mirror of
https://github.com/p2p-ld/nwb-linkml.git
synced 2024-11-12 17:54:29 +00:00
some baseline tests, fixing imports, coverage reports
This commit is contained in:
parent
ccc09de400
commit
da2eaea51e
29 changed files with 392 additions and 76 deletions
9
.github/workflows/tests.yml
vendored
9
.github/workflows/tests.yml
vendored
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@ -4,7 +4,7 @@ on:
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push:
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jobs:
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build:
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test:
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strategy:
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matrix:
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python-version: [3.11]
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@ -20,7 +20,7 @@ jobs:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: pip install .[tests] pytest-md pytest-emoji
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run: pip install .[tests]
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working-directory: nwb_linkml
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- uses: pavelzw/pytest-action@v2
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@ -29,3 +29,8 @@ jobs:
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emoji: true
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verbose: true
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job-summary: true
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- working-directory: nwb_linkml
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run: "coveralls --service=github"
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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0
nwb_linkml/README.md
Normal file
0
nwb_linkml/README.md
Normal file
141
nwb_linkml/poetry.lock
generated
141
nwb_linkml/poetry.lock
generated
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@ -212,6 +212,87 @@ files = [
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{file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
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]
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[[package]]
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name = "coverage"
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version = "6.5.0"
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description = "Code coverage measurement for Python"
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optional = false
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python-versions = ">=3.7"
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files = [
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{file = "coverage-6.5.0-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:83516205e254a0cb77d2d7bb3632ee019d93d9f4005de31dca0a8c3667d5bc04"},
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{file = "coverage-6.5.0-cp310-cp310-musllinux_1_1_i686.whl", hash = "sha256:a1170fa54185845505fbfa672f1c1ab175446c887cce8212c44149581cf2d466"},
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{file = "coverage-6.5.0-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:11b990d520ea75e7ee8dcab5bc908072aaada194a794db9f6d7d5cfd19661e5a"},
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{file = "coverage-6.5.0-cp310-cp310-win32.whl", hash = "sha256:5dbec3b9095749390c09ab7c89d314727f18800060d8d24e87f01fb9cfb40b32"},
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||||
{file = "coverage-6.5.0-cp310-cp310-win_amd64.whl", hash = "sha256:59f53f1dc5b656cafb1badd0feb428c1e7bc19b867479ff72f7a9dd9b479f10e"},
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{file = "coverage-6.5.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:4a5375e28c5191ac38cca59b38edd33ef4cc914732c916f2929029b4bfb50795"},
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{file = "coverage-6.5.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:c4ed2820d919351f4167e52425e096af41bfabacb1857186c1ea32ff9983ed75"},
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{file = "coverage-6.5.0-cp311-cp311-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:33a7da4376d5977fbf0a8ed91c4dffaaa8dbf0ddbf4c8eea500a2486d8bc4d7b"},
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{file = "coverage-6.5.0-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a8fb6cf131ac4070c9c5a3e21de0f7dc5a0fbe8bc77c9456ced896c12fcdad91"},
|
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{file = "coverage-6.5.0-cp311-cp311-musllinux_1_1_aarch64.whl", hash = "sha256:a6b7d95969b8845250586f269e81e5dfdd8ff828ddeb8567a4a2eaa7313460c4"},
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{file = "coverage-6.5.0-cp311-cp311-musllinux_1_1_i686.whl", hash = "sha256:1ef221513e6f68b69ee9e159506d583d31aa3567e0ae84eaad9d6ec1107dddaa"},
|
||||
{file = "coverage-6.5.0-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:cca4435eebea7962a52bdb216dec27215d0df64cf27fc1dd538415f5d2b9da6b"},
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{file = "coverage-6.5.0-cp311-cp311-win32.whl", hash = "sha256:98e8a10b7a314f454d9eff4216a9a94d143a7ee65018dd12442e898ee2310578"},
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||||
{file = "coverage-6.5.0-cp311-cp311-win_amd64.whl", hash = "sha256:bc8ef5e043a2af066fa8cbfc6e708d58017024dc4345a1f9757b329a249f041b"},
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{file = "coverage-6.5.0-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:4433b90fae13f86fafff0b326453dd42fc9a639a0d9e4eec4d366436d1a41b6d"},
|
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{file = "coverage-6.5.0-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:f4f05d88d9a80ad3cac6244d36dd89a3c00abc16371769f1340101d3cb899fc3"},
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{file = "coverage-6.5.0-cp37-cp37m-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:94e2565443291bd778421856bc975d351738963071e9b8839ca1fc08b42d4bef"},
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{file = "coverage-6.5.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:027018943386e7b942fa832372ebc120155fd970837489896099f5cfa2890f79"},
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{file = "coverage-6.5.0-cp37-cp37m-musllinux_1_1_aarch64.whl", hash = "sha256:255758a1e3b61db372ec2736c8e2a1fdfaf563977eedbdf131de003ca5779b7d"},
|
||||
{file = "coverage-6.5.0-cp37-cp37m-musllinux_1_1_i686.whl", hash = "sha256:851cf4ff24062c6aec510a454b2584f6e998cada52d4cb58c5e233d07172e50c"},
|
||||
{file = "coverage-6.5.0-cp37-cp37m-musllinux_1_1_x86_64.whl", hash = "sha256:12adf310e4aafddc58afdb04d686795f33f4d7a6fa67a7a9d4ce7d6ae24d949f"},
|
||||
{file = "coverage-6.5.0-cp37-cp37m-win32.whl", hash = "sha256:b5604380f3415ba69de87a289a2b56687faa4fe04dbee0754bfcae433489316b"},
|
||||
{file = "coverage-6.5.0-cp37-cp37m-win_amd64.whl", hash = "sha256:4a8dbc1f0fbb2ae3de73eb0bdbb914180c7abfbf258e90b311dcd4f585d44bd2"},
|
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{file = "coverage-6.5.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:d900bb429fdfd7f511f868cedd03a6bbb142f3f9118c09b99ef8dc9bf9643c3c"},
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{file = "coverage-6.5.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:2198ea6fc548de52adc826f62cb18554caedfb1d26548c1b7c88d8f7faa8f6ba"},
|
||||
{file = "coverage-6.5.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:6c4459b3de97b75e3bd6b7d4b7f0db13f17f504f3d13e2a7c623786289dd670e"},
|
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{file = "coverage-6.5.0-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:20c8ac5386253717e5ccc827caad43ed66fea0efe255727b1053a8154d952398"},
|
||||
{file = "coverage-6.5.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6b07130585d54fe8dff3d97b93b0e20290de974dc8177c320aeaf23459219c0b"},
|
||||
{file = "coverage-6.5.0-cp38-cp38-musllinux_1_1_aarch64.whl", hash = "sha256:dbdb91cd8c048c2b09eb17713b0c12a54fbd587d79adcebad543bc0cd9a3410b"},
|
||||
{file = "coverage-6.5.0-cp38-cp38-musllinux_1_1_i686.whl", hash = "sha256:de3001a203182842a4630e7b8d1a2c7c07ec1b45d3084a83d5d227a3806f530f"},
|
||||
{file = "coverage-6.5.0-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:e07f4a4a9b41583d6eabec04f8b68076ab3cd44c20bd29332c6572dda36f372e"},
|
||||
{file = "coverage-6.5.0-cp38-cp38-win32.whl", hash = "sha256:6d4817234349a80dbf03640cec6109cd90cba068330703fa65ddf56b60223a6d"},
|
||||
{file = "coverage-6.5.0-cp38-cp38-win_amd64.whl", hash = "sha256:7ccf362abd726b0410bf8911c31fbf97f09f8f1061f8c1cf03dfc4b6372848f6"},
|
||||
{file = "coverage-6.5.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:633713d70ad6bfc49b34ead4060531658dc6dfc9b3eb7d8a716d5873377ab745"},
|
||||
{file = "coverage-6.5.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:95203854f974e07af96358c0b261f1048d8e1083f2de9b1c565e1be4a3a48cfc"},
|
||||
{file = "coverage-6.5.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:b9023e237f4c02ff739581ef35969c3739445fb059b060ca51771e69101efffe"},
|
||||
{file = "coverage-6.5.0-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:265de0fa6778d07de30bcf4d9dc471c3dc4314a23a3c6603d356a3c9abc2dfcf"},
|
||||
{file = "coverage-6.5.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8f830ed581b45b82451a40faabb89c84e1a998124ee4212d440e9c6cf70083e5"},
|
||||
{file = "coverage-6.5.0-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:7b6be138d61e458e18d8e6ddcddd36dd96215edfe5f1168de0b1b32635839b62"},
|
||||
{file = "coverage-6.5.0-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:42eafe6778551cf006a7c43153af1211c3aaab658d4d66fa5fcc021613d02518"},
|
||||
{file = "coverage-6.5.0-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:723e8130d4ecc8f56e9a611e73b31219595baa3bb252d539206f7bbbab6ffc1f"},
|
||||
{file = "coverage-6.5.0-cp39-cp39-win32.whl", hash = "sha256:d9ecf0829c6a62b9b573c7bb6d4dcd6ba8b6f80be9ba4fc7ed50bf4ac9aecd72"},
|
||||
{file = "coverage-6.5.0-cp39-cp39-win_amd64.whl", hash = "sha256:fc2af30ed0d5ae0b1abdb4ebdce598eafd5b35397d4d75deb341a614d333d987"},
|
||||
{file = "coverage-6.5.0-pp36.pp37.pp38-none-any.whl", hash = "sha256:1431986dac3923c5945271f169f59c45b8802a114c8f548d611f2015133df77a"},
|
||||
{file = "coverage-6.5.0.tar.gz", hash = "sha256:f642e90754ee3e06b0e7e51bce3379590e76b7f76b708e1a71ff043f87025c84"},
|
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]
|
||||
|
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[package.extras]
|
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toml = ["tomli"]
|
||||
|
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[[package]]
|
||||
name = "coveralls"
|
||||
version = "3.3.1"
|
||||
description = "Show coverage stats online via coveralls.io"
|
||||
optional = true
|
||||
python-versions = ">= 3.5"
|
||||
files = [
|
||||
{file = "coveralls-3.3.1-py2.py3-none-any.whl", hash = "sha256:f42015f31d386b351d4226389b387ae173207058832fbf5c8ec4b40e27b16026"},
|
||||
{file = "coveralls-3.3.1.tar.gz", hash = "sha256:b32a8bb5d2df585207c119d6c01567b81fba690c9c10a753bfe27a335bfc43ea"},
|
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]
|
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|
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[package.dependencies]
|
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coverage = ">=4.1,<6.0.dev0 || >6.1,<6.1.1 || >6.1.1,<7.0"
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docopt = ">=0.6.1"
|
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requests = ">=1.0.0"
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[package.extras]
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yaml = ["PyYAML (>=3.10)"]
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[[package]]
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name = "curies"
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version = "0.6.0"
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@ -344,6 +425,16 @@ wrapt = ">=1.10,<2"
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[package.extras]
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||||
dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
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|
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[[package]]
|
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name = "docopt"
|
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version = "0.6.2"
|
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description = "Pythonic argument parser, that will make you smile"
|
||||
optional = true
|
||||
python-versions = "*"
|
||||
files = [
|
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{file = "docopt-0.6.2.tar.gz", hash = "sha256:49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491"},
|
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]
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[[package]]
|
||||
name = "et-xmlfile"
|
||||
version = "1.1.0"
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@ -1372,6 +1463,24 @@ pluggy = ">=0.12,<2.0"
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[package.extras]
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testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
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[[package]]
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name = "pytest-cov"
|
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version = "4.1.0"
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description = "Pytest plugin for measuring coverage."
|
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optional = false
|
||||
python-versions = ">=3.7"
|
||||
files = [
|
||||
{file = "pytest-cov-4.1.0.tar.gz", hash = "sha256:3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6"},
|
||||
{file = "pytest_cov-4.1.0-py3-none-any.whl", hash = "sha256:6ba70b9e97e69fcc3fb45bfeab2d0a138fb65c4d0d6a41ef33983ad114be8c3a"},
|
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]
|
||||
|
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[package.dependencies]
|
||||
coverage = {version = ">=5.2.1", extras = ["toml"]}
|
||||
pytest = ">=4.6"
|
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|
||||
[package.extras]
|
||||
testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
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[[package]]
|
||||
name = "pytest-depends"
|
||||
version = "1.0.1"
|
||||
|
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@ -1389,6 +1498,20 @@ future-fstrings = "*"
|
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networkx = "*"
|
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pytest = ">=3"
|
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|
||||
[[package]]
|
||||
name = "pytest-emoji"
|
||||
version = "0.2.0"
|
||||
description = "A pytest plugin that adds emojis to your test result report"
|
||||
optional = false
|
||||
python-versions = ">=3.4"
|
||||
files = [
|
||||
{file = "pytest-emoji-0.2.0.tar.gz", hash = "sha256:e1bd4790d87649c2d09c272c88bdfc4d37c1cc7c7a46583087d7c510944571e8"},
|
||||
{file = "pytest_emoji-0.2.0-py3-none-any.whl", hash = "sha256:6e34ed21970fa4b80a56ad11417456bd873eb066c02315fe9df0fafe6d4d4436"},
|
||||
]
|
||||
|
||||
[package.dependencies]
|
||||
pytest = ">=4.2.1"
|
||||
|
||||
[[package]]
|
||||
name = "pytest-logging"
|
||||
version = "2015.11.4"
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||||
|
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@ -1402,6 +1525,20 @@ files = [
|
|||
[package.dependencies]
|
||||
pytest = ">=2.8.1"
|
||||
|
||||
[[package]]
|
||||
name = "pytest-md"
|
||||
version = "0.2.0"
|
||||
description = "Plugin for generating Markdown reports for pytest results"
|
||||
optional = false
|
||||
python-versions = ">=3.6"
|
||||
files = [
|
||||
{file = "pytest-md-0.2.0.tar.gz", hash = "sha256:3b248d5b360ea5198e05b4f49c7442234812809a63137ec6cdd3643a40cf0112"},
|
||||
{file = "pytest_md-0.2.0-py3-none-any.whl", hash = "sha256:4c4cd16fea6d1485e87ee254558712c804a96d2aa9674b780e7eb8fb6526e1d1"},
|
||||
]
|
||||
|
||||
[package.dependencies]
|
||||
pytest = ">=4.2.1"
|
||||
|
||||
[[package]]
|
||||
name = "python-dateutil"
|
||||
version = "2.8.2"
|
||||
|
|
@ -2186,9 +2323,9 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
|
|||
[extras]
|
||||
dev = []
|
||||
plot = ["dash", "dash-cytoscape"]
|
||||
tests = ["pytest", "pytest-depends"]
|
||||
tests = ["coverage", "pytest", "pytest-cov", "pytest-depends", "pytest-emoji", "pytest-md"]
|
||||
|
||||
[metadata]
|
||||
lock-version = "2.0"
|
||||
python-versions = "^3.11"
|
||||
content-hash = "4b3073d732a5ddcc84db255baea64e2df0414967995d20bd902f83a39de0bc10"
|
||||
content-hash = "2d93043f4c9a191ba4a48ffed4739d027cc9b10f26b1f882326d1e385af462cb"
|
||||
|
|
|
|||
|
|
@ -17,17 +17,25 @@ linkml-runtime = "^1.5.6"
|
|||
#nwb_schema_language = { path = './nwb_schema_language', develop = true, optional = true }
|
||||
rich = "^13.5.2"
|
||||
linkml = "^1.5.7"
|
||||
pytest = { version="^7.4.0", optional=true}
|
||||
pytest-depends = {version="^1.0.1", optional=true}
|
||||
dash = {version="^2.12.1", optional=true}
|
||||
dash-cytoscape = {version="^0.3.0", optional=true}
|
||||
nptyping = "^2.5.0"
|
||||
pydantic = "^2.3.0"
|
||||
h5py = "^3.9.0"
|
||||
dash = {version="^2.12.1", optional=true}
|
||||
dash-cytoscape = {version="^0.3.0", optional=true}
|
||||
pytest = { version="^7.4.0", optional=true}
|
||||
pytest-depends = {version="^1.0.1", optional=true}
|
||||
coverage = {version = "^6.1.1", optional = true}
|
||||
pytest-md = {version = "^0.2.0", optional = true}
|
||||
pytest-emoji = {version="^0.2.0", optional = true}
|
||||
pytest-cov = {version = "^4.1.0", optional = true}
|
||||
coveralls = {version = "^3.3.1", optional = true}
|
||||
|
||||
[tool.poetry.extras]
|
||||
dev = ["nwb_schema_language"]
|
||||
tests = ["pytest", "pytest-depends"]
|
||||
tests = [
|
||||
"pytest", "pytest-depends", "coverage", "pytest-md",
|
||||
"pytest-emoji", "pytest-cov"
|
||||
]
|
||||
plot = ["dash", "dash-cytoscape"]
|
||||
|
||||
|
||||
|
|
@ -37,6 +45,10 @@ optional = true
|
|||
[tool.poetry.group.tests.dependencies]
|
||||
pytest = "^7.4.0"
|
||||
pytest-depends = "^1.0.1"
|
||||
coverage = "^6.1.1"
|
||||
pytest-md = "^0.2.0"
|
||||
pytest-emoji = "^0.2.0"
|
||||
pytest-cov = "^4.1.0"
|
||||
|
||||
[tool.poetry.group.plot]
|
||||
optional = true
|
||||
|
|
@ -51,3 +63,21 @@ build-backend = "poetry.core.masonry.api"
|
|||
|
||||
|
||||
[tool.pytest.ini_options]
|
||||
addopts = [
|
||||
"--cov",
|
||||
"--cov-append"
|
||||
]
|
||||
testpaths = [
|
||||
"tests"
|
||||
]
|
||||
|
||||
[tool.coverage.run]
|
||||
branch = true
|
||||
source = [
|
||||
"src/nwb_linkml"
|
||||
]
|
||||
omit = [
|
||||
"*/nwb_schema_language/*",
|
||||
"*/nwb_linkml/models/*"
|
||||
]
|
||||
|
||||
|
|
|
|||
|
|
@ -1 +1 @@
|
|||
from nwb_linkml.src.nwb_linkml.maps import preload
|
||||
from nwb_linkml.maps import preload
|
||||
|
|
@ -1 +1,4 @@
|
|||
from nwb_linkml.src.nwb_linkml.adapters.namespaces import NamespacesAdapter
|
||||
from nwb_linkml.adapters.namespaces import NamespacesAdapter
|
||||
from nwb_linkml.adapters.classes import ClassAdapter
|
||||
from nwb_linkml.adapters.group import GroupAdapter
|
||||
from nwb_linkml.adapters.schema import SchemaAdapter
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@ from typing import List, Optional
|
|||
from nwb_schema_language import Dataset, Group, ReferenceDtype, CompoundDtype, DTypeType
|
||||
from nwb_linkml.adapters.adapter import Adapter, BuildResult
|
||||
from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition
|
||||
from nwb_linkml.src.nwb_linkml.maps import QUANTITY_MAP
|
||||
from nwb_linkml.maps import QUANTITY_MAP
|
||||
|
||||
CAMEL_TO_SNAKE = re.compile('((?<=[a-z0-9])[A-Z]|(?!^)[A-Z](?=[a-z]))')
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ from pydantic import PrivateAttr
|
|||
from nwb_schema_language import Dataset, ReferenceDtype, CompoundDtype, DTypeType
|
||||
from nwb_linkml.adapters.classes import ClassAdapter, camel_to_snake
|
||||
from nwb_linkml.adapters.adapter import BuildResult
|
||||
from nwb_linkml.src.nwb_linkml.maps import QUANTITY_MAP
|
||||
from nwb_linkml.maps import QUANTITY_MAP
|
||||
|
||||
class DatasetAdapter(ClassAdapter):
|
||||
cls: Dataset
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@ from nwb_schema_language import Dataset, Group, ReferenceDtype, CompoundDtype, D
|
|||
from nwb_linkml.adapters.classes import ClassAdapter, camel_to_snake
|
||||
from nwb_linkml.adapters.dataset import DatasetAdapter
|
||||
from nwb_linkml.adapters.adapter import BuildResult
|
||||
from nwb_linkml.src.nwb_linkml.maps import QUANTITY_MAP
|
||||
from nwb_linkml.maps import QUANTITY_MAP
|
||||
|
||||
class GroupAdapter(ClassAdapter):
|
||||
cls: Group
|
||||
|
|
|
|||
|
|
@ -0,0 +1 @@
|
|||
from nwb_linkml.generators.pydantic import PydanticGenerator
|
||||
|
|
@ -25,7 +25,7 @@ from types import ModuleType
|
|||
from copy import deepcopy
|
||||
import warnings
|
||||
|
||||
from nwb_linkml.src.nwb_linkml.maps import flat_to_npytyping
|
||||
from nwb_linkml.maps import flat_to_npytyping
|
||||
from linkml.generators import PydanticGenerator
|
||||
from linkml_runtime.linkml_model.meta import (
|
||||
Annotation,
|
||||
|
|
|
|||
|
|
@ -0,0 +1 @@
|
|||
from nwb_linkml.io import schema
|
||||
|
|
@ -1,6 +1,8 @@
|
|||
"""
|
||||
Define and manage NWB namespaces in external repositories
|
||||
"""
|
||||
import pdb
|
||||
from typing import Optional
|
||||
import warnings
|
||||
from pathlib import Path
|
||||
import tempfile
|
||||
|
|
@ -50,7 +52,7 @@ class GitRepo:
|
|||
def __init__(self, namespace:NamespaceRepo, commit:str|None=None):
|
||||
self._temp_directory = None
|
||||
self.namespace = namespace
|
||||
self.commit = commit
|
||||
self._commit = commit
|
||||
|
||||
def _git_call(self, *args) -> subprocess.CompletedProcess:
|
||||
res = subprocess.run(
|
||||
|
|
@ -68,9 +70,7 @@ class GitRepo:
|
|||
"""
|
||||
if self._temp_directory is None:
|
||||
self._temp_directory = Path(tempfile.gettempdir()) / f'nwb_linkml__{self.namespace.name}'
|
||||
if self._temp_directory.exists():
|
||||
warnings.warn(f'Temporary directory already exists! {self._temp_directory}')
|
||||
else:
|
||||
if not self._temp_directory.exists():
|
||||
self._temp_directory.mkdir(parents=True)
|
||||
|
||||
return self._temp_directory
|
||||
|
|
@ -99,6 +99,23 @@ class GitRepo:
|
|||
"""
|
||||
return self.temp_directory / self.namespace.path
|
||||
|
||||
@property
|
||||
def commit(self) -> Optional[str]:
|
||||
"""
|
||||
The intended commit to check out.
|
||||
|
||||
If ``None``, should be the latest commit when the repo was checked out
|
||||
|
||||
Should match :prop:`.active_commit`, differs semantically in that it is used to
|
||||
set the active_commit, while :prop:`.active_commit` reads what commit is actually checked out
|
||||
"""
|
||||
return self._commit
|
||||
|
||||
@commit.setter
|
||||
def commit(self, commit:str):
|
||||
self._git_call('checkout', commit)
|
||||
self._commit = commit
|
||||
|
||||
def check(self) -> bool:
|
||||
"""
|
||||
Check if the repository is already cloned and checked out
|
||||
|
|
@ -120,7 +137,7 @@ class GitRepo:
|
|||
return False
|
||||
|
||||
# Check that the remote matches
|
||||
if self.remote.strip('.git') != self.namespace.repository:
|
||||
if self.remote != str(self.namespace.repository):
|
||||
warnings.warn(f'Repository exists, but has the wrong remote URL.\nExpected: {self.namespace.repository}\nGot:{self.remote.strip(".git")}')
|
||||
return False
|
||||
|
||||
|
|
@ -164,6 +181,8 @@ class GitRepo:
|
|||
self.cleanup()
|
||||
|
||||
res = subprocess.run(['git', 'clone', str(self.namespace.repository), str(self.temp_directory)])
|
||||
if self.commit:
|
||||
self.commit = self.commit
|
||||
if res.returncode != 0:
|
||||
raise GitError(f'Could not clone repository:\n{res.stderr}')
|
||||
|
||||
|
|
@ -4,15 +4,14 @@ Loading/saving NWB Schema yaml files
|
|||
from pathlib import Path
|
||||
from typing import Optional
|
||||
from pprint import pprint
|
||||
import warnings
|
||||
|
||||
from linkml_runtime.loaders import yaml_loader
|
||||
import yaml
|
||||
|
||||
from nwb_schema_language import Namespaces, Group, Dataset
|
||||
from nwb_linkml.namespaces import NamespaceRepo, NWB_CORE_REPO, HDMF_COMMON_REPO
|
||||
from nwb_linkml.src.nwb_linkml.map import PHASES, Map
|
||||
from nwb_linkml.src.nwb_linkml.adapters.namespaces import NamespacesAdapter
|
||||
from nwb_linkml.io.git import NamespaceRepo, NWB_CORE_REPO, HDMF_COMMON_REPO
|
||||
from nwb_linkml.map import PHASES, Map
|
||||
from nwb_linkml.adapters.namespaces import NamespacesAdapter
|
||||
from nwb_linkml.adapters.schema import SchemaAdapter
|
||||
|
||||
|
||||
|
|
@ -32,12 +31,9 @@ def load_namespaces(path:Path|NamespaceRepo) -> Namespaces:
|
|||
|
||||
ns_dict = load_yaml(path)
|
||||
|
||||
|
||||
namespaces = yaml_loader.load(ns_dict, target_class=Namespaces)
|
||||
return namespaces
|
||||
|
||||
|
||||
|
||||
def load_schema_file(path:Path, yaml:Optional[dict] = None) -> SchemaAdapter:
|
||||
if yaml is not None:
|
||||
source = yaml
|
||||
|
|
@ -89,7 +85,7 @@ def load_namespace_schema(namespace: Namespaces, path:Path=Path('..')) -> Namesp
|
|||
for ns in namespace.namespaces:
|
||||
for schema in ns.schema_:
|
||||
if schema.source is None:
|
||||
warnings.warn(f"No source specified for {schema}")
|
||||
# this is normal, we'll resolve later
|
||||
continue
|
||||
yml_file = (path / schema.source).resolve()
|
||||
sch.append(load_schema_file(yml_file))
|
||||
|
|
@ -12,7 +12,7 @@ from linkml_runtime.linkml_model import \
|
|||
TypeDefinition,\
|
||||
Prefix,\
|
||||
PermissibleValue
|
||||
from nwb_linkml.src.nwb_linkml.maps import flat_to_linkml
|
||||
from nwb_linkml.maps import flat_to_linkml
|
||||
|
||||
|
||||
FlatDType = EnumDefinition(
|
||||
|
|
@ -20,34 +20,6 @@ FlatDType = EnumDefinition(
|
|||
permissible_values=[PermissibleValue(p) for p in FlatDtype_source.__members__.keys()],
|
||||
)
|
||||
|
||||
# DimNameSlot = SlotDefinition(
|
||||
# name="dim_name",
|
||||
# range="string",
|
||||
# description="The name of a dimension"
|
||||
# )
|
||||
# DimShapeSlot = SlotDefinition(
|
||||
# name="dim_shape",
|
||||
# range="integer",
|
||||
# required=False
|
||||
# )
|
||||
# DimClass = ClassDefinition(
|
||||
# name="Dimension",
|
||||
# slots=[DimNameSlot.name, DimShapeSlot.name],
|
||||
# description="A single dimension within a shape"
|
||||
# )
|
||||
# DimSlot = SlotDefinition(
|
||||
# name="dim",
|
||||
# range=DimClass.name,
|
||||
# multivalued=True,
|
||||
# description="Slot representing the dimensions that a Shape can have"
|
||||
# )
|
||||
|
||||
# ShapeClass = ClassDefinition(
|
||||
# name="Shape",
|
||||
# description="A possible shape for an array-like dataset",
|
||||
# slots=[DimSlot.name]
|
||||
# )
|
||||
|
||||
DTypeTypes = []
|
||||
for nwbtype, linkmltype in flat_to_linkml.items():
|
||||
amin = None
|
||||
|
|
@ -85,7 +57,6 @@ NwbLangSchema = SchemaDefinition(
|
|||
id='nwb.language',
|
||||
description="Adapter objects to mimic the behavior of elements in the nwb-schema-language",
|
||||
enums=[FlatDType],
|
||||
# slots=[DimNameSlot, DimShapeSlot, DimSlot],
|
||||
classes=[Arraylike, AnyType],
|
||||
types=DTypeTypes,
|
||||
imports=['linkml:types'],
|
||||
|
|
|
|||
|
|
@ -1,3 +1,4 @@
|
|||
# Import everything so it's defined, but shoudlnt' necessarily be used from here
|
||||
from nwb_linkml.src.nwb_linkml.maps import MAP_HDMF_DATATYPE_DEF, MAP_HDMF_DATATYPE_INC
|
||||
from nwb_linkml.src.nwb_linkml.maps import QUANTITY_MAP
|
||||
from nwb_linkml.maps.preload import MAP_HDMF_DATATYPE_DEF, MAP_HDMF_DATATYPE_INC
|
||||
from nwb_linkml.maps.quantity import QUANTITY_MAP
|
||||
from nwb_linkml.maps.dtype import flat_to_linkml, flat_to_npytyping
|
||||
|
|
@ -2,7 +2,7 @@
|
|||
Maps to change the loaded .yaml from nwb schema before it's given to the nwb_schema_language models
|
||||
"""
|
||||
|
||||
from nwb_linkml.src.nwb_linkml.map import KeyMap, SCOPE_TYPES, PHASES
|
||||
from nwb_linkml.map import KeyMap, SCOPE_TYPES, PHASES
|
||||
|
||||
MAP_HDMF_DATATYPE_DEF = KeyMap(
|
||||
source="\'data_type_def\'",
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@ import dash_cytoscape as cyto
|
|||
cyto.load_extra_layouts()
|
||||
|
||||
from nwb_schema_language import Namespace, Group, Dataset
|
||||
from nwb_linkml.src.nwb_linkml.io import load_nwb_core
|
||||
from nwb_linkml.io import load_nwb_core
|
||||
|
||||
if TYPE_CHECKING:
|
||||
from nwb_linkml.adapters import NamespacesAdapter
|
||||
|
|
|
|||
|
|
@ -12,9 +12,9 @@ import h5py
|
|||
from linkml_runtime.dumpers import yaml_dumper
|
||||
|
||||
from nwb_schema_language import Namespaces
|
||||
from nwb_linkml.src.nwb_linkml.io import load_schema_file
|
||||
from nwb_linkml.io.schema import load_schema_file
|
||||
from nwb_linkml.generators.pydantic import NWBPydanticGenerator
|
||||
from nwb_linkml.src.nwb_linkml.map import apply_preload
|
||||
from nwb_linkml.map import apply_preload
|
||||
from nwb_linkml.adapters import SchemaAdapter, NamespacesAdapter
|
||||
|
||||
def make_namespace_adapter(schema: dict) -> NamespacesAdapter:
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
import pytest
|
||||
|
||||
from nwb_linkml.src.nwb_linkml import io
|
||||
from nwb_linkml.src.nwb_linkml.adapters.namespaces import NamespacesAdapter
|
||||
from nwb_linkml.io import schema as io
|
||||
from nwb_linkml.adapters.namespaces import NamespacesAdapter
|
||||
import shutil
|
||||
from pathlib import Path
|
||||
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
import pytest
|
||||
from .fixtures import nwb_core_fixture
|
||||
from ..fixtures import nwb_core_fixture
|
||||
|
||||
from nwb_schema_language import Dataset, Group, Schema
|
||||
|
||||
|
|
@ -20,3 +20,9 @@ def test_walk_types(nwb_core_fixture, walk_class, known_number):
|
|||
# pdb.set_trace()
|
||||
|
||||
|
||||
def test_build_result_add():
|
||||
"""
|
||||
Build results can
|
||||
Returns:
|
||||
|
||||
"""
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
import pytest
|
||||
|
||||
from .fixtures import nwb_core_fixture
|
||||
from ..fixtures import nwb_core_fixture
|
||||
|
||||
|
|
|
|||
|
|
@ -1,5 +1,7 @@
|
|||
import pytest
|
||||
from .fixtures import nwb_core_fixture
|
||||
from ..fixtures import nwb_core_fixture
|
||||
from nwb_schema_language import Dataset, Group
|
||||
from nwb_linkml.adapters import SchemaAdapter
|
||||
|
||||
@pytest.mark.parametrize(
|
||||
['class_name','schema_file','namespace_name'],
|
||||
|
|
@ -17,4 +19,17 @@ def test_find_type_source(nwb_core_fixture, class_name, schema_file, namespace_n
|
|||
|
||||
|
||||
def test_populate_imports(nwb_core_fixture):
|
||||
nwb_core_fixture.populate_imports()
|
||||
nwb_core_fixture.populate_imports()
|
||||
schema: SchemaAdapter
|
||||
assert len(nwb_core_fixture.schemas) > 0
|
||||
for schema in nwb_core_fixture.schemas:
|
||||
need_imports = [nwb_core_fixture.find_type_source(cls.neurodata_type_def).namespace for cls in schema.created_classes if cls.neurodata_type_inc is not None]
|
||||
need_imports = [i for i in need_imports if i != schema.namespace]
|
||||
for i in need_imports:
|
||||
assert i in schema.imports
|
||||
|
||||
|
||||
|
||||
|
||||
def test_build(nwb_core_fixture):
|
||||
pass
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
import pytest
|
||||
from .fixtures import nwb_core_fixture
|
||||
from ..fixtures import nwb_core_fixture
|
||||
|
||||
from nwb_schema_language import Dataset, Group, Schema
|
||||
|
||||
|
|
|
|||
|
|
@ -5,7 +5,6 @@ import warnings
|
|||
|
||||
from .fixtures import nwb_core_fixture, tmp_output_dir
|
||||
from linkml_runtime.dumpers import yaml_dumper
|
||||
from linkml.generators import PydanticGenerator
|
||||
from nwb_linkml.generators.pydantic import NWBPydanticGenerator
|
||||
|
||||
from nwb_linkml.lang_elements import NwbLangSchema
|
||||
|
|
|
|||
0
nwb_linkml/tests/test_io/__init__.py
Normal file
0
nwb_linkml/tests/test_io/__init__.py
Normal file
94
nwb_linkml/tests/test_io/test_io_git.py
Normal file
94
nwb_linkml/tests/test_io/test_io_git.py
Normal file
|
|
@ -0,0 +1,94 @@
|
|||
import pytest
|
||||
import tempfile
|
||||
import shutil
|
||||
|
||||
import yaml
|
||||
from nwb_linkml.io.git import GitRepo, GitError, NamespaceRepo, NWB_CORE_REPO, HDMF_COMMON_REPO
|
||||
from nwb_schema_language import Namespaces
|
||||
|
||||
@pytest.mark.parametrize(
|
||||
['source', 'commit'],
|
||||
[
|
||||
(NWB_CORE_REPO, 'b4f8838cbfbb7f8a117bd7e0aad19133d26868b4'),
|
||||
(HDMF_COMMON_REPO, '660b6ac0780dd9d2cb1e56fea8b62c671ca5e2c8')
|
||||
]
|
||||
)
|
||||
def test_gitrepo(source, commit):
|
||||
"""
|
||||
Basic functionality of GitRepo
|
||||
"""
|
||||
repo = GitRepo(source)
|
||||
|
||||
# make a temp directory that exists
|
||||
first_dir = repo.temp_directory
|
||||
assert repo.temp_directory.exists()
|
||||
|
||||
# find the same repository when it's deleted
|
||||
shutil.rmtree(str(repo.temp_directory))
|
||||
repo._temp_directory = None
|
||||
second_dir = repo.temp_directory
|
||||
assert first_dir == second_dir
|
||||
|
||||
# successfully clone the repository after its deleted
|
||||
assert not any(repo.temp_directory.iterdir())
|
||||
repo.clone()
|
||||
# check that the namespace file exists and has some expected fields
|
||||
assert repo.namespace_file.exists()
|
||||
with open(repo.namespace_file, 'r') as nsfile:
|
||||
ns = yaml.safe_load(nsfile)
|
||||
# correct model instantiation confirms the repo was cloned successfully
|
||||
ns_model = Namespaces(**ns)
|
||||
|
||||
# setting commit should change the active commit
|
||||
prior_commit = repo.active_commit
|
||||
repo.commit = commit
|
||||
assert prior_commit != repo.active_commit
|
||||
assert repo.active_commit == commit
|
||||
assert repo.commit == commit
|
||||
|
||||
# remote is gotten correctly
|
||||
assert repo.remote == str(source.repository)
|
||||
|
||||
# cleanup should remove files
|
||||
repo.cleanup()
|
||||
assert not any(repo.temp_directory.iterdir())
|
||||
|
||||
@pytest.mark.parametrize(
|
||||
['source', 'commit'],
|
||||
[
|
||||
(NWB_CORE_REPO, 'b4f8838cbfbb7f8a117bd7e0aad19133d26868b4')
|
||||
]
|
||||
)
|
||||
def test_gitrepo_check(source, commit):
|
||||
"""
|
||||
Our check method should flag common problems with the repo
|
||||
"""
|
||||
repo = GitRepo(NWB_CORE_REPO, commit=commit)
|
||||
# cleanup is tested separately
|
||||
repo.cleanup()
|
||||
|
||||
# check should fail without warning when the repo is empty
|
||||
assert not repo.check()
|
||||
|
||||
repo.clone()
|
||||
assert repo.check()
|
||||
|
||||
# check should fail when repo is at wrong commit
|
||||
assert repo.active_commit == commit
|
||||
repo._git_call('checkout', 'HEAD~10')
|
||||
with pytest.warns(UserWarning, match=".*wrong commit.*"):
|
||||
assert not repo.check()
|
||||
repo.commit = commit
|
||||
assert repo.active_commit == commit
|
||||
assert repo.check()
|
||||
|
||||
# check should fail on repo namespace mismatch
|
||||
old_repo = repo.namespace.repository
|
||||
repo.namespace.repository = "https://example.com/a/git/repository"
|
||||
with pytest.warns(UserWarning, match='.*wrong remote.*'):
|
||||
assert not repo.check()
|
||||
repo.namespace.repository = old_repo
|
||||
assert repo.check()
|
||||
|
||||
|
||||
|
||||
42
nwb_linkml/tests/test_maps.py
Normal file
42
nwb_linkml/tests/test_maps.py
Normal file
|
|
@ -0,0 +1,42 @@
|
|||
import pytest
|
||||
import shutil
|
||||
|
||||
import tempfile
|
||||
import yaml
|
||||
from yaml import CDumper as Dumper
|
||||
from pathlib import Path
|
||||
from nwb_linkml.io.schema import load_yaml
|
||||
|
||||
def test_preload_maps():
|
||||
hdmf_style_naming = {
|
||||
'groups': [
|
||||
{
|
||||
'data_type_def': 'Container',
|
||||
'data_type_inc': 'MainClass',
|
||||
'doc': 'Demo group',
|
||||
'datasets': [
|
||||
{
|
||||
'data_type_inc': 'Data'
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
|
||||
temp, temp_name = tempfile.mkstemp(suffix='.yaml')
|
||||
|
||||
with open(temp_name, 'w') as temp_f:
|
||||
yaml.dump(hdmf_style_naming, temp_f, Dumper=Dumper)
|
||||
loaded = load_yaml(Path(temp_name))
|
||||
|
||||
assert 'neurodata_type_def' in loaded['groups'][0].keys()
|
||||
assert 'data_type_def' not in loaded['groups'][0].keys()
|
||||
assert 'neurodata_type_inc' in loaded['groups'][0].keys()
|
||||
assert 'data_type_inc' not in loaded['groups'][0].keys()
|
||||
assert 'neurodata_type_inc' in loaded['groups'][0]['datasets'][0].keys()
|
||||
assert 'data_type_inc' not in loaded['groups'][0]['datasets'][0].keys()
|
||||
|
||||
shutil.rmtree(temp_name)
|
||||
|
||||
|
||||
|
||||
|
|
@ -1,4 +0,0 @@
|
|||
[pytest]
|
||||
|
||||
testpaths =
|
||||
nwb_linkml/tests
|
||||
Loading…
Reference in a new issue