Commit 5137d1b9 authored by Joel Collins's avatar Joel Collins
Browse files

Added basic unit tests of non-integrated functions

parent f54684b4

openflexure_microscope/api/default_extensions/scan.py

+1 −11
Original line number Diff line number Diff line
@@ -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

openflexure_microscope/utilities.py

+1 −34
Original line number Diff line number Diff line
@@ -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)

poetry.lock

+133 −1
Original line number Diff line number Diff line
@@ -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"
@@ -454,6 +507,29 @@ category = "main" 
optional = false

python-versions = "*"



[[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"
@@ -747,13 +823,25 @@ 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 = "e0aad912d5cb388d3ff395dc8a517f701ba2cbe4c2169771080a889906e91b41"

content-hash = "394961d14d2bd06da0a05b6c34db8db97d88ff2b3d12e0e149da4e2706169cab"



[metadata.files]

alabaster = [
@@ -776,6 +864,10 @@ 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"},
@@ -842,6 +934,14 @@ 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"},
@@ -909,6 +1009,11 @@ 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 = [
@@ -1003,6 +1108,10 @@ 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"},
@@ -1016,6 +1125,10 @@ 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"},
@@ -1036,6 +1149,10 @@ pyserial = [ 
    {file = "pyserial-3.4-py2.py3-none-any.whl", hash = "sha256:e0770fadba80c31013896c7e6ef703f72e7834965954a78e71a3049488d4d7d8"},

    {file = "pyserial-3.4.tar.gz", hash = "sha256:6e2d401fdee0eab996cf734e67773a0143b932772ca8b42451440cfed942c627"},

]

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 = [

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    {file = "python_dateutil-2.8.1-py2.py3-none-any.whl", hash = "sha256:75bb3f31ea686f1197762692a9ee6a7550b59fc6ca3a1f4b5d7e32fb98e2da2a"},
@@ -1055,6 +1172,8 @@ pyyaml = [ 
    {file = "PyYAML-5.3.1-cp37-cp37m-win_amd64.whl", hash = "sha256:73f099454b799e05e5ab51423c7bcf361c58d3206fa7b0d555426b1f4d9a3eaf"},

    {file = "PyYAML-5.3.1-cp38-cp38-win32.whl", hash = "sha256:06a0d7ba600ce0b2d2fe2e78453a470b5a6e000a985dd4a4e54e436cc36b0e97"},

    {file = "PyYAML-5.3.1-cp38-cp38-win_amd64.whl", hash = "sha256:95f71d2af0ff4227885f7a6605c37fd53d3a106fcab511b8860ecca9fcf400ee"},

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    {file = "PyYAML-5.3.1-cp39-cp39-win_amd64.whl", hash = "sha256:6034f55dab5fea9e53f436aa68fa3ace2634918e8b5994d82f3621c04ff5ed2e"},

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]

requests = [
@@ -1146,19 +1265,28 @@ typed-ast = [ 
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    {file = "typed_ast-1.4.1-cp39-cp39-win32.whl", hash = "sha256:b52ccf7cfe4ce2a1064b18594381bccf4179c2ecf7f513134ec2f993dd4ab395"},

    {file = "typed_ast-1.4.1-cp39-cp39-win_amd64.whl", hash = "sha256:3742b32cf1c6ef124d57f95be609c473d7ec4c14d0090e5a5e05a15269fb4d0c"},

    {file = "typed_ast-1.4.1.tar.gz", hash = "sha256:8c8aaad94455178e3187ab22c8b01a3837f8ee50e09cf31f1ba129eb293ec30b"},

]

urllib3 = [
@@ -1180,3 +1308,7 @@ 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"},

]

pyproject.toml

+1 −0
Original line number Diff line number Diff line
@@ -59,6 +59,7 @@ 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/)'

pytest.ini

0 → 100644
+2 −0
Original line number Diff line number Diff line 
[pytest]

norecursedirs = .git build node_modules
 
 No newline at end of file