From fbd84ff1dd8004d671d9c631e33c8a4a516b8a8d Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 16 Jul 2024 14:48:40 +0200 Subject: [PATCH] #357 synthcity test deps added --- 357_Synthcity/synthcity.eb | 94 ++++++++++++++++++++++++++++++++++++-- 1 file changed, 90 insertions(+), 4 deletions(-) diff --git a/357_Synthcity/synthcity.eb b/357_Synthcity/synthcity.eb index 1e6fa79c..162cc080 100644 --- a/357_Synthcity/synthcity.eb +++ b/357_Synthcity/synthcity.eb @@ -92,8 +92,21 @@ toolchain = {'name': 'foss', 'version': '2023a'} # fastapi 0.110.0 has requirement typing-extensions>=4.8.0, but you have typing-extensions 4.6.3. # -> add v typing-extensions v4.9.0 to exts # py7zr 0.20.6 has requirement pyppmd<1.1.0,>=0.18.1, but you have pyppmd 1.1.0. -> add pyppmd v1.0.0 ok + # TESTS + # black 24.4.2 requires mypy-extensions ok exts + # pre-commit 3.7.1 requires identify, ok exts + # pre-commit 3.7.1 requires nodeenv, ok exts + # bandit 1.7.9 requires stevedore, ok exts + # pytest-benchmark 4.0.0 requires py-cpuinfo, OK + # doc8 1.1.1 requires restructuredtext-lint, ok exts + # doc8 1.1.1 requires stevedore, ok exts + # flake8 7.1.0 requires mccabe, ok exts + # flake8 7.1.0 requires pycodestyle, OK + # flake8 7.1.0 requires pyflakes, ok exts + # pre-commit 3.7.1 requires cfgv, ok exts + # flake8 7.1.0 has requirement pycodestyle<2.13.0,>=2.12.0, but you have pycodestyle 2.11.1. -> flake8 v7.0.0 -# builddependencies = [('poetry', '1.5.1')] +builddependencies = [('poetry', '1.5.1')] dependencies = [ ('Python', '3.11.3'), ('Python-bundle-PyPI', '2023.06'), @@ -112,7 +125,7 @@ dependencies = [ # ('PyYAML', '6.0'), ('fastai', '2.7.15'), ('h5py', '3.9.0'), - # ('networkx', '3.1'), # v2.8.8 in exts + ('networkx', '3.1'), # ('protobuf', '3.19.4'), # ('Arrow', '8.0.0'), # ('pybind11', '2.9.2'), @@ -130,6 +143,14 @@ dependencies = [ ('MONAI', '1.3.0'), ('DECAF-synthetic-data', '0.1.6'), ('PyTorch-Lightning', '2.2.1'), + # TESTS + ('pytest', '7.4.2'), + ('Jupyter-bundle', '20230823'), + ('pytest-xdist', '3.3.1'), + ('python-igraph', '0.11.4'), + ('coverage', '7.2.3'), + ('py-cpuinfo', '9.0.0'), + ('pycodestyle', '2.11.1'), ] sanity_pip_check = True @@ -156,6 +177,64 @@ local_xgbse_preinstallopts = ( ) exts_list = [ + ('cfgv', '3.4.0', { + 'checksums': ['e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560'], + }), + ('pyflakes', '3.2.0', { + 'checksums': ['1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f'], + }), + ('mccabe', '0.7.0', { + 'checksums': ['348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325'], + }), + ('restructuredtext_lint', '1.4.0', { + 'checksums': ['1b235c0c922341ab6c530390892eb9e92f90b9b75046063e047cacfb0f050c45'], + }), + ('stevedore', '5.2.0', { + 'checksums': ['46b93ca40e1114cea93d738a6c1e365396981bb6bb78c27045b7587c9473544d'], + }), + ('nodeenv', '1.9.1', { + 'checksums': ['6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f'], + }), + ('identify', '2.6.0', { + 'checksums': ['cb171c685bdc31bcc4c1734698736a7d5b6c8bf2e0c15117f4d469c8640ae5cf'], + }), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + ('pytest-cov', '5.0.0', { + 'checksums': ['5837b58e9f6ebd335b0f8060eecce69b662415b16dc503883a02f45dfeb14857'], + }), + ('bandit', '1.7.9', { + 'checksums': ['7c395a436743018f7be0a4cbb0a4ea9b902b6d87264ddecf8cfdc73b4f78ff61'], + }), + ('black', '24.4.2', { + 'checksums': ['c872b53057f000085da66a19c55d68f6f8ddcac2642392ad3a355878406fbd4d'], + }), + ('black-nb', '0.7', { + 'checksums': ['8742a4f7c728302c91954325168d779f9444f8e3c31b19598ee8e98fc4bf4782'], + }), + ('darglint', '1.8.1', { + 'checksums': ['080d5106df149b199822e7ee7deb9c012b49891538f14a11be681044f0bb20da'], + }), + ('doc8', '1.1.1', { + 'checksums': ['d97a93e8f5a2efc4713a0804657dedad83745cca4cd1d88de9186f77f9776004'], + }), + ('flake8', '7.0.0', { + 'checksums': ['33f96621059e65eec474169085dc92bf26e7b2d47366b70be2f67ab80dc25132'], + }), + ('isort', '5.13.2', { + 'checksums': ['48fdfcb9face5d58a4f6dde2e72a1fb8dcaf8ab26f95ab49fab84c2ddefb0109'], + }), + ('pytest-benchmark', '4.0.0', { + 'checksums': ['fb0785b83efe599a6a956361c0691ae1dbb5318018561af10f3e915caa0048d1'], + }), + ('pytest-xprocess', '1.0.2', { + 'modulename': 'xprocess', + 'checksums': ['15e270637586eabc56755ee5fcc81c48bdb46ba7ef7c0d5b1b64302d080cc60f'], + }), + ('pre_commit', '3.7.1', { + 'checksums': ['8ca3ad567bc78a4972a3f1a477e94a79d4597e8140a6e0b651c5e33899c3654a'], + }), ('typing_extensions', '4.9.0', { 'checksums': ['23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783'], }), @@ -242,7 +321,7 @@ exts_list = [ 'checksums': ['824f10482581f5211d3a435d8b14adcc6c21b38d952f00b6a792fc7c089788b1'], }), ('xgbse', '0.2.3', { - 'preinstallopts': local_xgbse_preinstallopts, + 'preinstallopts': "sed -i -e '45,49d' -e 's/pandas>=1.0.\*/pandas>=1.0.0/' setup.py && ", 'source_urls': ['https://github.com/loft-br/xgboost-survival-embeddings/archive/'], 'sources': ['v%(version)s.tar.gz'], 'checksums': ['9e6b71539b2b533c00eddfe7681cdd541f393d9573594eca358d263b141c127d'], @@ -252,12 +331,13 @@ exts_list = [ }), (name, version, { 'preinstallopts': local_preinstallopts, + 'runtest': 'pytest -vvvs -m "not slow" --durations=50', 'source_urls': ['https://github.com/vanderschaarlab/synthcity/archive/'], 'sources': ['v%(version)s.tar.gz'], 'checksums': ['122a8546cad35e3ac5c74cf81281252dec4dd3c7b1d7afe0f45ef785f89cc682'], }), ] - + sanity_check_commands = [ "python -c 'from synthcity.plugins import Plugins'", "python -c 'from decaf import DECAF, DataModule'" @@ -265,6 +345,12 @@ sanity_check_commands = [ moduleclass = 'lib' +# ERROR3: + # -> add coverage to deps + # -> put runtest to exts - synthcity ext, not as runtest = ... + # tests/test_pytest_cov.py:12: in + # import coverage + # E ModuleNotFoundError: No module named 'coverage' # ERROR2: OK # -> fix pandas version in setup.py by local_xgbse_preinstallopts # == 2024-07-15 14:17:49,585 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): cmd "sed -i '45,49d' setup.py && /apps/gent/RHEL8/zen2-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/zen2-ib/software/synthcity/0.2.10-foss-2023a --no-deps --ignore-installed --no-index --no-build-isolation ." exited with exit code 1 and output: