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CI: fix mamba version and some test file paths #208

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merged 4 commits into from
Oct 3, 2024
Merged

CI: fix mamba version and some test file paths #208

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90136a5
Update some test file paths to fix CI errors
misialq Sep 27, 2024
e856caf
fixup! Update some test file paths to fix CI errors
misialq Sep 27, 2024
72b9f62
Fix mamba version in setup_miniconda
misialq Oct 2, 2024
a88b857
fixup! Update some test file paths to fix CI errors
misialq Oct 2, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ jobs:
uses: conda-incubator/setup-miniconda@v3
with:
python-version: 3.9
mamba-version: "*"
mamba-version: 1.5.10
channels: conda-forge,defaults
channel-priority: true
activate-environment: conda-env
Expand Down
8 changes: 3 additions & 5 deletions q2_moshpit/kraken2/tests/test_bracken.py
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Expand Up @@ -72,7 +72,7 @@ def test_run_bracken_one_sample(self, p1):
)

kraken2_report_fp = self.get_data_path(
'kraken2-report/sample1/sample1.report.txt'
'kraken2-reports-select/samples/sample1.report.txt'
)
bracken_report_dir = self.get_data_path('bracken-report')
obs_table = _run_bracken_one_sample(
Expand Down Expand Up @@ -113,15 +113,13 @@ def test_run_bracken_one_sample(self, p1):
side_effect=CalledProcessError(returncode=123, cmd='bracken')
)
def test_run_bracken_one_sample_error(self, p1):
kraken2_report_fp = self.get_data_path(
'kraken2-report/sample1/sample1.report.txt'
)
kraken2_report_fp = tempfile.NamedTemporaryFile()
bracken_report_dir = self.get_data_path('bracken-report')

with self.assertRaisesRegex(Exception, 'return code 123'):
_run_bracken_one_sample(
bracken_db=self.bracken_db_dir,
kraken2_report_fp=kraken2_report_fp,
kraken2_report_fp=kraken2_report_fp.name,
bracken_report_dir=bracken_report_dir,
tmp_dir=self.temp_dir,
threshold=self.kwargs['threshold'],
Expand Down
8 changes: 6 additions & 2 deletions q2_moshpit/kraken2/tests/test_database.py
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Original file line number Diff line number Diff line change
Expand Up @@ -203,7 +203,9 @@ def test_fetch_libraries_exception(self, p1):

@patch('q2_moshpit.kraken2.database.run_command')
def test_add_seqs_to_library(self, p1):
seqs = DNAFASTAFormat(self.get_data_path('mags/samp1/bin1.fa'), 'r')
seqs = DNAFASTAFormat(self.get_data_path(
'mags/sample1/3b72d1a7-ddb0-4dc7-ac36-080ceda04aaa.fasta'), 'r'
)

_add_seqs_to_library(self.kraken2_db_dir, seqs=seqs, no_masking=True)

Expand All @@ -218,7 +220,9 @@ def test_add_seqs_to_library(self, p1):
side_effect=CalledProcessError(123, 'cmd')
)
def test_add_seqs_to_library_exception(self, p1):
seqs = DNAFASTAFormat(self.get_data_path('mags/samp1/bin1.fa'), 'r')
seqs = DNAFASTAFormat(self.get_data_path(
'mags/sample1/3b72d1a7-ddb0-4dc7-ac36-080ceda04aaa.fasta'), 'r'
)

with self.assertRaisesRegex(
Exception,
Expand Down
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