use contextmanager for tempdir

broadinstitute · Mar 20, 2024 · 98ac0f8 · 98ac0f8
1 parent e3c9f8b
commit 98ac0f8
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Showing 2 changed files with 19 additions and 19 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -190,7 +190,7 @@ jobs:
           mkdir coverage
       - name: test with docker
         run: |
-          docker run -e _JAVA_OPTIONS -e PYTEST_ADDOPTS -v `pwd`/coverage:/coverage -v `pwd`/test:/opt/viral-ngs/source/test:rw --entrypoint /bin/bash $DOCKER_TAG -c 'set -e; cd /opt/viral-ngs/source; env; echo "LD_LIBRARY_PATH: $LD_LIBRARY_PATH"; export LD_LIBRARY_PATH="/opt/miniconda/envs/viral-ngs-env/lib:/usr/local/lib:${LD_LIBRARY_PATH}"; echo "$(nproc)"; python -c "import locale; print(locale.getpreferredencoding(False))"; pytest test/unit; cp .coverage /coverage'
+          docker run -e _JAVA_OPTIONS -e PYTEST_ADDOPTS -v `pwd`/coverage:/coverage -v `pwd`/test:/opt/viral-ngs/source/test:rw --entrypoint /bin/bash $DOCKER_TAG -c 'set -e; cd /opt/viral-ngs/source; env; echo "LD_LIBRARY_PATH: $LD_LIBRARY_PATH"; export LD_LIBRARY_PATH="/opt/miniconda/envs/viral-ngs-env/lib:/usr/local/lib:${LD_LIBRARY_PATH}"; echo "nproc: $(nproc)"; python -c "import locale; print(locale.getpreferredencoding(False))"; pytest test/unit; cp .coverage /coverage'
       - name: run coveralls
         run: |
           mv coverage/.coverage .

diff --git a/phylo/vphaser2.py b/phylo/vphaser2.py
@@ -59,21 +59,21 @@ def iterate(self, inBam, numThreads=None):
           SNP_or_LP_Profile1, SNP_or_LP_Profile2, ...]
         """
         #outdir = tempfile.mkdtemp('vphaser2')
-        outdir = util.file.tmp_dir(prefix='vphaser2')
-        try:
-            self.execute(inBam, outdir, numThreads)
-        finally:
-            # these V-Phaser droppings cause problems if they persist
-            bti = inBam + '.bti'
-            if os.path.isfile(bti):
-                os.unlink(bti)
-        chromNames = pysam.Samfile(inBam).references
-        for chromName in chromNames:
-            outfile = os.path.join(outdir, chromName + '.var.raw.txt')
-            if not os.path.exists(outfile):
-                continue
-            with open(outfile, 'rt') as inf:
-                for line in inf:
-                    if not line.startswith('#'):
-                        yield [chromName] + line.strip().split()
-        shutil.rmtree(outdir)
+        with util.file.tmp_dir(prefix='vphaser2') as outdir:
+            try:
+                self.execute(inBam, outdir, numThreads)
+            finally:
+                # these V-Phaser droppings cause problems if they persist
+                bti = inBam + '.bti'
+                if os.path.isfile(bti):
+                    os.unlink(bti)
+            chromNames = pysam.Samfile(inBam).references
+            for chromName in chromNames:
+                outfile = os.path.join(outdir, chromName + '.var.raw.txt')
+                if not os.path.exists(outfile):
+                    continue
+                with open(outfile, 'rt') as inf:
+                    for line in inf:
+                        if not line.startswith('#'):
+                            yield [chromName] + line.strip().split()
+            #shutil.rmtree(outdir)