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Donders-Institute / bidscoin

BIDScoin converts your source-level neuroimaging data to BIDS
https://bidscoin.readthedocs.io
GNU General Public License v3.0
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Document How to Run Tests/Set up Env #247

Open bendhouseart opened 6 hours ago

bendhouseart commented 6 hours ago

General summary Unable to run tests with pytest

(venv) galassiae@MH02276145MLI bidscoin % pytest tests             
ImportError while loading conftest '/Users/galassiae/Projects/bidscoin/tests/conftest.py'.
tests/conftest.py:10: in <module>
    from bidscoin.utilities import dicomsort
E   ModuleNotFoundError: No module named 'bidscoin.utilities'

Additional detail Might be related to pip install failing:

(venv) galassiae@MH02276145MLI bidscoin % pip install bidscoin[dev]
zsh: no matches found: bidscoin[dev]
(venv) galassiae@MH02276145MLI bidscoin % pytest tests 
ImportError while loading conftest '/Users/galassiae/Projects/bidscoin/tests/conftest.py'.
tests/conftest.py:10: in <module>
    from bidscoin.utilities import dicomsort
E   ModuleNotFoundError: No module named 'bidscoin.utilities'

Currently working off of commit 527d97b6f2d from 2024-11-04 at donders-institute/bidscoin:master

marcelzwiers commented 5 hours ago

Are you perhaps in a py3.13 environment? Because that fails here too

bendhouseart commented 5 hours ago

I'm on Python 3.11.0 (v3.11.0:deaf509e8f, Oct 24 2022, 14:43:23) [Clang 13.0.0 (clang-1300.0.29.30)] on darwin

What do you recommend?

marcelzwiers commented 5 hours ago

That should be ok, but it is unclear to me why your install fails? If you install without the dev extras, does that work?

marcelzwiers commented 5 hours ago

It works on GitHub...? https://github.com/Donders-Institute/bidscoin/actions/runs/11699151269/job/32580622420

bendhouseart commented 5 hours ago

Yeah, that's very odd....

I tried the same commands on the github runner for mac and got the same errors, but when I switch over to bash:

(venv) galassiae@MH02276145MLI bidscoin % pip install .[all] pytest    
zsh: no matches found: .[all]
(venv) galassiae@MH02276145MLI bidscoin % bash
bash: /Applications/freesurfer/7.2.0/SetUpFreeSurfer.sh: No such file or directory

The default interactive shell is now zsh.
To update your account to use zsh, please run `chsh -s /bin/zsh`.
For more details, please visit https://support.apple.com/kb/HT208050.
(venv) %n@%m %1~ %# pip install .[all] pytest
Processing /Users/galassiae/Projects/bidscoin
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting pytest
  Downloading pytest-8.3.3-py3-none-any.whl.metadata (7.5 kB)
Requirement already satisfied: pandas in ./venv/lib/python3.11/site-packages (from bidscoin==4.5.0) (2.2.3)
Requirement already satisfied: matplotlib in ./venv/lib/python3.11/site-packages (from bidscoin==4.5.0) (3.9.2)
Requirement already satisfied: numpy in ./venv/lib/python3.11/site-packages (from bidscoin==4.5.0) (1.26.4)
Requirement already satisfied: pydicom>=2 in ./venv/lib/python3.11/site-packages (from bidscoin==4.5.0) (2.4.4)
Requirement already satisfied: PyQt6 in ./venv/lib/python3.11/site-packages (from bidscoin==4.5.0) (6.7.1)
Requirement already satisfied: ruamel-yaml>0.17.2 in ./venv/lib/python3.11/site-packages (from bidscoin==4.5.0) (0.18.6)
Requirement already satisfied: coloredlogs in ./venv/lib/python3.11/site-packages (from bidscoin==4.5.0) (15.0.1)
Requirement already satisfied: tqdm>=4.60.0 in ./venv/lib/python3.11/site-packages (from bidscoin==4.5.0) (4.66.5)
Requirement already satisfied: multiecho>=0.25 in ./venv/lib/python3.11/site-packages (from bidscoin==4.5.0) (0.29)
Requirement already satisfied: python-dateutil in ./venv/lib/python3.11/site-packages (from bidscoin==4.5.0) (2.9.0.post0)
Requirement already satisfied: nibabel in ./venv/lib/python3.11/site-packages (from bidscoin==4.5.0) (5.3.2)
Requirement already satisfied: bids-validator in ./venv/lib/python3.11/site-packages (from bidscoin==4.5.0) (1.14.7.post0)
Requirement already satisfied: jsonschema in ./venv/lib/python3.11/site-packages (from bidscoin==4.5.0) (4.23.0)
Requirement already satisfied: bidsschematools in ./venv/lib/python3.11/site-packages (from bidscoin==4.5.0) (0.11.3)
Requirement already satisfied: drmaa in ./venv/lib/python3.11/site-packages (from bidscoin==4.5.0) (0.7.9)
Requirement already satisfied: duecredit in ./venv/lib/python3.11/site-packages (from bidscoin==4.5.0) (0.10.2)
Requirement already satisfied: pypet2bids in ./venv/lib/python3.11/site-packages (from bidscoin==4.5.0) (1.3.13)
Collecting iniconfig (from pytest)
  Downloading iniconfig-2.0.0-py3-none-any.whl.metadata (2.6 kB)
Requirement already satisfied: packaging in ./venv/lib/python3.11/site-packages (from pytest) (24.1)
Collecting pluggy<2,>=1.5 (from pytest)
  Using cached pluggy-1.5.0-py3-none-any.whl.metadata (4.8 kB)
Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in ./venv/lib/python3.11/site-packages (from ruamel-yaml>0.17.2->bidscoin==4.5.0) (0.2.12)
Requirement already satisfied: click in ./venv/lib/python3.11/site-packages (from bidsschematools->bidscoin==4.5.0) (8.1.7)
Requirement already satisfied: pyyaml in ./venv/lib/python3.11/site-packages (from bidsschematools->bidscoin==4.5.0) (6.0.2)
Collecting dcm2niix (from bidscoin==4.5.0)
  Downloading dcm2niix-1.0.20220715.tar.gz (451 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting pydeface (from bidscoin==4.5.0)
  Downloading pydeface-2.0.2-py3-none-any.whl.metadata (1.8 kB)
Collecting spec2nii>=0.6.1 (from bidscoin==4.5.0)
  Downloading spec2nii-0.8.5-py3-none-any.whl.metadata (11 kB)
Requirement already satisfied: joblib<2.0.0,>=1.2.0 in ./venv/lib/python3.11/site-packages (from pypet2bids->bidscoin==4.5.0) (1.4.2)
Requirement already satisfied: json-maj<0.0.9,>=0.0.8 in ./venv/lib/python3.11/site-packages (from pypet2bids->bidscoin==4.5.0) (0.0.8)
Requirement already satisfied: openpyxl<4.0.0,>=3.0.9 in ./venv/lib/python3.11/site-packages (from pypet2bids->bidscoin==4.5.0) (3.1.5)
Requirement already satisfied: pyparsing<4.0.0,>=3.0.4 in ./venv/lib/python3.11/site-packages (from pypet2bids->bidscoin==4.5.0) (3.2.0)
Requirement already satisfied: python-dotenv<0.20.0,>=0.19.1 in ./venv/lib/python3.11/site-packages (from pypet2bids->bidscoin==4.5.0) (0.19.2)
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Requirement already satisfied: scipy<2.0.0,>=1.7.1 in ./venv/lib/python3.11/site-packages (from pypet2bids->bidscoin==4.5.0) (1.14.1)
Requirement already satisfied: six<2.0.0,>=1.16.0 in ./venv/lib/python3.11/site-packages (from pypet2bids->bidscoin==4.5.0) (1.16.0)
Requirement already satisfied: toml>=0.10.2 in ./venv/lib/python3.11/site-packages (from pypet2bids->bidscoin==4.5.0) (0.10.2)
Requirement already satisfied: xlrd<3.0.0,>=2.0.1 in ./venv/lib/python3.11/site-packages (from pypet2bids->bidscoin==4.5.0) (2.0.1)
Requirement already satisfied: importlib-resources>=5.12 in ./venv/lib/python3.11/site-packages (from nibabel->bidscoin==4.5.0) (6.4.5)
Requirement already satisfied: typing-extensions>=4.6 in ./venv/lib/python3.11/site-packages (from nibabel->bidscoin==4.5.0) (4.12.2)
Requirement already satisfied: pytz>=2020.1 in ./venv/lib/python3.11/site-packages (from pandas->bidscoin==4.5.0) (2024.2)
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Requirement already satisfied: PyQt6-sip<14,>=13.8 in ./venv/lib/python3.11/site-packages (from PyQt6->bidscoin==4.5.0) (13.8.0)
Requirement already satisfied: PyQt6-Qt6<6.8.0,>=6.7.0 in ./venv/lib/python3.11/site-packages (from PyQt6->bidscoin==4.5.0) (6.7.3)
Requirement already satisfied: lxml in ./venv/lib/python3.11/site-packages (from citeproc-py>=0.4->duecredit->bidscoin==4.5.0) (5.3.0)
Requirement already satisfied: et-xmlfile in ./venv/lib/python3.11/site-packages (from openpyxl<4.0.0,>=3.0.9->pypet2bids->bidscoin==4.5.0) (1.1.0)
Collecting pyMapVBVD>=0.6.0 (from spec2nii>=0.6.1->bidscoin==4.5.0)
  Downloading pyMapVBVD-0.6.1-py3-none-any.whl.metadata (4.4 kB)
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  Downloading nifti_mrs-1.3.2-py3-none-any.whl.metadata (5.4 kB)
INFO: pip is looking at multiple versions of spec2nii to determine which version is compatible with other requirements. This could take a while.
Collecting spec2nii>=0.6.1 (from bidscoin==4.5.0)
  Downloading spec2nii-0.8.4-py3-none-any.whl.metadata (11 kB)
Collecting scipy<2.0.0,>=1.7.1 (from pypet2bids->bidscoin==4.5.0)
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Collecting spec2nii>=0.6.1 (from bidscoin==4.5.0)
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Collecting miutil[web] (from dcm2niix->bidscoin==4.5.0)
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Collecting nipype (from pydeface->bidscoin==4.5.0)
  Downloading nipype-1.9.0-py3-none-any.whl.metadata (6.6 kB)
Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (from pydeface->bidscoin==4.5.0) (65.5.0)
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Building wheels for collected packages: bidscoin, dcm2niix
  Building wheel for bidscoin (pyproject.toml) ... done
  Created wheel for bidscoin: filename=bidscoin-4.5.0-py3-none-any.whl size=759671 sha256=9bb45cebfad36749a28f41c554efb0de56fdbf8573b8c77e3ea85439402e95d1
  Stored in directory: /private/var/folders/5t/0cjjt4t10hz5_qk4tts9gkv40000gs/T/pip-ephem-wheel-cache-u6a2ktx2/wheels/1a/8c/f7/ef2d6820eb3bc359bfe9183dac437a42012870672461544f0a
  Building wheel for dcm2niix (pyproject.toml) ... /

It works fine...

bendhouseart commented 5 hours ago

Created PR #248 to close this.