removed import *

broadinstitute · Jan 30, 2019 · f8ce593 · f8ce593
1 parent d2ad5d4
commit f8ce593
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Showing 3 changed files with 15 additions and 9 deletions.
diff --git a/test/pipelines/snakemake/test_diamond.py b/test/pipelines/snakemake/test_diamond.py
@@ -1,17 +1,20 @@
 #!/usr/bin/env python
 
-import os
+import os, os.path
 import sys
 
 import pytest
 
 import tools
 from test.pipelines.snakemake import snake
-from test.integration.test_diamond import * # for pytest fixtures
+from test.integration.test_diamond import fastq_to_sam, sam_to_fastq, diamond, krona, db_type, input_bam, \
+    input_fastqs, taxonomy_db, diamond_db, krona_db, test_diamond
 
 @pytest.mark.skipif(tools.is_osx(), reason="not currently tested under OSX")
 @pytest.mark.skipif(sys.version_info < (3, 5), reason="Python version is too old for snakemake.")
 def test_pipes(tmpdir_function, diamond_db, taxonomy_db, krona_db, input_bam):
+    join = os.path.join
+
     runner = snake.SnakemakeRunner(workdir=tmpdir_function)
     override_config = {
         'diamond_db': diamond_db,
@@ -32,4 +35,4 @@ def test_pipes(tmpdir_function, diamond_db, taxonomy_db, krona_db, input_bam):
     )
     runner.run([krona_out])
     assert os.path.getsize(os.path.join(runner.workdir, diamond_out)) > 0
-    assert os.path.getsize(os.path.join(runner.workdir, krona_out)) > 0
+    assert os.path.getsize(os.path.join(runner.workdir, krona_out)) > 0
diff --git a/test/pipelines/snakemake/test_kraken.py b/test/pipelines/snakemake/test_kraken.py
@@ -1,15 +1,17 @@
 #!/usr/bin/env python
 
-import os
+import os, os.path
+
 import sys
 
 import pytest
 
 from test.pipelines.snakemake import snake
-from test.integration.test_kraken import * # for pytest fixtures
+from test.integration.test_kraken import input_bam, kraken, krona, db_type, kraken_db, krona_db
 
 @pytest.mark.skipif(sys.version_info < (3, 5), reason="Python version is too old for snakemake.")
 def test_pipes(tmpdir_function, kraken_db, krona_db, input_bam):
+    join = os.path.join
     runner = snake.SnakemakeRunner(workdir=tmpdir_function)
     override_config = {
         'kraken_db': kraken_db,
@@ -33,4 +35,4 @@ def test_pipes(tmpdir_function, kraken_db, krona_db, input_bam):
     # runner.run(['all_metagenomics'])
     runner.run([kraken_out, krona_out])
     assert os.path.getsize(os.path.join(runner.workdir, kraken_out)) > 0
-    assert os.path.getsize(os.path.join(runner.workdir, krona_out)) > 0
+    assert os.path.getsize(os.path.join(runner.workdir, krona_out)) > 0
diff --git a/test/pipelines/snakemake/test_metagenomics_align.py b/test/pipelines/snakemake/test_metagenomics_align.py
@@ -1,15 +1,16 @@
 #!/usr/bin/env python
 
-import os
+import os, os.path
 import sys
 
 import pytest
 
 from test.pipelines.snakemake import snake
-from test.integration.test_metagenomics_align import * # for pytest fixtures
+from test.integration.test_metagenomics_align import fastq_to_sam, taxonomy_db, input_bam, bwa, db_type, bwa_db
 
 @pytest.mark.skipif(sys.version_info < (3, 5), reason="Python version is too old for snakemake.")
 def test_pipes(tmpdir_function, bwa_db, taxonomy_db, input_bam):
+    join = os.path.join
     runner = snake.SnakemakeRunner(workdir=tmpdir_function)
     override_config = {
         'align_rna_db': bwa_db,
@@ -32,4 +33,4 @@ def test_pipes(tmpdir_function, bwa_db, taxonomy_db, input_bam):
 
     runner.run([report_out])
     assert os.path.getsize(os.path.join(runner.workdir, report_out)) > 0
-    assert os.path.getsize(os.path.join(runner.workdir, bam_out)) > 0
+    assert os.path.getsize(os.path.join(runner.workdir, bam_out)) > 0