Merge pull request #547 from BCDA-APS/447-pytest

refactor from unittest to pytest

.github/workflows/unit-tests-pytest.yml

@@ -88,19 +88,12 @@ jobs:
     - name: install test data catalogs
       shell: bash -l {0}
       run: |
-        ./tests/unpack.sh
+        ./resources/unpack.sh
 
     - name: Run tests with pytest
       run: |
         source $CONDA/bin/activate $ENV_NAME
-        pytest -vvv ./tests ./apstools/beamtime/tests
+        pytest -vvv .
       env:
         PY_VER: ${{ matrix.python-version }}
         ENV_NAME: anaconda-test-env-py-${{ matrix.python-version }}
-
-
-# These actions were done by travis after success of previous steps
-# TODO: coverage
-# https://github.com/marketplace/actions/codecov
-# TODO: coveralls
-# https://github.com/marketplace/actions/coveralls-github-action

apstools/__init__.py

@@ -24,7 +24,7 @@
 __license__ += u" (see LICENSE.txt file for details)"
 __platforms__ = "any"
 __zip_safe__ = False
-__exclude_project_dirs__ = "docs examples tests".split()
+__exclude_project_dirs__ = "docs examples resources".split()
 __python_version_required__ = ">=3.7"
 
 __package_name__ = __project__

apstools/_plans/tests/test_plans.py

@@ -0,0 +1,171 @@
+"""
+Unit testing of plans.
+"""
+
+from ... import plans as APS_plans
+from ...plans import _COMMAND_HANDLER_
+from ...plans import addDeviceDataAsStream
+from ...plans import execute_command_list
+from ...plans import get_command_list
+from ...plans import register_command_handler
+from ...plans import run_command_file
+from bluesky.simulators import summarize_plan
+
+import ophyd.sim
+import os
+import pytest
+import sys
+
+
+DATA_PATH = os.path.abspath(
+    os.path.join(os.path.dirname(__file__), "..", "..", "tests")
+)
+
+
+def test_myoutput(capsys):  # or use "capfd" for fd-level
+    print("hello")
+    sys.stderr.write("world\n")
+    captured = capsys.readouterr()
+    assert captured.out == "hello\n"
+    assert captured.err == "world\n"
+    print("next")
+    captured = capsys.readouterr()
+    assert captured.out == "next\n"
+
+
+@pytest.mark.parametrize(
+    "objects, name, expected",
+    [
+        ([ophyd.sim.motor1], "test-device", "  Read ['motor1']\n"),
+        (
+            [[ophyd.sim.motor2, ophyd.sim.motor3]],
+            "test-device-list",
+            "  Read ['motor2', 'motor3']\n",
+        ),
+    ],
+)
+def test_addDeviceDataAsStream(objects, name, expected, capsys):
+    summarize_plan(addDeviceDataAsStream(*objects, name))
+
+    captured = capsys.readouterr()
+    assert captured.out == expected
+
+
+def test_register_action_handler():
+    assert summarize_plan != execute_command_list
+    assert APS_plans._COMMAND_HANDLER_ == _COMMAND_HANDLER_
+
+    register_command_handler(summarize_plan)
+    assert APS_plans._COMMAND_HANDLER_ != _COMMAND_HANDLER_  # FIXME:
+    assert APS_plans._COMMAND_HANDLER_ == summarize_plan
+    assert APS_plans._COMMAND_HANDLER_ != execute_command_list
+
+    register_command_handler()
+    assert APS_plans._COMMAND_HANDLER_ == _COMMAND_HANDLER_
+    assert APS_plans._COMMAND_HANDLER_ == execute_command_list
+
+
+def test_get_command_list(capsys):
+    filename = os.path.join(DATA_PATH, "actions.txt")
+    assert os.path.exists(filename)
+
+    expected = [
+        "sample_slits 0 0 0.4 1.2",
+        "preusaxstune",
+        "FlyScan 0   0   0   blank",
+        'FlyScan 5   2   0   "empty container"',
+        "SAXS 0 0 0 blank",
+    ]
+
+    commands = get_command_list(filename)
+    assert len(commands) == len(expected)
+    for r, e in zip(commands, expected):
+        assert r[-1] == e
+
+
+def test_run_command_file_text(capsys):
+    filename = os.path.join(DATA_PATH, "actions.txt")
+    assert os.path.exists(filename)
+
+    expected = [
+        f"Command file: {filename}",
+        "====== ============ ========================",
+        "line # action       parameters              ",
+        "====== ============ ========================",
+        "5      sample_slits 0, 0, 0.4, 1.2          ",
+        "7      preusaxstune                         ",
+        "10     FlyScan      0, 0, 0, blank          ",
+        "11     FlyScan      5, 2, 0, empty container",
+        "12     SAXS         0, 0, 0, blank          ",
+        "====== ============ ========================",
+        "",
+        "file line 5: sample_slits 0 0 0.4 1.2",
+        "no handling for line 5: sample_slits 0 0 0.4 1.2",
+        "file line 7: preusaxstune",
+        "no handling for line 7: preusaxstune",
+        "file line 10: FlyScan 0   0   0   blank",
+        "no handling for line 10: FlyScan 0   0   0   blank",
+        'file line 11: FlyScan 5   2   0   "empty container"',
+        'no handling for line 11: FlyScan 5   2   0   "empty container"',
+        "file line 12: SAXS 0 0 0 blank",
+        "no handling for line 12: SAXS 0 0 0 blank",
+    ]
+
+    summarize_plan(run_command_file(filename))
+
+    captured = capsys.readouterr()
+    assert isinstance(captured.out, str)
+
+    received = captured.out.strip().split("\n")
+    assert len(received) == len(expected)
+
+    for r, e in zip(received[1:], expected[1:]):  # FIXME: first row?
+        assert r.find("\n") == -1
+        assert r == e
+
+
+def test_run_command_file_Excel(capsys):
+    filename = os.path.join(DATA_PATH, "actions.xlsx")
+    assert os.path.exists(filename)
+
+    expected = [
+        f"Command file: {filename}",
+        "====== ============ ===========================",
+        "line # action       parameters                 ",
+        "====== ============ ===========================",
+        "1      mono_shutter open                       ",
+        "2      USAXSscan    45.07, 98.3, 0, Water Blank",
+        "3      saxsExp      45.07, 98.3, 0, Water Blank",
+        "4      waxwsExp     45.07, 98.3, 0, Water Blank",
+        "5      USAXSscan    12, 12, 1.2, plastic       ",
+        "6      USAXSscan    12, 37, 0.1, Al foil       ",
+        "7      mono_shutter close                      ",
+        "====== ============ ===========================",
+        "",
+        "file line 1: ['mono_shutter', 'open', None, None, None]",
+        "no handling for line 1: ['mono_shutter', 'open', None, None, None]",
+        "file line 2: ['USAXSscan', 45.07, 98.3, 0, 'Water Blank']",
+        "no handling for line 2: ['USAXSscan', 45.07, 98.3, 0, 'Water Blank']",
+        "file line 3: ['saxsExp', 45.07, 98.3, 0, 'Water Blank']",
+        "no handling for line 3: ['saxsExp', 45.07, 98.3, 0, 'Water Blank']",
+        "file line 4: ['waxwsExp', 45.07, 98.3, 0, 'Water Blank']",
+        "no handling for line 4: ['waxwsExp', 45.07, 98.3, 0, 'Water Blank']",
+        "file line 5: ['USAXSscan', 12, 12, 1.2, 'plastic']",
+        "no handling for line 5: ['USAXSscan', 12, 12, 1.2, 'plastic']",
+        "file line 6: ['USAXSscan', 12, 37, 0.1, 'Al foil']",
+        "no handling for line 6: ['USAXSscan', 12, 37, 0.1, 'Al foil']",
+        "file line 7: ['mono_shutter', 'close', None, None, None]",
+        "no handling for line 7: ['mono_shutter', 'close', None, None, None]",
+    ]
+
+    summarize_plan(run_command_file(filename))
+
+    captured = capsys.readouterr()
+    assert isinstance(captured.out, str)
+
+    received = captured.out.strip().split("\n")
+    assert len(received) == len(expected)
+
+    for r, e in zip(received[1:], expected[1:]):  # FIXME: first row?
+        assert r.find("\n") == -1
+        assert r == e

apstools/_utils/tests/test_commandlist.py

@@ -0,0 +1,145 @@
+"""
+Test the command list support.
+"""
+
+import os
+import pyRestTable
+import pytest
+
+from ...plans import CommandFileReadError
+from ...plans import get_command_list
+from ...utils import command_list_as_table
+
+DATA_PATH = os.path.abspath(
+    os.path.join(os.path.dirname(__file__), "..", "..", "tests")
+)
+
+
+@pytest.fixture(scope="function")
+def text_command_file():
+    text_command_file = os.path.join(DATA_PATH, "actions.txt")
+    return text_command_file
+
+
+@pytest.fixture(scope="function")
+def xl_command_file():
+    xl_command_file = os.path.join(DATA_PATH, "actions.xlsx")
+    return xl_command_file
+
+
+@pytest.fixture(scope="function")
+def xl_file():
+    xl_file = os.path.join(DATA_PATH, "demo3.xlsx")
+    return xl_file
+
+
+def test_testfile_exists(text_command_file, xl_command_file, xl_file):
+    assert os.path.exists(text_command_file)
+    assert os.path.exists(xl_command_file)
+    assert os.path.exists(xl_file)
+
+
+def compare_tables_as_str(expected, received):
+    e_lines = expected.strip().splitlines()
+    r_lines = received.strip().splitlines()
+    assert len(e_lines) == len(r_lines)
+    for expect, got in zip(e_lines, r_lines):
+        assert expect.strip() == got.strip()
+
+
+def test_ExcelFile_commands(xl_file):
+    # just a spreadsheet for testing (early version of a command file)
+    commands = get_command_list(xl_file)
+    assert len(commands) == 9  # rows
+
+    table = command_list_as_table(commands, show_raw=False)
+    assert isinstance(table, pyRestTable.Table)
+    received = str(table).strip()
+    expected = """
+    ====== ====== =========================================
+    line # action parameters
+    ====== ====== =========================================
+    1      row1   91, 26, 85, None, blank, 8
+    2      row2   9, 39, 29, 85, sample, 60
+    3      row3   54, None, 38, 3, blank, 76
+    4      row4   71, 36, 95, 83, foil, 12
+    5      row5   55, 75, 59, 84, DNA, 34
+    6      row6   18, 49, 31, 34, lecithin, 47
+    7      row7   37, None, None, None, a big mix  of stuff
+    8      row8   37, 80, 79, 45, salt water, 36
+    9      row9   72, 98, 67, 89, surprises, 49
+    ====== ====== =========================================
+    """.strip()
+    compare_tables_as_str(expected, received)
+
+
+def test_ExcelCommandList(xl_command_file):
+    commands = get_command_list(xl_command_file)
+    assert len(commands) == 7
+    table = command_list_as_table(commands, show_raw=False)
+    received = str(table).strip()
+    expected = """
+    ====== ============ ===========================
+    line # action       parameters
+    ====== ============ ===========================
+    1      mono_shutter open
+    2      USAXSscan    45.07, 98.3, 0, Water Blank
+    3      saxsExp      45.07, 98.3, 0, Water Blank
+    4      waxwsExp     45.07, 98.3, 0, Water Blank
+    5      USAXSscan    12, 12, 1.2, plastic
+    6      USAXSscan    12, 37, 0.1, Al foil
+    7      mono_shutter close
+    ====== ============ ===========================
+    """.strip()
+    compare_tables_as_str(expected, received)
+
+
+def test_TextCommandList(text_command_file):
+    commands = get_command_list(text_command_file)
+    assert len(commands) == 5
+    table = command_list_as_table(commands, show_raw=False)
+    received = str(table).strip()
+    expected = """
+    ====== ============ ========================
+    line # action       parameters
+    ====== ============ ========================
+    5      sample_slits 0, 0, 0.4, 1.2
+    7      preusaxstune
+    10     FlyScan      0, 0, 0, blank
+    11     FlyScan      5, 2, 0, empty container
+    12     SAXS         0, 0, 0, blank
+    ====== ============ ========================
+    """.strip()
+    compare_tables_as_str(expected, received)
+
+
+def test_TextCommandListRaw(text_command_file):
+    commands = get_command_list(text_command_file)
+    assert len(commands) == 5
+    table = command_list_as_table(commands, show_raw=True)
+    received = str(table).strip()
+    expected = """
+    ====== ============ ======================== =====================================
+    line # action       parameters               raw input
+    ====== ============ ======================== =====================================
+    5      sample_slits 0, 0, 0.4, 1.2           sample_slits 0 0 0.4 1.2
+    7      preusaxstune                          preusaxstune
+    10     FlyScan      0, 0, 0, blank           FlyScan 0   0   0   blank
+    11     FlyScan      5, 2, 0, empty container FlyScan 5   2   0   "empty container"
+    12     SAXS         0, 0, 0, blank           SAXS 0 0 0 blank
+    ====== ============ ======================== =====================================
+    """.strip()
+    compare_tables_as_str(expected, received)
+
+
+@pytest.mark.parametrize(
+    "error, expected, item",
+    [
+        (IOError, "file not found: ", os.path.join(DATA_PATH, "none such")),
+        (CommandFileReadError, "could not read ", __file__),
+    ],
+)
+def test_known_exceptions(error, expected, item):
+    with pytest.raises(error) as exc:
+        get_command_list(item)
+    assert str(exc.value).startswith(expected)

apstools/_utils/tests/test_exceltable.py

@@ -0,0 +1,37 @@
+"""
+Test the Excel support.
+"""
+
+import os
+import pytest
+
+from ...utils import ExcelDatabaseFileGeneric
+
+
+DATA_PATH = os.path.abspath(
+    os.path.join(os.path.dirname(__file__), "..", "..", "tests")
+)
+
+
+@pytest.fixture(scope="function")
+def xl_file():
+    xl_file = os.path.join(DATA_PATH, "demo3.xlsx")
+    return xl_file
+
+
+def test_testfile_exists(xl_file):
+    assert os.path.exists(xl_file)
+
+
+def test_normal_read(xl_file):
+    xl = ExcelDatabaseFileGeneric(xl_file)
+    assert len(xl.db) == 9  # rows
+    assert len(xl.db["0"]) == 7  # columns
+    assert "Unnamed: 7" in xl.db["0"]
+    assert xl.db["0"]["Unnamed: 7"] == 8.0
+
+
+def test_ignore_extra_false(xl_file):
+    xl = ExcelDatabaseFileGeneric(xl_file, ignore_extra=False)
+    assert len(xl.db) == 16  # rows
+    assert len(xl.db["0"]) == 9  # columns