tests: give repack and split their own test module

tests/test_cli.py

@@ -45,150 +45,12 @@ def test_compressed(method):
     assert ccue.data["uncompressed"] == 0
 
 
-@pytest.mark.filterwarnings(
-    "ignore::dclab.rtdc_dataset.config.WrongConfigurationTypeWarning")
-def test_compressed_split():
-    """Make sure the split output data are compressed"""
-    path_in = retrieve_data("fmt-hdf5_mask-contour_2018.zip")
-    # same directory (will be cleaned up with path_in)
-    path_out = path_in.parent
-
-    paths = cli.split(path_in=path_in,
-                      path_out=path_out,
-                      split_events=3,
-                      ret_out_paths=True)
-
-    for pp in paths:
-        ic = rtdc_dataset.check.IntegrityChecker(pp)
-        ccue = ic.check_compression()[0]
-        assert ccue.data["uncompressed"] == 0
-
-
 def test_method_available():
     # DCOR depotize needs this
     assert hasattr(cli, "get_job_info")
     assert hasattr(cli, "get_command_log")
 
 
-@pytest.mark.filterwarnings(
-    "ignore::dclab.rtdc_dataset.config.WrongConfigurationTypeWarning")
-def test_repack_basic():
-    path_in = retrieve_data("fmt-hdf5_mask-contour_2018.zip")
-    # same directory (will be cleaned up with path_in)
-    path_out = path_in.with_name("repacked.rtdc")
-
-    cli.repack(path_out=path_out, path_in=path_in)
-
-    with new_dataset(path_out) as dsj, new_dataset(path_in) as ds0:
-        assert len(dsj)
-        assert len(dsj) == len(ds0)
-        for feat in ds0.features_innate:
-            if feat in ds0.features_scalar:
-                assert np.all(dsj[feat] == ds0[feat]), feat
-        for ii in range(len(ds0)):
-            assert np.all(dsj["contour"][ii] == ds0["contour"][ii])
-            assert np.all(dsj["image"][ii] == ds0["image"][ii])
-            assert np.all(dsj["mask"][ii] == ds0["mask"][ii])
-
-
-@pytest.mark.filterwarnings(
-    "ignore::dclab.rtdc_dataset.config.WrongConfigurationTypeWarning")
-def test_repack_remove_secrets():
-    path_in = retrieve_data("fmt-hdf5_mask-contour_2018.zip")
-    # same directory (will be cleaned up with path_in)
-    path_out = path_in.with_name("repacked.rtdc")
-
-    with h5py.File(path_in, "a") as h5:
-        h5.attrs["experiment:sample"] = "my dirty secret"
-
-    with h5py.File(path_in, "a") as h5:
-        h5.attrs["experiment:sample"] = "sunshine"
-
-    # test whether the dirty secret is still there
-    with open(str(path_in), "rb") as fd:
-        data = fd.read()
-        assert str(data).count("my dirty secret")
-
-    # now repack
-    cli.repack(path_out=path_out, path_in=path_in)
-
-    # clean?
-    with open(str(path_out), "rb") as fd:
-        data = fd.read()
-        assert not str(data).count("my dirty secret")
-
-
-@pytest.mark.filterwarnings(
-    "ignore::dclab.rtdc_dataset.config.WrongConfigurationTypeWarning")
-def test_repack_strip_logs():
-    path_in = retrieve_data("fmt-hdf5_mask-contour_2018.zip")
-    # same directory (will be cleaned up with path_in)
-    path_out = path_in.with_name("repacked.rtdc")
-
-    # write some logs
-    with h5py.File(path_in, "a") as h5:
-        hw = rtdc_dataset.RTDCWriter(h5)
-        hw.store_log("test_log", ["peter", "hans"])
-
-    cli.repack(path_out=path_out, path_in=path_in, strip_logs=True)
-
-    with new_dataset(path_out) as dsj, new_dataset(path_in) as ds0:
-        assert ds0.logs
-        assert not dsj.logs
-
-
-@pytest.mark.filterwarnings(
-    "ignore::dclab.rtdc_dataset.config.WrongConfigurationTypeWarning")
-def test_repack_user_metadata():
-    path_in = retrieve_data("fmt-hdf5_mask-contour_2018.zip")
-    with h5py.File(path_in, "a") as h5:
-        h5.attrs["user:peter"] = "hans"
-
-    # same directory (will be cleaned up with path_in)
-    path_out = path_in.with_name("repacked.rtdc")
-
-    cli.repack(path_out=path_out, path_in=path_in)
-
-    with new_dataset(path_out) as ds:
-        assert ds.config["user"]["peter"] == "hans"
-
-
-@pytest.mark.filterwarnings(
-    "ignore::dclab.rtdc_dataset.config.WrongConfigurationTypeWarning")
-def test_split():
-    path_in = retrieve_data("fmt-hdf5_mask-contour_2018.zip")
-    paths = cli.split(path_in=path_in, split_events=3, ret_out_paths=True)
-    with new_dataset(path_in) as ds:
-        ecount = 0
-        for pp in paths:
-            with new_dataset(pp) as di:
-                for feat in ds.features_scalar:
-                    if feat in ["index",
-                                "time",  # issue 204
-                                ]:
-                        continue
-                    assert np.all(
-                        ds[feat][ecount:ecount + len(di)] == di[feat]), feat
-                ecount += len(di)
-
-
-@pytest.mark.filterwarnings(
-    "ignore::dclab.rtdc_dataset.config.WrongConfigurationTypeWarning")
-def test_split_traces():
-    path_in = retrieve_data("fmt-hdf5_fl_2018.zip")
-    paths = cli.split(path_in=path_in, split_events=3, ret_out_paths=True)
-    with new_dataset(path_in) as ds:
-        ecount = 0
-        for pp in paths:
-            with new_dataset(pp) as di:
-                for flkey in ds["trace"].keys():
-                    trace1 = ds["trace"][flkey][ecount:ecount + len(di)]
-                    trace2 = di["trace"][flkey][:]
-                    assert len(trace1) == len(trace2)
-                    assert np.all(trace1 == trace2), flkey
-                ecount += len(di)
-
-
 def test_tdms2rtdc():
     pytest.importorskip("nptdms")
     path_in = retrieve_data("fmt-tdms_shapein-2.0.1-no-image_2017.zip")

tests/test_cli_repack.py

@@ -0,0 +1,90 @@
+from dclab import cli, new_dataset, rtdc_dataset
+
+import h5py
+import numpy as np
+import pytest
+
+from helper_methods import retrieve_data
+
+
+@pytest.mark.filterwarnings(
+    "ignore::dclab.rtdc_dataset.config.WrongConfigurationTypeWarning")
+def test_repack_basic():
+    path_in = retrieve_data("fmt-hdf5_mask-contour_2018.zip")
+    # same directory (will be cleaned up with path_in)
+    path_out = path_in.with_name("repacked.rtdc")
+
+    cli.repack(path_in=path_in, path_out=path_out)
+
+    with new_dataset(path_out) as dsj, new_dataset(path_in) as ds0:
+        assert len(dsj)
+        assert len(dsj) == len(ds0)
+        for feat in ds0.features_innate:
+            if feat in ds0.features_scalar:
+                assert np.all(dsj[feat] == ds0[feat]), feat
+        for ii in range(len(ds0)):
+            assert np.all(dsj["contour"][ii] == ds0["contour"][ii])
+            assert np.all(dsj["image"][ii] == ds0["image"][ii])
+            assert np.all(dsj["mask"][ii] == ds0["mask"][ii])
+
+
+@pytest.mark.filterwarnings(
+    "ignore::dclab.rtdc_dataset.config.WrongConfigurationTypeWarning")
+def test_repack_remove_secrets():
+    path_in = retrieve_data("fmt-hdf5_mask-contour_2018.zip")
+    # same directory (will be cleaned up with path_in)
+    path_out = path_in.with_name("repacked.rtdc")
+
+    with h5py.File(path_in, "a") as h5:
+        h5.attrs["experiment:sample"] = "my dirty secret"
+
+    with h5py.File(path_in, "a") as h5:
+        h5.attrs["experiment:sample"] = "sunshine"
+
+    # test whether the dirty secret is still there
+    with open(str(path_in), "rb") as fd:
+        data = fd.read()
+        assert str(data).count("my dirty secret")
+
+    # now repack
+    cli.repack(path_in=path_in, path_out=path_out)
+
+    # clean?
+    with open(str(path_out), "rb") as fd:
+        data = fd.read()
+        assert not str(data).count("my dirty secret")
+
+
+@pytest.mark.filterwarnings(
+    "ignore::dclab.rtdc_dataset.config.WrongConfigurationTypeWarning")
+def test_repack_strip_logs():
+    path_in = retrieve_data("fmt-hdf5_mask-contour_2018.zip")
+    # same directory (will be cleaned up with path_in)
+    path_out = path_in.with_name("repacked.rtdc")
+
+    # write some logs
+    with h5py.File(path_in, "a") as h5:
+        hw = rtdc_dataset.RTDCWriter(h5)
+        hw.store_log("test_log", ["peter", "hans"])
+
+    cli.repack(path_in=path_in, path_out=path_out, strip_logs=True)
+
+    with new_dataset(path_out) as dsj, new_dataset(path_in) as ds0:
+        assert ds0.logs
+        assert not dsj.logs
+
+
+@pytest.mark.filterwarnings(
+    "ignore::dclab.rtdc_dataset.config.WrongConfigurationTypeWarning")
+def test_repack_user_metadata():
+    path_in = retrieve_data("fmt-hdf5_mask-contour_2018.zip")
+    with h5py.File(path_in, "a") as h5:
+        h5.attrs["user:peter"] = "hans"
+
+    # same directory (will be cleaned up with path_in)
+    path_out = path_in.with_name("repacked.rtdc")
+
+    cli.repack(path_in=path_in, path_out=path_out)
+
+    with new_dataset(path_out) as ds:
+        assert ds.config["user"]["peter"] == "hans"

tests/test_cli_split.py

@@ -0,0 +1,73 @@
+import sys
+import tempfile
+import pathlib
+import shutil
+
+from dclab import cli, new_dataset, rtdc_dataset
+
+import h5py
+import numpy as np
+import pytest
+
+from helper_methods import retrieve_data
+
+
+
+@pytest.mark.filterwarnings(
+    "ignore::dclab.rtdc_dataset.config.WrongConfigurationTypeWarning")
+def test_compressed_split():
+    """Make sure the split output data are compressed"""
+    path_in = retrieve_data("fmt-hdf5_mask-contour_2018.zip")
+    # same directory (will be cleaned up with path_in)
+    path_out = path_in.parent
+
+    paths = cli.split(path_in=path_in,
+                      path_out=path_out,
+                      split_events=3,
+                      ret_out_paths=True)
+
+    for pp in paths:
+        ic = rtdc_dataset.check.IntegrityChecker(pp)
+        ccue = ic.check_compression()[0]
+        assert ccue.data["uncompressed"] == 0
+
+
+
+
+
+@pytest.mark.filterwarnings(
+    "ignore::dclab.rtdc_dataset.config.WrongConfigurationTypeWarning")
+def test_split():
+    path_in = retrieve_data("fmt-hdf5_mask-contour_2018.zip")
+    paths = cli.split(path_in=path_in, split_events=3, ret_out_paths=True)
+    with new_dataset(path_in) as ds:
+        ecount = 0
+        for pp in paths:
+            with new_dataset(pp) as di:
+                for feat in ds.features_scalar:
+                    if feat in ["index",
+                                "time",  # issue 204
+                                ]:
+                        continue
+                    assert np.all(
+                        ds[feat][ecount:ecount + len(di)] == di[feat]), feat
+                ecount += len(di)
+
+
+
+
+@pytest.mark.filterwarnings(
+    "ignore::dclab.rtdc_dataset.config.WrongConfigurationTypeWarning")
+def test_split_traces():
+    path_in = retrieve_data("fmt-hdf5_fl_2018.zip")
+    paths = cli.split(path_in=path_in, split_events=3, ret_out_paths=True)
+    with new_dataset(path_in) as ds:
+        ecount = 0
+        for pp in paths:
+            with new_dataset(pp) as di:
+                for flkey in ds["trace"].keys():
+                    trace1 = ds["trace"][flkey][ecount:ecount + len(di)]
+                    trace2 = di["trace"][flkey][:]
+                    assert len(trace1) == len(trace2)
+                    assert np.all(trace1 == trace2), flkey
+                ecount += len(di)