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Merged
cokelaer merged 1 commit into from
Mar 20, 2026
Merged

pin version #27

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2 changes: 2 additions & 0 deletions README.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -135,6 +135,8 @@ Changelog
========= ======================================================================
Version Description
========= ======================================================================
1.4.1 * update to use wrappers.shells and wrappers.snippets
drop wrappers usage
1.4.0 * update wrappers to v24.8.29
* update sequana_pipetools requirement to >=1.5
1.3.1 * remove temp on BWA BAM file (more practical to keep them)
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10 changes: 9 additions & 1 deletion pyproject.toml
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Expand Up @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"

[tool.poetry]
name = "sequana-mapper"
version = "1.4.0"
version = "1.4.1"
description = "A multi-sample mapper to map reads onto a reference"
authors = ["Sequana Team"]
license = "BSD-3"
Expand Down Expand Up @@ -51,3 +51,11 @@ mock = "^5.1.0"
pytest-mock = "^3.11.1"
pytest-cov = "^4.1.0"

[tool.pytest.ini_options]
filterwarnings = [
"ignore::pytest.PytestDeprecationWarning",
"ignore::DeprecationWarning:click_completion",
"ignore::DeprecationWarning:importlib",
]
asyncio_mode = "auto"

112 changes: 55 additions & 57 deletions test/test_main.py
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Expand Up @@ -13,72 +13,70 @@


def test_standalone_subprocess():
directory = tempfile.TemporaryDirectory()
cmd = """sequana_mapper --input-directory {}
--working-directory {} --force""".format(
sharedir, directory.name
)
subprocess.call(cmd.split())
with tempfile.TemporaryDirectory() as directory:
cmd = """sequana_mapper --input-directory {}
--working-directory {} --force""".format(
sharedir, directory
)
subprocess.call(cmd.split())


def test_standalone_script():
directory = tempfile.TemporaryDirectory()

runner = CliRunner()
results = runner.invoke(
main,
[
"--input-directory",
sharedir,
"--reference-file",
sharedir + "/measles.fa",
"--working-directory",
directory.name,
"--force",
],
)
assert results.exit_code == 0
with tempfile.TemporaryDirectory() as directory:
runner = CliRunner()
results = runner.invoke(
main,
[
"--input-directory",
sharedir,
"--reference-file",
sharedir + "/measles.fa",
"--working-directory",
directory,
"--force",
],
)
assert results.exit_code == 0


def test_standalone_script_minimap2():
directory = tempfile.TemporaryDirectory()
runner = CliRunner()
results = runner.invoke(
main,
[
"--input-directory",
sharedir,
"--reference-file",
sharedir + "/measles.fa",
"--working-directory",
directory.name,
"--force",
"--aligner-choice",
"minimap2",
],
)
assert results.exit_code == 0
with tempfile.TemporaryDirectory() as directory:
runner = CliRunner()
results = runner.invoke(
main,
[
"--input-directory",
sharedir,
"--reference-file",
sharedir + "/measles.fa",
"--working-directory",
directory,
"--force",
"--aligner-choice",
"minimap2",
],
)
assert results.exit_code == 0


def test_standalone_script_saf(tmpdir):
directory = tempfile.TemporaryDirectory()

runner = CliRunner()
results = runner.invoke(
main,
[
"--input-directory",
sharedir,
"--reference-file",
sharedir + "/measles.fa",
"--working-directory",
directory.name,
"--force",
"--capture-annotation-file",
sharedir + "/test.saf",
],
)
assert results.exit_code == 0
with tempfile.TemporaryDirectory() as directory:
runner = CliRunner()
results = runner.invoke(
main,
[
"--input-directory",
sharedir,
"--reference-file",
sharedir + "/measles.fa",
"--working-directory",
directory,
"--force",
"--capture-annotation-file",
sharedir + "/test.saf",
],
)
assert results.exit_code == 0


def test_full():
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