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Merge pull request easybuilders#25111 from boegel/MDTraj_fix_tests_https
add patch to use `https` instead of `http` to fix failing MDTraj tests
2 parents deb72dd + 714ff70 commit cf797a5

7 files changed

Lines changed: 103 additions & 5 deletions

‎easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.3-foss-2023b.eb‎

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@@ -28,8 +28,12 @@ exts_list = [
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'checksums': ['b9c13f1ab8b3b542f72e28f634bad4de758ab3ce4546e4301970ad6fa77c38be'],
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}),
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('mdtraj', version, {
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'patches': ['MDTraj-1.11.0_fix-tests-https.patch'],
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'use_pip_extras': 'optional',
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'checksums': ['d14a35009263725b784c436a8ac63fb6ceeb2bb366a526715dac6590d21025e5'],
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'checksums': [
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{'mdtraj-1.10.3.tar.gz': 'd14a35009263725b784c436a8ac63fb6ceeb2bb366a526715dac6590d21025e5'},
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{'MDTraj-1.11.0_fix-tests-https.patch': 'bb4384205f67f3c65a5e003c97ef6e47d4fe3f545cc4a0f5017ee953a4a641e7'},
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],
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}),
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]
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‎easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.3-foss-2024a.eb‎

Lines changed: 5 additions & 1 deletion
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@@ -28,8 +28,12 @@ exts_list = [
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'checksums': ['b9c13f1ab8b3b542f72e28f634bad4de758ab3ce4546e4301970ad6fa77c38be'],
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}),
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('mdtraj', version, {
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'checksums': ['d14a35009263725b784c436a8ac63fb6ceeb2bb366a526715dac6590d21025e5'],
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'patches': ['MDTraj-1.11.0_fix-tests-https.patch'],
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'use_pip_extras': 'optional',
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'checksums': [
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{'mdtraj-1.10.3.tar.gz': 'd14a35009263725b784c436a8ac63fb6ceeb2bb366a526715dac6590d21025e5'},
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{'MDTraj-1.11.0_fix-tests-https.patch': 'bb4384205f67f3c65a5e003c97ef6e47d4fe3f545cc4a0f5017ee953a4a641e7'},
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],
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}),
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]
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‎easybuild/easyconfigs/m/MDTraj/MDTraj-1.11.0-foss-2025a.eb‎

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -28,8 +28,12 @@ exts_list = [
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'checksums': ['b9c13f1ab8b3b542f72e28f634bad4de758ab3ce4546e4301970ad6fa77c38be'],
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}),
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('mdtraj', version, {
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'patches': ['MDTraj-1.11.0_fix-tests-https.patch'],
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'use_pip_extras': 'optional',
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'checksums': ['2cf0ed2ee9a603dc4599743b1806e1387c655e2a1e9d013841b99fb137ad852e'],
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'checksums': [
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{'mdtraj-1.11.0.tar.gz': '2cf0ed2ee9a603dc4599743b1806e1387c655e2a1e9d013841b99fb137ad852e'},
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{'MDTraj-1.11.0_fix-tests-https.patch': 'bb4384205f67f3c65a5e003c97ef6e47d4fe3f545cc4a0f5017ee953a4a641e7'},
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],
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}),
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]
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‎easybuild/easyconfigs/m/MDTraj/MDTraj-1.11.0-foss-2025b.eb‎

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@@ -32,12 +32,16 @@ exts_list = [
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'checksums': ['c38b266db8a808953ebd71ac25c381cb1981a78ff9340a14bcb9f1b9bff1899e'],
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}),
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('mdtraj', version, {
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'patches': ['MDTraj-1.11.0_fix-tests-https.patch'],
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'runtest': "cd tests && pytest -v --numprocesses %(parallel)s",
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'source_urls': ['https://github.com/mdtraj/mdtraj/archive/'],
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'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s-github.tar.gz'}],
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'testinstall': True,
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'use_pip_extras': 'optional',
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'checksums': ['fefca787f882d0716a7aeb01b4d8e30caddbd2be0b2893acfa7201c31d13c786'],
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'checksums': [
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{'mdtraj-1.11.0-github.tar.gz': 'fefca787f882d0716a7aeb01b4d8e30caddbd2be0b2893acfa7201c31d13c786'},
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{'MDTraj-1.11.0_fix-tests-https.patch': 'bb4384205f67f3c65a5e003c97ef6e47d4fe3f545cc4a0f5017ee953a4a641e7'},
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],
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}),
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]
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‎easybuild/easyconfigs/m/MDTraj/MDTraj-1.11.0_fix-tests-https.patch‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,39 @@
1+
use https rather than http for download URLs, to fix broken tests;
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see https://github.com/mdtraj/mdtraj/issues/2126 and https://github.com/mdtraj/mdtraj/pull/2106
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diff -ru mdtraj-1.11.0.orig/tests/test_dssp.py mdtraj-1.11.0/tests/test_dssp.py
4+
--- mdtraj-1.11.0.orig/tests/test_dssp.py 2025-05-20 19:25:49.000000000 +0200
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+++ mdtraj-1.11.0/tests/test_dssp.py 2026-01-21 08:12:36.196184875 +0100
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@@ -66,7 +66,7 @@
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def test_3(get_fn, tmpdir, pdbid):
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"""This test checks dssp assignments on pdb files downloaded from rcsb"""
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# 1COY gives a small error, due to a broken chain.
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- t = md.load_pdb("http://www.rcsb.org/pdb/files/%s.pdb" % pdbid)
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+ t = md.load_pdb("https://www.rcsb.org/pdb/files/%s.pdb" % pdbid)
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t = t.atom_slice(t.top.select_atom_indices("minimal"))
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assert_(call_dssp(get_fn, pdbid), md.compute_dssp(t, simplified=False)[0])
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diff -ru mdtraj-1.11.0.orig/tests/test_pdb.py mdtraj-1.11.0/tests/test_pdb.py
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--- mdtraj-1.11.0.orig/tests/test_pdb.py 2025-06-25 03:43:58.000000000 +0200
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+++ mdtraj-1.11.0/tests/test_pdb.py 2026-01-21 08:12:36.196184875 +0100
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@@ -211,8 +211,8 @@
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@flaky_pdb_dl
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def test_pdb_from_url():
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# load pdb from URL
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- t1 = load_pdb("http://www.rcsb.org/pdb/files/4ZUO.pdb.gz")
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- t2 = load_pdb("http://www.rcsb.org/pdb/files/4ZUO.pdb")
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+ t1 = load_pdb("https://www.rcsb.org/pdb/files/4ZUO.pdb.gz")
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+ t2 = load_pdb("https://www.rcsb.org/pdb/files/4ZUO.pdb")
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eq(t1.n_frames, 1)
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eq(t2.n_frames, 1)
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eq(t1.n_atoms, 6200)
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@@ -258,8 +258,8 @@
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def test_1vii_url_and_gz(get_fn):
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- t1 = load_pdb("http://www.rcsb.org/pdb/files/1vii.pdb.gz")
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- t2 = load_pdb("http://www.rcsb.org/pdb/files/1vii.pdb")
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+ t1 = load_pdb("https://www.rcsb.org/pdb/files/1vii.pdb.gz")
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+ t2 = load_pdb("https://www.rcsb.org/pdb/files/1vii.pdb")
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t3 = load_pdb(get_fn("1vii.pdb.gz"))
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t4 = load_pdb(get_fn("1vii.pdb"))
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eq(t1.n_frames, 1)

‎easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.9-gfbf-2023a.eb‎

Lines changed: 5 additions & 1 deletion
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@@ -25,7 +25,11 @@ exts_list = [
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'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'],
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}),
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('mdtraj', version, {
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'checksums': ['1b03f7ac753af5ca07cf874842689c8d49e791ee1242510875581df6100ca15e'],
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'patches': ['MDTraj-1.9.9_fix-tests-https.patch'],
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'checksums': [
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{'mdtraj-1.9.9.tar.gz': '1b03f7ac753af5ca07cf874842689c8d49e791ee1242510875581df6100ca15e'},
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{'MDTraj-1.9.9_fix-tests-https.patch': 'b80303ee805df6681d2e9b284250cca468c781e37a25101bd08d81ad579118e4'},
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],
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}),
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]
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‎easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.9_fix-tests-https.patch‎

Lines changed: 39 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,39 @@
1+
use https rather than http for download URLs, to fix broken tests;
2+
see https://github.com/mdtraj/mdtraj/issues/2126 and https://github.com/mdtraj/mdtraj/pull/2106
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diff -ru mdtraj-1.9.9.orig/tests/test_dssp.py mdtraj-1.9.9/tests/test_dssp.py
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--- mdtraj-1.9.9.orig/tests/test_dssp.py 2022-10-27 17:00:03.000000000 +0200
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+++ mdtraj-1.9.9/tests/test_dssp.py 2026-01-21 07:54:50.601558615 +0100
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@@ -61,7 +61,7 @@
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# 1COY gives a small error, due to a broken chain.
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pdbids = ['1GAI', '6gsv', '2AAC']
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for pdbid in pdbids:
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- t = md.load_pdb('http://www.rcsb.org/pdb/files/%s.pdb' % pdbid)
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+ t = md.load_pdb('https://www.rcsb.org/pdb/files/%s.pdb' % pdbid)
12+
t = t.atom_slice(t.top.select_atom_indices('minimal'))
13+
assert_(call_dssp(tmpdir, t), md.compute_dssp(t, simplified=False)[0])
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diff -ru mdtraj-1.9.9.orig/tests/test_pdb.py mdtraj-1.9.9/tests/test_pdb.py
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--- mdtraj-1.9.9.orig/tests/test_pdb.py 2022-11-06 02:55:17.000000000 +0100
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+++ mdtraj-1.9.9/tests/test_pdb.py 2026-01-21 07:54:50.601558615 +0100
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@@ -195,8 +195,8 @@
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20+
def test_pdb_from_url():
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# load pdb from URL
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- t1 = load_pdb('http://www.rcsb.org/pdb/files/4ZUO.pdb.gz')
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- t2 = load_pdb('http://www.rcsb.org/pdb/files/4ZUO.pdb')
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+ t1 = load_pdb('https://www.rcsb.org/pdb/files/4ZUO.pdb.gz')
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+ t2 = load_pdb('https://www.rcsb.org/pdb/files/4ZUO.pdb')
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eq(t1.n_frames, 1)
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eq(t2.n_frames, 1)
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eq(t1.n_atoms, 6200)
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@@ -238,8 +238,8 @@
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t1 = load_pdb(get_fn('1ncw.pdb.gz'))
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32+
def test_1vii_url_and_gz(get_fn):
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- t1 = load_pdb('http://www.rcsb.org/pdb/files/1vii.pdb.gz')
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- t2 = load_pdb('http://www.rcsb.org/pdb/files/1vii.pdb')
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+ t1 = load_pdb('https://www.rcsb.org/pdb/files/1vii.pdb.gz')
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+ t2 = load_pdb('https://www.rcsb.org/pdb/files/1vii.pdb')
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t3 = load_pdb(get_fn('1vii.pdb.gz'))
38+
t4 = load_pdb(get_fn('1vii.pdb'))
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eq(t1.n_frames, 1)

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