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scipion-em / scipion-em-sphire

Plugin to use Sphire programs within the Scipion framework
GNU General Public License v3.0
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Fixing error related to numpy #67

Closed pconesa closed 1 year ago

pconesa commented 2 years ago

This has been reported today:

scipionuser@scipion-master:~/ScipionUserData/projects$ more 2022_02_21_dunia-asensio_000081/Runs/003508_SphireProtCRYOLOPicking/logs/run.stderr Traceback (most recent call last): File "/home/scipionuser/miniconda3/envs/cryolo-1.8.2/bin/cryolo_predict.py", line 5, in from cryolo.predict import main File "/home/scipionuser/miniconda3/envs/cryolo-1.8.2/lib/python3.7/site-packages/cryolo/predict.py", line 31, in from cryolo.utils import BoundBox File "/home/scipionuser/miniconda3/envs/cryolo-1.8.2/lib/python3.7/site-packages/cryolo/utils.py", line 25, in from . import imagereader File "/home/scipionuser/miniconda3/envs/cryolo-1.8.2/lib/python3.7/site-packages/cryolo/imagereader.py", line 13, in import imageio File "/home/scipionuser/miniconda3/envs/cryolo-1.8.2/lib/python3.7/site-packages/imageio/init.py", line 22, in from .core import FormatManager, RETURN_BYTES File "/home/scipionuser/miniconda3/envs/cryolo-1.8.2/lib/python3.7/site-packages/imageio/core/init.py", line 16, in from .format import Format, FormatManager File "/home/scipionuser/miniconda3/envs/cryolo-1.8.2/lib/python3.7/site-packages/imageio/core/format.py", line 40, in from ..config import known_plugins, known_extensions, PluginConfig, FileExtension File "/home/scipionuser/miniconda3/envs/cryolo-1.8.2/lib/python3.7/site-packages/imageio/config/init.py", line 7, in from .plugins import known_plugins, PluginConfig File "/home/scipionuser/miniconda3/envs/cryolo-1.8.2/lib/python3.7/site-packages/imageio/config/plugins.py", line 4, in from ..core.legacy_plugin_wrapper import LegacyPlugin File "/home/scipionuser/miniconda3/envs/cryolo-1.8.2/lib/python3.7/site-packages/imageio/core/legacy_plugin_wrapper.py", line 6, in from .v3_plugin_api import PluginV3, ImageProperties File "/home/scipionuser/miniconda3/envs/cryolo-1.8.2/lib/python3.7/site-packages/imageio/core/v3_plugin_api.py", line 2, in from numpy.typing import ArrayLike ModuleNotFoundError: No module named 'numpy.typing' Traceback (most recent call last): File "/home/scipionuser/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 201, in run self._run() File "/home/scipionuser/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 252, in _run resultFiles = self._runFunc() File "/home/scipionuser/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _runFunc return self._func(self._args) File "/home/scipionuser/miniconda3/envs/scipion3/lib/python3.8/site-packages/pwem/protocols/protocol_particles_picking.py", line 286, in pickMicrographListStep self._pickMicrographList(micList, args) File "/home/scipionuser/miniconda3/envs/scipion3/lib/python3.8/site-packages/sphire/protocols/protocol_cryolo_picking.py", line 216, in _pickMicrographList Plugin.runCryolo(self, 'cryolo_predict.py', args, useCpu=self.usingCpu()) File "/home/scipionuser/miniconda3/envs/scipion3/lib/python3.8/site-packages/sphire/init.py", line 195, in runCryolo protocol.runJob(fullProgram, args, env=cls.getEnviron(), cwd=cwd, File "/home/scipionuser/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1441, in runJob self._stepsExecutor.runJob(self._log, program, arguments, **kwargs) File "/home/scipionuser/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob process.runJob(log, programName, params, File "/home/scipionuser/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob return runCommand(command, env, cwd) File "/home/scipionuser/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, File "/home/scipionuser/miniconda3/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command ' eval "$(/home/scipionuser/miniconda3/bin/conda shell.bash hook)"&& conda activate cryolo-1.8.2 && cryolo_predict.py -c Runs/003508_SphireProtCRYOLOPicking/extra/config.json -w /home/sci pionuser/scipion3/software/em/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 -i Runs/003508_SphireProtCRYOLOPicking/tmp/micrographs_1-16/ -o Runs/003508_SphireProtCRYOLOPicking/tmp/micrographs_1-16/ -t 0.300 -g 0 -nc 4 --otf' returned non-zero exit status 1. Protocol failed: Command ' eval "$(/home/scipionuser/miniconda3/bin/conda shell.bash hook)"&& conda activate cryolo-1.8.2 && cryolo_predict.py -c Runs/003508_SphireProtCRYOLOPicking/extra/config.json -w /home/scipionuser/s cipion3/software/em/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 -i Runs/003508_SphireProtCRYOLOPicking/tmp/micrographs_1-16/ -o Runs/003508_SphireProtCRYOLOPicking/tmp/micrographs_1-16/ -t 0.300 -g 0 -nc 4 --o tf' returned non-zero exit status 1.

'numpy.typing' was introduced in 1.20

Maybe imageio has to be fixed. I don't know.

azazellochg commented 1 year ago

Hi @pconesa , the error is because imageio is too new (https://github.com/imageio/imageio/blob/v2.16.0/setup.py#L174). Imageio must be fixed at <= 2.15.0. Numpy is fixed by cryolo now and cannot be updated. I'll report the error to Thorsten.