[Mne_analysis] conda upgrade error
Megan Schendel
mschendel at mrn.org
Thu Sep 10 18:04:09 EDT 2020
External Email - Use Caution
Hi all,
I managed to install a new anaconda package.
I tried modifying the environment file to leave off dipy and PyQt, but I
discovered I also can't install pyvistaqt. I actually was able to include
dipy once I got the updated conda.
However, now I'm getting an error using mne.sys_info(), and I can't use
that command over a terminal without X11 forwarding (I am working remotely,
so sometimes it's nice to just work on the python terminal and not get
slowed down with the graphics forwarding). Not a deal breaker, though.
From what I can tell from the mne.sys_info, it looks like some form of pyqt
installed
conda --version && python --version
conda 4.8.4
Python 3.8.5
I created an environment from everything in the environment file under
dependencies and with just mne for pip. Then I iteratively updated the
environment, adding one line to the list of pip installs from the
environment file at a time. I got some errors with pyvistaqt and PyQt.
Just terminal:
mne.sys_info()
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to
'/tmp/runtime-mschendel'
qt.qpa.screen: QXcbConnection: Could not connect to display
Could not connect to any X display.
(ipython3 quits)
Using python over a vnc with X11 forwarding enabled...
mne.sys_info()
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to
'/tmp/runtime-mschendel'
Platform: Linux-2.6.32-573.7.1.el6.x86_64-x86_64-with-glibc2.10
Python: 3.8.5 (default, Sep 4 2020, 07:30:14) [GCC 7.3.0]
Executable:
/export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne20/bin/python
CPU: x86_64: 24 cores
Memory: 126.0 GB
mne: 0.20.8
numpy: 1.19.1 {blas=mkl_rt, lapack=mkl_rt}
scipy: 1.5.2
matplotlib: 3.3.1 {backend=Qt5Agg}
sklearn: Not found
numba: 0.50.1
nibabel: 3.1.1
cupy: Not found
pandas: 1.1.1
dipy: 1.1.1
mayavi: 4.7.2 {qt_api=pyqt5, PyQt5=5.9.2}
pyvista: 0.26.0
vtk: 9.0.1
I also tried to create an environment without pyvistaqt and PyQt.
mne.sys_info() looks identical
Successfully installed PySurfer-0.11.0 appdirs-1.4.4 apptools-4.5.0
configobj-5.0.6 dipy-1.1.1 envisage-4.9.2 imageio-ffmpeg-0.4.2 mayavi-4.7.2
meshio-4.2.0 mne-0.20.8 neo-0.8.0 nibabel-3.1.1 nilearn-0.6.2
python-picard-0.4 pyvista-0.26.0 quantities-0.12.4 scooby-0.5.6 sklearn-0.0
vtk-9.0.1
Megan
MEG Technician
The Mind Research Network
1101 Yale Blvd. NE
Albuquerque, New Mexico 87106
On Sat, Sep 5, 2020 at 11:00 AM Eric Larson <larson.eric.d at gmail.com> wrote:
> External Email - Use Caution
>
> I would just remove the `dipy` line from the environment file to see if
> that will install properly. If it doesn't, you could iteratively remove
> requirements or as Alex says, try just installing numpy, scipy, matplotlib,
> and mne.
>
> FYI CentOS 6 reaches end-of-life for even security updates in November, so
> it might not be a bad time to consider upgrading. (Of course this is not
> the easiest solution, though!)
>
> Eric
>
>
>
> On Sat, Sep 5, 2020 at 7:52 AM Alexandre Gramfort <
> alexandre.gramfort at inria.fr> wrote:
>
>> External Email - Use Caution
>>
>> hi Megan,
>>
>> thanks for the details. Unfortunately it's going to be really hard to
>> debug for us
>> without accessing your system. Note however that you can still use
>> mne-python
>> with just numpy, scipy and matplotlib. It will cover 90% of what you can
>> do with
>> mne-python. What you will not have is 3D support but if it's remove
>> compute
>> cluster maybe it's not a real issue.
>>
>> Alex
>>
>>
>>
>>
>> On Sat, Sep 5, 2020 at 1:45 AM Megan Schendel <mschendel at mrn.org> wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hi all,
>> > The PyQt5 list helped me track down that error a bit more. The wheel
>> build for PyQt5 depends on something called manylinux2014, which depends on
>> CentOS7. The server I'm trying to use is CentOS 6.7.
>> >
>> > It sounds like my environment/pip dipy issue is related to the anaconda
>> version I have (may also be why mne was broken when I tried to create the
>> environment).
>> > There are issues with the environment file using pip in older anaconda
>> versions.
>> > However, this is after I do "conda update --all" in my mne
>> environment. I'm having trouble figuring out how to get a newer anaconda
>> package. The mne install page suggests conda version 4.6.2. It looks like
>> I have 4.3.30. The github issue page says the pip options issue is fixed
>> with 4.6.9
>> > Sorry to ask a conda question here, but when I try "conda update
>> anaconda" I get an error saying "PackageNotInstalledError: Package is not
>> installed in prefix." From searching, it sounds like I need to update my
>> base/root anaconda environment, but I'm not sure I want to do that?
>> >
>> > Also, FWIW I was able to get dipy to install using "pip install dipy
>> --only-binary dipy", which sort of led me down the rabbit hole of why my
>> environment didn't seem to be working with the pip options... I was also
>> able to install mne using pip.
>> >
>> > Just thought I'd update. It seems it is an issue with my system, not
>> with your environment file.
>> > Thanks,
>> > Megan
>> >
>> > conda info
>> > Current conda install:
>> >
>> > platform : linux-64
>> > conda version : 4.3.30
>> > conda is private : False
>> > conda-env version : 4.3.30
>> > conda-build version : 1.19.0
>> > python version : 3.5.4.final.0
>> > requests version : 2.12.4
>> > root environment :
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3
>> (writable)
>> > default environment :
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne
>> > envs directories :
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs
>> > /na/homes/mschendel/.conda/envs
>> > package cache :
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/pkgs
>> > /na/homes/mschendel/.conda/pkgs
>> > channel URLs : https://repo.continuum.io/pkgs/main/linux-64
>> > https://repo.continuum.io/pkgs/main/noarch
>> > https://repo.continuum.io/pkgs/free/linux-64
>> > https://repo.continuum.io/pkgs/free/noarch
>> > https://repo.continuum.io/pkgs/r/linux-64
>> > https://repo.continuum.io/pkgs/r/noarch
>> > https://repo.continuum.io/pkgs/pro/linux-64
>> > https://repo.continuum.io/pkgs/pro/noarch
>> > config file : None
>> > netrc file : None
>> > offline mode : False
>> > user-agent : conda/4.3.30 requests/2.12.4 CPython/3.5.4
>> Linux/2.6.32-573.7.1.el6.x86_64 CentOS/6.7 glibc/2.12
>> > UID:GID : 10263:8000
>> >
>> >
>> > I was able to get dipy to install...
>> >
>> > (mne) [mschendel at earth python]$ pip --version
>> > pip 20.2.2 from
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/lib/python3.8/site-packages/pip
>> (python 3.8)
>> >
>> > (mne) [mschendel at earth envs]$ pip install dipy --only-binary dipy
>> > Collecting dipy
>> > Using cached dipy-1.1.1-cp38-cp38-manylinux1_x86_64.whl (8.0 MB)
>> > Collecting nibabel>=3.0.0
>> > Using cached nibabel-3.1.1-py3-none-any.whl (3.3 MB)
>> > Requirement already satisfied: scipy>=1.0 in
>> ./mne/lib/python3.8/site-packages (from dipy) (1.5.2)
>> > Requirement already satisfied: h5py>=2.4.0 in
>> ./mne/lib/python3.8/site-packages (from dipy) (2.10.0)
>> > Requirement already satisfied: numpy>=1.13 in
>> ./mne/lib/python3.8/site-packages (from nibabel>=3.0.0->dipy) (1.19.1)
>> > Requirement already satisfied: packaging>=14.3 in
>> ./mne/lib/python3.8/site-packages (from nibabel>=3.0.0->dipy) (20.4)
>> > Requirement already satisfied: six in ./mne/lib/python3.8/site-packages
>> (from h5py>=2.4.0->dipy) (1.15.0)
>> > Requirement already satisfied: pyparsing>=2.0.2 in
>> ./mne/lib/python3.8/site-packages (from
>> packaging>=14.3->nibabel>=3.0.0->dipy) (2.4.7)
>> > Installing collected packages: nibabel, dipy
>> > Successfully installed dipy-1.1.1 nibabel-3.1.1
>> >
>> > Here's where I am now:
>> > mne.sys_info()
>> > Platform: Linux-2.6.32-573.7.1.el6.x86_64-x86_64-with-glibc2.10
>> > Python: 3.8.5 (default, Sep 4 2020, 07:30:14) [GCC 7.3.0]
>> > Executable:
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/bin/python3
>> > CPU: x86_64: 24 cores
>> > Memory: 126.0 GB
>> >
>> > mne: 0.20.8
>> > numpy: 1.19.1 {blas=mkl_rt, lapack=mkl_rt}
>> > scipy: 1.5.2
>> > matplotlib: 3.3.1 {backend=agg}
>> >
>> > sklearn: 0.23.2
>> > numba: 0.50.1
>> > nibabel: 3.1.1
>> > cupy: Not found
>> > pandas: 1.1.1
>> > dipy: 1.1.1
>> > mayavi: Not found
>> > pyvista: Not found
>> > vtk: Not found
>> >
>> >
>> > MEG Technician
>> > The Mind Research Network
>> > 1101 Yale Blvd. NE
>> > Albuquerque, New Mexico 87106
>> >
>> >
>> >
>> > On Fri, Sep 4, 2020 at 2:36 PM Megan Schendel <mschendel at mrn.org>
>> wrote:
>> >>
>> >> Hi all,
>> >> I am getting the same PyQt5 error when I try the install via create
>> environment.
>> >> So attempting to creating a new environment did nothing to solve
>> either of the errors I was getting trying to update the environment.
>> >> In the new environment, I can import the mne module, but it doesn't
>> have a .__version__ attribute or a .sysinfo() attribute, so it's still
>> broken.
>> >>
>> >> I also heard back from the dipy devs that the environment line for
>> dipy is wrong. They suggest either drop either the first or second 'dipy',
>> see their response below... Has anyone had success using the
>> environment.yml file on the mne install page with the dipy dependency as
>> written? I guess I'll also try to check with the PyQt5 devs to see about
>> the error I'm getting on that.
>> >>
>> >> Thanks for any help,
>> >> Megan
>> >>
>> >> PyQt5 error...
>> >> Collecting PyQt5>=5.10
>> >> Using cached PyQt5-5.15.0.tar.gz (3.3 MB)
>> >> Installing build dependencies: started
>> >> Installing build dependencies: finished with status 'done'
>> >> Getting requirements to build wheel: started
>> >> Getting requirements to build wheel: finished with status 'done'
>> >> Preparing wheel metadata: started
>> >> Preparing wheel metadata: finished with status 'error'
>> >> ERROR: Command errored out with exit status 1:
>> >> command:
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/bin/python
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py
>> prepare_metadata_for_build_wheel /tmp/tmpdqxe1zsu
>> >> cwd: /tmp/pip-install-02yoibkc/pyqt5
>> >> Complete output (35 lines):
>> >> Querying qmake about your Qt installation...
>> >>
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/bin/qmake
>> -query
>> >> Traceback (most recent call last):
>> >> File
>> "/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py",
>> line 126, in prepare_metadata_for_build_wheel
>> >> hook = backend.prepare_metadata_for_build_wheel
>> >> AttributeError: module 'sipbuild.api' has no attribute
>> 'prepare_metadata_for_build_wheel'
>> >>
>> >> During handling of the above exception, another exception occurred:
>> >>
>> >> Traceback (most recent call last):
>> >> File
>> "/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py",
>> line 280, in <module>
>> >> main()
>> >> File
>> "/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py",
>> line 263, in main
>> >> json_out['return_val'] = hook(**hook_input['kwargs'])
>> >> File
>> "/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py",
>> line 130, in prepare_metadata_for_build_wheel
>> >> return _get_wheel_metadata_from_wheel(backend,
>> metadata_directory,
>> >> File
>> "/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py",
>> line 159, in _get_wheel_metadata_from_wheel
>> >> whl_basename = backend.build_wheel(metadata_directory,
>> config_settings)
>> >> File
>> "/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/sipbuild/api.py",
>> line 51, in build_wheel
>> >> project = AbstractProject.bootstrap('pep517')
>> >> File
>> "/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/sipbuild/abstract_project.py",
>> line 82, in bootstrap
>> >> project.setup(pyproject, tool, tool_description)
>> >> File
>> "/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/sipbuild/project.py",
>> line 479, in setup
>> >> self.apply_user_defaults(tool)
>> >> File "project.py", line 62, in apply_user_defaults
>> >> super().apply_user_defaults(tool)
>> >> File
>> "/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/pyqtbuild/project.py",
>> line 89, in apply_user_defaults
>> >> super().apply_user_defaults(tool)
>> >> File
>> "/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/sipbuild/project.py",
>> line 225, in apply_user_defaults
>> >> self.builder.apply_user_defaults(tool)
>> >> File
>> "/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/pyqtbuild/builder.py",
>> line 77, in apply_user_defaults
>> >> self._get_qt_configuration()
>> >> File
>> "/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/pyqtbuild/builder.py",
>> line 450, in _get_qt_configuration
>> >> raise UserException(
>> >> sipbuild.exceptions.UserException
>> >> ----------------------------------------
>> >> ERROR: Command errored out with exit status 1:
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/bin/python
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py
>> prepare_metadata_for_build_wheel /tmp/tmpdqxe1zsu Check the logs for full
>> command output.
>> >> Using Anaconda Cloud api site https://api.anaconda.org
>> >>
>> >> CondaValueError: pip returned an error.
>> >>
>> >>
>> >> Response from Mathew at dipy
>> >>>
>> >>> I don't use conda myself - but I guess that line must be wrong, and
>> >>> you need to drop either the first or the second 'dipy' , as in:
>> >>> dependencies:
>> >>> - pip:
>> >>> - --only-binary dipy
>> >>> or:
>> >>> dependencies:
>> >>> - pip:
>> >>> - dipy --only-binary
>> >>
>> >>
>> >> MEG Technician
>> >> The Mind Research Network
>> >> 1101 Yale Blvd. NE
>> >> Albuquerque, New Mexico 87106
>> >>
>> >>
>> >>
>> >> On Thu, Sep 3, 2020 at 5:33 PM Megan Schendel <mschendel at mrn.org>
>> wrote:
>> >>>
>> >>> Hi Dan,
>> >>> I tried creating a new environment, and I'm still getting the dipy
>> error. I'll try again removing the dipy line...
>> >>> Thanks,
>> >>> Megan
>> >>>
>> >>> conda env create --name mne --file environment.yml
>> >>> Using Anaconda Cloud api site https://api.anaconda.org
>> >>> Fetching package metadata ...........
>> >>> Solving package specifications: .
>> >>> pyzmq-19.0.1-p 100%
>> |#######################################################################################################|
>> Time: 0:00:00 2.75 MB/s
>> >>> jedi-0.17.2-py 100%
>> |#######################################################################################################|
>> Time: 0:00:00 7.84 MB/s
>> >>> ERROR: Invalid requirement: 'dipy --only-binary dipy'
>> >>>
>> >>> CondaValueError: pip returned an error.
>> >>>
>> >>>
>> >>> MEG Technician
>> >>> The Mind Research Network
>> >>> 1101 Yale Blvd. NE
>> >>> Albuquerque, New Mexico 87106
>> >>>
>> >>>
>> >>>
>> >>> On Thu, Sep 3, 2020 at 4:16 PM Dan McCloy <dan at mccloy.info> wrote:
>> >>>>
>> >>>> External Email - Use Caution
>> >>>>
>> >>>> If faced with this, I'd recommend creating a *new* conda environment
>> rather than trying to update an old one. If it works cleanly, it's
>> possible to delete the old one and rename the new one later if desired.
>> The only reason I can think of *not* to do it this way is if your disk
>> space is highly constrained, or if your MNE-Python environment has a lot of
>> extra packages added that aren't in our environment.yml file (in which case
>> it might be a bit annoying to have to manually re-install those afterward).
>> >>>>
>> >>>> -- dan
>> >>>> Daniel McCloy
>> >>>> https://dan.mccloy.info
>> >>>> Research Scientist
>> >>>> Institute for Learning and Brain Sciences
>> >>>> University of Washington
>> >>>>
>> >>>>
>> >>>> ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
>> >>>> On Thursday, September 3, 2020 5:05 PM, Megan Schendel <
>> mschendel at mrn.org> wrote:
>> >>>>
>> >>>> External Email - Use Caution
>> >>>>
>> >>>>
>> >>>> Hi Eric,
>> >>>>
>> >>>> Thanks for the questions. See terminal commands and outputs below.
>> I'm on Linux.
>> >>>> Since pip is listed in the environment.yml file, it should have been
>> upgraded by the conda env -update command, right?
>> >>>> In the environment I'm trying to update, mne is broken, so I can't
>> use the python -c "import mne; mne.sys_info()" command. The results below
>> are from the environment where I have a working mne 0.15 package, but I'm
>> not sure which other modules have been updated there.
>> >>>>
>> >>>> Thanks again,
>> >>>> Megan
>> >>>>
>> >>>> updated environment:
>> >>>> pip --version
>> >>>> pip 20.2.2 from
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip
>> (python 3.8)
>> >>>>
>> >>>> python -c "import setuptools; print(setuptools.__version__)"
>> >>>> 49.6.0.post20200814
>> >>>> /updated environment
>> >>>>
>> >>>>
>> >>>> old environment:
>> >>>> conda --version && python --version
>> >>>> conda 4.3.30
>> >>>> Python 3.5.4 :: Anaconda 2.5.0 (64-bit)
>> >>>> python -c "import mne; mne.sys_info()"
>> >>>> Platform:
>> Linux-2.6.32-573.7.1.el6.x86_64-x86_64-with-centos-6.7-Final
>> >>>> Python: 3.5.4 |Anaconda 2.5.0 (64-bit)| (default, Aug 14
>> 2017, 13:26:58) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
>> >>>> Executable:
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/bin/python
>> >>>> CPU: x86_64: 24 cores
>> >>>> Memory: 126.0 GB
>> >>>>
>> >>>> mne: 0.15.2
>> >>>> numpy: 1.10.4 {lapack=SCIPY_MKL_H, blas=SCIPY_MKL_H}
>> >>>> scipy: 0.17.0
>> >>>> matplotlib: 3.0.3
>> >>>>
>> >>>> sklearn: 0.17.1
>> >>>> nibabel: 2.3.3
>> >>>> mayavi: Not found
>> >>>> pycuda: Not found
>> >>>> skcuda: Not found
>> >>>> pandas: 0.17.1
>> >>>> /old environment
>> >>>>
>> >>>> On Thu, Sep 3, 2020 at 3:37 PM Eric Larson <larson.eric.d at gmail.com>
>> wrote:
>> >>>>>
>> >>>>> External Email - Use Caution
>> >>>>>
>> >>>>>
>> >>>>> Building PyQt5 from source shouldn't happen. What platform are you
>> on? Windows/Linux/macOS should in principle all work. Maybe you need to
>> `pip install --upgrade pip`?
>> >>>>>
>> >>>>> Can you also try:
>> >>>>>
>> >>>>> $ python -c "import setuptools; print(setuptools.__version__)"
>> >>>>>
>> >>>>> Setuptools 50.0 has broken things in SciPy lately, it's possible
>> there are other bugs. If it's 50.0, try `pip install "setuptools<50.0"`.
>> >>>>>
>> >>>>> Eric
>> >>>>>
>> >>>>>
>> >>>>> On Thu, Sep 3, 2020 at 5:23 PM Megan Schendel <mschendel at mrn.org>
>> wrote:
>> >>>>>>
>> >>>>>> External Email - Use Caution
>> >>>>>>
>> >>>>>>
>> >>>>>> Hi all,
>> >>>>>> Ok, I've asked the dipy people about that error, but I could still
>> use help with the update.
>> >>>>>> Should install instructions work for update, too? Should I just
>> use pip to update mne instead of trying to use the new environment file?
>> >>>>>>
>> >>>>>> I took the dipy line out of the environment file. Here is the
>> error I'm getting from PyQt5....
>> >>>>>> Any ideas/suggestions?
>> >>>>>> Thank you,
>> >>>>>> Megan
>> >>>>>>
>> >>>>>> Collecting PyQt5>=5.10
>> >>>>>> Using cached PyQt5-5.15.0.tar.gz (3.3 MB)
>> >>>>>> Installing build dependencies: started
>> >>>>>> Installing build dependencies: finished with status 'done'
>> >>>>>> Getting requirements to build wheel: started
>> >>>>>> Getting requirements to build wheel: finished with status 'done'
>> >>>>>> Preparing wheel metadata: started
>> >>>>>> Preparing wheel metadata: finished with status 'error'
>> >>>>>> ERROR: Command errored out with exit status 1:
>> >>>>>> command:
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/bin/python
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py
>> prepare_metadata_for_build_wheel /tmp/tmperieq8r7
>> >>>>>> cwd: /tmp/pip-install-ci617d3e/pyqt5
>> >>>>>> Complete output (35 lines):
>> >>>>>> Querying qmake about your Qt installation...
>> >>>>>>
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/bin/qmake
>> -query
>> >>>>>> Traceback (most recent call last):
>> >>>>>> File
>> "/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py",
>> line 126, in prepare_metadata_for_build_wheel
>> >>>>>> hook = backend.prepare_metadata_for_build_wheel
>> >>>>>> AttributeError: module 'sipbuild.api' has no attribute
>> 'prepare_metadata_for_build_wheel'
>> >>>>>>
>> >>>>>> During handling of the above exception, another exception
>> occurred:
>> >>>>>>
>> >>>>>> Traceback (most recent call last):
>> >>>>>> File
>> "/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py",
>> line 280, in <module>
>> >>>>>> main()
>> >>>>>> File
>> "/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py",
>> line 263, in main
>> >>>>>> json_out['return_val'] = hook(**hook_input['kwargs'])
>> >>>>>> File
>> "/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py",
>> line 130, in prepare_metadata_for_build_wheel
>> >>>>>> return _get_wheel_metadata_from_wheel(backend,
>> metadata_directory,
>> >>>>>> File
>> "/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py",
>> line 159, in _get_wheel_metadata_from_wheel
>> >>>>>> whl_basename = backend.build_wheel(metadata_directory,
>> config_settings)
>> >>>>>> File
>> "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/sipbuild/api.py",
>> line 51, in build_wheel
>> >>>>>> project = AbstractProject.bootstrap('pep517')
>> >>>>>> File
>> "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/sipbuild/abstract_project.py",
>> line 82, in bootstrap
>> >>>>>> project.setup(pyproject, tool, tool_description)
>> >>>>>> File
>> "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/sipbuild/project.py",
>> line 479, in setup
>> >>>>>> self.apply_user_defaults(tool)
>> >>>>>> File "project.py", line 62, in apply_user_defaults
>> >>>>>> super().apply_user_defaults(tool)
>> >>>>>> File
>> "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/pyqtbuild/project.py",
>> line 89, in apply_user_defaults
>> >>>>>> super().apply_user_defaults(tool)
>> >>>>>> File
>> "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/sipbuild/project.py",
>> line 225, in apply_user_defaults
>> >>>>>> self.builder.apply_user_defaults(tool)
>> >>>>>> File
>> "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/pyqtbuild/builder.py",
>> line 77, in apply_user_defaults
>> >>>>>> self._get_qt_configuration()
>> >>>>>> File
>> "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/pyqtbuild/builder.py",
>> line 450, in _get_qt_configuration
>> >>>>>> raise UserException(
>> >>>>>> sipbuild.exceptions.UserException
>> >>>>>> ----------------------------------------
>> >>>>>> ERROR: Command errored out with exit status 1:
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/bin/python
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne20conda4/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py
>> prepare_metadata_for_build_wheel /tmp/tmperieq8r7 Check the logs for full
>> command output.
>> >>>>>> Using Anaconda Cloud api site https://api.anaconda.org
>> >>>>>>
>> >>>>>> CondaValueError: pip returned an error.
>> >>>>>> MEG Technician
>> >>>>>> The Mind Research Network
>> >>>>>> 1101 Yale Blvd. NE
>> >>>>>> Albuquerque, New Mexico 87106
>> >>>>>>
>> >>>>>>
>> >>>>>> On Thu, Sep 3, 2020 at 1:18 AM Alexandre Gramfort <
>> alexandre.gramfort at inria.fr> wrote:
>> >>>>>>>
>> >>>>>>> External Email - Use Caution
>> >>>>>>>
>> >>>>>>> hi Megan,
>> >>>>>>>
>> >>>>>>> you should ask this question to the dipy developpers. We are just
>> users here.
>> >>>>>>>
>> >>>>>>> Alex
>> >>>>>>>
>> >>>>>>> On Thu, Sep 3, 2020 at 1:54 AM Megan Schendel <mschendel at mrn.org>
>> wrote:
>> >>>>>>> >
>> >>>>>>> > External Email - Use Caution
>> >>>>>>> >
>> >>>>>>> > HI all,
>> >>>>>>> > I'm wondering if this is an error because I already have things
>> installed. The dipy page says to uninstall dipy before installing using
>> pip.
>> >>>>>>> > Are there separate instructions for upgrades? I realized I'm
>> trying to follow install instructions.
>> >>>>>>> >
>> >>>>>>> > >>> import dipy
>> >>>>>>> > >>> dipy.__file__
>> >>>>>>> >
>> '/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/lib/python3.5/site-packages/dipy/__init__.py'
>> >>>>>>> >
>> >>>>>>> > I also tried to do the upgrade after removing the dipy line
>> from the .yml file, but I got errors relating to PyQt
>> >>>>>>> > Collecting PyQt5>=5.10
>> >>>>>>> > Using cached PyQt5-5.15.0.tar.gz (3.3 MB)
>> >>>>>>> > Installing build dependencies: started
>> >>>>>>> > Installing build dependencies: finished with status 'done'
>> >>>>>>> > Getting requirements to build wheel: started
>> >>>>>>> > Getting requirements to build wheel: finished with status
>> 'done'
>> >>>>>>> > Preparing wheel metadata: started
>> >>>>>>> > Preparing wheel metadata: finished with status 'error'
>> >>>>>>> >
>> >>>>>>> > I may have more details on the error tomorrow. I lost my
>> connection to the remote server I'm working on.
>> >>>>>>> >
>> >>>>>>> > Thanks,
>> >>>>>>> > Megan
>> >>>>>>> > MEG Technician
>> >>>>>>> > The Mind Research Network
>> >>>>>>> > 1101 Yale Blvd. NE
>> >>>>>>> > Albuquerque, New Mexico 87106
>> >>>>>>> >
>> >>>>>>> >
>> >>>>>>> >
>> >>>>>>> > On Wed, Sep 2, 2020 at 4:58 PM Megan Schendel <
>> mschendel at mrn.org> wrote:
>> >>>>>>> >>
>> >>>>>>> >> Hi all,
>> >>>>>>> >> I am attempting to follow upgrade instructions. I was able to
>> upgrade conda, and I succeeded in using curl to get the yml file.
>> >>>>>>> >> However, when I try the conda env update, I eventually get an
>> error when the update gets to dipy. See below. Any suggestions?
>> >>>>>>> >>
>> >>>>>>> >> Thanks for your help,
>> >>>>>>> >> Megan
>> >>>>>>> >>
>> >>>>>>> >> conda env update --file environment.yml
>> >>>>>>> >> Using Anaconda Cloud api site https://api.anaconda.org
>> >>>>>>> >> Fetching package metadata ...........
>> >>>>>>> >> Solving package specifications: .
>> >>>>>>> >> ...
>> >>>>>>> >> ERROR: Invalid requirement: 'dipy --only-binary dipy'
>> >>>>>>> >>
>> >>>>>>> >> conda --version && python --version
>> >>>>>>> >> conda 4.3.30
>> >>>>>>> >> Python 3.8.5
>> >>>>>>> >>
>> >>>>>>> >> Here is the contents of my environment.yml file:
>> >>>>>>> >>
>> >>>>>>> >> name: mne
>> >>>>>>> >> channels:
>> >>>>>>> >> - defaults
>> >>>>>>> >> dependencies:
>> >>>>>>> >> - python>=3.8
>> >>>>>>> >> - pip
>> >>>>>>> >> - numpy
>> >>>>>>> >> - scipy
>> >>>>>>> >> - matplotlib
>> >>>>>>> >> - numba
>> >>>>>>> >> - pandas
>> >>>>>>> >> - xlrd
>> >>>>>>> >> - scikit-learn
>> >>>>>>> >> - h5py
>> >>>>>>> >> - pillow
>> >>>>>>> >> - statsmodels
>> >>>>>>> >> - jupyter
>> >>>>>>> >> - joblib
>> >>>>>>> >> - psutil
>> >>>>>>> >> - numexpr
>> >>>>>>> >> - traits
>> >>>>>>> >> - pyface
>> >>>>>>> >> - traitsui
>> >>>>>>> >> - imageio
>> >>>>>>> >> - tqdm
>> >>>>>>> >> - spyder-kernels
>> >>>>>>> >> - pip:
>> >>>>>>> >> - mne
>> >>>>>>> >> - imageio-ffmpeg>=0.4.1
>> >>>>>>> >> - vtk>=9.0.1
>> >>>>>>> >> - pyvista>=0.24
>> >>>>>>> >> - pyvistaqt
>> >>>>>>> >> - mayavi
>> >>>>>>> >> - PySurfer[save_movie]
>> >>>>>>> >> - dipy --only-binary dipy
>> >>>>>>> >> - nibabel
>> >>>>>>> >> - nilearn
>> >>>>>>> >> - neo
>> >>>>>>> >> - python-picard
>> >>>>>>> >> - PyQt5>=5.10,<5.14; platform_system == "Darwin"
>> >>>>>>> >> - PyQt5>=5.10; platform_system != "Darwin"
>> >>>>>>> >>
>> >>>>>>> >> MEG Technician
>> >>>>>>> >> The Mind Research Network
>> >>>>>>> >> 1101 Yale Blvd. NE
>> >>>>>>> >> Albuquerque, New Mexico 87106
>> >>>>>>> >>
>> >>>>>>> > _______________________________________________
>> >>>>>>> > Mne_analysis mailing list
>> >>>>>>> > Mne_analysis at nmr.mgh.harvard.edu
>> >>>>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>> >>>>>>>
>> >>>>>>> _______________________________________________
>> >>>>>>> Mne_analysis mailing list
>> >>>>>>> Mne_analysis at nmr.mgh.harvard.edu
>> >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>> >>>>>>
>> >>>>>> _______________________________________________
>> >>>>>> Mne_analysis mailing list
>> >>>>>> Mne_analysis at nmr.mgh.harvard.edu
>> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>> >>>>>
>> >>>>> _______________________________________________
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>> >>>>> Mne_analysis at nmr.mgh.harvard.edu
>> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>> >>>>
>> >>>>
>> >>>> _______________________________________________
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>> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
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