fix: tests no longer create files in working directory or test data dirs

[Copilot]

Pytest tests were writing output files into the repo working directory and tests/graphics/data/ — particularly graphics tests that produced PDFs with no post-test cleanup — requiring manual removal before commits.

Changes

Redirect file creation to tmp_path

• test_cbook.py::test_depends, test_sizes.py::test_sizes: pass tmp_path-rooted paths instead of bare filenames
• test_obo.py::test_oboreader, test_allmaps.py, test_base.py (test_cleanup, test_need_update, test_download, test_getpath), test_fetch.py::test_get_cookies: add monkeypatch.chdir(tmp_path) so all output lands in pytest's auto-cleaned temp dir; remove now-redundant manual cleanup() calls

Graphics tests: symlink data → tmp_path, redirect output

Tests that chdir into tests/graphics/data/ and produce PDFs there now symlink the data directory contents into tmp_path and monkeypatch.chdir there instead. Output files (PDFs, intermediate images) are written to tmp_path and cleaned up automatically.

Affected: test_karyotype.py, test_landscape.py, test_synteny.py, test_grabseeds.py, test_tree.py

# Before — pollutes tests/graphics/data/
def test_main():
    cwd = os.getcwd()
    os.chdir(op.join(op.dirname(__file__), "data"))
    cleanup("karyotype.pdf")
    image_name = karyotype_main(["seqids", "layout"])
    assert op.exists(image_name)
    os.chdir(cwd)

# After — output goes to pytest tmp_path, auto-cleaned
def test_main(tmp_path, monkeypatch):
    data_dir = op.join(op.dirname(__file__), "data")
    for fname in os.listdir(data_dir):
        os.symlink(op.join(data_dir, fname), op.join(str(tmp_path), fname))
    monkeypatch.chdir(tmp_path)
    image_name = karyotype_main(["seqids", "layout"])
    assert op.exists(image_name)

tests/config.py

LOG = open("test_scripts.log", "a") was executed at module import time, creating the file in CWD. Changed to write to tempfile.gettempdir().

tests/formats/test_bed.py

Removed os.chdir entirely; passes the absolute path to the bed file directly to summary().

[Copilot]

Pull request overview

This pull request updates the test suite to avoid writing generated output files into the repository working directory or committed test-data directories, primarily by redirecting output into pytest-managed temporary directories. It also adds small CLI affordances to support directing outputs to temp locations for script-based tests.

Changes:

• Redirect test-generated outputs to tmp_path (via passing tmp-rooted filenames and/or monkeypatch.chdir(tmp_path)) and remove now-unneeded manual cleanup calls.
• Update graphics tests to run from tmp_path by symlinking required data files into the temp directory before execution.
• Add explicit output controls for CLI utilities used by tests (synteny liftover --outfile, hic bam2mat --outdir) and refresh pre-commit hook versions.

Reviewed changes

Copilot reviewed 26 out of 34 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tests/utils/test_cbook.py	Writes depends-test inputs/outputs under tmp_path instead of CWD.
tests/graphics/test_tree.py	Uses monkeypatch.chdir(tmp_path) to keep generated images out of the repo.
tests/graphics/test_synteny.py	Symlinks graphics data into tmp_path and runs from there.
tests/graphics/test_landscape.py	Symlinks graphics data into tmp_path and runs from there.
tests/graphics/test_karyotype.py	Symlinks graphics data into tmp_path and runs from there.
tests/graphics/test_grabseeds.py	Runs from tmp_path so PDFs/JSON land in temp.
tests/graphics/test_glyph.py	Runs from tmp_path to avoid writing into the repo.
tests/formats/test_sizes.py	Writes FASTA under tmp_path (avoids CWD pollution).
tests/formats/test_obo.py	Runs from tmp_path so downloaded OBO file lands in temp.
tests/formats/test_bed.py	Avoids chdir; passes absolute input path to summary().
tests/config.py	Moves test_scripts.log to system temp; runs script tests inside a temp working dir with try/finally restore.
tests/compara/synteny.py/tests.yml	Routes synteny test outputs to __TMP__ and uses --outfile.
tests/compara/synfind.py/tests.yml	Routes synfind test outputs to __TMP__.
tests/assembly/test_allmaps.py	Runs allmaps tests from tmp_path and avoids writing to inputs dir.
tests/assembly/hic.py/tests.yml	Uses new --outdir=__TMP__ so bam2mat outputs land in temp.
tests/assembly/hic.py/inputs/test.resolution_500000.json	Adds reference JSON fixture for bam2mat tests.
tests/assembly/allmaps.py/inputs/scaffolds.fasta.gz.sizes	Adds sizes fixture to avoid generating it during tests.
tests/assembly/allmaps.py/inputs/JM-2.unplaced.fasta	Adds/updates allmaps test fixture input.
tests/assembly/allmaps.py/inputs/JM-2.unplaced.agp	Adds/updates allmaps test fixture input.
tests/assembly/allmaps.py/inputs/JM-2.summary.txt	Adds summary fixture output for allmaps-related testing.
tests/assembly/allmaps.py/inputs/JM-2.lifted.bed	Adds lifted BED fixture output for allmaps-related testing.
tests/assembly/allmaps.py/inputs/JM-2.fasta.sizes	Adds FASTA sizes fixture output for allmaps-related testing.
tests/assembly/allmaps.py/inputs/JM-2.chr.agp	Adds AGP fixture output for allmaps-related testing.
tests/assembly/allmaps.py/inputs/JM-2.agp	Adds AGP fixture output for allmaps-related testing.
tests/apps/test_fetch.py	Runs cookie-writing logic from tmp_path to avoid polluting repo CWD.
tests/apps/test_base.py	Runs file-writing tests from tmp_path to avoid polluting repo CWD.
src/jcvi/compara/synteny.py	Adds --outfile support to liftover() output naming.
src/jcvi/assembly/hic.py	Adds --outdir support to bam2mat() so outputs can be redirected.
.pre-commit-config.yaml	Bumps pre-commit hook revisions.

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[Copilot]

Fixed in the latest commit by changing p.set_outfile() to p.set_outfile(outfile=None), so opts.outfile is None by default and the .lifted.anchors fallback filename is used correctly when no --outfile flag is provided.

[Adamtaranto]

@tanghaibao ready for review