fix: tests no longer create files in working directory or test data dirs (#853)

* Initial plan

* Initial commit

* fix: prevent pytest tests from creating files in working directory or data dirs

* Fix test side effects: isolate file I/O in tmp dirs

* update pre-commit hooks

* Fix liftover outfile default to None to prevent stdout fallback

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: Adam Taranto <adam.p.taranto@gmail.com>

Author: Copilot

.pre-commit-config.yaml

@@ -18,19 +18,19 @@ repos:
       - id: check-executables-have-shebangs
         #- id: debug-statements
   - repo: https://github.com/rhysd/actionlint
-    rev: v1.7.9
+    rev: v1.7.12
     hooks:
       - id: actionlint
   - repo: https://github.com/google/yamlfmt
-    rev: v0.20.0
+    rev: v0.21.0
     hooks:
       - id: yamlfmt
   - repo: https://github.com/psf/black
-    rev: 25.12.0
+    rev: 26.5.1
     hooks:
       - id: black
   - repo: https://github.com/PyCQA/isort
-    rev: 7.0.0
+    rev: 9.0.0a3
     hooks:
       - id: isort
         args: ["--profile", "black"]

src/jcvi/assembly/hic.py

@@ -946,6 +946,10 @@ def bam2mat(args):
         "--seqids",
         help="Use a given seqids file, a single line with seqids joined by comma",
     )
+    p.add_argument(
+        "--outdir",
+        help="Output directory for generated files (default: same dir as input BAM)",
+    )
     opts, args = p.parse_args(args)
 
     if len(args) != 1:
@@ -954,7 +958,8 @@ def bam2mat(args):
     (bamfilename,) = args
     pf = bamfilename.rsplit(".", 1)[0]
     N = opts.resolution
-    pf += f".resolution_{N}"
+    pf_name = op.basename(pf) + f".resolution_{N}"
+    pf = op.join(opts.outdir, pf_name) if opts.outdir else pf + f".resolution_{N}"
     bins = 1500  # Distance distribution bins
     minsize = 100  # Record distance if it is at least minsize
     seqids = opts.seqids

src/jcvi/compara/synteny.py

@@ -1930,6 +1930,7 @@ def liftover(args):
     """
     p = OptionParser(liftover.__doc__)
     p.set_stripnames()
+    p.set_outfile(outfile=None)
 
     blast_file, anchor_file, dist, opts = add_arguments(p, args)
     qbed, sbed, qorder, sorder, is_self = check_beds(blast_file, p, opts)
@@ -1961,7 +1962,7 @@ def liftover(args):
             lifted += 1
 
     logger.debug("%d new pairs found (dist=%d).", lifted, dist)
-    newanchorfile = anchor_file.rsplit(".", 1)[0] + ".lifted.anchors"
+    newanchorfile = opts.outfile or anchor_file.rsplit(".", 1)[0] + ".lifted.anchors"
     if accepted:
         ac.filter_blocks(accepted)
     ac.print_to_file(filename=newanchorfile)

tests/apps/test_base.py

@@ -35,10 +35,11 @@ def test_sample_N():
     assert a == [2, 3, 1, 2]
 
 
-def test_download():
+def test_download(tmp_path, monkeypatch):
     from jcvi.apps.base import cleanup, download
     from jcvi.apps.vecscreen import ECOLI_URL, UNIVEC_URL
 
+    monkeypatch.chdir(tmp_path)
     ret = download("http://www.google.com")
     assert ret == "index.html"
     cleanup(ret)
@@ -83,10 +84,11 @@ def test_flatten(input_list, output_list):
     assert flatten(input_list) == output_list
 
 
-def test_cleanup():
+def test_cleanup(tmp_path, monkeypatch):
     from jcvi.apps.base import cleanup, mkdir
     from jcvi.formats.base import write_file
 
+    monkeypatch.chdir(tmp_path)
     write_file("a", "content_a", skipcheck=True)
     write_file("b", "content_b", skipcheck=True)
     write_file("c", "content_c", skipcheck=True)
@@ -109,11 +111,11 @@ def test_cleanup():
         assert not op.exists(path)
 
 
-def test_need_update():
+def test_need_update(tmp_path, monkeypatch):
     from jcvi.apps.base import cleanup, need_update
     from jcvi.formats.base import write_file
 
-    cleanup("a", "b", "c")
+    monkeypatch.chdir(tmp_path)
     assert need_update("does_not_exist.txt", "does_not_exist.txt")
 
     write_file("a", "content_a", skipcheck=True)
@@ -130,7 +132,6 @@ def test_need_update():
     assert need_update(["c", "b"], "a")
     assert not need_update("a", ["b", "c"])
     assert need_update(["a", "b"], ["c", "d"])
-    cleanup("a", "b", "c")
 
 
 def test_set_image_options():
@@ -155,9 +156,10 @@ def test_set_image_options():
     g.add_argument("--group", default="jcvi", help="pytest coverage")
 
 
-def test_getpath():
+def test_getpath(tmp_path, monkeypatch):
     from jcvi.apps.base import getpath
 
+    monkeypatch.chdir(tmp_path)
     with mock.patch("builtins.input", lambda _: "e\rvvvvvvvv = zzzzzzzz\n"):
         assert getpath("not-part-of-path", name="CLUSTALW2", warn="warn") is None
 

tests/apps/test_fetch.py

@@ -8,16 +8,15 @@
 
 @patch("builtins.input", return_value="username")
 @patch("getpass.getpass", return_value="password")
-def test_get_cookies(mock_username, mock_password):
+def test_get_cookies(mock_username, mock_password, tmp_path, monkeypatch):
     from jcvi.apps.fetch import get_cookies, PHYTOZOME_COOKIES
-    from jcvi.apps.base import cleanup, which
+    from jcvi.apps.base import which
 
-    cleanup(PHYTOZOME_COOKIES)
+    monkeypatch.chdir(tmp_path)
     if which("curl"):
         assert get_cookies() == PHYTOZOME_COOKIES
     else:
         assert get_cookies() is None  # errored out with "curl not found"
-    cleanup(PHYTOZOME_COOKIES)
 
 
 def test_usage_with_percent_prog():

tests/assembly/allmaps.py/inputs/JM-2.agp

@@ -0,0 +1,47 @@
+##agp-version 2.1
+# COMMENT: Generated by ALLMAPS 0.1.dev2+g2ce5bee02 (2026-07-05)
+# COMMAND: python -m jcvi.assembly.allmaps path /home/runner/work/jcvi/jcvi/tests/assembly/allmaps.py/inputs/JM-2.bed /home/runner/work/jcvi/jcvi/tests/assembly/allmaps.py/inputs/scaffolds.fasta.gz -w /home/runner/work/jcvi/jcvi/tests/assembly/allmaps.py/inputs/weights.txt
+# FIELDS: object, object_beg, object_end, part_number, component_type, component_id/gap_length, component_beg/gap_type, component_end/linkage, orientation/linkage_evidence
+chr23	1	137336	1	W	scaffold_821	1	137336	?
+chr23	137337	137436	2	U	100	scaffold	yes	map
+chr23	137437	284865	3	W	scaffold_792	1	147429	?
+chr23	284866	284965	4	U	100	scaffold	yes	map
+chr23	284966	412560	5	W	scaffold_866	1	127595	?
+chr23	412561	412660	6	U	100	scaffold	yes	map
+chr23	412661	484207	7	W	scaffold_1189	1	71547	-
+chr23	484208	484307	8	U	100	scaffold	yes	map
+chr23	484308	891092	9	W	scaffold_375	1	406785	-
+chr23	891093	891192	10	U	100	scaffold	yes	map
+chr23	891193	1393339	11	W	scaffold_310	1	502147	-
+chr23	1393340	1393439	12	U	100	scaffold	yes	map
+chr23	1393440	2982363	13	W	scaffold_95	1	1588924	?
+chr23	2982364	2982463	14	U	100	scaffold	yes	map
+chr23	2982464	4080317	15	W	scaffold_148	1	1097854	-
+chr23	4080318	4080417	16	U	100	scaffold	yes	map
+chr23	4080418	4781064	17	W	scaffold_225	1	700647	?
+chr23	4781065	4781164	18	U	100	scaffold	yes	map
+chr23	4781165	5760583	19	W	scaffold_164	1	979419	-
+chr23	5760584	5760683	20	U	100	scaffold	yes	map
+chr23	5760684	6999179	21	W	scaffold_129	1	1238496	+
+chr23	6999180	6999279	22	U	100	scaffold	yes	map
+chr23	6999280	9562302	23	W	scaffold_43	1	2563023	-
+chr23	9562303	9562402	24	U	100	scaffold	yes	map
+chr23	9562403	11388199	25	W	scaffold_80	1	1825797	-
+chr23	11388200	11388299	26	U	100	scaffold	yes	map
+chr23	11388300	12471757	27	W	scaffold_150	1	1083458	-
+chr23	12471758	12471857	28	U	100	scaffold	yes	map
+chr23	12471858	12942229	29	W	scaffold_331	1	470372	?
+chr23	12942230	12942329	30	U	100	scaffold	yes	map
+chr23	12942330	13145841	31	W	scaffold_642	1	203512	?
+chr23	13145842	13145941	32	U	100	scaffold	yes	map
+chr23	13145942	13277112	33	W	scaffold_829	1	131171	-
+chr23	13277113	13277212	34	U	100	scaffold	yes	map
+chr23	13277213	13540514	35	W	scaffold_513	1	263302	-
+chr23	13540515	13540614	36	U	100	scaffold	yes	map
+chr23	13540615	13742295	37	W	scaffold_648	1	201681	?
+chr23	13742296	13742395	38	U	100	scaffold	yes	map
+chr23	13742396	14146998	39	W	scaffold_382	1	404603	+
+chr23	14146999	14147098	40	U	100	scaffold	yes	map
+chr23	14147099	14246084	41	W	scaffold_1006	1	98986	?
+chr23	14246085	14246184	42	U	100	scaffold	yes	map
+chr23	14246185	15272643	43	W	scaffold_158	1	1026459	?

tests/assembly/allmaps.py/inputs/JM-2.chr.agp

@@ -0,0 +1,47 @@
+##agp-version 2.1
+# COMMENT: Generated by ALLMAPS 0.1.dev2+g2ce5bee02 (2026-07-05)
+# COMMAND: python -m jcvi.assembly.allmaps path /home/runner/work/jcvi/jcvi/tests/assembly/allmaps.py/inputs/JM-2.bed /home/runner/work/jcvi/jcvi/tests/assembly/allmaps.py/inputs/scaffolds.fasta.gz -w /home/runner/work/jcvi/jcvi/tests/assembly/allmaps.py/inputs/weights.txt
+# FIELDS: object, object_beg, object_end, part_number, component_type, component_id/gap_length, component_beg/gap_type, component_end/linkage, orientation/linkage_evidence
+chr23	1	137336	1	W	scaffold_821	1	137336	?
+chr23	137337	137436	2	U	100	scaffold	yes	map
+chr23	137437	284865	3	W	scaffold_792	1	147429	?
+chr23	284866	284965	4	U	100	scaffold	yes	map
+chr23	284966	412560	5	W	scaffold_866	1	127595	?
+chr23	412561	412660	6	U	100	scaffold	yes	map
+chr23	412661	484207	7	W	scaffold_1189	1	71547	-
+chr23	484208	484307	8	U	100	scaffold	yes	map
+chr23	484308	891092	9	W	scaffold_375	1	406785	-
+chr23	891093	891192	10	U	100	scaffold	yes	map
+chr23	891193	1393339	11	W	scaffold_310	1	502147	-
+chr23	1393340	1393439	12	U	100	scaffold	yes	map
+chr23	1393440	2982363	13	W	scaffold_95	1	1588924	?
+chr23	2982364	2982463	14	U	100	scaffold	yes	map
+chr23	2982464	4080317	15	W	scaffold_148	1	1097854	-
+chr23	4080318	4080417	16	U	100	scaffold	yes	map
+chr23	4080418	4781064	17	W	scaffold_225	1	700647	?
+chr23	4781065	4781164	18	U	100	scaffold	yes	map
+chr23	4781165	5760583	19	W	scaffold_164	1	979419	-
+chr23	5760584	5760683	20	U	100	scaffold	yes	map
+chr23	5760684	6999179	21	W	scaffold_129	1	1238496	+
+chr23	6999180	6999279	22	U	100	scaffold	yes	map
+chr23	6999280	9562302	23	W	scaffold_43	1	2563023	-
+chr23	9562303	9562402	24	U	100	scaffold	yes	map
+chr23	9562403	11388199	25	W	scaffold_80	1	1825797	-
+chr23	11388200	11388299	26	U	100	scaffold	yes	map
+chr23	11388300	12471757	27	W	scaffold_150	1	1083458	-
+chr23	12471758	12471857	28	U	100	scaffold	yes	map
+chr23	12471858	12942229	29	W	scaffold_331	1	470372	?
+chr23	12942230	12942329	30	U	100	scaffold	yes	map
+chr23	12942330	13145841	31	W	scaffold_642	1	203512	?
+chr23	13145842	13145941	32	U	100	scaffold	yes	map
+chr23	13145942	13277112	33	W	scaffold_829	1	131171	-
+chr23	13277113	13277212	34	U	100	scaffold	yes	map
+chr23	13277213	13540514	35	W	scaffold_513	1	263302	-
+chr23	13540515	13540614	36	U	100	scaffold	yes	map
+chr23	13540615	13742295	37	W	scaffold_648	1	201681	?
+chr23	13742296	13742395	38	U	100	scaffold	yes	map
+chr23	13742396	14146998	39	W	scaffold_382	1	404603	+
+chr23	14146999	14147098	40	U	100	scaffold	yes	map
+chr23	14147099	14246084	41	W	scaffold_1006	1	98986	?
+chr23	14246085	14246184	42	U	100	scaffold	yes	map
+chr23	14246185	15272643	43	W	scaffold_158	1	1026459	?