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

Author: Copilot

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()
 
     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/assembly/hic.py/tests.yml

@@ -1,13 +1,13 @@
 bam2mat:
   action: bam2mat
-  opts:
+  opts: --outdir=__TMP__
   args: __DIR__/inputs/test.bam
-  outputs: [__DIR__/inputs/test.resolution_500000.json]
+  outputs: [__TMP__/test.resolution_500000.json]
   references: [references/test.resolution_500000.json]
 
 bam2mat_seqids:
   action: bam2mat
-  opts: --seqids=__DIR__/inputs/seqids
+  opts: --seqids=__DIR__/inputs/seqids --outdir=__TMP__
   args: __DIR__/inputs/test.bam
-  outputs: [__DIR__/inputs/test.resolution_500000.json]
+  outputs: [__TMP__/test.resolution_500000.json]
   references: [references/test.resolution_500000.seqids.json]

tests/assembly/test_allmaps.py

@@ -1,6 +1,4 @@
-import os
 import os.path as op
-from jcvi.apps.base import mkdir
 from jcvi.assembly.allmaps import path
 
 
@@ -34,14 +32,13 @@ def test_liftover(tmp_path, monkeypatch):
 
 
 def test_path(tmp_path, monkeypatch):
+    import shutil
+
     monkeypatch.chdir(tmp_path)
-    bedfile = datafile("inputs/JM-2.bed")
+    bedfile = str(tmp_path / "JM-2.bed")
+    shutil.copy(datafile("inputs/JM-2.bed"), bedfile)
     fastafile = datafile("inputs/scaffolds.fasta.gz")
     weightsfile = datafile("inputs/weights.txt")
-    output_image = "chr23.pdf"
-    testdir = str(tmp_path / "chr23")
-    mkdir(testdir)
-    os.chdir(testdir)
     path(
         [
             bedfile,
@@ -50,4 +47,4 @@ def test_path(tmp_path, monkeypatch):
             weightsfile,
         ]
     )
-    assert op.exists(output_image)
+    assert op.exists("chr23.pdf")

tests/compara/synfind.py/tests.yml

@@ -1,7 +1,7 @@
 synfind:
   script: synfind
   action: main
-  opts: -o __DIR__/inputs/testtigs.testchr.synfind
+  opts: -o __TMP__/testtigs.testchr.synfind
   args: __DIR__/inputs/testtigs.testchr.last
-  outputs: [__DIR__/inputs/testtigs.testchr.synfind]
+  outputs: [__TMP__/testtigs.testchr.synfind]
   references: [references/testtigs.testchr.synfind]

tests/compara/synteny.py/tests.yml

@@ -14,7 +14,7 @@ depth:
 
 liftover:
   action: liftover
-  opts: --qbed=__DIR__/inputs/test_empty_blocks.a.bed --sbed=__DIR__/inputs/test_empty_blocks.b.bed
+  opts: --qbed=__DIR__/inputs/test_empty_blocks.a.bed --sbed=__DIR__/inputs/test_empty_blocks.b.bed --outfile=__TMP__/test_empty_blocks.lifted.anchors
   args: __DIR__/inputs/test_empty_blocks.last __DIR__/inputs/test_empty_blocks.anchors
-  outputs: [__DIR__/inputs/test_empty_blocks.lifted.anchors]
+  outputs: [__TMP__/test_empty_blocks.lifted.anchors]
   references: [references/test_empty_blocks.lifted.anchors]

tests/config.py

@@ -13,6 +13,7 @@
 """
 
 import sys
+import os
 import os.path as op
 import glob
 import re
@@ -134,8 +135,13 @@ def test_script(
     func = getattr(module, action)
     args = " ".join((opts, args)).split()
 
-    with Capturing(stdout) as output:
-        func(args)
+    original_dir = os.getcwd()
+    os.chdir(tmp_dir)
+    try:
+        with Capturing(stdout) as output:
+            func(args)
+    finally:
+        os.chdir(original_dir)
 
     if not fail:
         for output, reference in zip(outputs, references):

tests/graphics/test_glyph.py

@@ -4,5 +4,6 @@
 from jcvi.graphics.glyph import demo
 
 
-def test_demo():
+def test_demo(tmp_path, monkeypatch):
+    monkeypatch.chdir(tmp_path)
     demo([])