varcode 9.2.5__tar.gz → 9.2.7__tar.gz

{varcode-9.2.5/varcode.egg-info → varcode-9.2.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: varcode
-Version: 9.2.5
+Version: 9.2.7
 Summary: Variant annotation in Python
 Author-email: Alex Rubinsteyn <alex.rubinsteyn@unc.edu>
 Project-URL: Homepage, https://github.com/openvax/varcode

varcode-9.2.7/tests/test_documentation_examples.py

@@ -0,0 +1,205 @@
+"""Keep the reader-facing examples executable, using their actual Markdown."""
+
+from pathlib import Path
+import ast
+import re
+import shutil
+
+import pytest
+from pyensembl import cached_release
+
+import varcode
+from varcode import EffectCandidate, StructuralVariant, Variant
+from varcode.effects.effect_classes import HaplotypeEffect
+from varcode.effect_hypotheses import RealizedEffectCandidate
+
+
+ROOT = Path(__file__).resolve().parents[1]
+
+
+def _blocks(path, heading=None):
+    text = (ROOT / path).read_text()
+    if heading is not None:
+        text = text.split(heading + "\n", 1)[1]
+    return re.findall(r"```python\n(.*?)```", text, re.S)
+
+
+def _run(blocks, namespace=None):
+    namespace = {} if namespace is None else namespace
+    for block in blocks:
+        exec(compile(block, "documentation example", "exec"), namespace)
+    return namespace
+
+
+@pytest.fixture
+def input_directory(tmp_path, monkeypatch):
+    for fixture in (ROOT / "tests/data/documentation").glob("*.vcf"):
+        shutil.copy(fixture, tmp_path / fixture.name)
+    shutil.copy(tmp_path / "variants.vcf", tmp_path / "tumor.vcf")
+    monkeypatch.chdir(tmp_path)
+    return tmp_path
+
+
+@pytest.mark.parametrize("path,count", [
+    ("README.md", 2),
+    ("docs/getting_started.md", 4),
+    ("docs/index.md", 1),
+    ("docs/effect_annotation.md", 3),
+    ("docs/structural_variants.md", 1),
+    ("docs/transforms.md", 1),
+    ("docs/germline.md", 1),
+    ("docs/phasing.md", 1),
+])
+def test_documentation_first_steps(path, count, input_directory):
+    namespace = _run(_blocks(path)[:count])
+    if path == "docs/transforms.md":
+        assert len(namespace["paired"]) == len(namespace["normalized"]) == 1
+    else:
+        assert len(namespace["effects"]) > 0
+    if path in ("README.md", "docs/getting_started.md"):
+        assert namespace["protein"][158] == "M"
+    if path == "docs/getting_started.md":
+        assert (input_directory / "effects.csv").is_file()
+    if path == "docs/structural_variants.md":
+        assert namespace["variants"][0].is_structural
+    if path == "docs/phasing.md":
+        variants = namespace["phased_variants"]
+        assert namespace["phaser"].in_cis(*variants) is True
+        assert any(isinstance(effect, HaplotypeEffect)
+                   for effect in namespace["effects"])
+
+
+def test_documentation_germline_scenarios():
+    namespace = _run(_blocks(
+        "docs/phasing.md", "## Two variants in one codon")[:4])
+    assert namespace["eff_cis"].short_description == "p.S159T"
+    assert namespace["eff_trans"].short_description == "p.L159M"
+    assert {c.effect.short_description for c in namespace["eff"].candidates} == {
+        "p.S159T", "p.L159M"}
+
+    namespace["effects"] = varcode.VariantCollection(
+        [namespace["germline"]]).effects(germline=namespace["ctx"])
+    _run(_blocks("docs/germline.md", "## Loss of heterozygosity (LOH)")[:1], namespace)
+    assert any(getattr(effect, "is_loh", False) for effect in namespace["effects"])
+
+    validation = _blocks("docs/germline.md", "## Cross-VCF build mismatch")[:1]
+    namespace["somatic_variants"] = varcode.VariantCollection([namespace["somatic"]])
+    namespace["germline_ctx"] = namespace["ctx"]
+    _run(validation, namespace)
+    namespace["germline_ctx"] = varcode.GermlineContext.from_variants(
+        [namespace["germline"]], reference_name="GRCh37")
+    with pytest.raises(varcode.GenomeBuildMismatchError):
+        _run(validation, namespace)
+
+
+def test_documentation_germline_with_vcf_phase(input_directory):
+    namespace = _run(_blocks("docs/germline.md")[:1])
+    _run(_blocks("docs/phasing.md", "## Phased VCF")[:1], namespace)
+    namespace["rna"] = varcode.NullRNAEvidenceResolver()
+    _run(_blocks("docs/phasing.md", "## Combining evidence")[:1], namespace)
+    cftr = [effect for effect in namespace["effects"]
+            if effect.transcript_id == "ENST00000003084"]
+    assert len(cftr) == 1
+    assert cftr[0].short_description == "p.S159T"
+
+
+def test_documentation_effect_families_keep_all_classes():
+    source = ast.parse((ROOT / "varcode/effects/effect_classes.py").read_text())
+    classes = {node.name for node in source.body if isinstance(node, ast.ClassDef)}
+    guide = (ROOT / "docs/effect_types.md").read_text()
+    documented = re.findall(r"^::: varcode.effects.effect_classes\.(\w+)$", guide, re.M)
+    assert set(documented) == classes
+    assert len(documented) == len(classes)
+    assert "::: varcode.SpliceOutcomeSet" in guide
+
+
+@pytest.mark.parametrize("path,anchor,destination", [
+    ("structural_variants.md", "alleles-coordinates-and-exports", "sv_reference.md"),
+    ("structural_variants.md", "importing-observed-rna-structures", "rna_structures.md"),
+    ("germline.md", "concrete-example-same-codon-three-scenarios", "phasing.md"),
+    ("germline.md", "known-deletion-haplotypes-in-rna-alignments", "phasing.md"),
+    ("api.md", "varcode.Variant.effects", "api_variants.md"),
+    ("api.md", "varcode.MutantTranscript", "api_rna.md"),
+    ("api.md", "varcode.VCFPhaseResolver", "api_phasing.md"),
+])
+def test_documentation_topic_links_preserve_old_fragments(path, anchor, destination):
+    guide = (ROOT / "docs" / path).read_text()
+    row = next(line for line in guide.splitlines() if f'id="{anchor}"' in line)
+    assert f"]({destination}" in row
+    assert (ROOT / "docs" / destination).is_file()
+
+
+def test_documentation_api_objects_have_one_heading():
+    topics = list((ROOT / "docs").glob("api_*.md"))
+    assert len(topics) == 5
+    for topic in topics:
+        text = topic.read_text()
+        assert "::: varcode." in text
+        assert not re.search(r"^### `varcode\.", text, re.M)
+
+
+def test_documentation_splice_accessors():
+    namespace = _run(_blocks("docs/splice_variants.md"))
+    assert isinstance(namespace["splice_set"], varcode.SpliceOutcomeSet)
+    assert namespace["coding"] is not None
+    assert namespace["preferred"] is not None
+
+
+def test_documentation_moved_sections_keep_incoming_links():
+    guide = (ROOT / "docs/effect_annotation.md").read_text()
+    destinations = {
+        "splice-disrupting-variants": "splice_variants.md",
+        "how-it-composes": "transcript_models.md",
+        "annotator-selection": "experimental_annotators.md",
+        "writing-an-annotator": "annotator_contract.md",
+        "provenance": "csv.md#annotation-provenance",
+    }
+    for anchor, destination in destinations.items():
+        # Old fragment URLs land beside a link to the relocated content.
+        row = next(line for line in guide.splitlines() if f'id="{anchor}"' in line)
+        assert f"]({destination})" in row
+        assert (ROOT / "docs" / destination.split("#")[0]).is_file()
+
+
+def test_documentation_custom_annotator_adapter():
+    namespace = _run(_blocks("docs/annotator_contract.md")[:1])
+    adapter = namespace["MyAnnotator"]
+    variant = Variant("7", 117531100, "T", "A", genome=81)
+    transcript = variant.genome.transcript_by_id("ENST00000003084")
+    effect = variant.effect_on_transcript(transcript)
+    supported = adapter(lambda variant, transcript: effect)
+    unsupported = adapter(lambda variant, transcript: None)
+    assert supported.annotate_on_transcript(variant, transcript) is effect
+    assert unsupported.annotate_on_transcript(variant, transcript) is NotImplemented
+
+
+@pytest.mark.parametrize("kind", ["point", "BND", "CNV"])
+def test_documentation_experimental_result_access(kind):
+    genome = cached_release(81)
+    transcript = genome.transcript_by_id("ENST00000003084")
+    if kind == "point":
+        variant = Variant("7", 117531100, "T", "A", genome)
+    elif kind == "BND":
+        variant = StructuralVariant(
+            "7", transcript.start + 50, "BND", alt="N]22:15500000]",
+            mate_contig="22", mate_start=15500000, genome=genome)
+    else:
+        variant = StructuralVariant(
+            "7", transcript.start + 50, "CNV", end=transcript.start + 100,
+            genome=genome)
+    namespace = dict(varcode=varcode, variant=variant, transcript=transcript)
+    advanced_blocks = _blocks("docs/experimental_annotators.md")
+    assert "comparison =" in advanced_blocks[0]
+    assert "candidate.outcomes" in advanced_blocks[1]
+    _run(advanced_blocks[:2], namespace)
+    _run(_blocks("docs/transcript_models.md"), namespace)
+    candidates = getattr(namespace["experimental"], "candidates", ())
+    if kind == "point":
+        assert candidates and all(isinstance(c, RealizedEffectCandidate)
+                                  for c in candidates)
+        assert namespace["protein"][158] == "M"
+    elif kind == "BND":
+        assert candidates and all(isinstance(c, EffectCandidate) for c in candidates)
+    else:
+        assert not candidates
+        assert isinstance(namespace["experimental"], varcode.Unresolved)

varcode-9.2.7/varcode/version.py

@@ -0,0 +1 @@
+__version__ = "9.2.7"

{varcode-9.2.5 → varcode-9.2.7/varcode.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: varcode
-Version: 9.2.5
+Version: 9.2.7
 Summary: Variant annotation in Python
 Author-email: Alex Rubinsteyn <alex.rubinsteyn@unc.edu>
 Project-URL: Homepage, https://github.com/openvax/varcode

varcode-9.2.5/tests/test_documentation_examples.py

@@ -1,127 +0,0 @@
-"""Keep the reader-facing examples executable, using their actual Markdown."""
-
-from pathlib import Path
-import re
-import shutil
-
-import pytest
-from pyensembl import cached_release
-
-import varcode
-from varcode import EffectCandidate, StructuralVariant, Variant
-from varcode.effect_hypotheses import RealizedEffectCandidate
-
-
-ROOT = Path(__file__).resolve().parents[1]
-
-
-def _blocks(path, heading=None):
-    text = (ROOT / path).read_text()
-    if heading is not None:
-        text = text.split(heading + "\n", 1)[1]
-    return re.findall(r"```python\n(.*?)```", text, re.S)
-
-
-def _run(blocks, namespace=None):
-    namespace = {} if namespace is None else namespace
-    for block in blocks:
-        exec(compile(block, "documentation example", "exec"), namespace)
-    return namespace
-
-
-@pytest.fixture
-def input_directory(tmp_path, monkeypatch):
-    for fixture in (ROOT / "tests/data/documentation").glob("*.vcf"):
-        shutil.copy(fixture, tmp_path / fixture.name)
-    shutil.copy(tmp_path / "variants.vcf", tmp_path / "tumor.vcf")
-    monkeypatch.chdir(tmp_path)
-    return tmp_path
-
-
-@pytest.mark.parametrize("path,count", [
-    ("README.md", 2),
-    ("docs/getting_started.md", 4),
-    ("docs/index.md", 1),
-    ("docs/effect_annotation.md", 3),
-    ("docs/structural_variants.md", 1),
-    ("docs/transforms.md", 1),
-    ("docs/germline.md", 1),
-])
-def test_documentation_first_steps(path, count, input_directory):
-    namespace = _run(_blocks(path)[:count])
-    if path == "docs/transforms.md":
-        assert len(namespace["paired"]) == len(namespace["normalized"]) == 1
-    else:
-        assert len(namespace["effects"]) > 0
-    if path in ("README.md", "docs/getting_started.md"):
-        assert namespace["protein"][158] == "M"
-    if path == "docs/getting_started.md":
-        assert (input_directory / "effects.csv").is_file()
-    if path == "docs/structural_variants.md":
-        assert namespace["variants"][0].is_structural
-
-
-def test_documentation_germline_scenarios():
-    namespace = _run(_blocks(
-        "docs/germline.md", "## Concrete example: same codon, three scenarios")[:4])
-    assert namespace["eff_cis"].short_description == "p.S159T"
-    assert namespace["eff_trans"].short_description == "p.L159M"
-    assert {c.effect.short_description for c in namespace["eff"].candidates} == {
-        "p.S159T", "p.L159M"}
-
-    _run(_blocks("docs/germline.md", "## Loss of heterozygosity (LOH)")[:1],
-         namespace)
-    assert any(getattr(effect, "is_loh", False)
-               for effect in namespace["overlap"].effects(germline=namespace["ctx"]))
-
-    validation = _blocks("docs/germline.md", "## Cross-VCF build mismatch")[:1]
-    _run(validation, namespace)
-    namespace["ctx"] = varcode.GermlineContext.from_variants(
-        [namespace["germline"]], reference_name="GRCh37")
-    with pytest.raises(varcode.GenomeBuildMismatchError):
-        _run(validation, namespace)
-
-
-def test_documentation_splice_accessors():
-    text = (ROOT / "docs/effect_annotation.md").read_text()
-    section = text.split("### The `SpliceOutcomeSet` shape\n", 1)[1]
-    section = section.split("### RNA evidence reconciliation\n", 1)[0]
-    blocks = re.findall(r"```python\n(.*?)```", section, re.S)
-    namespace = _run(blocks[:1])
-    namespace["effect"] = namespace["splice_set"]
-    _run(blocks[1:], namespace)
-    assert isinstance(namespace["splice_set"], varcode.SpliceOutcomeSet)
-    assert namespace["coding"] is not None
-
-
-@pytest.mark.parametrize("kind", ["point", "BND", "CNV"])
-def test_documentation_experimental_result_access(kind):
-    genome = cached_release(81)
-    transcript = genome.transcript_by_id("ENST00000003084")
-    if kind == "point":
-        variant = Variant("7", 117531100, "T", "A", genome)
-    elif kind == "BND":
-        variant = StructuralVariant(
-            "7", transcript.start + 50, "BND", alt="N]22:15500000]",
-            mate_contig="22", mate_start=15500000, genome=genome)
-    else:
-        variant = StructuralVariant(
-            "7", transcript.start + 50, "CNV", end=transcript.start + 100,
-            genome=genome)
-    namespace = dict(varcode=varcode, variant=variant, transcript=transcript)
-    advanced_blocks = _blocks("docs/effect_annotation.md",
-                              "## Advanced: annotators and implementation limits")
-    assert "comparison =" in advanced_blocks[0]
-    assert "candidate.outcomes" in advanced_blocks[1]
-    _run(advanced_blocks[:2], namespace)
-    _run(_blocks("docs/effect_annotation.md", "## Read an effect")[:1], namespace)
-    candidates = getattr(namespace["experimental"], "candidates", ())
-    if kind == "point":
-        assert candidates and all(isinstance(c, RealizedEffectCandidate)
-                                  for c in candidates)
-        assert namespace["protein"][158] == "M"
-    elif kind == "BND":
-        assert candidates and all(isinstance(c, EffectCandidate) for c in candidates)
-    else:
-        assert not candidates
-        assert isinstance(namespace["experimental"], varcode.Unresolved)

varcode-9.2.5/varcode/version.py

@@ -1 +0,0 @@
-__version__ = "9.2.5"