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Fix FileNotFoundErrors to support windows #1

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Fix FileNotFoundErrors to support windows #1

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fc112b8
Fix FileNotFoundErrors to support windows
mataton Apr 4, 2024
1a116cd
Merge branch 'qiyun_windows' into windows
mataton Apr 5, 2024
e656012
Use dirname over rsplit
mataton Apr 5, 2024
8ae53dd
Fix temp file opening issues
mataton Apr 8, 2024
4b3adc9
Fix other temp file issues
mataton Apr 8, 2024
d00f947
Supporting NumPy 2.0 (#950)
qiyunzhu Apr 10, 2024
50b6908
removed dependency on natsort (#953)
qiyunzhu Apr 10, 2024
bdbc4db
Fix linting and put unlink in tearDown
mataton Apr 11, 2024
b0654ba
Testing workflow failure of python3.7 on windows
mataton Apr 11, 2024
07236ff
Remove test line for python3.7
mataton Apr 11, 2024
e38dae5
Merge branch 'master' into windows
mataton Apr 15, 2024
563eda1
Utilize setUp and tearDown for removing tmp files
mataton Apr 15, 2024
00a532e
Update changelog
mataton Apr 15, 2024
bf11bfd
Update ChangeLog.md
wasade Apr 15, 2024
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13 changes: 7 additions & 6 deletions biom/tests/test_cli/test_subset_table.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,9 +55,10 @@ def test_invalid_input(self):
def test_subset_samples_hdf5(self):
"""Correctly subsets samples in a hdf5 table"""
cwd = os.getcwd()
if '/' in __file__:
os.chdir(__file__.rsplit('/', 1)[0])
obs = _subset_table(hdf5_biom='test_data/test.biom', axis='sample',
if os.path.sep in __file__:
os.chdir(__file__.rsplit(os.path.sep, 1)[0])
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__file__.rsplit(os.path.sep, 1)[0] can be os.path.dirname(__file__), I guess.

obs = _subset_table(hdf5_biom=os.path.join('test_data', 'test.biom'),
axis='sample',
ids=['Sample1', 'Sample2', 'Sample3'],
json_table_str=None)
os.chdir(cwd)
Expand All @@ -71,9 +72,9 @@ def test_subset_samples_hdf5(self):
def test_subset_observations_hdf5(self):
"""Correctly subsets samples in a hdf5 table"""
cwd = os.getcwd()
if '/' in __file__:
os.chdir(__file__.rsplit('/', 1)[0])
obs = _subset_table(hdf5_biom='test_data/test.biom',
if os.path.sep in __file__:
os.chdir(__file__.rsplit(os.path.sep, 1)[0])
obs = _subset_table(hdf5_biom=os.path.join('test_data', 'test.biom'),
axis='observation',
ids=['GG_OTU_1', 'GG_OTU_3', 'GG_OTU_5'],
json_table_str=None)
Expand Down
6 changes: 3 additions & 3 deletions biom/tests/test_cli/test_table_normalizer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,9 +24,9 @@ def setUp(self):
self.cmd = _normalize_table

cwd = os.getcwd()
if '/' in __file__:
os.chdir(__file__.rsplit('/', 1)[0])
self.table = biom.load_table('test_data/test.json')
if os.path.sep in __file__:
os.chdir(__file__.rsplit(os.path.sep, 1)[0])
self.table = biom.load_table(os.path.join('test_data', 'test.json'))
os.chdir(cwd)

def test_bad_inputs(self):
Expand Down
3 changes: 2 additions & 1 deletion biom/tests/test_cli/test_validate_table.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,8 @@ def setUp(self):
self.to_remove = []

cur_path = os.path.split(os.path.abspath(__file__))[0]
examples_path = os.path.join(cur_path.rsplit('/', 3)[0], 'examples')
examples_path = os.path.join(cur_path.rsplit(os.path.sep, 3)[0],
'examples')
self.hdf5_file_valid = os.path.join(examples_path,
'min_sparse_otu_table_hdf5.biom')
self.hdf5_file_valid_md = os.path.join(examples_path,
Expand Down
31 changes: 16 additions & 15 deletions biom/tests/test_parse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -281,9 +281,10 @@ def test_parse_adjacency_table_no_header(self):
def test_parse_biom_table_hdf5(self):
"""Make sure we can parse a HDF5 table through the same loader"""
cwd = os.getcwd()
if '/' in __file__[1:]:
os.chdir(__file__.rsplit('/', 1)[0])
Table.from_hdf5(h5py.File('test_data/test.biom', 'r'))
if os.path.sep in __file__[1:]:
os.chdir(__file__.rsplit(os.path.sep, 1)[0])
Table.from_hdf5(h5py.File(os.path.join('test_data', 'test.biom'),
'r'))
os.chdir(cwd)

def test_save_table_filepath(self):
Expand All @@ -296,23 +297,23 @@ def test_save_table_filepath(self):

def test_load_table_filepath(self):
cwd = os.getcwd()
if '/' in __file__[1:]:
os.chdir(__file__.rsplit('/', 1)[0])
load_table('test_data/test.biom')
if os.path.sep in __file__[1:]:
os.chdir(__file__.rsplit(os.path.sep, 1)[0])
load_table(os.path.join('test_data', 'test.biom'))
os.chdir(cwd)

def test_load_table_inmemory(self):
cwd = os.getcwd()
if '/' in __file__[1:]:
os.chdir(__file__.rsplit('/', 1)[0])
load_table(h5py.File('test_data/test.biom', 'r'))
if os.path.sep in __file__[1:]:
os.chdir(__file__.rsplit(os.path.sep, 1)[0])
load_table(h5py.File(os.path.join('test_data', 'test.biom'), 'r'))
os.chdir(cwd)

def test_load_table_inmemory_json(self):
cwd = os.getcwd()
if '/' in __file__[1:]:
os.chdir(__file__.rsplit('/', 1)[0])
load_table(open('test_data/test.json'))
if os.path.sep in __file__[1:]:
os.chdir(__file__.rsplit(os.path.sep, 1)[0])
load_table(open(os.path.join('test_data', 'test.json')))
os.chdir(cwd)

def test_load_table_inmemory_stringio(self):
Expand Down Expand Up @@ -350,10 +351,10 @@ def test_parse_biom_table_with_hdf5(self):
"""tests for parse_biom_table when we have h5py"""
# We will round-trip the HDF5 file to several different formats, and
# make sure we can recover the same table using parse_biom_table
if '/' in __file__[1:]:
os.chdir(__file__.rsplit('/', 1)[0])
if os.path.sep in __file__[1:]:
os.chdir(__file__.rsplit(os.path.sep, 1)[0])

t = parse_biom_table(h5py.File('test_data/test.biom', 'r'))
t = parse_biom_table(h5py.File(os.path.join('test_data', 'test.biom'), 'r'))

# These things are not round-trippable using the general-purpose
# parse_biom_table function
Expand Down