data for sequence-to-function models, from alignments. + +A sequence-to-function model consumes pairs of a one-hot DNA sequence +over an input window and a measured signal profile over a shorter, +concentric output window. Everything between a set of alignments and a +batch of such pairs is independent of the architecture downstream, and +that is what this package implements. + +The vocabulary used throughout: + +``locus`` + A genomic coordinate, typically a peak summit or a sampled + background position. + +``window`` + A fixed-length interval centred on a locus, in two nested + lengths, i.e., an input window supplying sequence and a shorter + output window supplying signal. + +``channel`` + One measured track. + +``cut-site table`` + The intermediate representation: a per-contig, position-sorted + Parquet table of ``(position, value)`` pairs for one channel, + written once by the pileup and read many times by the loader. + +``draw`` + One ``(locus, jitter offset, strand)`` triple the sampler emits, so + a locus yields many draws under jitter and reverse-complement + augmentation. + +Nothing the ``pileup`` extra installs is imported at package import +time, so a caller who already has cut-site tables pays for none of it. +The engine behind that extra reads alignments through polars-bio and +transpiles its aggregate with giql, and loads what it needs when a +pileup runs. +""" + +from importlib.metadata import version + +__all__ = ["__version__"] + +# public +__version__ = version("quadrat") diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000..1dcdc8c --- /dev/null +++ b/uv.lock @@ -0,0 +1,3067 @@ +version = 1 +revision = 3 +requires-python = ">=3.11" +resolution-markers = [ + "python_full_version >= '3.14' and sys_platform == 'win32'", + "python_full_version >= '3.14' and sys_platform == 'emscripten'", + "python_full_version >= '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'", + "python_full_version == '3.13.*' and sys_platform == 'win32'", + "python_full_version == '3.13.*' and sys_platform == 'emscripten'", + "python_full_version == '3.13.*' and sys_platform != 'emscripten' and sys_platform != 'win32'", + "python_full_version == '3.12.*' and 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"sha256:dc2b495a92b3971966bf102e73589f950db3ec1ca6713265355ce7771d97b199", size = 212375, upload-time = "2026-10-19T16:58:04.483Z" }, +] From cda1e4593f905d38ad1ceb2fa29db06ff9818d76 Mon Sep 17 00:00:00 2001 From: Conrad Date: Thu, 29 Oct 2026 14:19:27 -0400 Subject: [PATCH 3/7] test: Add the synthetic-data builders and the shared fixture layer Every later assertion about the pileup, the window cache or the sampler is an assertion about data these builders produced, so a builder that silently writes the wrong thing would make the suite agree with itself and with nothing else. Cherimoya has no data-path fixtures in conftest -- every one is module-local, and the FASTA, BAM and BED quintet is duplicated five ways differing only in chromosome sizes and window geometry. Porting that duplication would multiply it, so the builders take the geometry as arguments and the five sets collapse onto one factory. Cut-site builders arrive with the writer they need, in the pileup slice. Each builder states what it guarantees where a caller reads it rather than where a test happens to assert it. write_fasta clips a mask interval to the contig it names at both ends of each coordinate, because a negative start truncates to an empty slice while a negative stop is counted back from the end of the sequence, and it applies its N runs after its soft mask, so a position covered by both reads as an upper-case N. write_random_bam reserves one read length rather than two, so a read may start anywhere a record of that length still ends inside its contig, and skews the surplus toward the first contig deliberately, because a uniform draw satisfies neither the per-contig floor nor the unevenness a suite splitting batches per contig needs. aligned_read carries the CIGAR it is given whether or not the record is placed, falls back to twenty bases only for a CIGAR consuming no query, and produces a half-placed record for a contig the header does not declare. pysam is imported under a guard so the module imports without it, and the skip has two owners that between them cover every path: the suite's pysam fixture for a test that touches a builder directly, and corpus_factory on its own behalf when a call asks for an alignment or a FASTA index. The factory rejects header contigs that do not cover the reference at its declared length, since reads are placed against the reference and a narrower header yields records it cannot resolve inside a corpus a later suite would assert against. It copies the chromosome sizes it is built from, because it is session-scoped and a corpus built from a module constant would otherwise hold that constant, so one test mutating what looks like its own attribute would corrupt it for every test after it. The cache directory has two tiers. A session directory is assigned at import time, before anything imports the package, because the function that will read it reads it per call: set later, the first reader would still see the user's own cache, and an entry surviving from an earlier run would satisfy a test written to exercise a cold build. It is assigned rather than defaulted, since defaulting would honour an exported value and an exported value is exactly that surviving entry. It is removed at exit rather than on a fixture teardown, which the subprocess tests reach and a fixture would not. During a test body an autouse fixture supersedes it with a directory that test alone can see. TQDM_DISABLE is the other way round and defers to the environment, because a developer who turns progress bars back on to watch a hang changes nothing a test can observe. What the test modules share lives in the package init rather than per module: the geometries, immutably, so a corpus built from one cannot alter the geometry a later corpus is built from; the project root; the BAM reader the assertions compare placements through; the child-process runner that reports the stderr a failed subprocess would otherwise swallow; and the Hypothesis settings every file-writing property test runs under. Those settings carry no deadline, because such a test spends about a second in pysam's sort and index on a cold first call against a 200ms default, which Hypothesis then reports as a falsifying example; the properties that stay in memory keep theirs. The loader that reads a build hook from its path lives here as well, since build-hooks is not a legal module name and two test modules need to reach it. --- tests/__init__.py | 90 ++++++++++++++++++ tests/builders.py | 231 +++++++++++++++++++++++++++++++++++++++++++++ tests/conftest.py | 233 ++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 554 insertions(+) create mode 100644 tests/__init__.py create mode 100644 tests/builders.py create mode 100644 tests/conftest.py diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..2952a76 --- /dev/null +++ b/tests/__init__.py @@ -0,0 +1,90 @@ +"""The geometries, paths and readers every test module shares. + +Declared here rather than per module so no two test modules can +drift, and the geometries immutably so a corpus built from one cannot +alter the geometry a later corpus is built from. + +`builders` writes the suite's synthetic data; what lives here is what +reads it back, locates the project, or runs a child process, none of +which belongs to any one module. +""" + +import importlib.util +import subprocess +from pathlib import Path +from types import MappingProxyType + +import pytest +from hypothesis import HealthCheck, settings + +# Two contigs is the default: the smallest geometry in which a contig +# boundary exists at all. Three is what a non-uniform contig split +# needs, because across two contigs "more on the first than on any +# other" has only one comparison to make. +TWO_CONTIGS = MappingProxyType({"chr1": 1000, "chr2": 500}) +THREE_CONTIGS = MappingProxyType({"chr1": 1000, "chr2": 500, "chr3": 400}) + +PROJECT_ROOT = Path(__file__).resolve().parent.parent + +# The settings every property test that writes real files runs under. +# Two decisions live here rather than once per test: the health check +# has to be suppressed because `tmp_path` and `pysam` are requested +# per test, and the deadline has to go because a cold first call spends +# a second in pysam's sort and index against Hypothesis's 200ms +# default -- which then reports a filesystem timing as a falsifying +# example. The properties that stay in memory keep the deadline. +FILE_BACKED = settings( + deadline=None, suppress_health_check=[HealthCheck.function_scoped_fixture] +) + + +def load_build_hook(name): + """Return the build hook module ``name``, loaded from its path. + + The hooks are build-time infrastructure rather than part of the + package, and ``build-hooks`` is not a legal module name, so they + are loaded from a path the way hatchling itself loads them. + """ + + path = PROJECT_ROOT / "build-hooks" / "{}.py".format(name) + spec = importlib.util.spec_from_file_location(name, path) + module = importlib.util.module_from_spec(spec) + spec.loader.exec_module(module) + return module + + +def record_placements(path, pysam, until_eof=False): + """Return ``(contig, start)`` for every record in a BAM, in file order. + + ``until_eof`` is what makes this a count of records rather than of + records the index can find: a plain `fetch` drops the unplaced + ones without saying so. + """ + + with pysam.AlignmentFile(path, "rb") as bam: + return [ + (read.reference_name, read.reference_start) + for read in bam.fetch(until_eof=until_eof) + ] + + +def run_child(command, failure, cwd=None, environment=None): + """Run ``command`` to completion and return it, failing with its stderr. + + `subprocess.CalledProcessError` carries the stderr but does not + print it, so a caller that lets it propagate reports an argv and an + exit status with no diagnosis -- which in a CI log is the whole of + what there is to read. + """ + + try: + return subprocess.run( + command, + cwd=cwd, + capture_output=True, + text=True, + check=True, + env=environment, + ) + except subprocess.CalledProcessError as error: + pytest.fail("{}:\n{}".format(failure, error.stderr)) diff --git a/tests/builders.py b/tests/builders.py new file mode 100644 index 0000000..4948acb --- /dev/null +++ b/tests/builders.py @@ -0,0 +1,231 @@ +"""Synthetic genomics inputs for the test suite. + +Not a ``test_`` module, so pytest does not collect it. Everything here +is a plain function taking an output path and the geometry to render at +it, so one builder serves every fixture that needs that shape of input +rather than each fixture carrying its own copy. + +`pysam` is imported under a guard, so this module imports without it. +""" + +import gzip +import os +import random + +try: + import pysam +except ImportError: + # Left unbound rather than re-raised, because the suite's `pysam` + # fixture owns the skip and nothing reaches a builder below without + # requesting it. + pysam = None + + +def write_fasta( + path, chrom_sizes, *, seed=0, soft_mask=(), n_runs=(), index=False, line_width=60 +): + """Write a random FASTA over ``chrom_sizes`` and return its path. + + ``soft_mask`` and ``n_runs`` are iterables of ``(chrom, start, + stop)`` half-open intervals, lowercased and replaced with ``N`` + respectively, so masked sequence is something a caller can ask for + rather than something a real reference happens to carry. An + interval running past either end of its contig is clipped to it, + and every contig is written at exactly its declared length. Where + the two overlap ``n_runs`` wins, so a position in both reads as an + upper-case ``N`` rather than a lower-case base. + + ``index`` writes a ``.fai`` beside the file. It needs pysam, so it + is off by default. + + .. rubric:: Implementation notes + + Both coordinates are clamped at both ends rather than left to + slice truncation, which diverges from the stated contract at every + negative one. A negative start truncates to an empty slice, so + ``bases[-5:3]`` would mask nothing instead of masking from the + contig's start; a negative stop is instead counted back from the + end, so ``bases[0:-10]`` is a slice of almost the whole contig — + which lowercases positions no interval named and, where the + replacement is built from the clamped width rather than from the + slice, deletes bases from a contig whose length is a guarantee. + + The masks are applied in the order the contract states rather than + merged, so the precedence is the loop order and nothing has to + reconcile an overlap. A caller wanting the other precedence has + both inputs and can subtract. + """ + + rng = random.Random(seed) + sequences = {} + for chrom, size in chrom_sizes.items(): + sequences[chrom] = [rng.choice("ACGT") for _ in range(size)] + + # Both loops clip to the contig; see this function's docstring. + for chrom, start, stop in soft_mask: + bases = sequences[chrom] + start = min(max(start, 0), len(bases)) + stop = min(max(stop, 0), len(bases)) + bases[start:stop] = [base.lower() for base in bases[start:stop]] + for chrom, start, stop in n_runs: + bases = sequences[chrom] + start = min(max(start, 0), len(bases)) + stop = min(max(stop, 0), len(bases)) + bases[start:stop] = ["N"] * max(0, stop - start) + + with open(path, "w") as handle: + for chrom, size in chrom_sizes.items(): + handle.write(">{}\n".format(chrom)) + bases = "".join(sequences[chrom]) + for offset in range(0, size, line_width): + handle.write(bases[offset : offset + line_width] + "\n") + + if index: + pysam.faidx(path) + return path + + +def alignment_header(chrom_sizes): + """Build a coordinate-sorted header over ``chrom_sizes``. + + A contig the reference does not declare is accepted without + complaint, so a header-versus-reference mismatch is constructible. + """ + + return pysam.AlignmentHeader.from_dict( + { + "HD": {"VN": "1.6", "SO": "coordinate"}, + "SQ": [{"SN": chrom, "LN": size} for chrom, size in chrom_sizes.items()], + } + ) + + +def aligned_read(header, name, chrom, pos, cigar="20M", flag=0, mapq=30): + """Build one aligned segment with a dummy query and qualities. + + ``chrom=None`` builds an unplaced record: no reference id and no + start, but the CIGAR it was given either way. Query length follows + the CIGAR, so soft clips and deletions stay self-consistent, and + falls back to 20 bases for a CIGAR that consumes no query at all. + + A ``chrom`` the header does not declare builds a half-placed + record: no reference id, because the header resolves an unknown + contig to one, while the start and the CIGAR are kept. That is how + a header-versus-reference mismatch reaches a reader. + """ + + read = pysam.AlignedSegment(header) + read.query_name = name + read.flag = flag + if chrom is None: + read.reference_id = -1 + read.reference_start = -1 + else: + read.reference_id = header.get_tid(chrom) + read.reference_start = pos + read.cigarstring = cigar + + length = read.infer_query_length() or 20 + read.query_sequence = "A" * length + read.query_qualities = pysam.qualitystring_to_array("I" * length) + read.mapping_quality = mapq + return read + + +def write_bam(path, reads, header): + """Sort ``reads`` into ``path``, index it, and return the path. + + The file is coordinate-sorted and indexed on return whatever order + the reads arrive in, and no intermediate survives beside it. + + .. rubric:: Implementation notes + + Written unsorted and sorted afterwards rather than sorted in + memory, because the index is what the sort exists to make valid, + and a BAM whose order disagrees with its index is a failure mode + worth being unable to produce by accident. + """ + + staging = path + ".unsorted.bam" + with pysam.AlignmentFile(staging, "wb", header=header) as out: + for read in reads: + out.write(read) + pysam.sort("-o", path, staging) + pysam.index(path) + os.remove(staging) + return path + + +def write_random_bam(path, header, chrom_sizes, *, n_reads=40, seed=0, read_length=20): + """Write a BAM of ``n_reads`` randomly placed records, half per strand. + + Every contig holds at least one read once ``n_reads`` reaches the + contig count and, once ``n_reads`` exceeds it, the first contig + holds more than any other, so a per-contig count is not the same + number everywhere. A read may start anywhere a record of + ``read_length`` still ends inside its contig, so no stretch of a + contig is systematically uncovered. + + Raises `ValueError` for a contig shorter than ``read_length``, which + cannot hold a read at all without running past the end the header + declares. + + .. rubric:: Implementation notes + + The skew is deliberate: a uniform draw over contigs would satisfy + neither the per-contig floor nor the unevenness, and a suite that + splits work per contig needs both at once to be worth testing + against. + """ + + rng = random.Random(seed) + chroms = list(chrom_sizes) + short = [chrom for chrom in chroms if chrom_sizes[chrom] < read_length] + if short: + raise ValueError( + "contig shorter than the read length of {}: {}".format( + read_length, ", ".join(short) + ) + ) + + reads = [] + for index in range(n_reads): + if index < len(chroms): + chrom = chroms[index] + else: + offset = index - len(chroms) + chrom = chroms[0] if offset % 3 else chroms[(offset // 3) % len(chroms)] + span = chrom_sizes[chrom] - read_length + 1 + reads.append( + aligned_read( + header, + "r{}".format(index), + chrom, + rng.randrange(0, span), + cigar="{}M".format(read_length), + flag=16 if index % 2 else 0, + ) + ) + return write_bam(path, reads, header) + + +def write_bed(path, rows): + """Write ``(chrom, start, stop)`` rows, gzipped when ``path`` says so. + + Exclusion lists are conventionally gzipped and locus files + conventionally are not, and both readers have to cope, so the + suffix decides rather than a flag. + """ + + opener = gzip.open if str(path).endswith(".gz") else open + with opener(path, "wt") as handle: + for row in rows: + chrom, start, stop = row[:3] + handle.write("{}\t{}\t{}\n".format(chrom, start, stop)) + return path + + +def intervals(chrom, start, stop, step, width): + """Return ``(chrom, start, stop)`` rows every ``step`` bases over a range.""" + + return [(chrom, pos, pos + width) for pos in range(start, stop, step)] diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..730d6dc --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,233 @@ +"""Suite-wide setup and the one fixture every data-path module wants. + +The environment block runs at import time, before anything imports +`quadrat`, because the package resolves its cache directory from the +environment on every call rather than once at import, so a later +assignment would leave the first reader pointed at the real user cache. + +The cache directory has two tiers and the import-time one is what this +block owns: a session directory that is in place before the first +import and is what the two subprocess tests observe, since neither +starts a pytest session. During a test body `_per_test_cache_dir` +supersedes it, and that fixture's docstring states what it guarantees. + +.. rubric:: Implementation notes + +Two reasons the session directory is not the user's own, and the +second is the one that bites: writing to the user's cache pollutes a +real install, and an entry surviving from an earlier run would satisfy +a test written to exercise a cold build, which then passes while +testing nothing. + +``QUADRAT_CACHE_DIR`` is therefore assigned rather than defaulted, +since defaulting would honour an exported value and an exported value +is exactly the surviving entry a fresh directory exists to rule out. +``TQDM_DISABLE`` is the other way round: a developer who turns progress +bars back on to watch a hang changes nothing a test can observe, so +that one defers to the environment. +""" + +import atexit +import os +import shutil +import tempfile + +import pytest + +from tests import builders + +# Progress bars in a captured suite are noise that also slows it down. +os.environ.setdefault("TQDM_DISABLE", "1") + +# Fresh per session and never the user's own; see the module docstring. +# The variable's name is the whole contract until `quadrat` grows the +# function that reads it, so a port that renames it breaks this guard +# silently and must keep the name or change both. +_CACHE_DIR = tempfile.mkdtemp(prefix="quadrat-test-cache-") +os.environ["QUADRAT_CACHE_DIR"] = _CACHE_DIR + +# Removed at exit rather than on a fixture's teardown, because the +# subprocess tests re-run this module in a fresh interpreter and never +# start a session for a fixture to hang off. +atexit.register(shutil.rmtree, _CACHE_DIR, True) + + +class Corpus: + """Paths to one synthetic genome and whatever was built over it. + + ``fasta``, ``peaks``, ``negatives`` and ``exclusion`` stay ``None`` + until something builds them, where ``None`` means nothing built + that rather than built and empty. ``bams`` is an empty list for the + same reason. + + :param root: The directory holding this corpus's files, as a + `pathlib.Path`. `Corpus.path` returns members of it as strings, + which is the form the builders take. + :param chrom_sizes: The geometry the corpus was built to, copied + rather than aliased, so a caller mutating its own mapping + afterwards cannot alter what this corpus reports. + + .. rubric:: Implementation notes + + A plain attribute bag rather than a dict, so a typo is an + `AttributeError` at the point of use rather than a key that is + silently missing. + """ + + __slots__ = ( + "root", + "chrom_sizes", + "fasta", + "bams", + "peaks", + "negatives", + "exclusion", + ) + + def __init__(self, root, chrom_sizes): + self.root = root + self.chrom_sizes = dict(chrom_sizes) + self.fasta = None + self.bams = [] + self.peaks = None + self.negatives = None + self.exclusion = None + + def path(self, name): + """Return a path inside this corpus's directory, as a string.""" + + return str(self.root / name) + + +@pytest.fixture(autouse=True) +def _per_test_cache_dir(tmp_path, monkeypatch): + """Point the cache at a directory this test alone can see. + + Autouse, so this is the value in force for every test body and the + session directory the module docstring describes is only ever what + an import observes. One test cannot reach another's cache entries, + which is the cold-build guarantee at test rather than session + granularity. + """ + + monkeypatch.setenv("QUADRAT_CACHE_DIR", str(tmp_path / "cache")) + + +@pytest.fixture(scope="session") +def pysam(): + """Return the `pysam` module, skipping the requesting test without it. + + Requested per test rather than imported at a test module's top, so + a test module that needs no alignment still runs without `pysam`. + """ + + return pytest.importorskip("pysam") + + +@pytest.fixture(scope="session") +def corpus_factory(tmp_path_factory): + """Build a synthetic corpus to a given geometry. + + Each call gets its own directory, so two corpora never share a file + even when their chromosome sizes agree, which is what makes one + session-scoped factory safe for the whole suite to share. + + Window geometry is not a parameter: nothing here renders a window, + so a suite that needs one supplies it itself. + + :param name: Prefix for the corpus's own temporary directory. + :param chrom_sizes: Contig name to length, rendered into every + artifact the call asks for. + :param n_bams: How many alignment files to write; ``0`` writes none + and leaves ``bams`` empty. + :param n_reads: Reads per alignment file. + :param seed: Base seed. The sequence is rendered with it and sample + ``n`` is written with ``seed + n``, so two samples of one corpus + differ. + :param index_fasta: Reaches `builders.write_fasta` as ``index``. + :param soft_mask: Reaches `builders.write_fasta` unchanged, which + owns the interval semantics and the clipping guarantee. + :param n_runs: Reaches `builders.write_fasta` unchanged. + :param header_contigs: Contigs to declare in the alignment header + in place of ``chrom_sizes``, which may name one the reference + does not have. It must cover every contig in ``chrom_sizes`` at + no less than its length, or the call raises `ValueError`. + :param peaks: Rows for a peak BED; empty leaves ``peaks`` unset. + :param negatives: Rows for a background BED; empty leaves + ``negatives`` unset. + :param exclusion: Rows for an exclusion BED; empty leaves + ``exclusion`` unset. The path this factory gives it ends + ``.bed.gz``. + + Requesting an alignment or a FASTA index needs ``pysam``, so a call + that asks for either skips without it. The rest of the surface has + no such requirement. + """ + + def build( + name, + chrom_sizes, + *, + n_bams=0, + n_reads=40, + seed=0, + index_fasta=False, + soft_mask=(), + n_runs=(), + header_contigs=None, + peaks=(), + negatives=(), + exclusion=(), + ): + if n_bams or index_fasta: + pytest.importorskip("pysam") + if header_contigs is not None: + uncovered = [ + chrom + for chrom, size in chrom_sizes.items() + if header_contigs.get(chrom, -1) < size + ] + if uncovered: + raise ValueError( + "header contigs do not cover the reference at {}: {}".format( + "its declared length", ", ".join(uncovered) + ) + ) + + root = tmp_path_factory.mktemp(name) + corpus = Corpus(root, chrom_sizes) + corpus.fasta = builders.write_fasta( + corpus.path("genome.fa"), + chrom_sizes, + seed=seed, + soft_mask=soft_mask, + n_runs=n_runs, + index=index_fasta, + ) + + if n_bams: + header = builders.alignment_header(header_contigs or chrom_sizes) + corpus.bams = [ + builders.write_random_bam( + corpus.path("s{}.bam".format(index)), + header, + chrom_sizes, + n_reads=n_reads, + seed=seed + index, + ) + for index in range(n_bams) + ] + + if peaks: + corpus.peaks = builders.write_bed(corpus.path("peaks.bed"), peaks) + if negatives: + corpus.negatives = builders.write_bed( + corpus.path("negatives.bed"), negatives + ) + if exclusion: + corpus.exclusion = builders.write_bed( + corpus.path("exclusion.bed.gz"), exclusion + ) + return corpus + + return build From e0b32b25e3e4306b6d0a094c002a4d1412c0716f Mon Sep 17 00:00:00 2001 From: Conrad Date: Thu, 29 Oct 2026 14:19:27 -0400 Subject: [PATCH 4/7] test: Pin the builders' contracts Forty-three tests over the seven builders, example-based where the input has one shape and property-based where the domain is wide: that a FASTA holds its declared lengths and masks exactly the intervals it is given, over a domain reaching past either of a contig's ends; that intervals tile their range; that a header declares any contig mapping; that a query and its qualities match any CIGAR; that a BAM round-trips any reads in sorted order; that every random read starts far enough from its contig's end to finish inside it; that every contig receives one; and that the surplus skews toward the first. Ordered foundational to derived, so a run that stops at the first failure stops at the deepest one rather than at whichever caller came first alphabetically. The pysam fixture is requested per test rather than imported at the module top. A module-level importorskip would abort collection of every test in the file when only some of them need pysam, and report it as a single line, so a reader could not tell how many had gone. Without pysam the FASTA, BED and interval builders still run, which is what importing pysam lazily was for. --- tests/test_builders.py | 1327 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 1327 insertions(+) create mode 100644 tests/test_builders.py diff --git a/tests/test_builders.py b/tests/test_builders.py new file mode 100644 index 0000000..10cf308 --- /dev/null +++ b/tests/test_builders.py @@ -0,0 +1,1327 @@ +"""Tests for the synthetic-input builders the suite is built on. + +The builders are test infrastructure, which is exactly why they are +tested: every later assertion about the data path is an assertion about +data these functions produced, so a builder that silently writes the +wrong thing makes the suite agree with itself and with nothing else. + +Tests that read an alignment back request the `pysam` fixture, which +owns the skip. + +Ordered foundational to derived, so ``pytest -x`` stops at the most +fundamental failure. +""" + +import gzip +import os +from collections import Counter + +import pytest +from hypothesis import given, settings +from hypothesis import strategies as st + +from tests import FILE_BACKED, THREE_CONTIGS, TWO_CONTIGS, builders, record_placements + +# Contig names over lowercase letters only, so a generated name cannot +# collide with FASTA or BED syntax. Lengths stay small because every +# draw writes a real file, and never zero, because `faidx` refuses a +# contig with no sequence. +contig_names = st.text( + st.characters(min_codepoint=97, max_codepoint=122), min_size=1, max_size=4 +) +contig_sizes = st.dictionaries( + contig_names, st.integers(min_value=1, max_value=200), min_size=1, max_size=4 +) + +# Contigs of at least the default read length, which is the floor +# `write_random_bam` refuses to go below: a shorter contig cannot hold +# a 20M record ending before the end its own header declares. +alignment_sizes = st.dictionaries( + contig_names, st.integers(min_value=20, max_value=200), min_size=1, max_size=4 +) + +bed_rows = st.lists( + st.tuples( + contig_names, + st.integers(min_value=0, max_value=10**6), + st.integers(min_value=0, max_value=10**6), + ), + max_size=10, +) + + +@st.composite +def geometries(draw): + """Draw a contig mapping with masked intervals that may overrun their contigs. + + The intervals are drawn against the widest contig the mapping + allows rather than against each contig's own length, and either + coordinate may fall below zero, so an interval running off either + end — or lying wholly outside the contig on either side — is a + case the invariant sees rather than one it is protected from. Soft + masks and N runs are drawn from one domain because either may + appear anywhere. + """ + + sizes = draw(contig_sizes) + intervals = st.lists( + st.tuples( + st.sampled_from(sorted(sizes)), + st.integers(min_value=-50, max_value=250), + st.integers(min_value=-50, max_value=250), + ), + max_size=3, + ) + return sizes, draw(intervals), draw(intervals) + + +@st.composite +def alignments(draw, read_length=20): + """Draw a contig mapping with reads placed on it, some of them unplaced. + + A placement of ``None`` is an unplaced record, which the sort has + to carry rather than locate. Placed reads sit far enough inside + their contig to end before it does, so no draw asks the writer to + produce a record the header contradicts. + """ + + sizes = draw(alignment_sizes) + names = sorted(sizes) + placements = [] + for chrom in draw(st.lists(st.sampled_from(names + [None]), max_size=8)): + if chrom is None: + placements.append((None, None)) + else: + stop = sizes[chrom] - read_length + placements.append((chrom, draw(st.integers(min_value=0, max_value=stop)))) + return sizes, placements + + +@st.composite +def cigars(draw): + """Draw a CIGAR whose soft clips sit only at the ends and that consumes query. + + At least one ``M`` is forced, because a CIGAR of pure deletions + infers a query length of zero and the builder's fallback would then + disagree with the CIGAR for reasons that are not a defect. + """ + + middle = draw( + st.lists( + st.tuples(st.sampled_from("MID"), st.integers(min_value=1, max_value=20)), + min_size=1, + max_size=3, + ) + ) + if not any(operation == "M" for operation, _ in middle): + middle.append(("M", draw(st.integers(min_value=1, max_value=20)))) + + operations = [] + leading = draw(st.integers(min_value=0, max_value=10)) + if leading: + operations.append(("S", leading)) + operations.extend(middle) + trailing = draw(st.integers(min_value=0, max_value=10)) + if trailing: + operations.append(("S", trailing)) + return "".join("{}{}".format(length, op) for op, length in operations) + + +def parse_fasta(path): + """Return contig name to sequence, read back from a FASTA on disk.""" + + sequences = {} + name = None + with open(path) as handle: + for line in handle: + if line.startswith(">"): + name = line[1:].strip() + sequences[name] = [] + else: + sequences[name].append(line.strip()) + return {name: "".join(parts) for name, parts in sequences.items()} + + +def sequence_lines(path): + """Return the sequence lines of a FASTA, headers dropped.""" + + with open(path) as handle: + return [line.strip() for line in handle if not line.startswith(">")] + + +def read_bed(path): + """Return ``(chrom, start, stop)`` rows read back from a BED, gzipped or not.""" + + opener = gzip.open if str(path).endswith(".gz") else open + with opener(path, "rt") as handle: + rows = [] + for line in handle: + if not line.strip(): + continue + chrom, start, stop = line.rstrip("\n").split("\t") + rows.append((chrom, int(start), int(stop))) + return rows + + +def covered_positions(intervals, sizes): + """Return the ``(contig, offset)`` pairs a set of intervals covers. + + Clamped to each contig, because an interval is allowed to name + coordinates past the end of the one it masks. + """ + + return { + (chrom, offset) + for chrom, start, stop in intervals + for offset in range( + min(max(start, 0), sizes[chrom]), min(max(stop, 0), sizes[chrom]) + ) + } + + +@pytest.fixture +def two_contig_header(pysam): + """Return an alignment header over the suite's two-contig geometry.""" + + return builders.alignment_header(TWO_CONTIGS) + + +def test_write_fasta_should_write_every_contig_at_its_declared_length(tmp_path): + """Test that the FASTA holds exactly the requested bases. + + Given: + A mapping of two contig names to lengths. + When: + The builder renders it. + Then: + It should write each contig at its declared length over the + DNA alphabet. + """ + + # Arrange + path = str(tmp_path / "genome.fa") + + # Act + builders.write_fasta(path, TWO_CONTIGS) + + # Assert + sequences = parse_fasta(path) + assert {name: len(bases) for name, bases in sequences.items()} == TWO_CONTIGS + assert set("".join(sequences.values())) <= set("ACGT") + + +def test_write_fasta_should_mask_only_the_intervals_it_is_given(tmp_path): + """Test that soft masking and N runs land where they were asked for. + + Given: + A soft-masked interval and an N run on a known contig, with + unmasked sequence on both sides of each. + When: + The builder renders it. + Then: + It should lowercase only the first interval, fill only the + second with N, and leave every base outside them an uppercase + ACGT. + """ + + # Arrange + path = str(tmp_path / "masked.fa") + + # Act + builders.write_fasta( + path, TWO_CONTIGS, soft_mask=[("chr1", 100, 120)], n_runs=[("chr1", 200, 210)] + ) + + # Assert + bases = parse_fasta(path)["chr1"] + assert bases[100:120] == bases[100:120].lower() + assert bases[200:210] == "N" * 10 + untouched = bases[:100] + bases[120:200] + bases[210:] + assert set(untouched) <= set("ACGT") + assert len(bases) == TWO_CONTIGS["chr1"] + + +def test_write_fasta_should_produce_identical_bases_when_the_seed_is_reused(tmp_path): + """Test that one seed renders one sequence. + + Given: + Two renders of one geometry under the same seed. + When: + The bases are compared. + Then: + It should produce identical bases, so every later assertion + about this data is reproducible. + """ + + # Arrange + first = str(tmp_path / "a.fa") + second = str(tmp_path / "b.fa") + + # Act + builders.write_fasta(first, TWO_CONTIGS, seed=7) + builders.write_fasta(second, TWO_CONTIGS, seed=7) + + # Assert + assert parse_fasta(first) == parse_fasta(second) + + +def test_write_fasta_should_produce_different_bases_when_the_seed_differs(tmp_path): + """Test that the seed actually reaches the generator. + + Given: + Two renders of one geometry under different seeds. + When: + The bases are compared. + Then: + It should produce different bases, so a geometry can be + rendered more than one way. + """ + + # Arrange + first = str(tmp_path / "a.fa") + second = str(tmp_path / "b.fa") + + # Act + builders.write_fasta(first, TWO_CONTIGS, seed=7) + builders.write_fasta(second, TWO_CONTIGS, seed=8) + + # Assert + assert parse_fasta(first) != parse_fasta(second) + + +def test_write_fasta_should_wrap_every_line_at_the_requested_width(tmp_path): + """Test that the line width reaches the file rather than the default. + + Given: + A contig longer than the requested line width. + When: + The builder renders it. + Then: + It should wrap every sequence line but the last at that width, + which is what makes the file indexable. + """ + + # Arrange + path = str(tmp_path / "wrapped.fa") + + # Act + builders.write_fasta(path, {"chr1": 25}, line_width=10) + + # Assert + assert [len(line) for line in sequence_lines(path)] == [10, 10, 5] + + +def test_write_fasta_should_preserve_the_length_when_an_n_run_overruns(tmp_path): + """Test that an out-of-range N run cannot lengthen a contig. + + Given: + An N run whose stop lies past the end of its contig. + When: + The builder renders it. + Then: + It should still write the contig at its declared length, with + the run clipped to the end, because a contig longer than its own + header would make the suite agree with itself and nothing else. + """ + + # Arrange + path = str(tmp_path / "overrun.fa") + + # Act + builders.write_fasta(path, {"chr1": 100}, n_runs=[("chr1", 90, 120)]) + + # Assert + bases = parse_fasta(path)["chr1"] + assert len(bases) == 100 + assert bases[90:] == "N" * 10 + + +def test_write_fasta_should_mask_from_the_contig_start_when_a_soft_mask_underruns( + tmp_path, +): + """Test that a soft mask beginning before a contig still masks it. + + Given: + A soft mask whose start lies before the beginning of its contig. + When: + The builder renders it. + Then: + It should lowercase from the contig's first base to the mask's + stop, because a negative start truncates to an empty slice and + would otherwise mask nothing at all. + """ + + # Arrange + path = str(tmp_path / "underrun.fa") + + # Act + builders.write_fasta(path, {"chr1": 100}, soft_mask=[("chr1", -5, 10)]) + + # Assert + bases = parse_fasta(path)["chr1"] + assert bases[:10].islower() + assert bases[10:].isupper() + + +def test_write_fasta_should_preserve_the_length_when_an_n_run_lies_wholly_before_its_contig( + tmp_path, +): + """Test that an N run entirely below zero masks nothing and removes nothing. + + Given: + An N run whose start and stop both lie before the beginning of + its contig. + When: + The builder renders it. + Then: + It should write the contig at its declared length with no base + masked, because a negative stop counts back from the end of the + sequence and would otherwise fill a slice of almost the whole + contig with a run narrow enough to delete the rest of it. + """ + + # Arrange + path = str(tmp_path / "before.fa") + + # Act + builders.write_fasta(path, {"chr1": 100}, n_runs=[("chr1", -50, -10)]) + + # Assert + bases = parse_fasta(path)["chr1"] + assert len(bases) == 100 + assert "N" not in bases + + +def test_write_fasta_should_mask_nothing_when_a_soft_mask_lies_wholly_before_its_contig( + tmp_path, +): + """Test that a soft mask entirely below zero lowercases nothing. + + Given: + A soft mask whose start and stop both lie before the beginning + of its contig. + When: + The builder renders it. + Then: + It should leave every base upper case, because a negative stop + counts back from the end of the sequence and would otherwise + lowercase positions the interval never named. + """ + + # Arrange + path = str(tmp_path / "before.fa") + + # Act + builders.write_fasta(path, {"chr1": 100}, soft_mask=[("chr1", -50, -10)]) + + # Assert + bases = parse_fasta(path)["chr1"] + assert len(bases) == 100 + assert bases.isupper() + + +def test_write_fasta_should_write_an_index_when_indexing_is_requested(tmp_path, pysam): + """Test that an index is written beside the sequence. + + Given: + A two-contig geometry with indexing requested. + When: + The builder renders it. + Then: + It should write an index beside the file from which each + contig's full sequence can be fetched, which is the path the + sequence stores read through. + """ + + # Arrange + path = str(tmp_path / "indexed.fa") + + # Act + builders.write_fasta(path, TWO_CONTIGS, index=True) + + # Assert + assert os.path.exists(path + ".fai") + with pysam.FastaFile(path) as reference: + lengths = {chrom: len(reference.fetch(chrom)) for chrom in reference.references} + assert lengths == TWO_CONTIGS + + +@settings(FILE_BACKED, max_examples=25) +@given(geometry=geometries(), line_width=st.integers(min_value=1, max_value=80)) +def test_write_fasta_should_hold_its_declared_lengths_for_any_geometry( + tmp_path, geometry, line_width +): + """Test the length invariant across arbitrary geometries. + + Given: + Any mapping of contig names to positive lengths, any soft + masks and any N runs over them including intervals past a + contig's end, at any line width. + When: + The builder renders it and the file is parsed back. + Then: + It should hold every contig at exactly its declared length, + within the masked and unmasked DNA alphabet, with no line + longer than the width. + """ + + # Arrange + sizes, soft_mask, n_runs = geometry + path = str(tmp_path / "property.fa") + + # Act + builders.write_fasta( + path, + sizes, + soft_mask=soft_mask, + n_runs=n_runs, + line_width=line_width, + ) + + # Assert + sequences = parse_fasta(path) + assert {name: len(bases) for name, bases in sequences.items()} == sizes + assert set("".join(sequences.values())) <= set("ACGTNacgt") + assert max(len(line) for line in sequence_lines(path)) <= line_width + + +@settings(FILE_BACKED, max_examples=25) +@given(geometry=geometries()) +def test_write_fasta_should_mask_every_interval_it_is_given(tmp_path, geometry): + """Test that both masking kinds reach every base they name. + + Given: + Any contig mapping with any soft masks and N runs over it, + including intervals reaching past a contig's end. + When: + The builder renders it and the file is parsed back. + Then: + It should leave no position inside a requested interval + unmasked, i.e., ``N`` where a run covers it and lower case + where only a soft mask does. + """ + + # Arrange + sizes, soft_mask, n_runs = geometry + path = str(tmp_path / "masked.fa") + + # Act + builders.write_fasta(path, sizes, soft_mask=soft_mask, n_runs=n_runs) + + # Assert + sequences = parse_fasta(path) + runs = covered_positions(n_runs, sizes) + soft = covered_positions(soft_mask, sizes) - runs + assert all(sequences[chrom][offset] == "N" for chrom, offset in runs) + assert all(sequences[chrom][offset].islower() for chrom, offset in soft) + + +@pytest.mark.parametrize("suffix", [".bed", ".bed.gz"]) +def test_write_bed_should_round_trip_a_row_for_either_suffix(tmp_path, suffix): + """Test that the path suffix decides the compression. + + Given: + One row and a path whose suffix is plain or gzipped. + When: + The builder writes it and the matching reader reads it back. + Then: + It should produce the same tab-separated line either way, so a + caller reads back what it wrote whichever suffix it chose. + """ + + # Arrange + path = str(tmp_path / ("x" + suffix)) + + # Act + builders.write_bed(path, [("chr1", 500, 600)]) + + # Assert + assert read_bed(path) == [("chr1", 500, 600)] + + +def test_write_bed_should_keep_only_the_leading_three_fields(tmp_path): + """Test that wider rows are narrowed rather than written through. + + Given: + Several rows, the first carrying a name, score and strand + beyond the leading three fields. + When: + The builder writes them. + Then: + It should write one line per row in order, keeping only the + contig, start and stop. + """ + + # Arrange + path = str(tmp_path / "wide.bed") + rows = [("chr1", 100, 200, "peak", 50, "+"), ("chr2", 10, 20)] + + # Act + builders.write_bed(path, rows) + + # Assert + assert read_bed(path) == [("chr1", 100, 200), ("chr2", 10, 20)] + + +@settings(FILE_BACKED, max_examples=25) +@given(rows=bed_rows) +def test_write_bed_should_round_trip_any_rows(tmp_path, rows): + """Test the write-and-read roundtrip over arbitrary rows. + + Given: + Any list of contig, start and stop rows, written to both a + plain and a gzipped path. + When: + Each file is read back with its matching reader. + Then: + It should return the original rows in order from both. + """ + + # Arrange + plain = str(tmp_path / "rows.bed") + packed = str(tmp_path / "rows.bed.gz") + + # Act + builders.write_bed(plain, rows) + builders.write_bed(packed, rows) + + # Assert + assert read_bed(plain) == rows + assert read_bed(packed) == rows + + +def test_intervals_should_step_across_the_range_at_a_fixed_width(): + """Test that the interval helper tiles a range as asked. + + Given: + A range of 400 to 600 at a step of 75 and a width of 20. + When: + The builder builds the rows. + Then: + It should return every start in the range, each paired with a + stop one width along. + """ + + # Act + rows = builders.intervals("chr1", 400, 600, 75, 20) + + # Assert + assert rows == [("chr1", 400, 420), ("chr1", 475, 495), ("chr1", 550, 570)] + + +@settings(max_examples=50) +@given( + start=st.integers(min_value=-1000, max_value=1000), + stop=st.integers(min_value=-1000, max_value=1000), + step=st.integers(min_value=1, max_value=100), + width=st.integers(min_value=1, max_value=100), +) +def test_intervals_should_tile_the_range_for_any_geometry(start, stop, step, width): + """Test the tiling invariant across the helper's whole domain. + + Given: + Any start, stop, positive step and positive width. + When: + The builder tiles the range. + Then: + It should return one row per step across the range, each + spanning exactly one width, and nothing at all once the start + has caught the stop. + """ + + # Act + rows = builders.intervals("chr1", start, stop, step, width) + + # Assert + assert [row[1] for row in rows] == list(range(start, stop, step)) + assert all(row[2] - row[1] == width for row in rows) + assert all(row[0] == "chr1" for row in rows) + + +def test_alignment_header_should_declare_its_contigs_in_order(pysam): + """Test that the header names every contig at its length. + + Given: + A mapping of two contig names to lengths. + When: + The builder builds a header. + Then: + It should mark the order coordinate-sorted and declare each + contig at its length in insertion order, each resolving to its + insertion index. + """ + + # Act + header = builders.alignment_header(TWO_CONTIGS) + + # Assert + as_dict = header.to_dict() + assert as_dict["HD"]["SO"] == "coordinate" + assert [entry["SN"] for entry in as_dict["SQ"]] == list(TWO_CONTIGS) + assert [entry["LN"] for entry in as_dict["SQ"]] == list(TWO_CONTIGS.values()) + for index, chrom in enumerate(TWO_CONTIGS): + assert header.get_tid(chrom) == index + + +@settings(max_examples=25) +@given(sizes=contig_sizes) +def test_alignment_header_should_declare_any_contig_mapping(pysam, sizes): + """Test that the header echoes whatever mapping it is given. + + Given: + Any mapping of contig names to positive lengths. + When: + The builder builds a header from it. + Then: + It should declare every contig at its length in the mapping's + own order and resolve each name to that position, so a read + placed by name lands on the contig the caller named. + """ + + # Act + header = builders.alignment_header(sizes) + + # Assert + declared = [(entry["SN"], entry["LN"]) for entry in header.to_dict()["SQ"]] + assert declared == list(sizes.items()) + assert [header.get_tid(chrom) for chrom in sizes] == list(range(len(sizes))) + + +def test_aligned_read_should_size_the_query_from_the_cigar(two_contig_header): + """Test that a soft-clipped CIGAR gets a query long enough for it. + + Given: + A read with five soft-clipped and fifteen matched bases. + When: + The builder builds it. + Then: + It should give the record a twenty-base query, so the CIGAR and + the sequence agree. + """ + + # Act + read = builders.aligned_read( + two_contig_header, "clipped", "chr1", 300, cigar="5S15M" + ) + + # Assert + assert read.query_length == 20 + + +def test_aligned_read_should_place_the_read_at_the_requested_position(two_contig_header): + """Test that the contig and position reach the record. + + Given: + A read placed at a known position on a known contig. + When: + The builder builds it. + Then: + It should resolve the contig to its header id and start at that + position. + """ + + # Act + read = builders.aligned_read(two_contig_header, "placed", "chr2", 300) + + # Assert + assert read.reference_id == two_contig_header.get_tid("chr2") + assert read.reference_start == 300 + + +def test_aligned_read_should_build_an_unplaced_record_when_the_contig_is_none( + two_contig_header, +): + """Test that passing no contig yields an unplaced read. + + Given: + A read whose contig is None. + When: + The builder builds it. + Then: + It should carry no reference and no start while keeping the + CIGAR it was given, so a record with no coordinates is + something a caller can construct rather than only encounter, + and the query length still follows the CIGAR there. + """ + + # Act + read = builders.aligned_read(two_contig_header, "unplaced", None, None, cigar="35M") + + # Assert + assert read.reference_id == -1 + assert read.reference_start == -1 + assert read.cigarstring == "35M" + assert read.query_length == 35 + + +def test_aligned_read_should_carry_the_flag_and_mapping_quality_given(two_contig_header): + """Test that the flag and mapping quality are not defaulted away. + + Given: + A read given the reverse flag and an explicit mapping quality. + When: + The builder builds it. + Then: + It should mark the record reverse and carry that mapping + quality. + """ + + # Act + read = builders.aligned_read(two_contig_header, "rev", "chr1", 100, flag=16, mapq=7) + + # Assert + assert read.is_reverse + assert read.mapping_quality == 7 + + +def test_aligned_read_should_exclude_hard_clipped_bases_from_the_query( + two_contig_header, +): + """Test that a hard clip is absent from the query it sizes. + + Given: + A hard-clipped CIGAR over a fifteen-base match. + When: + The builder builds it. + Then: + It should size the query from the matched span alone, because + a hard clip names bases the record does not carry. + """ + + # Act + read = builders.aligned_read(two_contig_header, "hard", "chr1", 100, cigar="5H15M") + + # Assert + assert read.query_length == 15 + + +def test_aligned_read_should_leave_the_record_unreferenced_when_unknown( + two_contig_header, +): + """Test that an undeclared contig gives a half-placed record. + + Given: + A contig name the header does not declare. + When: + The builder builds it. + Then: + It should leave the record without a reference while keeping + its start and CIGAR -- a half-placed record, distinct from the + unplaced one a None contig produces. + """ + + # Act + read = builders.aligned_read(two_contig_header, "stray", "chrZ", 250) + + # Assert + assert read.reference_id == -1 + assert read.reference_start == 250 + assert read.cigarstring == "20M" + + +@settings(FILE_BACKED, max_examples=25) +@given(cigar=cigars()) +def test_aligned_read_should_match_query_and_qualities_to_any_cigar( + two_contig_header, cigar +): + """Test that the sequence and qualities always agree with the CIGAR. + + Given: + Any CIGAR assembled from match, soft-clip, insert and delete + operations, consuming at least one query base. + When: + The builder builds the record. + Then: + It should give the sequence and the qualities equal length, + both matching the length the CIGAR consumes -- an invariant + pysam raises on rather than tolerates. + """ + + # Act + read = builders.aligned_read( + two_contig_header, "generated", "chr1", 100, cigar=cigar + ) + + # Assert + assert read.query_length == read.infer_query_length() + assert len(read.query_qualities) == read.query_length + + +def test_write_bam_should_write_a_sorted_indexed_file( + tmp_path, pysam, two_contig_header +): + """Test that reads handed over out of order come back sorted. + + Given: + Three reads supplied in descending coordinate order. + When: + The builder writes them. + Then: + It should emit them in ascending coordinate order beside an + index, and return the path. + """ + + # Arrange + reads = [ + builders.aligned_read(two_contig_header, "r{}".format(index), "chr1", pos) + for index, pos in enumerate((400, 200, 100)) + ] + path = str(tmp_path / "reads.bam") + + # Act + written = builders.write_bam(path, reads, two_contig_header) + + # Assert + assert written == path + assert os.path.exists(path + ".bai") + assert [start for _, start in record_placements(path, pysam)] == [100, 200, 400] + + +def test_write_bam_should_remove_its_staging_file(tmp_path, two_contig_header): + """Test that the unsorted intermediate does not outlive the call. + + Given: + Reads written through the staging file the builder sorts from. + When: + The builder finishes. + Then: + It should leave only the BAM and its index, so nothing later + reaching into the directory can pick up a file whose order + disagrees with that index. + """ + + # Arrange + reads = [builders.aligned_read(two_contig_header, "r0", "chr1", 100)] + path = str(tmp_path / "reads.bam") + + # Act + builders.write_bam(path, reads, two_contig_header) + + # Assert + assert sorted(os.listdir(tmp_path)) == ["reads.bam", "reads.bam.bai"] + + +def test_write_bam_should_sort_by_contig_before_position( + tmp_path, pysam, two_contig_header +): + """Test that the sort key is the contig order, then the position. + + Given: + Four reads across two contigs in scrambled order. + When: + The builder writes them. + Then: + It should order them by contig as the header declares them, + then by position within each. + """ + + # Arrange + placements = [("chr2", 400), ("chr1", 900), ("chr2", 100), ("chr1", 50)] + reads = [ + builders.aligned_read(two_contig_header, "r{}".format(index), chrom, pos) + for index, (chrom, pos) in enumerate(placements) + ] + path = str(tmp_path / "multi.bam") + + # Act + builders.write_bam(path, reads, two_contig_header) + + # Assert + with pysam.AlignmentFile(path, "rb") as bam: + observed = [(read.reference_name, read.reference_start) for read in bam.fetch()] + assert observed == [("chr1", 50), ("chr1", 900), ("chr2", 100), ("chr2", 400)] + + +@settings(FILE_BACKED, max_examples=25) +@given(alignment=alignments()) +def test_write_bam_should_sort_and_preserve_any_reads(tmp_path, pysam, alignment): + """Test that the file holds its input, in coordinate order. + + Given: + Any reads over any contig mapping, handed over in any order, + including unplaced ones. + When: + The builder writes them and every record is read back. + Then: + It should hold exactly those reads with the placed ones in + contig then position order, so no input can produce a file + whose order disagrees with its index. + """ + + # Arrange + sizes, placements = alignment + header = builders.alignment_header(sizes) + reads = [ + builders.aligned_read(header, "r{}".format(index), chrom, start) + for index, (chrom, start) in enumerate(placements) + ] + path = str(tmp_path / "property.bam") + + # Act + builders.write_bam(path, reads, header) + + # Assert + # Unplaced records sort last, which is the coordinate-sort + # convention rather than what a plain ``(tid, start)`` key over a + # reference id of -1 would give. + placed = sorted( + [row for row in placements if row[0] is not None], + key=lambda row: (header.get_tid(row[0]), row[1]), + ) + unplaced = [(None, -1) for row in placements if row[0] is None] + assert record_placements(path, pysam, until_eof=True) == placed + unplaced + + +def test_write_bam_should_keep_an_unplaced_record(tmp_path, pysam, two_contig_header): + """Test that a record with no contig survives the round trip. + + Given: + One placed read and one unplaced one. + When: + The builder writes them and every record is read back. + Then: + It should hold both with the unplaced one last, so a count + taken over the file counts records written rather than records + the index can find. + """ + + # Arrange + reads = [ + builders.aligned_read(two_contig_header, "placed", "chr1", 100), + builders.aligned_read(two_contig_header, "unplaced", None, None), + ] + path = str(tmp_path / "mixed.bam") + + # Act + builders.write_bam(path, reads, two_contig_header) + + # Assert + assert record_placements(path, pysam, until_eof=True) == [ + ("chr1", 100), + (None, -1), + ] + + +def test_write_random_bam_should_raise_when_a_contig_is_shorter_than_one_read( + tmp_path, pysam +): + """Test that a contig too short to hold a read is refused. + + Given: + A geometry whose only contig is shorter than the read length. + When: + The builder is asked to place reads on it. + Then: + It should raise ValueError naming that contig, because a random + offset on it would put the record past the end the header + declares. + """ + + # Arrange + sizes = {"chr1": 10} + header = builders.alignment_header(sizes) + + # Act & assert + with pytest.raises(ValueError, match="shorter than the read length of 20: chr1"): + builders.write_random_bam(str(tmp_path / "short.bam"), header, sizes) + + +def test_write_random_bam_should_accept_a_contig_as_long_as_one_read(tmp_path, pysam): + """Test that the shortest usable contig is not refused. + + Given: + A contig exactly as long as the read length. + When: + The builder places one read on it. + Then: + It should write that read across the whole contig, because a + contig that can hold a read is one the builder has no reason to + turn down. + """ + + # Arrange + sizes = {"chr1": 20} + header = builders.alignment_header(sizes) + path = str(tmp_path / "exact.bam") + + # Act + builders.write_random_bam(path, header, sizes, n_reads=1) + + # Assert + assert record_placements(path, pysam) == [("chr1", 0)] + + +def test_write_random_bam_should_reach_the_last_base_of_a_contig(tmp_path, pysam): + """Test that no stretch of a contig is out of reach of a read. + + Given: + A contig twice the read length, and a seed that draws the + latest start the contig admits. + When: + The builder places one read on it. + Then: + It should end at the contig's last base, so a suite expecting + signal near a boundary is not handed a region no read can ever + occupy. + """ + + # Arrange + sizes = {"chr1": 40} + header = builders.alignment_header(sizes) + path = str(tmp_path / "tail.bam") + + # Act + builders.write_random_bam(path, header, sizes, n_reads=1, seed=27) + + # Assert + with pysam.AlignmentFile(path, "rb") as bam: + (read,) = bam.fetch() + assert read.reference_end == 40 + + +def test_write_random_bam_should_write_the_requested_number_of_reads( + tmp_path, pysam, two_contig_header +): + """Test that the record count is the count that was asked for. + + Given: + A request for twelve randomly placed reads. + When: + The builder writes them. + Then: + It should write exactly that many records and return the path. + """ + + # Arrange + path = str(tmp_path / "random.bam") + + # Act + written = builders.write_random_bam(path, two_contig_header, TWO_CONTIGS, n_reads=12) + + # Assert + assert written == path + assert len(record_placements(path, pysam)) == 12 + + +def test_write_random_bam_should_split_the_reads_evenly_between_strands( + tmp_path, pysam, two_contig_header +): + """Test that half the reads come back on the reverse strand. + + Given: + A request for an even number of randomly placed reads. + When: + The builder writes them. + Then: + It should put half on each strand, so a suite reading strand + from the data sees both without arranging for either. + """ + + # Arrange + path = str(tmp_path / "stranded.bam") + + # Act + builders.write_random_bam(path, two_contig_header, TWO_CONTIGS, n_reads=12) + + # Assert + with pysam.AlignmentFile(path, "rb") as bam: + assert sum(read.is_reverse for read in bam.fetch()) == 6 + + +def test_write_random_bam_should_place_reads_identically_for_one_seed( + tmp_path, pysam, two_contig_header +): + """Test that a seeded random BAM is reproducible. + + Given: + Two renders of one geometry under the same seed. + When: + The placements are compared. + Then: + It should place every read identically, so a suite that + depends on where a read landed can depend on the seed instead. + """ + + # Arrange + first = str(tmp_path / "a.bam") + second = str(tmp_path / "b.bam") + + # Act + builders.write_random_bam(first, two_contig_header, TWO_CONTIGS, n_reads=12, seed=3) + builders.write_random_bam(second, two_contig_header, TWO_CONTIGS, n_reads=12, seed=3) + + # Assert + assert record_placements(first, pysam) == record_placements(second, pysam) + + +def test_write_random_bam_should_place_reads_differently_when_the_seed_differs( + tmp_path, pysam, two_contig_header +): + """Test that the seed is what decides the placement. + + Given: + Two renders of one geometry under different seeds. + When: + The placements are compared. + Then: + It should place them differently, so the seed is a real knob + rather than a parameter the builder ignores. + """ + + # Arrange + first = str(tmp_path / "a.bam") + second = str(tmp_path / "b.bam") + + # Act + builders.write_random_bam(first, two_contig_header, TWO_CONTIGS, n_reads=12, seed=3) + builders.write_random_bam(second, two_contig_header, TWO_CONTIGS, n_reads=12, seed=4) + + # Assert + assert record_placements(first, pysam) != record_placements(second, pysam) + + +def test_write_random_bam_should_put_reads_on_every_contig(tmp_path, pysam): + """Test that a contig split is neither empty nor uniform. + + Given: + A three-contig geometry and forty reads. + When: + The builder places them. + Then: + It should put at least one read on every contig and more on the + first than on any other, so a per-contig count is neither zero + anywhere nor the same number everywhere. + """ + + # Arrange + header = builders.alignment_header(THREE_CONTIGS) + path = str(tmp_path / "spread.bam") + + # Act + builders.write_random_bam(path, header, THREE_CONTIGS, n_reads=40) + + # Assert + with pysam.AlignmentFile(path, "rb") as bam: + counts = {chrom: 0 for chrom in THREE_CONTIGS} + for read in bam.fetch(): + counts[read.reference_name] += 1 + first, *rest = [counts[chrom] for chrom in THREE_CONTIGS] + assert all(count > 0 for count in counts.values()) + assert all(first > count for count in rest) + + +@settings(FILE_BACKED, max_examples=25) +@given(sizes=alignment_sizes) +def test_write_random_bam_should_place_every_read_inside_its_contig_for_any_geometry( + tmp_path, pysam, sizes +): + """Test that no read is placed where it could not end inside its contig. + + Given: + Any contig mapping the builder accepts. + When: + The builder places reads across it. + Then: + It should start every read far enough from the end that a + record of the read length still finishes inside the contig, so + the bound the refusal protects holds across geometries rather + than only at the two sizes an example can pin. + """ + + # Arrange + header = builders.alignment_header(sizes) + path = str(tmp_path / "bounds.bam") + + # Act + builders.write_random_bam(path, header, sizes) + + # Assert + for chrom, start in record_placements(path, pysam): + assert 0 <= start <= sizes[chrom] - 20 + + +@settings(FILE_BACKED, max_examples=25) +@given(sizes=alignment_sizes, extra=st.integers(min_value=0, max_value=20)) +def test_write_random_bam_should_put_reads_on_every_contig_for_any_geometry( + tmp_path, pysam, sizes, extra +): + """Test that contig coverage holds for any geometry. + + Given: + Any contig mapping, and any read count at or above the contig + count, i.e., the condition under which the builder promises it. + When: + The builder places them. + Then: + It should put at least one read on every contig, so no caller + asking for more reads than contigs is handed an empty one. + """ + + # Arrange + header = builders.alignment_header(sizes) + path = str(tmp_path / "property.bam") + + # Act + builders.write_random_bam(path, header, sizes, n_reads=len(sizes) + extra) + + # Assert + assert {chrom for chrom, _ in record_placements(path, pysam)} == set(sizes) + + +@settings(FILE_BACKED, max_examples=25) +@given(sizes=alignment_sizes, extra=st.integers(min_value=1, max_value=20)) +def test_write_random_bam_should_skew_toward_the_first_contig_for_any_geometry( + tmp_path, pysam, sizes, extra +): + """Test that the contig skew holds wherever it is promised. + + Given: + Any contig mapping, and any read count above the contig count, + i.e., the condition under which the builder promises a skew. + When: + The builder places them. + Then: + It should put more reads on the first contig than on any other, + so a suite that splits work per contig sees an uneven split + rather than one it only assumes is uneven. + """ + + # Arrange + header = builders.alignment_header(sizes) + path = str(tmp_path / "skew.bam") + first = next(iter(sizes)) + + # Act + builders.write_random_bam(path, header, sizes, n_reads=len(sizes) + extra) + + # Assert + counts = Counter(chrom for chrom, _ in record_placements(path, pysam)) + assert all(counts[first] > counts[chrom] for chrom in sizes if chrom != first) + + +def test_write_random_bam_should_size_its_reads_from_the_read_length( + tmp_path, pysam, two_contig_header +): + """Test that the read length reaches every record. + + Given: + An explicit read length. + When: + The builder writes the reads. + Then: + It should give every record a CIGAR and a query of that length. + """ + + # Arrange + path = str(tmp_path / "sized.bam") + + # Act + builders.write_random_bam( + path, two_contig_header, TWO_CONTIGS, n_reads=8, read_length=35 + ) + + # Assert + with pysam.AlignmentFile(path, "rb") as bam: + reads = list(bam.fetch()) + assert [read.cigarstring for read in reads] == ["35M"] * 8 + assert [read.query_length for read in reads] == [35] * 8 From a12a52a365097560564a071046b0c826a41241ba Mon Sep 17 00:00:00 2001 From: Conrad Date: Thu, 29 Oct 2026 14:19:27 -0400 Subject: [PATCH 5/7] test: Pin the fixture layer's contracts corpus_factory is the one builder every data-path suite draws its inputs from, which makes its keyword surface load-bearing: a keyword that silently stopped reaching the builders would leave every later suite asserting against data it did not ask for. So each one is exercised here rather than trusted, along with Corpus and the suite's own environment block. The environment block is tested in a subprocess, because the only claim worth making about it concerns what is true at import time, and by the time a test body runs the import has long since happened. Those tests carry the packaging marker, so a run can select or exclude the ones that spawn a fresh interpreter. --- tests/test_conftest.py | 633 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 633 insertions(+) create mode 100644 tests/test_conftest.py diff --git a/tests/test_conftest.py b/tests/test_conftest.py new file mode 100644 index 0000000..cc4487f --- /dev/null +++ b/tests/test_conftest.py @@ -0,0 +1,633 @@ +"""Tests for the shared fixture layer and the suite's own environment. + +`corpus_factory` is the one builder every data-path suite draws its +inputs from, which makes its keyword surface load-bearing: a keyword +that silently stopped reaching the builders would leave every later +suite asserting against data it did not ask for. So each one is +exercised here rather than trusted. + +The environment block is tested in a subprocess, because the only claim +worth making about it concerns what is true at *import* time, and by the +time a test body runs the import has long since happened. +""" + +import gzip +import os +import sys +import tempfile + +import pytest +from hypothesis import given, settings +from hypothesis import strategies as st + +from tests import ( + FILE_BACKED, + PROJECT_ROOT, + TWO_CONTIGS, + builders, + record_placements, + run_child, +) +from tests.conftest import Corpus + +# Contig names from the suite's own vocabulary rather than arbitrary +# text: the builders beneath this factory already property-test +# arbitrary names, and what this factory adds is forwarding a geometry +# it did not choose. +corpus_sizes = st.dictionaries( + st.sampled_from(["chr1", "chr2", "chr3", "chrX"]), + st.integers(min_value=1, max_value=200), + min_size=1, + max_size=4, +) + + +def import_conftest(environment): + """Import the suite's conftest in a fresh interpreter. + + Returns a mapping of what the child could observe and the parent + cannot: ``cache_dir``, whether it ``existed`` at import time, whether + the package was ``imported`` by the time the import finished, and the + ``tqdm_disable`` the environment was left with. Existence is reported + from inside the child because the child removes the directory when it + exits. + """ + + program = ( + "import os, sys\n" + "import tests.conftest\n" + "cache_dir = os.environ['QUADRAT_CACHE_DIR']\n" + "print(cache_dir)\n" + "print(os.path.isdir(cache_dir))\n" + "print('quadrat' in sys.modules)\n" + "print(os.environ['TQDM_DISABLE'])\n" + ) + env = dict(os.environ) + for name, value in environment.items(): + if value is None: + env.pop(name, None) + else: + env[name] = value + + result = run_child( + [sys.executable, "-c", program], + "importing the conftest failed", + cwd=PROJECT_ROOT, + environment=env, + ) + + cache_dir, existed, imported, tqdm_disable = result.stdout.splitlines() + return { + "cache_dir": cache_dir, + "existed": existed == "True", + "imported": imported == "True", + "tqdm_disable": tqdm_disable, + } + + +class TestCorpus: + """The attribute bag the factory hands back.""" + + def test___init___should_leave_every_optional_slot_unset(self, tmp_path): + """Test that a fresh corpus claims nothing it was not given. + + Given: + A root directory and a chromosome mapping. + When: + A corpus is instantiated. + Then: + It should expose that root and mapping with no alignments + and no locus files, so a test cannot read a file nothing + built. + """ + + # Act + corpus = Corpus(tmp_path, TWO_CONTIGS) + + # Assert + assert corpus.root == tmp_path + assert corpus.chrom_sizes == TWO_CONTIGS + assert corpus.fasta is None + assert corpus.bams == [] + assert corpus.peaks is None + assert corpus.negatives is None + assert corpus.exclusion is None + + def test___init___should_copy_the_chromosome_sizes_it_is_given(self, tmp_path): + """Test that a corpus does not alias the caller's mapping. + + Given: + A caller's chromosome mapping. + When: + A corpus is built from it. + Then: + It should hold an equal but separate mapping, so a test + that mutates its own geometry cannot corrupt a constant + every later corpus in the session is built from. + """ + + # Arrange + sizes = dict(TWO_CONTIGS) + + # Act + corpus = Corpus(tmp_path, sizes) + + # Assert + assert corpus.chrom_sizes == sizes + assert corpus.chrom_sizes is not sizes + + def test_path_should_resolve_a_name_inside_the_corpus_root(self, tmp_path): + """Test that a corpus resolves paths against its own directory. + + Given: + A corpus rooted at a known directory. + When: + A name is resolved through it. + Then: + It should return that name inside the corpus directory as a + string, which is what the builders take. + """ + + # Arrange + corpus = Corpus(tmp_path, TWO_CONTIGS) + + # Act + resolved = corpus.path("genome.fa") + + # Assert + assert resolved == str(tmp_path / "genome.fa") + assert isinstance(resolved, str) + + def test___setattr___should_raise_when_the_attribute_is_undeclared(self, tmp_path): + """Test that a misspelt field fails where it is written. + + Given: + A corpus. + When: + An attribute outside its declared slots is assigned. + Then: + It should raise AttributeError, which is the whole reason + the class is an attribute bag rather than a dict. + """ + + # Arrange + corpus = Corpus(tmp_path, TWO_CONTIGS) + + # Act & assert + with pytest.raises(AttributeError): + corpus.peeks = "typo" + + +def test_corpus_factory_should_build_only_what_it_was_asked_for(corpus_factory): + """Test that unrequested pieces of a corpus stay absent. + + Given: + A corpus requested with peaks and nothing else. + When: + The factory builds it. + Then: + It should populate the peaks and leave the rest unset, beside + the FASTA it writes unconditionally, so a test cannot read a + file it never asked to exist. + """ + + # Act + corpus = corpus_factory("minimal", TWO_CONTIGS, peaks=[("chr1", 100, 140)]) + + # Assert + assert os.path.exists(corpus.fasta) + assert os.path.exists(corpus.peaks) + assert corpus.bams == [] + assert corpus.negatives is None + assert corpus.exclusion is None + + +def test_corpus_factory_should_build_every_locus_file_it_is_asked_for(corpus_factory): + """Test that the requested locus files are all written. + + Given: + A corpus requested with peaks, negatives and an exclusion + list. + When: + The factory builds it. + Then: + It should write all three, with only the exclusion list + gzipped, as the suffix the factory gives each one dictates. + """ + + # Act + corpus = corpus_factory( + "populated", + TWO_CONTIGS, + peaks=[("chr1", 100, 140)], + negatives=[("chr1", 500, 540)], + exclusion=[("chr2", 10, 60)], + ) + + # Assert + with open(corpus.peaks) as handle: + assert handle.read() == "chr1\t100\t140\n" + with open(corpus.negatives) as handle: + assert handle.read() == "chr1\t500\t540\n" + assert corpus.exclusion.endswith(".bed.gz") + with gzip.open(corpus.exclusion, "rt") as handle: + assert handle.read() == "chr2\t10\t60\n" + + +def test_corpus_factory_should_leave_an_empty_locus_request_unset(corpus_factory): + """Test that asking for no loci is not the same as asking for some. + + Given: + A corpus requested with an empty peaks iterable. + When: + The factory builds it. + Then: + It should leave the peaks attribute unset, so asking for no + loci is today indistinguishable from not asking -- a + limitation worth pinning, because the underlying writer does + accept an empty row list. + """ + + # Act + corpus = corpus_factory("empty-peaks", TWO_CONTIGS, peaks=[]) + + # Assert + assert corpus.peaks is None + + +def test_corpus_factory_should_give_each_corpus_its_own_directory(corpus_factory): + """Test that two corpora of one geometry do not share files. + + Given: + Two corpora requested under one name and identical chromosome + sizes. + When: + Both are built. + Then: + It should give each its own directory, so neither can observe + the other's writes even though the factory itself lives for the + whole session. + """ + + # Act + first = corpus_factory("twin", TWO_CONTIGS) + second = corpus_factory("twin", TWO_CONTIGS) + + # Assert + assert first.root != second.root + + +def test_corpus_factory_should_copy_the_chromosome_sizes_it_is_given(corpus_factory): + """Test that a built corpus does not alias the caller's mapping. + + Given: + A corpus built from a caller's chromosome mapping. + When: + That mapping is compared to the corpus's own. + Then: + It should hold an equal but separate mapping, so a test cannot + corrupt a shared constant for the rest of the session. + """ + + # Arrange + sizes = dict(TWO_CONTIGS) + + # Act + corpus = corpus_factory("copied", sizes) + + # Assert + assert corpus.chrom_sizes == sizes + assert corpus.chrom_sizes is not sizes + + +def test_corpus_factory_should_pass_the_fasta_geometry_through( + corpus_factory, tmp_path, pysam +): + """Test that the sequence keywords reach the FASTA builder. + + Given: + A corpus requested with a seed, a soft mask, an N run and + FASTA indexing. + When: + The factory builds it. + Then: + It should produce a FASTA matching a direct render of the same + request, with an index beside it. + """ + + # Arrange + geometry = { + "seed": 11, + "soft_mask": [("chr1", 100, 120)], + "n_runs": [("chr1", 200, 210)], + } + expected = builders.write_fasta( + str(tmp_path / "expected.fa"), TWO_CONTIGS, **geometry + ) + + # Act + corpus = corpus_factory("geometry", TWO_CONTIGS, index_fasta=True, **geometry) + + # Assert + with open(corpus.fasta) as built, open(expected) as reference: + assert built.read() == reference.read() + assert os.path.exists(corpus.fasta + ".fai") + + +def test_corpus_factory_should_write_one_indexed_alignment_per_sample( + corpus_factory, pysam +): + """Test that every sample gets an alignment file of its own. + + Given: + A corpus requested with two alignments. + When: + The factory builds it. + Then: + It should write two separately named BAMs with an index beside + each, so a later suite can open either by name and seek in it. + """ + + # Act + corpus = corpus_factory("samples", TWO_CONTIGS, n_bams=2, n_reads=6) + + # Assert + assert [os.path.basename(path) for path in corpus.bams] == ["s0.bam", "s1.bam"] + for path in corpus.bams: + assert os.path.exists(path + ".bai") + + +def test_corpus_factory_should_forward_the_read_count_to_every_alignment( + corpus_factory, pysam +): + """Test that the requested read count reaches each alignment. + + Given: + A corpus requested with two alignments of a given read count. + When: + The factory builds it. + Then: + It should write that many records to each of them, so the + keyword reaches the builder rather than stopping here. + """ + + # Act + corpus = corpus_factory("counted", TWO_CONTIGS, n_bams=2, n_reads=6) + + # Assert + for path in corpus.bams: + assert len(record_placements(path, pysam)) == 6 + + +def test_corpus_factory_should_place_each_sample_differently(corpus_factory, pysam): + """Test that two samples are not one alignment written twice. + + Given: + A corpus requested with two alignments. + When: + Their placements are compared. + Then: + It should have placed them differently, so a suite reading two + samples sees two. + """ + + # Arrange + corpus = corpus_factory("distinct", TWO_CONTIGS, n_bams=2, n_reads=6) + + # Act + placements = [record_placements(path, pysam) for path in corpus.bams] + + # Assert + assert placements[0] != placements[1] + + +def test_corpus_factory_should_place_alignment_reads_identically_for_one_seed( + corpus_factory, pysam +): + """Test that one seed gives two corpora the same placements. + + Given: + Two corpora of one geometry requested under the same seed. + When: + Their alignments are compared. + Then: + It should place every read identically, so a suite that rebuilds + a corpus reasons about the same data twice. + """ + + # Arrange + first = corpus_factory("one-seed-a", TWO_CONTIGS, n_bams=1, n_reads=6, seed=5) + second = corpus_factory("one-seed-b", TWO_CONTIGS, n_bams=1, n_reads=6, seed=5) + + # Act + placements = [record_placements(c.bams[0], pysam) for c in (first, second)] + + # Assert + assert placements[0] == placements[1] + + +def test_corpus_factory_should_place_alignment_reads_differently_for_another_seed( + corpus_factory, pysam +): + """Test that the seed reaches the reads the factory places. + + Given: + Two corpora of one geometry requested under different seeds. + When: + Their alignments are compared. + Then: + It should place the reads differently, so the seed is a real + knob on the alignment path rather than one the factory accepts + and drops. + """ + + # Arrange + first = corpus_factory("two-seeds-a", TWO_CONTIGS, n_bams=1, n_reads=6, seed=5) + second = corpus_factory("two-seeds-b", TWO_CONTIGS, n_bams=1, n_reads=6, seed=6) + + # Act + placements = [record_placements(c.bams[0], pysam) for c in (first, second)] + + # Assert + assert placements[0] != placements[1] + + +@pytest.mark.parametrize( + "header_contigs", + [{"chr1": 1000}, {"chr1": 1000, "chr2": 400}], + ids=["omitted", "shorter"], +) +def test_corpus_factory_should_raise_when_header_contigs_do_not_cover_the_reference( + corpus_factory, header_contigs +): + """Test that a header narrower than the reference is refused. + + Given: + Header contigs that leave out a contig the chromosome sizes + declare, or declare one of them shorter than it is. + When: + The factory is asked to build an alignment over them. + Then: + It should raise ValueError naming the uncovered contig, because + reads are placed against the reference and would otherwise be + written half-placed or past the end the header declares. + """ + + # Act & assert + with pytest.raises(ValueError, match="do not cover the reference.*chr2"): + corpus_factory("uncovered", TWO_CONTIGS, n_bams=1, header_contigs=header_contigs) + + +def test_corpus_factory_should_declare_header_contigs_the_reference_lacks( + corpus_factory, pysam +): + """Test that a BAM header may name a contig outside the reference. + + Given: + A corpus whose header contigs include one absent from the + chromosome sizes the FASTA was built from. + When: + The factory builds an alignment over it. + Then: + It should write the BAM with that contig in its header, so a + header-versus-reference mismatch is something a suite can + construct rather than only hope to encounter. + """ + + # Arrange + header_contigs = dict(TWO_CONTIGS, chrZ=800) + + # Act + corpus = corpus_factory( + "asymmetric", TWO_CONTIGS, n_bams=1, header_contigs=header_contigs + ) + + # Assert + with pysam.AlignmentFile(corpus.bams[0], "rb") as bam: + assert "chrZ" in set(bam.references) + assert "chrZ" not in corpus.chrom_sizes + + +def test_corpus_factory_should_default_header_contigs_to_the_reference( + corpus_factory, pysam +): + """Test that the header follows the reference unless overridden. + + Given: + A corpus requested with one alignment and no header contigs. + When: + The factory builds it. + Then: + It should give the BAM a header whose contigs and lengths equal + the chromosome sizes, so the symmetric case needs no argument. + """ + + # Act + corpus = corpus_factory("symmetric", TWO_CONTIGS, n_bams=1) + + # Assert + with pysam.AlignmentFile(corpus.bams[0], "rb") as bam: + assert list(bam.references) == list(TWO_CONTIGS) + assert list(bam.lengths) == list(TWO_CONTIGS.values()) + + +@settings(FILE_BACKED, max_examples=15) +@given(sizes=corpus_sizes) +def test_corpus_factory_should_render_a_corpus_to_any_geometry( + corpus_factory, tmp_path, sizes +): + """Test that any geometry reaches the artifacts built from it. + + Given: + An arbitrary contig mapping and a request for peaks and an + exclusion list over it. + When: + The factory builds a corpus. + Then: + It should report that geometry and write a sequence identical + to a direct render of it, with both locus files present, so the + one parameter the factory exists to take is not assumed at a + single value. + """ + + # Arrange + rows = [(chrom, 0, 10) for chrom in sizes] + expected = builders.write_fasta(str(tmp_path / "expected.fa"), sizes, seed=3) + + # Act + corpus = corpus_factory("any-geometry", sizes, seed=3, peaks=rows, exclusion=rows) + + # Assert + assert corpus.chrom_sizes == dict(sizes) + with open(corpus.fasta) as built, open(expected) as reference: + assert built.read() == reference.read() + assert os.path.exists(corpus.peaks) + assert os.path.exists(corpus.exclusion) + + +@pytest.mark.packaging +def test_quadrat_cache_dir_should_be_set_before_the_package_is_imported(): + """Test that nothing can read the variable before it is in place. + + Given: + A fresh interpreter with no cache variable set. + When: + The suite's conftest is imported and nothing else. + Then: + It should set the variable while leaving the package + unimported, so any later import of it sees the variable already + there, for the reason the conftest module docstring gives. + """ + + # Act + observed = import_conftest({"QUADRAT_CACHE_DIR": None}) + + # Assert + assert observed["existed"] + assert not observed["imported"] + + +@pytest.mark.packaging +def test_quadrat_cache_dir_should_replace_a_value_the_caller_exported(): + """Test that an exported cache directory does not survive. + + Given: + A fresh interpreter with the cache variable already exported to + a path of the caller's own. + When: + The suite's conftest is imported. + Then: + It should replace that value with a fresh temporary directory, + for the reason the conftest module docstring gives. + """ + + # Arrange + exported = os.path.join(tempfile.gettempdir(), "quadrat-caller-cache") + + # Act + observed = import_conftest({"QUADRAT_CACHE_DIR": exported}) + + # Assert + assert observed["cache_dir"] != exported + assert observed["existed"] + + +@pytest.mark.packaging +def test_tqdm_disable_should_defer_to_a_value_the_caller_exported(): + """Test that a developer may turn progress bars back on. + + Given: + A fresh interpreter with progress bars explicitly enabled. + When: + The suite's conftest is imported. + Then: + It should leave that value in place, because a progress bar + changes nothing a test can observe and watching one is how a + hang gets diagnosed. + """ + + # Act + observed = import_conftest({"TQDM_DISABLE": "0"}) + + # Assert + assert observed["tqdm_disable"] == "0" From 24d0d20f44791d699ab51d602c066fee31f675fe Mon Sep 17 00:00:00 2001 From: Conrad Date: Thu, 29 Oct 2026 14:19:28 -0400 Subject: [PATCH 6/7] test: Pin the package surface and the built distribution The package surface is a docstring, a version and an __all__, so what is worth pinning is not behaviour but the wiring: that __version__ matches the installed distribution, that a star import binds only the names __all__ declares, and that __all__ names every symbol the source marks public -- read out of the module's syntax tree, so a symbol marked public but never re-exported, or re-exported without the marker, fails here rather than in a caller. The import guarantee gets a test of its own: a fresh interpreter imports quadrat and asserts that none of the pileup engine's modules arrived with it. That is the claim the README, the package docstring and the manifest comment all rest on, and it is the one a later slice can break by adding a single module-level import. The distribution is built and read back rather than described: that its metadata declares the licence once, that the sdist carries the test tree, and that notebook checkpoints are excluded at any depth. The version the build derives is pinned twice over. End to end, by building a wheel and comparing its metadata version with what the hook derives from the same repository, so a manifest that stopped naming the hook fails here rather than shipping whatever the backend fell back to. And per branch of the derivation, in a module of its own against repositories built for each case: a tagged commit, a commit past the tag, a modified file, an untracked file, no tag at all, a tag outside the release shape, an unpacked distribution, one nested inside an unrelated checkout, and a tree that is none of those. The staged tree the checkpoint exclusion is measured against carries the hook too, because that tree holds exactly what the sdist declares it includes and the build fails without it. --- tests/test_build_hooks.py | 275 +++++++++++++++++++++++++++++ tests/test_quadrat.py | 360 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 635 insertions(+) create mode 100644 tests/test_build_hooks.py create mode 100644 tests/test_quadrat.py diff --git a/tests/test_build_hooks.py b/tests/test_build_hooks.py new file mode 100644 index 0000000..147cfb5 --- /dev/null +++ b/tests/test_build_hooks.py @@ -0,0 +1,275 @@ +"""Tests for the version the build backend derives from the repository. + +Releasing is pushing a tag, so the derivation is the whole of the +release process and every branch of it is exercised here against a +real repository rather than a mocked one: what git reports is the +thing under test. +""" + +from tests import load_build_hook, run_child + +version = load_build_hook("_git").version + + +def git(root, *arguments): + """Run a git command in ``root`` and return its stdout. + + The identity is supplied per invocation so a machine with no + configured committer still builds the repositories these tests + need. + """ + + command = [ + "git", + "-C", + str(root), + "-c", + "user.email=suite@example.invalid", + "-c", + "user.name=Test Suite", + *arguments, + ] + return run_child(command, "git {} failed".format(arguments[0])).stdout.strip() + + +def repository(root, *, tag=None): + """Build a one-commit git repository at ``root``, optionally tagged.""" + + root.mkdir(parents=True) + git(root, "init") + (root / "tracked.txt").write_text("one\n") + git(root, "add", "tracked.txt") + git(root, "commit", "-m", "one") + if tag is not None: + git(root, "tag", tag) + return root + + +def commit(root, message): + """Add one empty commit to ``root`` and return its abbreviated sha.""" + + git(root, "commit", "--allow-empty", "-m", message) + return git(root, "rev-parse", "--short=7", "HEAD") + + +def test_version_should_report_the_release_when_the_commit_is_tagged(tmp_path): + """Test that a tagged, clean commit is exactly its release. + + Given: + A clean repository whose head commit carries a release tag. + When: + The version is derived. + Then: + It should be the tag's release and nothing else, because a + tagged commit is the release rather than a build on top of one. + """ + + # Arrange + root = repository(tmp_path / "repo", tag="v1.2.3") + + # Act + derived = version(root) + + # Assert + assert derived == "1.2.3" + + +def test_version_should_add_the_commit_when_the_tag_is_behind_the_head(tmp_path): + """Test that an untagged commit reports the release it follows. + + Given: + A clean repository with a release tag and a later commit. + When: + The version is derived. + Then: + It should be the tagged release plus the head's abbreviated + commit, so the build is traceable to a commit without claiming + a release of its own. + """ + + # Arrange + root = repository(tmp_path / "repo", tag="v1.2.3") + head = commit(root, "two") + + # Act + derived = version(root) + + # Assert + assert derived == "1.2.3+{}".format(head) + + +def test_version_should_add_dirty_when_the_tree_has_uncommitted_content(tmp_path): + """Test that a modified tracked file marks the version dirty. + + Given: + A repository tagged at its head with one tracked file modified. + When: + The version is derived. + Then: + It should append a dirty segment, so an artifact built from a + tree that no commit describes says so. + """ + + # Arrange + root = repository(tmp_path / "repo", tag="v1.2.3") + (root / "tracked.txt").write_text("two\n") + + # Act + derived = version(root) + + # Assert + assert derived == "1.2.3+dirty" + + +def test_version_should_add_dirty_when_the_tree_has_untracked_content(tmp_path): + """Test that an untracked file marks the version dirty too. + + Given: + A repository tagged at its head with one untracked file added. + When: + The version is derived. + Then: + It should append a dirty segment, because the build's default + include is broad enough that an untracked file can reach the + artifact. + """ + + # Arrange + root = repository(tmp_path / "repo", tag="v1.2.3") + (root / "untracked.txt").write_text("two\n") + + # Act + derived = version(root) + + # Assert + assert derived == "1.2.3+dirty" + + +def test_version_should_report_the_initial_release_when_no_tag_is_reachable(tmp_path): + """Test that an untagged repository still names its commit. + + Given: + A clean repository carrying no tags at all. + When: + The version is derived. + Then: + It should be the initial release plus the head's abbreviated + commit, so a repository before its first release still + produces a version that orders and identifies the build. + """ + + # Arrange + root = repository(tmp_path / "repo") + head = git(root, "rev-parse", "--short=7", "HEAD") + + # Act + derived = version(root) + + # Assert + assert derived == "0.0.0+{}".format(head) + + +def test_version_should_ignore_a_tag_that_does_not_name_a_release(tmp_path): + """Test that only a release-shaped tag is read as a release. + + Given: + A clean repository whose head carries a tag that is not a + three-part version. + When: + The version is derived. + Then: + It should fall back to the initial release and the commit, + because a tag outside the release shape is somebody's pointer + rather than a version to publish. + """ + + # Arrange + root = repository(tmp_path / "repo", tag="latest") + head = git(root, "rev-parse", "--short=7", "HEAD") + + # Act + derived = version(root) + + # Assert + assert derived == "0.0.0+{}".format(head) + + +def test_version_should_read_the_packaged_version_when_there_is_no_repository(tmp_path): + """Test that an unpacked distribution reports the version it carries. + + Given: + A directory that is no repository, holding the metadata a + source distribution ships. + When: + The version is derived. + Then: + It should be the version recorded in that metadata, so a wheel + built from a distribution reports the tree it came from rather + than failing for want of a repository. + """ + + # Arrange + root = tmp_path / "unpacked" + root.mkdir() + (root / "PKG-INFO").write_text( + "Metadata-Version: 2.4\nName: quadrat\nVersion: 4.5.6+abc1234\n" + ) + + # Act + derived = version(root) + + # Assert + assert derived == "4.5.6+abc1234" + + +def test_version_should_prefer_the_packaged_version_to_an_enclosing_repository(tmp_path): + """Test that a distribution inside a checkout ignores its tags. + + Given: + A repository tagged with one release, containing an unpacked + distribution directory whose metadata names another. + When: + The version of that inner directory is derived. + Then: + It should be the version the distribution carries, because git + searches upward and would otherwise hand the distribution a + release belonging to a project it has nothing to do with. + """ + + # Arrange + outer = repository(tmp_path / "outer", tag="v9.9.9") + root = outer / "unpacked" + root.mkdir() + (root / "PKG-INFO").write_text("Version: 4.5.6\n") + + # Act + derived = version(root) + + # Assert + assert derived == "4.5.6" + + +def test_version_should_report_the_initial_release_when_nothing_names_a_version( + tmp_path, +): + """Test that an unversionable tree still builds. + + Given: + A directory that is neither a repository nor an unpacked + distribution. + When: + The version is derived. + Then: + It should be the initial release, so a build from an exported + tree produces an artifact rather than an error. + """ + + # Arrange + root = tmp_path / "bare" + root.mkdir() + + # Act + derived = version(root) + + # Assert + assert derived == "0.0.0" diff --git a/tests/test_quadrat.py b/tests/test_quadrat.py new file mode 100644 index 0000000..c69e747 --- /dev/null +++ b/tests/test_quadrat.py @@ -0,0 +1,360 @@ +"""Tests for the package surface and the distribution built from it. + +The package surface is a docstring, a version and an `__all__`, so what +is worth pinning is not behaviour but the wiring +between the source tree and the artifact a user installs: the version +the build backend reads, the export list and the marker convention it +agrees with, what an import of the package costs, and what reaches a +source distribution. + +The last of those spawn a subprocess or a real build, because once +pytest is running, its plugins and the suite's own modules have already +populated `sys.modules` and the question cannot be asked. +""" + +import ast +import importlib.metadata +import shutil +import sys +import tarfile +import zipfile +from pathlib import Path + +import pytest + +import quadrat +from tests import PROJECT_ROOT, load_build_hook, run_child + +# The import names of what the ``pileup`` extra installs. The package +# docstring states the guarantee these are checked against. +PILEUP_MODULES = ("polars", "polars_bio", "giql", "pyfaidx") + + +def declared_names(node): + """Return the names one top-level declaration binds.""" + + if isinstance(node, (ast.FunctionDef, ast.AsyncFunctionDef, ast.ClassDef)): + return {node.name} + if isinstance(node, ast.AnnAssign): + targets = [node.target] + elif isinstance(node, ast.Assign): + targets = node.targets + else: + return set() + + names = set() + for target in targets: + if isinstance(target, ast.Name): + names.add(target.id) + elif isinstance(target, (ast.Tuple, ast.List)): + names.update( + element.id for element in target.elts if isinstance(element, ast.Name) + ) + return names + + +def marked_public(source): + """Return the names declared under a ``# public`` marker in ``source``. + + A decorated declaration is measured from its first decorator, since + that is where the marker has to sit to read as marking it. + """ + + lines = source.splitlines() + names = set() + for node in ast.parse(source).body: + decorators = getattr(node, "decorator_list", []) + first = min([node.lineno] + [item.lineno for item in decorators]) + if first > 1 and lines[first - 2].strip() == "# public": + names.update(declared_names(node)) + return names + + +def uv_build(project, out_dir, kind): + """Build a ``"sdist"`` or ``"wheel"`` from ``project`` and return its path. + + A failed build is reported with its stderr, which + `subprocess.CalledProcessError` carries but does not print: without + it a cold uv cache reads as an unexplained non-zero exit. + """ + + command = [ + "uv", + "build", + "--offline", + "--" + kind, + "--out-dir", + str(out_dir), + str(project), + ] + run_child(command, "uv build --{} failed".format(kind)) + + (archive,) = Path(out_dir).glob("*.tar.gz" if kind == "sdist" else "*.whl") + return archive + + +def sdist_members(project, out_dir): + """Return the member paths of a source distribution built from ``project``. + + The archive's leading version directory is stripped, so a member + reads as the path it occupies in the project tree. + """ + + with tarfile.open(uv_build(project, out_dir, "sdist")) as handle: + return {name.split("/", 1)[1] for name in handle.getnames() if "/" in name} + + +def wheel_metadata(project, out_dir): + """Return the metadata of a wheel built from ``project``, as text.""" + + with zipfile.ZipFile(uv_build(project, out_dir, "wheel")) as handle: + (name,) = [ + member + for member in handle.namelist() + if member.endswith(".dist-info/METADATA") + ] + return handle.read(name).decode() + + +derived_version = load_build_hook("_git").version + + +class TestDistribution: + """The package's public surface and its built artifacts.""" + + def test___version___should_match_the_installed_distribution(self): + """Test that the declared version is the one that ships. + + Given: + An installed distribution of the package. + When: + The declared version and the distribution metadata version + are compared. + Then: + It should report the same version from both, so the + attribute reads the version the build resolved rather than + carrying a literal that can drift from it. + """ + + # Act + declared = quadrat.__version__ + packaged = importlib.metadata.version("quadrat") + + # Assert + assert declared == packaged + + def test___all___should_bind_only_its_names_when_star_imported(self): + """Test that the export list is the whole public contract. + + Given: + The package's declared export list. + When: + The package is star-imported into a fresh namespace. + Then: + It should bind exactly the declared names, so `__all__` is + enforced rather than documentary. + """ + + # Arrange + namespace = {} + + # Act + exec("from quadrat import *", namespace) + + # Assert + bound = set(namespace) - {"__builtins__"} + assert bound == set(quadrat.__all__) + + def test___all___should_name_every_symbol_marked_public(self): + """Test that the marker convention and the export list agree. + + Given: + Every module of the installed package. + When: + The top-level declarations carrying a ``# public`` marker + are collected across all of them. + Then: + It should name exactly the package's export list, so a + symbol marked public but never re-exported -- or + re-exported without the marker -- fails here rather than + drifting until someone reads both files. + """ + + # Arrange + root = Path(quadrat.__file__).parent + + # Act + marked = set() + for path in sorted(root.rglob("*.py")): + marked |= marked_public(path.read_text()) + + # Assert + assert marked == set(quadrat.__all__) + + @pytest.mark.packaging + def test_quadrat_should_import_none_of_the_pileup_engine(self): + """Test that a base install never pays for the pileup engine. + + Given: + A fresh interpreter in an environment where the optional + dependencies are installed. + When: + The package is imported and the loaded modules inspected. + Then: + It should have loaded none of polars, polars-bio, giql or + pyfaidx, so a caller who already has cut-site tables never + pays for the engine that builds them. + """ + + # Arrange + # An absent module is indistinguishable from one the package + # declined to import, so a base install skips rather than fails. + for name in PILEUP_MODULES: + pytest.importorskip(name) + + program = ( + "import sys, quadrat\n" + "names = {!r}\n" + "print(' '.join(n for n in names if n in sys.modules))\n".format( + PILEUP_MODULES + ) + ) + + # Act + result = run_child( + [sys.executable, "-c", program], "the child interpreter failed" + ) + + # Assert + assert result.stdout.split() == [] + + @pytest.mark.packaging + @pytest.mark.skipif( + shutil.which("uv") is None, + reason="uv builds the wheel under test", + ) + @pytest.mark.packaging + @pytest.mark.skipif( + shutil.which("uv") is None, + reason="uv builds the wheel under test", + ) + def test_metadata_should_carry_the_version_the_repository_derives(self, tmp_path): + """Test that the artifact is versioned by the tag history. + + Given: + A wheel built from the repository, and the version the + build hook derives from that same repository. + When: + The wheel's metadata version is compared with it. + Then: + It should be that version, so the hook the manifest names + is the one that versioned the artifact rather than some + default the backend fell back to. + """ + + # Act + metadata = wheel_metadata(PROJECT_ROOT, tmp_path) + + # Assert + expected = "Version: {}".format(derived_version(PROJECT_ROOT)) + assert expected in metadata.splitlines() + + def test_metadata_should_declare_the_license_once(self, tmp_path): + """Test that the built metadata names the licence exactly once. + + Given: + A wheel built from the repository. + When: + Its metadata is inspected. + Then: + It should carry a licence expression and no licence + classifier, because PEP 639 directs tools not to combine the + two and PyPI rejects a distribution that does. + """ + + # Act + metadata = wheel_metadata(PROJECT_ROOT, tmp_path) + + # Assert + assert "License-Expression: MIT" in metadata + classifiers = [ + line + for line in metadata.splitlines() + if line.startswith("Classifier: License") + ] + assert classifiers == [] + + @pytest.mark.packaging + @pytest.mark.skipif( + shutil.which("uv") is None, + reason="uv builds the source distribution under test", + ) + def test_sdist_should_carry_the_test_tree(self, tmp_path): + """Test that the suite ships inside a source distribution. + + Given: + A source distribution built from the repository. + When: + Its members are inspected. + Then: + It should carry the test package including conftest, so the + suite runs from an sdist exactly as it does from the + repository. + """ + + # Act + members = sdist_members(PROJECT_ROOT, tmp_path) + + # Assert + assert "tests/__init__.py" in members + assert "tests/conftest.py" in members + assert "tests/builders.py" in members + assert "src/quadrat/__init__.py" in members + + @pytest.mark.packaging + @pytest.mark.skipif( + shutil.which("uv") is None, + reason="uv builds the source distribution under test", + ) + def test_sdist_should_exclude_notebook_checkpoints_at_any_depth(self, tmp_path): + """Test that no notebook checkpoint ships, however deep it sits. + + Given: + A staged tree holding exactly what the sdist declares it + includes, with checkpoint directories planted one and two + levels inside those roots. The copy carries no + ``.gitignore``, whose own checkpoint entry would otherwise + keep them out of the archive and leave this unable to fail. + When: + A source distribution is built from that tree. + Then: + It should ship none of them, so the exclusion rests on the + build configuration the distribution declares rather than on + an ignore file that is no part of it. + """ + + # Arrange + staged = tmp_path / "project" + staged.mkdir() + for name in ("pyproject.toml", "README.md", "LICENSE"): + shutil.copy(PROJECT_ROOT / name, staged / name) + for name in ("src", "tests", "build-hooks"): + shutil.copytree( + PROJECT_ROOT / name, + staged / name, + ignore=shutil.ignore_patterns("__pycache__"), + ) + planted = ( + staged / "src" / ".ipynb_checkpoints", + staged / "src" / "quadrat" / ".ipynb_checkpoints", + staged / "tests" / "sub" / ".ipynb_checkpoints", + ) + for directory in planted: + directory.mkdir(parents=True) + (directory / "notebook-checkpoint.py").write_text("x = 1\n") + + # Act + members = sdist_members(staged, tmp_path / "dist") + + # Assert + assert [name for name in members if ".ipynb_checkpoints" in name] == [] From a3fa880574009a4ef895ed4e628587d3dbe3c4dc Mon Sep 17 00:00:00 2001 From: Conrad Date: Thu, 29 Oct 2026 14:19:28 -0400 Subject: [PATCH 7/7] ci: Run the suite on every supported interpreter Modelled on giql's workflow -- empty permissions, checkout without persisted credentials, a concurrency group that cancels superseded runs, and both actions pinned to full commit SHAs so a re-tagged release cannot execute in CI without a repository change. The sync passes --locked, so a green run says the committed lock resolves rather than that some resolution uv wrote and discarded did. The bare install runs as a job of its own rather than as a step, because that is the install the package's import guarantee is about and syncing without extras would strip the venv the test job then needs. Both checkouts fetch the whole history rather than a shallow one. The version comes from the tag history, which a shallow clone does not carry, so at the default depth every build would report the initial release plus a commit whatever tag it was built from -- and nothing in the suite would fail, because the version test compares the installed metadata with itself. Lint and format cover the build hooks as well as the package and the suite, so the code that versions the artifact is held to the standard the rest of the repository is. --- .github/workflows/test.yml | 88 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 .github/workflows/test.yml diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 0000000..380de68 --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,88 @@ +name: Run tests + +on: + pull_request: + branches: + - main + push: + branches: + - main + +permissions: {} + +concurrency: + group: ${{ github.workflow }}-${{ github.head_ref || github.ref }} + cancel-in-progress: true + +jobs: + test: + name: Python ${{ matrix.python-version }} + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: + - '3.11' + - '3.12' + - '3.13' + steps: + - name: Checkout code + uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262 # v4 + with: + persist-credentials: false + # The version comes from the tag history, which a shallow + # clone does not carry: at the default depth every build + # would report the initial release plus a commit, whatever + # tag it was actually built from. + fetch-depth: 0 + + - name: Install uv + uses: astral-sh/setup-uv@d4b2f3b6ecc6e67c4457f6d3e41ec42d3d0fcb86 # v5 + with: + python-version: ${{ matrix.python-version }} + + # The pileup extra resolves giql from a git revision, so the + # install needs network here. See the comment on + # `[tool.uv.sources]` in pyproject.toml. + # + # `--locked` so a green run says the committed lock resolves, + # rather than that some resolution uv wrote and discarded did. + - name: Install + run: uv sync --locked --all-extras + + - name: Lint + run: | + uv run ruff format --check src tests build-hooks + uv run ruff check src tests build-hooks + + - name: Test + run: uv run pytest -q + + base-install: + name: Base install + runs-on: ubuntu-latest + steps: + - name: Checkout code + uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262 # v4 + with: + persist-credentials: false + # The version comes from the tag history, which a shallow + # clone does not carry: at the default depth every build + # would report the initial release plus a commit, whatever + # tag it was actually built from. + fetch-depth: 0 + + - name: Install uv + uses: astral-sh/setup-uv@d4b2f3b6ecc6e67c4457f6d3e41ec42d3d0fcb86 # v5 + with: + python-version: '3.11' + + # No extras and no dev group, which is the install the README and + # the package docstring call sufficient. It is a job of its own + # because syncing without extras would strip the venv the test job + # needs. + - name: Install + run: uv sync --locked --no-dev + + - name: Import + run: uv run --no-sync python -c "import quadrat; print(quadrat.__version__)"