refactor: move test suite out of caput (#274)

And fix the pytest.fixture things I was complaining about.

.github/workflows/main.yml

@@ -57,21 +57,18 @@ jobs:
 
     - name: Install pip dependencies
       run: |
-        pip install -e .
-        pip install -e .[mpi]
-        pip install -e .[compression]
-        pip install -e .[test]
+        pip install -e .[compression,mpi,test]
 
     - name: Run serial tests
-      run: pytest --doctest-modules caput/
+      run: pytest --doctest-modules .
 
     - name: Run parallel tests
       run: |
-        mpirun --oversubscribe -np 4 pytest caput/tests/test_memh5_parallel.py
-        mpirun --oversubscribe -np 4 pytest caput/tests/test_mpiarray.py
-        mpirun -np 1 pytest caput/tests/test_selection_parallel.py
-        mpirun --oversubscribe -np 2 pytest caput/tests/test_selection_parallel.py
-        mpirun --oversubscribe -np 4 pytest caput/tests/test_selection_parallel.py
+        mpirun --oversubscribe -np 4 pytest tests/test_memh5_parallel.py
+        mpirun --oversubscribe -np 4 pytest tests/test_mpiarray.py
+        mpirun -np 1 pytest tests/test_selection_parallel.py
+        mpirun --oversubscribe -np 2 pytest tests/test_selection_parallel.py
+        mpirun --oversubscribe -np 4 pytest tests/test_selection_parallel.py
 
   build-docs:
 

doc/conf.py

@@ -21,7 +21,7 @@
 import caput
 
 # Mock up modules missing on readthedocs.
-from mock import Mock as MagicMock
+from unittest.mock import Mock as MagicMock
 
 
 class Mock(MagicMock):

caput/tests/conftest.py → tests/conftest.py

@@ -6,9 +6,9 @@
 import numpy as np
 import pytest
 
-from ..pipeline import PipelineStopIteration, TaskBase, IterBase
-from ..scripts.runner import cli
-from .. import config, fileformats, mpiutil
+from caput.pipeline import PipelineStopIteration, TaskBase, IterBase
+from caput.scripts.runner import cli
+from caput import config, fileformats, mpiutil
 
 
 @pytest.fixture(scope="session")
@@ -106,16 +106,19 @@ def write_output(self, filename, output, file_format=None, **kwargs):
         raise NotImplementedError()
 
 
-eggs_pipeline_conf = """
+@pytest.fixture
+def run_pipeline():
+    """Provides the `run_pipeline` function which will run the pipeline."""
+    eggs_pipeline_conf = """
 ---
 pipeline:
   tasks:
-    - type: caput.tests.conftest.PrintEggs
+    - type: tests.conftest.PrintEggs
       params: eggs_params
-    - type: caput.tests.conftest.GetEggs
+    - type: tests.conftest.GetEggs
       params: eggs_params
       out: egg
-    - type: caput.tests.conftest.CookEggs
+    - type: tests.conftest.CookEggs
       params: cook_params
       in: egg
 eggs_params:
@@ -124,71 +127,53 @@ def write_output(self, filename, output, file_format=None, **kwargs):
   style: 'fried'
 """
 
-multi_eggs_pipeline_conf = """
----
-pipeline:
-  tasks:
-    - type: caput.tests.conftest.GetEggs
-      params: eggs_params
-      out: [color, egg]
-    - type: caput.tests.conftest.CookEggs
-      params: cook_params
-      in: egg
-    - type: caput.tests.conftest.CookEggs
-      params: cook_params
-      in: color
-eggs_params:
-  eggs: [['green', 'duck'], ['blue', 'ostrich']]
-cook_params:
-  style: 'fried'
-"""
-
+    def _run_pipeline(parameters=None, configstr=eggs_pipeline_conf):
+        """Run `caput.scripts.runner run` with given parameters and config.
 
-def run_pipeline(parameters=None, configstr=eggs_pipeline_conf):
-    """Run `caput.scripts.runner run` with given parameters and config.
+        Parameters
+        ----------
+        parameters : List[str]
+            Parameters to pass to the cli, for example `["--profile"]` (see `--help`).
+        configstr : str
+            YAML string to use as a config. This function will write it to a file that is then passed to the cli.
 
-    Parameters
-    ----------
-    parameters : List[str]
-        Parameters to pass to the cli, for example `["--profile"]` (see `--help`).
-    configstr : str
-        YAML string to use as a config. This function will write it to a file that is then passed to the cli.
+        Returns
+        -------
+        result : `click.testing.Result`
+            Holds the captured result. Try accessing e.g. `result.exit_code`, `result.output`.
+        """
+        with tempfile.NamedTemporaryFile("w+") as configfile:
+            configfile.write(configstr)
+            configfile.flush()
+            from click.testing import CliRunner
 
-    Returns
-    -------
-    result : `click.testing.Result`
-        Holds the captured result. Try accessing e.g. `result.exit_code`, `result.output`.
-    """
-    with tempfile.NamedTemporaryFile("w+") as configfile:
-        configfile.write(configstr)
-        configfile.flush()
-        from click.testing import CliRunner
+            runner = CliRunner()
+            if parameters is None:
+                return runner.invoke(cli, ["run", configfile.name])
+            else:
+                return runner.invoke(cli, ["run", *parameters, configfile.name])
 
-        runner = CliRunner()
-        if parameters is None:
-            return runner.invoke(cli, ["run", configfile.name])
-        else:
-            return runner.invoke(cli, ["run", *parameters, configfile.name])
+    return _run_pipeline
 
 
 @pytest.fixture
-def h5_file():
+def h5_file(rm_all_files):
     """Provides a file name and removes all files/dirs with the same prefix later."""
     fname = "tmp_test_memh5.h5"
     yield fname
     rm_all_files(fname)
 
 
 @pytest.fixture
-def zarr_file():
+def zarr_file(rm_all_files):
     """Provides a directory name and removes all files/dirs with the same prefix later."""
     fname = "tmp_test_memh5.zarr"
     yield fname
     rm_all_files(fname)
 
 
 @pytest.fixture
-def h5_file_distributed():
+def h5_file_distributed(rm_all_files):
     """Provides a file name and removes all files/dirs with the same prefix later."""
     fname = "tmp_test_memh5_distributed.h5"
     yield fname
@@ -197,16 +182,22 @@ def h5_file_distributed():
 
 
 @pytest.fixture
-def zarr_file_distributed():
+def zarr_file_distributed(rm_all_files):
     """Provides a directory name and removes all files/dirs with the same prefix later."""
     fname = "tmp_test_memh5.zarr"
     yield fname
     if mpiutil.rank == 0:
         rm_all_files(fname)
 
 
-def rm_all_files(file_name):
-    """Remove all files and directories starting with `file_name`."""
-    file_names = glob.glob(file_name + "*")
-    for fname in file_names:
-        fileformats.remove_file_or_dir(fname)
+@pytest.fixture
+def rm_all_files():
+    """Provides the `rm_all_files` function."""
+
+    def _rm_all_files(file_name):
+        """Remove all files and directories starting with `file_name`."""
+        file_names = glob.glob(file_name + "*")
+        for fname in file_names:
+            fileformats.remove_file_or_dir(fname)
+
+    return _rm_all_files

caput/tests/test_lint.py → tests/test_lint.py

@@ -23,16 +23,16 @@ def simple_config():
         "pipeline": {
             "tasks": [
                 {
-                    "type": "caput.tests.test_lint.DoNothing",
+                    "type": "tests.test_lint.DoNothing",
                     "out": "out1",
                 },
                 {
-                    "type": "caput.tests.test_lint.DoNothing",
+                    "type": "tests.test_lint.DoNothing",
                     "out": "out2",
                     "in": "out1",
                 },
                 {
-                    "type": "caput.tests.test_lint.DoNothing2",
+                    "type": "tests.test_lint.DoNothing2",
                     "in": "out2",
                     "out": "out3",
                     "requires": "out1",

tests/test_pipeline.py

@@ -0,0 +1,35 @@
+"""Test running the caput.pipeline."""
+
+
+def test_pipeline(run_pipeline):
+    """Test running a very simple pipeline."""
+    result = run_pipeline()
+    print(result.output)
+    assert result.exit_code == 0
+
+
+def test_pipeline_multiple_outputs(run_pipeline):
+    """Test running a very simple pipeline with a multi-output task."""
+
+    multi_eggs_pipeline_conf = """
+---
+pipeline:
+  tasks:
+    - type: tests.conftest.GetEggs
+      params: eggs_params
+      out: [color, egg]
+    - type: tests.conftest.CookEggs
+      params: cook_params
+      in: egg
+    - type: tests.conftest.CookEggs
+      params: cook_params
+      in: color
+eggs_params:
+  eggs: [['green', 'duck'], ['blue', 'ostrich']]
+cook_params:
+  style: 'fried'
+"""
+
+    result = run_pipeline(configstr=multi_eggs_pipeline_conf)
+    print(result.output)
+    assert result.exit_code == 0

caput/tests/test_psutilprofiler.py → tests/test_psutilprofiler.py

@@ -1,10 +1,8 @@
 """Test running the caput.pipeline."""
 
-from caput.tests import conftest
 
-
-def test_pipeline():
+def test_pipeline(run_pipeline):
     """Test profiling a very simple pipeline."""
-    result = conftest.run_pipeline(["--psutil"])
+    result = run_pipeline(["--psutil"])
     print(result.output)
     assert result.exit_code == 0

caput/tests/test_selection.py → tests/test_selection.py

@@ -6,7 +6,6 @@
 
 from caput.memh5 import MemGroup
 from caput import fileformats
-from caput.tests.conftest import rm_all_files
 
 fsel = slice(1, 8, 2)
 isel = slice(1, 4)
@@ -16,7 +15,7 @@
 
 
 @pytest.fixture
-def h5_file_select(datasets, h5_file):
+def h5_file_select(datasets, h5_file, rm_all_files):
     """Provides an HDF5 file with some content for testing."""
     container = MemGroup()
     container.create_dataset("dset1", data=datasets[0].view())
@@ -27,7 +26,7 @@ def h5_file_select(datasets, h5_file):
 
 
 @pytest.fixture
-def zarr_file_select(datasets, zarr_file):
+def zarr_file_select(datasets, zarr_file, rm_all_files):
     """Provides a Zarr file with some content for testing."""
     container = MemGroup()
     container.create_dataset("dset1", data=datasets[0].view())

caput/tests/test_selection_parallel.py → tests/test_selection_parallel.py

@@ -10,14 +10,13 @@
 
 from caput import mpiutil, mpiarray, fileformats
 from caput.memh5 import MemGroup
-from caput.tests.conftest import rm_all_files
 
 
 comm = MPI.COMM_WORLD
 
 
 @pytest.fixture
-def container_on_disk(datasets, file_name, file_format):
+def container_on_disk(datasets, file_name, file_format, rm_all_files):
     """Prepare a file for the select_parallel tests."""
     if comm.rank == 0:
         m1 = mpiarray.MPIArray.wrap(datasets[0], axis=0, comm=MPI.COMM_SELF)