rename package (#473)

broadinstitute · Oct 17, 2024 · 5ad8d58 · 5ad8d58
1 parent 8af26a7
commit 5ad8d58
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Showing 16 changed files with 20 additions and 20 deletions.
diff --git a/...rkflows/python-dropseq_metadata-conda.yml → ...lows/python-dropseq_aggregation-conda.yml b/...rkflows/python-dropseq_metadata-conda.yml → ...lows/python-dropseq_aggregation-conda.yml
@@ -6,7 +6,7 @@ on:
   pull_request:
     branches: [ "master" ]
     paths:
-      - 'src/python/dropseq_metadata/**'
+      - 'src/python/dropseq_aggregation/**'
 
 
 jobs:
@@ -44,11 +44,11 @@ jobs:
         echo "use_lockfiles: false" >> ~/.mambarc
     - name: Install dependencies
       run: |
-        cd src/python/dropseq_metadata
+        cd src/python/dropseq_aggregation
         conda env update --file environment.yml --name base
     - name: Lint with flake8
       run: |
-        cd src/python/dropseq_metadata
+        cd src/python/dropseq_aggregation
 
         # Explicitly using the classic solver to avoid:
         #   a) "libarchive.so.20: cannot open shared object", and
@@ -65,5 +65,5 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with unittest
       run: |
-        cd src/python/dropseq_metadata
+        cd src/python/dropseq_aggregation
         PYTHONPATH=src python -m unittest discover -s tests
diff --git a/src/python/dropseq_metadata/LICENSE → src/python/dropseq_aggregation/LICENSE b/src/python/dropseq_metadata/LICENSE → src/python/dropseq_aggregation/LICENSE
diff --git a/src/python/dropseq_metadata/README.md → src/python/dropseq_aggregation/README.md b/src/python/dropseq_metadata/README.md → src/python/dropseq_aggregation/README.md
diff --git a/src/python/dropseq_metadata/environment.yml → ...ython/dropseq_aggregation/environment.yml b/src/python/dropseq_metadata/environment.yml → ...ython/dropseq_aggregation/environment.yml
@@ -1,4 +1,4 @@
-name: dropseq_metadata
+name: dropseq_aggregation
 channels:
   - conda-forge
   - nodefaults

diff --git a/src/python/dropseq_metadata/pyproject.toml → ...python/dropseq_aggregation/pyproject.toml b/src/python/dropseq_metadata/pyproject.toml → ...python/dropseq_aggregation/pyproject.toml
diff --git a/...metadata/src/dropseq_metadata/__init__.py → ...ation/src/dropseq_aggregation/__init__.py b/...metadata/src/dropseq_metadata/__init__.py → ...ation/src/dropseq_aggregation/__init__.py
diff --git a/...pseq_metadata/src/dropseq_metadata/cli.py → ...ggregation/src/dropseq_aggregation/cli.py b/...pseq_metadata/src/dropseq_metadata/cli.py → ...ggregation/src/dropseq_aggregation/cli.py
@@ -47,7 +47,7 @@
 
 
 def main(args=None):
-    parser = argparse.ArgumentParser(prog="dropseq_metadata", description=__doc__)
+    parser = argparse.ArgumentParser(prog="dropseq_aggregation", description=__doc__)
     parser.add_argument("--log-level", "-l", default="INFO", choices=dctLogLevel.keys(),
                         help="Set the logging level.  (default: %(default)s)")
     subparsers = parser.add_subparsers(

diff --git a/...c/dropseq_metadata/join_and_filter_tsv.py → ...ropseq_aggregation/join_and_filter_tsv.py b/...c/dropseq_metadata/join_and_filter_tsv.py → ...ropseq_aggregation/join_and_filter_tsv.py
diff --git a/...etadata/tests/test_join_and_filter_tsv.py → ...egation/tests/test_join_and_filter_tsv.py b/...etadata/tests/test_join_and_filter_tsv.py → ...egation/tests/test_join_and_filter_tsv.py
@@ -30,7 +30,7 @@
 
 import pandas.testing
 
-import dropseq_metadata.join_and_filter_tsv
+import dropseq_aggregation.join_and_filter_tsv
 
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
@@ -40,7 +40,7 @@
 
 class TestJoinAndFilterTSV(unittest.TestCase):
     def setUp(self):
-        self.testDataDir = "../../../testdata/python/dropseq_metadata/join_and_filter_tsv"
+        self.testDataDir = "../../../testdata/python/dropseq_aggregation/join_and_filter_tsv"
         self.tmpDir = tempfile.mkdtemp(".tmp", "join_and_filter_tsv.")
         self.outputFile = os.path.join(self.tmpDir, "output.tsv")
         self.options = OptionsTuple(open(self.outputFile, "w"))
@@ -53,7 +53,7 @@ def test_basic(self):
         secondary = os.path.join(self.testDataDir, "sample1.100.scPred.txt")
         options = self.options._replace(input=open(primary),
                                         join=[(secondary, "CELL_BARCODE", "CELL_BARCODE")])
-        self.assertEqual(dropseq_metadata.join_and_filter_tsv.main(options), 0)
+        self.assertEqual(dropseq_aggregation.join_and_filter_tsv.main(options), 0)
         self.assertSharedColumnsEqual(self.outputFile, primary)
         self.assertSharedColumnsEqual(self.outputFile, secondary)
 
@@ -62,7 +62,7 @@ def test_fewer_secondary(self):
         secondary = os.path.join(self.testDataDir, "sample1.50.scPred.txt")
         options = self.options._replace(input=open(primary),
                                         join=[(secondary, "CELL_BARCODE", "CELL_BARCODE")])
-        self.assertEqual(dropseq_metadata.join_and_filter_tsv.main(options), 0)
+        self.assertEqual(dropseq_aggregation.join_and_filter_tsv.main(options), 0)
         self.assertSharedColumnsEqual(self.outputFile, primary)
         self.assertSharedColumnsEqual(self.outputFile, secondary, wideRows=49)
 
@@ -71,7 +71,7 @@ def test_fewer_primary(self):
         secondary = os.path.join(self.testDataDir, "sample1.100.scPred.txt")
         options = self.options._replace(input=open(primary),
                                         join=[(secondary, "CELL_BARCODE", "CELL_BARCODE")])
-        self.assertEqual(dropseq_metadata.join_and_filter_tsv.main(options), 0)
+        self.assertEqual(dropseq_aggregation.join_and_filter_tsv.main(options), 0)
         self.assertSharedColumnsEqual(self.outputFile, primary)
         self.assertSharedColumnsEqual(self.outputFile, secondary, narrowRows=49)
 
@@ -82,7 +82,7 @@ def test_additional_join(self):
         options = self.options._replace(input=open(primary),
                                         join=[(secondary1, "CELL_BARCODE", "CELL_BARCODE"),
                                               (secondary2, "DONOR", "DONOR")])
-        self.assertEqual(dropseq_metadata.join_and_filter_tsv.main(options), 0)
+        self.assertEqual(dropseq_aggregation.join_and_filter_tsv.main(options), 0)
         self.assertSharedColumnsEqual(self.outputFile, primary)
         self.assertSharedColumnsEqual(self.outputFile, secondary1)
         self.assertMultiJoin(self.outputFile, secondary2, "DONOR", "DONOR")
@@ -94,7 +94,7 @@ def test_set(self):
         options = self.options._replace(input=open(primary),
                                         join=[(secondary, "CELL_BARCODE", "CELL_BARCODE")],
                                         set=setTuples)
-        self.assertEqual(dropseq_metadata.join_and_filter_tsv.main(options), 0)
+        self.assertEqual(dropseq_aggregation.join_and_filter_tsv.main(options), 0)
         outputDf = pd.read_csv(self.outputFile, sep='\t')
         for column, value in setTuples:
             self.assertTrue((outputDf[column] == value).all())
@@ -107,7 +107,7 @@ def test_min(self):
         options = self.options._replace(input=open(primary),
                                         join=[(secondary, "CELL_BARCODE", "CELL_BARCODE")],
                                         min=[("max.prob", "0.8")])
-        self.assertEqual(dropseq_metadata.join_and_filter_tsv.main(options), 0)
+        self.assertEqual(dropseq_aggregation.join_and_filter_tsv.main(options), 0)
         outputDf = pd.read_csv(self.outputFile, sep='\t')
         self.assertTrue((outputDf["max.prob"] >= 0.8).all())
         primaryDf = pd.read_csv(primary, sep='\t')
@@ -119,7 +119,7 @@ def test_max(self):
         options = self.options._replace(input=open(primary),
                                         join=[(secondary, "CELL_BARCODE", "CELL_BARCODE")],
                                         max=[("max.prob", "0.8")])
-        self.assertEqual(dropseq_metadata.join_and_filter_tsv.main(options), 0)
+        self.assertEqual(dropseq_aggregation.join_and_filter_tsv.main(options), 0)
         outputDf = pd.read_csv(self.outputFile, sep='\t')
         self.assertTrue((outputDf["max.prob"] <= 0.8).all())
         primaryDf = pd.read_csv(primary, sep='\t')
@@ -130,7 +130,7 @@ def test_include_file(self):
         includeFile = os.path.join(self.testDataDir, "donor_subset.txt")
         options = self.options._replace(input=open(primary),
                                         include_file=[("DONOR", includeFile)])
-        self.assertEqual(dropseq_metadata.join_and_filter_tsv.main(options), 0)
+        self.assertEqual(dropseq_aggregation.join_and_filter_tsv.main(options), 0)
         outputDf = pd.read_csv(self.outputFile, sep='\t')
         includeValues = pd.read_csv(includeFile, sep='\t', header=None).iloc[0]
         self.assertTrue((outputDf["DONOR"].isin(includeValues)).all())
@@ -140,7 +140,7 @@ def test_exclude_file(self):
         excludeFile = os.path.join(self.testDataDir, "donor_subset.txt")
         options = self.options._replace(input=open(primary),
                                         exclude_file=[("DONOR", excludeFile)])
-        self.assertEqual(dropseq_metadata.join_and_filter_tsv.main(options), 0)
+        self.assertEqual(dropseq_aggregation.join_and_filter_tsv.main(options), 0)
         outputDf = pd.read_csv(self.outputFile, sep='\t')
         excludeValues = pd.read_csv(excludeFile, sep='\t', header=None).iloc[0]
         self.assertFalse((outputDf["DONOR"].isin(excludeValues)).any())
@@ -152,7 +152,7 @@ def test_include_exclude(self):
         options = self.options._replace(input=open(primary),
                                         include=[["DONOR"] + donorsToInclude],
                                         exclude=[["predClass"] + predClassesToExclude])
-        self.assertEqual(dropseq_metadata.join_and_filter_tsv.main(options), 0)
+        self.assertEqual(dropseq_aggregation.join_and_filter_tsv.main(options), 0)
         outputDf = pd.read_csv(self.outputFile, sep='\t')
         self.assertTrue((outputDf["DONOR"].isin(donorsToInclude)).all())
         self.assertFalse((outputDf["predClass"].isin(predClassesToExclude)).any())
@@ -162,13 +162,13 @@ def test_negative_non_unique_join(self):
         secondary = os.path.join(self.testDataDir, "sample1.nonunique.scPred.txt")
         options = self.options._replace(input=open(primary),
                                         join=[(secondary, "CELL_BARCODE", "CELL_BARCODE")])
-        self.assertEqual(dropseq_metadata.join_and_filter_tsv.main(options), 1)
+        self.assertEqual(dropseq_aggregation.join_and_filter_tsv.main(options), 1)
 
     def test_boolean(self):
         primary = os.path.join(self.testDataDir, "sample1.100.cell_metadata.txt")
         options = self.options._replace(input=open(primary),
                                         exclude=[["doublet", "true"]])
-        self.assertEqual(dropseq_metadata.join_and_filter_tsv.main(options), 0)
+        self.assertEqual(dropseq_aggregation.join_and_filter_tsv.main(options), 0)
         outputDf = pd.read_csv(self.outputFile, sep='\t')
         self.assertFalse(outputDf["doublet"].any())
 

diff --git a/...data/join_and_filter_tsv/donor_subset.txt → ...tion/join_and_filter_tsv/donor_subset.txt b/...data/join_and_filter_tsv/donor_subset.txt → ...tion/join_and_filter_tsv/donor_subset.txt
diff --git a/..._filter_tsv/sample1.100.cell_metadata.txt → ..._filter_tsv/sample1.100.cell_metadata.txt b/..._filter_tsv/sample1.100.cell_metadata.txt → ..._filter_tsv/sample1.100.cell_metadata.txt
diff --git a/...oin_and_filter_tsv/sample1.100.scPred.txt → ...oin_and_filter_tsv/sample1.100.scPred.txt b/...oin_and_filter_tsv/sample1.100.scPred.txt → ...oin_and_filter_tsv/sample1.100.scPred.txt
diff --git a/...d_filter_tsv/sample1.50.cell_metadata.txt → ...d_filter_tsv/sample1.50.cell_metadata.txt b/...d_filter_tsv/sample1.50.cell_metadata.txt → ...d_filter_tsv/sample1.50.cell_metadata.txt
diff --git a/...join_and_filter_tsv/sample1.50.scPred.txt → ...join_and_filter_tsv/sample1.50.scPred.txt b/...join_and_filter_tsv/sample1.50.scPred.txt → ...join_and_filter_tsv/sample1.50.scPred.txt
diff --git a/...join_and_filter_tsv/sample1.donor_age.txt → ...join_and_filter_tsv/sample1.donor_age.txt b/...join_and_filter_tsv/sample1.donor_age.txt → ...join_and_filter_tsv/sample1.donor_age.txt
diff --git a/...d_filter_tsv/sample1.nonunique.scPred.txt → ...d_filter_tsv/sample1.nonunique.scPred.txt b/...d_filter_tsv/sample1.nonunique.scPred.txt → ...d_filter_tsv/sample1.nonunique.scPred.txt