Merge pull request #26 from klarman-cell-observatory/yiming

Modify dockerfile to enable unit test
lilab-bcb · Jun 19, 2020 · 1a39d90 · 1a39d90
2 parents 72df0e0 + c11cd9d
commit 1a39d90
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Showing 2 changed files with 8 additions and 6 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -33,6 +33,8 @@ RUN apt-get -qq -y remove curl gnupg && \
 
 COPY . /pegasusio/
 WORKDIR /pegasusio/tests
-RUN git clone https://github.com/klarman-cell-observatory/pegasus-test-data.git
+RUN git clone https://github.com/klarman-cell-observatory/pegasusio-test-data.git
 WORKDIR /pegasusio/
 RUN pip3 install -e .
+
+WORKDIR /pegasusio/tests
diff --git a/tests/test_io.py b/tests/test_io.py
@@ -5,26 +5,26 @@
 class TestIO(unittest.TestCase):
 
     def test_read_h5ad(self):
-        data = io.read_input("tests/pegasusio-test-data/case1/pbmc3k.h5ad", genome = 'hg19')
+        data = io.read_input("pegasusio-test-data/case1/pbmc3k.h5ad", genome = 'hg19')
         self.assertEqual(data.shape, (2638, 1838))
 
     def test_mixture_data(self):
-        data = io.read_input("tests/pegasusio-test-data/case2/1k_hgmm_v3_filtered_feature_bc_matrix.h5")
+        data = io.read_input("pegasusio-test-data/case2/1k_hgmm_v3_filtered_feature_bc_matrix.h5")
         data.select_data('mm10-rna')
         self.assertEqual(data.shape, (1063, 54232))
         data.select_data('hg19-rna')
         self.assertEqual(data.shape, (1063, 57905))
 
     def test_read_10x_mtx(self):
-        data = io.read_input("tests/pegasusio-test-data/case3/42468c97-1c5a-4c9f-86ea-9eaa1239445a.mtx", genome = 'hg19')
+        data = io.read_input("pegasusio-test-data/case3/42468c97-1c5a-4c9f-86ea-9eaa1239445a.mtx", genome = 'hg19')
         self.assertEqual(data.shape, (2544, 58347))
 
     def test_read_loom(self):
-        data = io.read_input("tests/pegasusio-test-data/case3/pancreas.loom", genome = 'hg19')
+        data = io.read_input("pegasusio-test-data/case3/pancreas.loom", genome = 'hg19')
         self.assertEqual(data.shape, (2544, 58347))
 
     def test_read_zarr(self):
-        data = io.read_input("tests/pegasusio-test-data/case4/MantonBM1_1_dbls.zarr")
+        data = io.read_input("pegasusio-test-data/case4/MantonBM1_1_dbls.zarr")
         self.assertEqual(data.shape, (4274, 19360))
 
 if __name__ == '__main__':