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Merge branch 'pytest' into 'master'

Browse source 
Added basic unit tests of non-integrated functions

See merge request openflexure/openflexure-microscope-server!97
This commit is contained in:
Joel Collins 2020-11-25 15:26:46 +00:00
commit 51a0813d22
7 changed files with 228 additions and 46 deletions
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12
openflexure_microscope/api/default_extensions/scan.py
View file

@ -33,7 +33,7 @@ def construct_grid(initial, step_sizes, n_steps, style="raster"):
if style == "spiral":
# deal with the centre image immediately
coord = initial
arr.append(initial)
arr.append([initial])
# for spiral, n_steps is the number of shells, and so only requires n_steps[0]
for i in range(2, n_steps[0] + 1):
arr.append([])
@ -66,16 +66,6 @@ def construct_grid(initial, step_sizes, n_steps, style="raster"):
return arr
def flatten_grid(grid):
"""
Convert a 3D list of scan positions into a flat list
of sequential positions.
"""
grid = list(itertools.chain(*grid))
return grid
### Capturing

35
openflexure_microscope/utilities.py
View file

@ -26,7 +26,7 @@ class Timer(object):
def deserialise_array_b64(b64_string, dtype, shape):
flat_arr = np.fromstring(base64.b64decode(b64_string), dtype)
flat_arr = np.frombuffer(base64.b64decode(b64_string), dtype)
return flat_arr.reshape(shape)
@ -106,16 +106,6 @@ def axes_to_array(
return base_array
def filter_dict(dictionary: dict, keys: list):
# Get value by recursively applying getitem
val = reduce(operator.getitem, keys, dictionary)
# Create new dictionary by running reduce on key, val pairs
out = reduce(lambda x, y: {y: x}, reversed(keys), val)
return out
def entry_by_uuid(entry_id: str, object_list: list):
"""Return an object from a list, if <object>.id matches id argument."""
found = None
@ -132,26 +122,3 @@ def entry_by_uuid(entry_id: str, object_list: list):
if converter(o.id) == converter(entry_id):
found = o
return found
def recursively_apply(data, func):
"""
Recursively apply a function to a dictionary, list, array, or tuple
Args:
data: Input iterable data
func: Function to apply to all non-iterable values
"""
# If the object is a dictionary
if isinstance(data, abc.Mapping):
return {key: recursively_apply(val, func) for key, val in data.items()}
# If the object is iterable but NOT a dictionary or a string
elif (
isinstance(data, abc.Iterable)
and not isinstance(data, abc.Mapping)
and not isinstance(data, str)
):
return [recursively_apply(x, func) for x in data]
# if the object is neither a map nor iterable
else:
return func(data)

134
poetry.lock generated
View file

@ -63,6 +63,14 @@ six = ">=1.12,<2.0"
typed-ast = {version = ">=1.4.0,<1.5", markers = "implementation_name == \"cpython\" and python_version < \"3.8\""}
wrapt = ">=1.11,<2.0"
[[package]]
name = "atomicwrites"
version = "1.4.0"
description = "Atomic file writes."
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
name = "attrs"
version = "20.3.0"
@ -246,6 +254,29 @@ category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
name = "importlib-metadata"
version = "3.1.0"
description = "Read metadata from Python packages"
category = "dev"
optional = false
python-versions = ">=3.6"
[package.dependencies]
zipp = ">=0.5"
[package.extras]
docs = ["sphinx", "rst.linker"]
testing = ["packaging", "pep517", "unittest2", "importlib-resources (>=1.3)"]
[[package]]
name = "iniconfig"
version = "1.1.1"
description = "iniconfig: brain-dead simple config-ini parsing"
category = "dev"
optional = false
python-versions = "*"
[[package]]
name = "isort"
version = "5.6.4"
@ -391,6 +422,20 @@ category = "main"
optional = false
python-versions = ">=3.5"
[[package]]
name = "pluggy"
version = "0.13.1"
description = "plugin and hook calling mechanisms for python"
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[package.dependencies]
importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
[package.extras]
dev = ["pre-commit", "tox"]
[[package]]
name = "psutil"
version = "5.7.3"
@ -402,6 +447,14 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[package.extras]
test = ["ipaddress", "mock", "unittest2", "enum34", "pywin32", "wmi"]
[[package]]
name = "py"
version = "1.9.0"
description = "library with cross-python path, ini-parsing, io, code, log facilities"
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
name = "pygments"
version = "2.7.2"
@ -457,6 +510,29 @@ python-versions = "*"
[package.extras]
cp2110 = ["hidapi"]
[[package]]
name = "pytest"
version = "6.1.2"
description = "pytest: simple powerful testing with Python"
category = "dev"
optional = false
python-versions = ">=3.5"
[package.dependencies]
atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
attrs = ">=17.4.0"
colorama = {version = "*", markers = "sys_platform == \"win32\""}
importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
iniconfig = "*"
packaging = "*"
pluggy = ">=0.12,<1.0"
py = ">=1.8.2"
toml = "*"
[package.extras]
checkqa_mypy = ["mypy (==0.780)"]
testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
[[package]]
name = "python-dateutil"
version = "2.8.1"
@ -750,13 +826,25 @@ python-versions = "*"
[package.dependencies]
ifaddr = ">=0.1.7"
[[package]]
name = "zipp"
version = "3.4.0"
description = "Backport of pathlib-compatible object wrapper for zip files"
category = "dev"
optional = false
python-versions = ">=3.6"
[package.extras]
docs = ["sphinx", "jaraco.packaging (>=3.2)", "rst.linker (>=1.9)"]
testing = ["pytest (>=3.5,!=3.7.3)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "jaraco.test (>=3.2.0)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
[extras]
rpi = ["RPi.GPIO"]
[metadata]
lock-version = "1.1"
python-versions = "^3.6.1"
content-hash = "60f1064b6af35d65d45ec835b4e3032316732e4859a5c81a3fab8e06091f2892"
content-hash = "394961d14d2bd06da0a05b6c34db8db97d88ff2b3d12e0e149da4e2706169cab"
[metadata.files]
alabaster = [
@ -779,6 +867,10 @@ astroid = [
{file = "astroid-2.4.2-py3-none-any.whl", hash = "sha256:bc58d83eb610252fd8de6363e39d4f1d0619c894b0ed24603b881c02e64c7386"},
{file = "astroid-2.4.2.tar.gz", hash = "sha256:2f4078c2a41bf377eea06d71c9d2ba4eb8f6b1af2135bec27bbbb7d8f12bb703"},
]
atomicwrites = [
{file = "atomicwrites-1.4.0-py2.py3-none-any.whl", hash = "sha256:6d1784dea7c0c8d4a5172b6c620f40b6e4cbfdf96d783691f2e1302a7b88e197"},
{file = "atomicwrites-1.4.0.tar.gz", hash = "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"},
]
attrs = [
{file = "attrs-20.3.0-py2.py3-none-any.whl", hash = "sha256:31b2eced602aa8423c2aea9c76a724617ed67cf9513173fd3a4f03e3a929c7e6"},
{file = "attrs-20.3.0.tar.gz", hash = "sha256:832aa3cde19744e49938b91fea06d69ecb9e649c93ba974535d08ad92164f700"},
@ -845,6 +937,14 @@ imagesize = [
{file = "imagesize-1.2.0-py2.py3-none-any.whl", hash = "sha256:6965f19a6a2039c7d48bca7dba2473069ff854c36ae6f19d2cde309d998228a1"},
{file = "imagesize-1.2.0.tar.gz", hash = "sha256:b1f6b5a4eab1f73479a50fb79fcf729514a900c341d8503d62a62dbc4127a2b1"},
]
importlib-metadata = [
{file = "importlib_metadata-3.1.0-py2.py3-none-any.whl", hash = "sha256:590690d61efdd716ff82c39ca9a9d4209252adfe288a4b5721181050acbd4175"},
{file = "importlib_metadata-3.1.0.tar.gz", hash = "sha256:d9b8a46a0885337627a6430db287176970fff18ad421becec1d64cfc763c2099"},
]
iniconfig = [
{file = "iniconfig-1.1.1-py2.py3-none-any.whl", hash = "sha256:011e24c64b7f47f6ebd835bb12a743f2fbe9a26d4cecaa7f53bc4f35ee9da8b3"},
{file = "iniconfig-1.1.1.tar.gz", hash = "sha256:bc3af051d7d14b2ee5ef9969666def0cd1a000e121eaea580d4a313df4b37f32"},
]
isort = [
{file = "isort-5.6.4-py3-none-any.whl", hash = "sha256:dcab1d98b469a12a1a624ead220584391648790275560e1a43e54c5dceae65e7"},
{file = "isort-5.6.4.tar.gz", hash = "sha256:dcaeec1b5f0eca77faea2a35ab790b4f3680ff75590bfcb7145986905aab2f58"},
@ -912,6 +1012,11 @@ markupsafe = [
{file = "MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:ba59edeaa2fc6114428f1637ffff42da1e311e29382d81b339c1817d37ec93c6"},
{file = "MarkupSafe-1.1.1-cp37-cp37m-win32.whl", hash = "sha256:b00c1de48212e4cc9603895652c5c410df699856a2853135b3967591e4beebc2"},
{file = "MarkupSafe-1.1.1-cp37-cp37m-win_amd64.whl", hash = "sha256:9bf40443012702a1d2070043cb6291650a0841ece432556f784f004937f0f32c"},
{file = "MarkupSafe-1.1.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:6788b695d50a51edb699cb55e35487e430fa21f1ed838122d722e0ff0ac5ba15"},
{file = "MarkupSafe-1.1.1-cp38-cp38-manylinux1_i686.whl", hash = "sha256:cdb132fc825c38e1aeec2c8aa9338310d29d337bebbd7baa06889d09a60a1fa2"},
{file = "MarkupSafe-1.1.1-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:13d3144e1e340870b25e7b10b98d779608c02016d5184cfb9927a9f10c689f42"},
{file = "MarkupSafe-1.1.1-cp38-cp38-win32.whl", hash = "sha256:596510de112c685489095da617b5bcbbac7dd6384aeebeda4df6025d0256a81b"},
{file = "MarkupSafe-1.1.1-cp38-cp38-win_amd64.whl", hash = "sha256:e8313f01ba26fbbe36c7be1966a7b7424942f670f38e666995b88d012765b9be"},
{file = "MarkupSafe-1.1.1.tar.gz", hash = "sha256:29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b"},
]
marshmallow = [
@ -1006,6 +1111,10 @@ pillow = [
{file = "Pillow-7.2.0-pp36-pypy36_pp73-win32.whl", hash = "sha256:25930fadde8019f374400f7986e8404c8b781ce519da27792cbe46eabec00c4d"},
{file = "Pillow-7.2.0.tar.gz", hash = "sha256:97f9e7953a77d5a70f49b9a48da7776dc51e9b738151b22dacf101641594a626"},
]
pluggy = [
{file = "pluggy-0.13.1-py2.py3-none-any.whl", hash = "sha256:966c145cd83c96502c3c3868f50408687b38434af77734af1e9ca461a4081d2d"},
{file = "pluggy-0.13.1.tar.gz", hash = "sha256:15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0"},
]
psutil = [
{file = "psutil-5.7.3-cp27-none-win32.whl", hash = "sha256:1cd6a0c9fb35ece2ccf2d1dd733c1e165b342604c67454fd56a4c12e0a106787"},
{file = "psutil-5.7.3-cp27-none-win_amd64.whl", hash = "sha256:e02c31b2990dcd2431f4524b93491941df39f99619b0d312dfe1d4d530b08b4b"},
@ -1019,6 +1128,10 @@ psutil = [
{file = "psutil-5.7.3-cp38-cp38-win_amd64.whl", hash = "sha256:2cb55ef9591b03ef0104bedf67cc4edb38a3edf015cf8cf24007b99cb8497542"},
{file = "psutil-5.7.3.tar.gz", hash = "sha256:af73f7bcebdc538eda9cc81d19db1db7bf26f103f91081d780bbacfcb620dee2"},
]
py = [
{file = "py-1.9.0-py2.py3-none-any.whl", hash = "sha256:366389d1db726cd2fcfc79732e75410e5fe4d31db13692115529d34069a043c2"},
{file = "py-1.9.0.tar.gz", hash = "sha256:9ca6883ce56b4e8da7e79ac18787889fa5206c79dcc67fb065376cd2fe03f342"},
]
pygments = [
{file = "Pygments-2.7.2-py3-none-any.whl", hash = "sha256:88a0bbcd659fcb9573703957c6b9cff9fab7295e6e76db54c9d00ae42df32773"},
{file = "Pygments-2.7.2.tar.gz", hash = "sha256:381985fcc551eb9d37c52088a32914e00517e57f4a21609f48141ba08e193fa0"},
@ -1039,6 +1152,10 @@ pyserial = [
{file = "pyserial-3.5-py2.py3-none-any.whl", hash = "sha256:c4451db6ba391ca6ca299fb3ec7bae67a5c55dde170964c7a14ceefec02f2cf0"},
{file = "pyserial-3.5.tar.gz", hash = "sha256:3c77e014170dfffbd816e6ffc205e9842efb10be9f58ec16d3e8675b4925cddb"},
]
pytest = [
{file = "pytest-6.1.2-py3-none-any.whl", hash = "sha256:4288fed0d9153d9646bfcdf0c0428197dba1ecb27a33bb6e031d002fa88653fe"},
{file = "pytest-6.1.2.tar.gz", hash = "sha256:c0a7e94a8cdbc5422a51ccdad8e6f1024795939cc89159a0ae7f0b316ad3823e"},
]
python-dateutil = [
{file = "python-dateutil-2.8.1.tar.gz", hash = "sha256:73ebfe9dbf22e832286dafa60473e4cd239f8592f699aa5adaf10050e6e1823c"},
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@ -1058,6 +1175,8 @@ pyyaml = [
{file = "PyYAML-5.3.1-cp37-cp37m-win_amd64.whl", hash = "sha256:73f099454b799e05e5ab51423c7bcf361c58d3206fa7b0d555426b1f4d9a3eaf"},
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{file = "PyYAML-5.3.1-cp38-cp38-win_amd64.whl", hash = "sha256:95f71d2af0ff4227885f7a6605c37fd53d3a106fcab511b8860ecca9fcf400ee"},
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]
requests = [
@ -1149,19 +1268,28 @@ typed-ast = [
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]
urllib3 = [
@ -1183,3 +1311,7 @@ zeroconf = [
{file = "zeroconf-0.28.6-py3-none-any.whl", hash = "sha256:17ae1e1681091b91b0337517db222eae1807003154c01b0bd0ab99572dfeafd8"},
{file = "zeroconf-0.28.6.tar.gz", hash = "sha256:70f10f0f16e3a8c4eb5e1a106b812b8d052253041cf1ee1195933df706f5261c"},
]
zipp = [
{file = "zipp-3.4.0-py3-none-any.whl", hash = "sha256:102c24ef8f171fd729d46599845e95c7ab894a4cf45f5de11a44cc7444fb1108"},
{file = "zipp-3.4.0.tar.gz", hash = "sha256:ed5eee1974372595f9e416cc7bbeeb12335201d8081ca8a0743c954d4446e5cb"},
]

1
pyproject.toml
View file

@ -57,6 +57,7 @@ sphinxcontrib-httpdomain = "^1.7"
rope = "^0.14.0"
pylint = "^2.3"
black = {version = "^18.3-alpha.0",allow-prereleases = true}
pytest = "^6.1.2"
[tool.black]
exclude = '(\.eggs|\.git|\.venv|node_modules/)'

2
pytest.ini Normal file
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@ -0,0 +1,2 @@
[pytest]
norecursedirs = .git build node_modules

59
tests/test_extension_scan.py Normal file
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@ -0,0 +1,59 @@
from pprint import pprint
from openflexure_microscope.api.default_extensions import scan
def test_construct_grid_raster():
grid = scan.construct_grid((0, 0), (100, 100), (3, 3), style="raster")
assert grid == [
[(0, 0), (0, 100), (0, 200)],
[(100, 0), (100, 100), (100, 200)],
[(200, 0), (200, 100), (200, 200)],
]
def test_construct_grid_snake():
grid = scan.construct_grid((0, 0), (100, 100), (3, 3), style="snake")
assert grid == [
[(0, 0), (0, 100), (0, 200)],
[(100, 200), (100, 100), (100, 0)],
[(200, 0), (200, 100), (200, 200)],
]
def test_construct_grid_spiral():
grid = scan.construct_grid((0, 0), (100, 100), (3, 0), style="spiral")
assert grid == [
[(0, 0)],
[
(0, 100),
(100, 100),
(100, 0),
(100, -100),
(0, -100),
(-100, -100),
(-100, 0),
(-100, 100),
],
[
(-100, 200),
(0, 200),
(100, 200),
(200, 200),
(200, 100),
(200, 0),
(200, -100),
(200, -200),
(100, -200),
(0, -200),
(-100, -200),
(-200, -200),
(-200, -100),
(-200, 0),
(-200, 100),
(-200, 200),
],
]
# Ensure second n_steps value makes no difference
assert grid == scan.construct_grid((0, 0), (100, 100), (3, 3), style="spiral")

31
tests/test_utilities.py Normal file
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@ -0,0 +1,31 @@
import numpy as np
from openflexure_microscope import utilities
def test_serialise_array_b64():
shape_in = (3, 2)
arr_in = np.random.randint(100, size=shape_in, dtype=np.int)
b64_string, dtype, shape = utilities.serialise_array_b64(arr_in)
assert b64_string
assert dtype == "int32"
assert shape == shape_in
arr_out = utilities.deserialise_array_b64(b64_string, dtype, shape)
assert np.array_equal(arr_out, arr_in)
def test_ndarray_to_json():
shape_in = (3, 2)
arr_in = np.random.randint(100, size=shape_in, dtype=np.int)
json_out = utilities.ndarray_to_json(arr_in)
arr_out = utilities.json_to_ndarray(json_out)
assert np.array_equal(arr_out, arr_in)
def test_axes_to_array():
dict_in = {"x": 1, "y": 2, "z": 3}
assert utilities.axes_to_array(dict_in) == [1, 2, 3]