<p><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;"> External Email - Use Caution </span></p><p></p><div dir="ltr">Hi all,<div>I managed to install a new anaconda package. </div><div>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. </div><div><br></div><div>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. </div><div><br></div><div>From what I can tell from the mne.sys_info, it looks like some form of pyqt installed </div><div><br></div><div>conda --version && python --version<br>conda 4.8.4<br>Python 3.8.5<br></div><div><br></div><div>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.</div><div><br></div><div>Just terminal:</div><div><font face="monospace"> mne.sys_info()<br>QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-mschendel'<br>qt.qpa.screen: QXcbConnection: Could not connect to display <br>Could not connect to any X display.<br></font></div><div><br></div><div>(ipython3 quits)</div><div><br></div><div>Using python over a vnc with X11 forwarding enabled...</div><div><font face="monospace">mne.sys_info()<br></font></div><div><font face="monospace">QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-mschendel'<br>Platform: Linux-2.6.32-573.7.1.el6.x86_64-x86_64-with-glibc2.10<br>Python: 3.8.5 (default, Sep 4 2020, 07:30:14) [GCC 7.3.0]<br>Executable: /export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne20/bin/python<br>CPU: x86_64: 24 cores<br>Memory: 126.0 GB<br><br>mne: 0.20.8<br>numpy: 1.19.1 {blas=mkl_rt, lapack=mkl_rt}<br>scipy: 1.5.2<br>matplotlib: 3.3.1 {backend=Qt5Agg}<br><br>sklearn: Not found<br>numba: 0.50.1<br>nibabel: 3.1.1<br>cupy: Not found<br>pandas: 1.1.1<br>dipy: 1.1.1<br>mayavi: 4.7.2 {qt_api=pyqt5, PyQt5=5.9.2}<br>pyvista: 0.26.0<br>vtk: 9.0.1<br></font></div><div><br></div><div>I also tried to create an environment without pyvistaqt and PyQt. mne.sys_info() looks identical</div><div><font face="monospace">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<br></font></div><div><font face="monospace"><br></font></div><div>Megan<br></div><div><div><div dir="ltr" data-smartmail="gmail_signature"><div dir="ltr"><div>MEG Technician<br>The Mind Research Network<br>1101 Yale Blvd. NE<br>Albuquerque, New Mexico 87106<br><br></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Sep 5, 2020 at 11:00 AM Eric Larson <<a href="mailto:larson.eric.d@gmail.com" target="_blank">larson.eric.d@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)"> External Email - Use Caution </span></p><p></p><div dir="ltr">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.<div><br></div><div>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!)<br><div><br></div><div>Eric</div><div><br></div></div></div><div dir="ltr"><div dir="ltr"><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Sep 5, 2020 at 7:52 AM Alexandre Gramfort <<a href="mailto:alexandre.gramfort@inria.fr" target="_blank">alexandre.gramfort@inria.fr</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"> External Email - Use Caution <br>
<br>
hi Megan,<br>
<br>
thanks for the details. Unfortunately it's going to be really hard to<br>
debug for us<br>
without accessing your system. Note however that you can still use mne-python<br>
with just numpy, scipy and matplotlib. It will cover 90% of what you can do with<br>
mne-python. What you will not have is 3D support but if it's remove compute<br>
cluster maybe it's not a real issue.<br>
<br>
Alex<br>
<br>
<br>
<br>
<br>
On Sat, Sep 5, 2020 at 1:45 AM Megan Schendel <<a href="mailto:mschendel@mrn.org" target="_blank">mschendel@mrn.org</a>> wrote:<br>
><br>
> External Email - Use Caution<br>
><br>
> Hi all,<br>
> 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.<br>
><br>
> 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).<br>
> There are issues with the environment file using pip in older anaconda versions.<br>
> 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<br>
> 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?<br>
><br>
> 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.<br>
><br>
> Just thought I'd update. It seems it is an issue with my system, not with your environment file.<br>
> Thanks,<br>
> Megan<br>
><br>
> conda info<br>
> Current conda install:<br>
><br>
> platform : linux-64<br>
> conda version : 4.3.30<br>
> conda is private : False<br>
> conda-env version : 4.3.30<br>
> conda-build version : 1.19.0<br>
> python version : 3.5.4.final.0<br>
> requests version : 2.12.4<br>
> root environment : /export/research/analysis/human/jstephen/shared/programs/python/anaconda3 (writable)<br>
> default environment : /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne<br>
> envs directories : /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs<br>
> /na/homes/mschendel/.conda/envs<br>
> package cache : /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/pkgs<br>
> /na/homes/mschendel/.conda/pkgs<br>
> channel URLs : <a href="https://repo.continuum.io/pkgs/main/linux-64" rel="noreferrer" target="_blank">https://repo.continuum.io/pkgs/main/linux-64</a><br>
> <a href="https://repo.continuum.io/pkgs/main/noarch" rel="noreferrer" target="_blank">https://repo.continuum.io/pkgs/main/noarch</a><br>
> <a href="https://repo.continuum.io/pkgs/free/linux-64" rel="noreferrer" target="_blank">https://repo.continuum.io/pkgs/free/linux-64</a><br>
> <a href="https://repo.continuum.io/pkgs/free/noarch" rel="noreferrer" target="_blank">https://repo.continuum.io/pkgs/free/noarch</a><br>
> <a href="https://repo.continuum.io/pkgs/r/linux-64" rel="noreferrer" target="_blank">https://repo.continuum.io/pkgs/r/linux-64</a><br>
> <a href="https://repo.continuum.io/pkgs/r/noarch" rel="noreferrer" target="_blank">https://repo.continuum.io/pkgs/r/noarch</a><br>
> <a href="https://repo.continuum.io/pkgs/pro/linux-64" rel="noreferrer" target="_blank">https://repo.continuum.io/pkgs/pro/linux-64</a><br>
> <a href="https://repo.continuum.io/pkgs/pro/noarch" rel="noreferrer" target="_blank">https://repo.continuum.io/pkgs/pro/noarch</a><br>
> config file : None<br>
> netrc file : None<br>
> offline mode : False<br>
> 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<br>
> UID:GID : 10263:8000<br>
><br>
><br>
> I was able to get dipy to install...<br>
><br>
> (mne) [mschendel@earth python]$ pip --version<br>
> 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)<br>
><br>
> (mne) [mschendel@earth envs]$ pip install dipy --only-binary dipy<br>
> Collecting dipy<br>
> Using cached dipy-1.1.1-cp38-cp38-manylinux1_x86_64.whl (8.0 MB)<br>
> Collecting nibabel>=3.0.0<br>
> Using cached nibabel-3.1.1-py3-none-any.whl (3.3 MB)<br>
> Requirement already satisfied: scipy>=1.0 in ./mne/lib/python3.8/site-packages (from dipy) (1.5.2)<br>
> Requirement already satisfied: h5py>=2.4.0 in ./mne/lib/python3.8/site-packages (from dipy) (2.10.0)<br>
> Requirement already satisfied: numpy>=1.13 in ./mne/lib/python3.8/site-packages (from nibabel>=3.0.0->dipy) (1.19.1)<br>
> Requirement already satisfied: packaging>=14.3 in ./mne/lib/python3.8/site-packages (from nibabel>=3.0.0->dipy) (20.4)<br>
> Requirement already satisfied: six in ./mne/lib/python3.8/site-packages (from h5py>=2.4.0->dipy) (1.15.0)<br>
> 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)<br>
> Installing collected packages: nibabel, dipy<br>
> Successfully installed dipy-1.1.1 nibabel-3.1.1<br>
><br>
> Here's where I am now:<br>
> mne.sys_info()<br>
> Platform: Linux-2.6.32-573.7.1.el6.x86_64-x86_64-with-glibc2.10<br>
> Python: 3.8.5 (default, Sep 4 2020, 07:30:14) [GCC 7.3.0]<br>
> Executable: /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne/bin/python3<br>
> CPU: x86_64: 24 cores<br>
> Memory: 126.0 GB<br>
><br>
> mne: 0.20.8<br>
> numpy: 1.19.1 {blas=mkl_rt, lapack=mkl_rt}<br>
> scipy: 1.5.2<br>
> matplotlib: 3.3.1 {backend=agg}<br>
><br>
> sklearn: 0.23.2<br>
> numba: 0.50.1<br>
> nibabel: 3.1.1<br>
> cupy: Not found<br>
> pandas: 1.1.1<br>
> dipy: 1.1.1<br>
> mayavi: Not found<br>
> pyvista: Not found<br>
> vtk: Not found<br>
><br>
><br>
> MEG Technician<br>
> The Mind Research Network<br>
> 1101 Yale Blvd. NE<br>
> Albuquerque, New Mexico 87106<br>
><br>
><br>
><br>
> On Fri, Sep 4, 2020 at 2:36 PM Megan Schendel <<a href="mailto:mschendel@mrn.org" target="_blank">mschendel@mrn.org</a>> wrote:<br>
>><br>
>> Hi all,<br>
>> I am getting the same PyQt5 error when I try the install via create environment.<br>
>> So attempting to creating a new environment did nothing to solve either of the errors I was getting trying to update the environment.<br>
>> 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.<br>
>><br>
>> 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.<br>
>><br>
>> Thanks for any help,<br>
>> Megan<br>
>><br>
>> PyQt5 error...<br>
>> Collecting PyQt5>=5.10<br>
>> Using cached PyQt5-5.15.0.tar.gz (3.3 MB)<br>
>> Installing build dependencies: started<br>
>> Installing build dependencies: finished with status 'done'<br>
>> Getting requirements to build wheel: started<br>
>> Getting requirements to build wheel: finished with status 'done'<br>
>> Preparing wheel metadata: started<br>
>> Preparing wheel metadata: finished with status 'error'<br>
>> ERROR: Command errored out with exit status 1:<br>
>> 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<br>
>> cwd: /tmp/pip-install-02yoibkc/pyqt5<br>
>> Complete output (35 lines):<br>
>> Querying qmake about your Qt installation...<br>
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/bin/qmake -query<br>
>> Traceback (most recent call last):<br>
>> 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<br>
>> hook = backend.prepare_metadata_for_build_wheel<br>
>> AttributeError: module 'sipbuild.api' has no attribute 'prepare_metadata_for_build_wheel'<br>
>><br>
>> During handling of the above exception, another exception occurred:<br>
>><br>
>> Traceback (most recent call last):<br>
>> 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><br>
>> main()<br>
>> 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<br>
>> json_out['return_val'] = hook(**hook_input['kwargs'])<br>
>> 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<br>
>> return _get_wheel_metadata_from_wheel(backend, metadata_directory,<br>
>> 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<br>
>> whl_basename = backend.build_wheel(metadata_directory, config_settings)<br>
>> File "/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/sipbuild/api.py", line 51, in build_wheel<br>
>> project = AbstractProject.bootstrap('pep517')<br>
>> File "/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/sipbuild/abstract_project.py", line 82, in bootstrap<br>
>> project.setup(pyproject, tool, tool_description)<br>
>> File "/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/sipbuild/project.py", line 479, in setup<br>
>> self.apply_user_defaults(tool)<br>
>> File "project.py", line 62, in apply_user_defaults<br>
>> super().apply_user_defaults(tool)<br>
>> File "/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/pyqtbuild/project.py", line 89, in apply_user_defaults<br>
>> super().apply_user_defaults(tool)<br>
>> File "/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/sipbuild/project.py", line 225, in apply_user_defaults<br>
>> self.builder.apply_user_defaults(tool)<br>
>> File "/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/pyqtbuild/builder.py", line 77, in apply_user_defaults<br>
>> self._get_qt_configuration()<br>
>> File "/tmp/pip-build-env-6gc1wdbn/overlay/lib/python3.8/site-packages/pyqtbuild/builder.py", line 450, in _get_qt_configuration<br>
>> raise UserException(<br>
>> sipbuild.exceptions.UserException<br>
>> ----------------------------------------<br>
>> 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.<br>
>> Using Anaconda Cloud api site <a href="https://api.anaconda.org" rel="noreferrer" target="_blank">https://api.anaconda.org</a><br>
>><br>
>> CondaValueError: pip returned an error.<br>
>><br>
>><br>
>> Response from Mathew at dipy<br>
>>><br>
>>> I don't use conda myself - but I guess that line must be wrong, and<br>
>>> you need to drop either the first or the second 'dipy' , as in:<br>
>>> dependencies:<br>
>>> - pip:<br>
>>> - --only-binary dipy<br>
>>> or:<br>
>>> dependencies:<br>
>>> - pip:<br>
>>> - dipy --only-binary<br>
>><br>
>><br>
>> MEG Technician<br>
>> The Mind Research Network<br>
>> 1101 Yale Blvd. NE<br>
>> Albuquerque, New Mexico 87106<br>
>><br>
>><br>
>><br>
>> On Thu, Sep 3, 2020 at 5:33 PM Megan Schendel <<a href="mailto:mschendel@mrn.org" target="_blank">mschendel@mrn.org</a>> wrote:<br>
>>><br>
>>> Hi Dan,<br>
>>> I tried creating a new environment, and I'm still getting the dipy error. I'll try again removing the dipy line...<br>
>>> Thanks,<br>
>>> Megan<br>
>>><br>
>>> conda env create --name mne --file environment.yml<br>
>>> Using Anaconda Cloud api site <a href="https://api.anaconda.org" rel="noreferrer" target="_blank">https://api.anaconda.org</a><br>
>>> Fetching package metadata ...........<br>
>>> Solving package specifications: .<br>
>>> pyzmq-19.0.1-p 100% |#######################################################################################################| Time: 0:00:00 2.75 MB/s<br>
>>> jedi-0.17.2-py 100% |#######################################################################################################| Time: 0:00:00 7.84 MB/s<br>
>>> ERROR: Invalid requirement: 'dipy --only-binary dipy'<br>
>>><br>
>>> CondaValueError: pip returned an error.<br>
>>><br>
>>><br>
>>> MEG Technician<br>
>>> The Mind Research Network<br>
>>> 1101 Yale Blvd. NE<br>
>>> Albuquerque, New Mexico 87106<br>
>>><br>
>>><br>
>>><br>
>>> On Thu, Sep 3, 2020 at 4:16 PM Dan McCloy <<a href="mailto:dan@mccloy.info" target="_blank">dan@mccloy.info</a>> wrote:<br>
>>>><br>
>>>> External Email - Use Caution<br>
>>>><br>
>>>> 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).<br>
>>>><br>
>>>> -- dan<br>
>>>> Daniel McCloy<br>
>>>> <a href="https://dan.mccloy.info" rel="noreferrer" target="_blank">https://dan.mccloy.info</a><br>
>>>> Research Scientist<br>
>>>> Institute for Learning and Brain Sciences<br>
>>>> University of Washington<br>
>>>><br>
>>>><br>
>>>> ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐<br>
>>>> On Thursday, September 3, 2020 5:05 PM, Megan Schendel <<a href="mailto:mschendel@mrn.org" target="_blank">mschendel@mrn.org</a>> wrote:<br>
>>>><br>
>>>> External Email - Use Caution<br>
>>>><br>
>>>><br>
>>>> Hi Eric,<br>
>>>><br>
>>>> Thanks for the questions. See terminal commands and outputs below. I'm on Linux.<br>
>>>> Since pip is listed in the environment.yml file, it should have been upgraded by the conda env -update command, right?<br>
>>>> 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.<br>
>>>><br>
>>>> Thanks again,<br>
>>>> Megan<br>
>>>><br>
>>>> updated environment:<br>
>>>> pip --version<br>
>>>> 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)<br>
>>>><br>
>>>> python -c "import setuptools; print(setuptools.__version__)"<br>
>>>> 49.6.0.post20200814<br>
>>>> /updated environment<br>
>>>><br>
>>>><br>
>>>> old environment:<br>
>>>> conda --version && python --version<br>
>>>> conda 4.3.30<br>
>>>> Python 3.5.4 :: Anaconda 2.5.0 (64-bit)<br>
>>>> python -c "import mne; mne.sys_info()"<br>
>>>> Platform: Linux-2.6.32-573.7.1.el6.x86_64-x86_64-with-centos-6.7-Final<br>
>>>> 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)]<br>
>>>> Executable: /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/bin/python<br>
>>>> CPU: x86_64: 24 cores<br>
>>>> Memory: 126.0 GB<br>
>>>><br>
>>>> mne: 0.15.2<br>
>>>> numpy: 1.10.4 {lapack=SCIPY_MKL_H, blas=SCIPY_MKL_H}<br>
>>>> scipy: 0.17.0<br>
>>>> matplotlib: 3.0.3<br>
>>>><br>
>>>> sklearn: 0.17.1<br>
>>>> nibabel: 2.3.3<br>
>>>> mayavi: Not found<br>
>>>> pycuda: Not found<br>
>>>> skcuda: Not found<br>
>>>> pandas: 0.17.1<br>
>>>> /old environment<br>
>>>><br>
>>>> On Thu, Sep 3, 2020 at 3:37 PM Eric Larson <<a href="mailto:larson.eric.d@gmail.com" target="_blank">larson.eric.d@gmail.com</a>> wrote:<br>
>>>>><br>
>>>>> External Email - Use Caution<br>
>>>>><br>
>>>>><br>
>>>>> 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`?<br>
>>>>><br>
>>>>> Can you also try:<br>
>>>>><br>
>>>>> $ python -c "import setuptools; print(setuptools.__version__)"<br>
>>>>><br>
>>>>> 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"`.<br>
>>>>><br>
>>>>> Eric<br>
>>>>><br>
>>>>><br>
>>>>> On Thu, Sep 3, 2020 at 5:23 PM Megan Schendel <<a href="mailto:mschendel@mrn.org" target="_blank">mschendel@mrn.org</a>> wrote:<br>
>>>>>><br>
>>>>>> External Email - Use Caution<br>
>>>>>><br>
>>>>>><br>
>>>>>> Hi all,<br>
>>>>>> Ok, I've asked the dipy people about that error, but I could still use help with the update.<br>
>>>>>> Should install instructions work for update, too? Should I just use pip to update mne instead of trying to use the new environment file?<br>
>>>>>><br>
>>>>>> I took the dipy line out of the environment file. Here is the error I'm getting from PyQt5....<br>
>>>>>> Any ideas/suggestions?<br>
>>>>>> Thank you,<br>
>>>>>> Megan<br>
>>>>>><br>
>>>>>> Collecting PyQt5>=5.10<br>
>>>>>> Using cached PyQt5-5.15.0.tar.gz (3.3 MB)<br>
>>>>>> Installing build dependencies: started<br>
>>>>>> Installing build dependencies: finished with status 'done'<br>
>>>>>> Getting requirements to build wheel: started<br>
>>>>>> Getting requirements to build wheel: finished with status 'done'<br>
>>>>>> Preparing wheel metadata: started<br>
>>>>>> Preparing wheel metadata: finished with status 'error'<br>
>>>>>> ERROR: Command errored out with exit status 1:<br>
>>>>>> 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<br>
>>>>>> cwd: /tmp/pip-install-ci617d3e/pyqt5<br>
>>>>>> Complete output (35 lines):<br>
>>>>>> Querying qmake about your Qt installation...<br>
>>>>>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/bin/qmake -query<br>
>>>>>> Traceback (most recent call last):<br>
>>>>>> 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<br>
>>>>>> hook = backend.prepare_metadata_for_build_wheel<br>
>>>>>> AttributeError: module 'sipbuild.api' has no attribute 'prepare_metadata_for_build_wheel'<br>
>>>>>><br>
>>>>>> During handling of the above exception, another exception occurred:<br>
>>>>>><br>
>>>>>> Traceback (most recent call last):<br>
>>>>>> 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><br>
>>>>>> main()<br>
>>>>>> 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<br>
>>>>>> json_out['return_val'] = hook(**hook_input['kwargs'])<br>
>>>>>> 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<br>
>>>>>> return _get_wheel_metadata_from_wheel(backend, metadata_directory,<br>
>>>>>> 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<br>
>>>>>> whl_basename = backend.build_wheel(metadata_directory, config_settings)<br>
>>>>>> File "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/sipbuild/api.py", line 51, in build_wheel<br>
>>>>>> project = AbstractProject.bootstrap('pep517')<br>
>>>>>> File "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/sipbuild/abstract_project.py", line 82, in bootstrap<br>
>>>>>> project.setup(pyproject, tool, tool_description)<br>
>>>>>> File "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/sipbuild/project.py", line 479, in setup<br>
>>>>>> self.apply_user_defaults(tool)<br>
>>>>>> File "project.py", line 62, in apply_user_defaults<br>
>>>>>> super().apply_user_defaults(tool)<br>
>>>>>> File "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/pyqtbuild/project.py", line 89, in apply_user_defaults<br>
>>>>>> super().apply_user_defaults(tool)<br>
>>>>>> File "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/sipbuild/project.py", line 225, in apply_user_defaults<br>
>>>>>> self.builder.apply_user_defaults(tool)<br>
>>>>>> File "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/pyqtbuild/builder.py", line 77, in apply_user_defaults<br>
>>>>>> self._get_qt_configuration()<br>
>>>>>> File "/tmp/pip-build-env-uvtea85d/overlay/lib/python3.8/site-packages/pyqtbuild/builder.py", line 450, in _get_qt_configuration<br>
>>>>>> raise UserException(<br>
>>>>>> sipbuild.exceptions.UserException<br>
>>>>>> ----------------------------------------<br>
>>>>>> 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.<br>
>>>>>> Using Anaconda Cloud api site <a href="https://api.anaconda.org" rel="noreferrer" target="_blank">https://api.anaconda.org</a><br>
>>>>>><br>
>>>>>> CondaValueError: pip returned an error.<br>
>>>>>> MEG Technician<br>
>>>>>> The Mind Research Network<br>
>>>>>> 1101 Yale Blvd. NE<br>
>>>>>> Albuquerque, New Mexico 87106<br>
>>>>>><br>
>>>>>><br>
>>>>>> On Thu, Sep 3, 2020 at 1:18 AM Alexandre Gramfort <<a href="mailto:alexandre.gramfort@inria.fr" target="_blank">alexandre.gramfort@inria.fr</a>> wrote:<br>
>>>>>>><br>
>>>>>>> External Email - Use Caution<br>
>>>>>>><br>
>>>>>>> hi Megan,<br>
>>>>>>><br>
>>>>>>> you should ask this question to the dipy developpers. We are just users here.<br>
>>>>>>><br>
>>>>>>> Alex<br>
>>>>>>><br>
>>>>>>> On Thu, Sep 3, 2020 at 1:54 AM Megan Schendel <<a href="mailto:mschendel@mrn.org" target="_blank">mschendel@mrn.org</a>> wrote:<br>
>>>>>>> ><br>
>>>>>>> > External Email - Use Caution<br>
>>>>>>> ><br>
>>>>>>> > HI all,<br>
>>>>>>> > 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.<br>
>>>>>>> > Are there separate instructions for upgrades? I realized I'm trying to follow install instructions.<br>
>>>>>>> ><br>
>>>>>>> > >>> import dipy<br>
>>>>>>> > >>> dipy.__file__<br>
>>>>>>> > '/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/lib/python3.5/site-packages/dipy/__init__.py'<br>
>>>>>>> ><br>
>>>>>>> > I also tried to do the upgrade after removing the dipy line from the .yml file, but I got errors relating to PyQt<br>
>>>>>>> > Collecting PyQt5>=5.10<br>
>>>>>>> > Using cached PyQt5-5.15.0.tar.gz (3.3 MB)<br>
>>>>>>> > Installing build dependencies: started<br>
>>>>>>> > Installing build dependencies: finished with status 'done'<br>
>>>>>>> > Getting requirements to build wheel: started<br>
>>>>>>> > Getting requirements to build wheel: finished with status 'done'<br>
>>>>>>> > Preparing wheel metadata: started<br>
>>>>>>> > Preparing wheel metadata: finished with status 'error'<br>
>>>>>>> ><br>
>>>>>>> > I may have more details on the error tomorrow. I lost my connection to the remote server I'm working on.<br>
>>>>>>> ><br>
>>>>>>> > Thanks,<br>
>>>>>>> > Megan<br>
>>>>>>> > MEG Technician<br>
>>>>>>> > The Mind Research Network<br>
>>>>>>> > 1101 Yale Blvd. NE<br>
>>>>>>> > Albuquerque, New Mexico 87106<br>
>>>>>>> ><br>
>>>>>>> ><br>
>>>>>>> ><br>
>>>>>>> > On Wed, Sep 2, 2020 at 4:58 PM Megan Schendel <<a href="mailto:mschendel@mrn.org" target="_blank">mschendel@mrn.org</a>> wrote:<br>
>>>>>>> >><br>
>>>>>>> >> Hi all,<br>
>>>>>>> >> I am attempting to follow upgrade instructions. I was able to upgrade conda, and I succeeded in using curl to get the yml file.<br>
>>>>>>> >> However, when I try the conda env update, I eventually get an error when the update gets to dipy. See below. Any suggestions?<br>
>>>>>>> >><br>
>>>>>>> >> Thanks for your help,<br>
>>>>>>> >> Megan<br>
>>>>>>> >><br>
>>>>>>> >> conda env update --file environment.yml<br>
>>>>>>> >> Using Anaconda Cloud api site <a href="https://api.anaconda.org" rel="noreferrer" target="_blank">https://api.anaconda.org</a><br>
>>>>>>> >> Fetching package metadata ...........<br>
>>>>>>> >> Solving package specifications: .<br>
>>>>>>> >> ...<br>
>>>>>>> >> ERROR: Invalid requirement: 'dipy --only-binary dipy'<br>
>>>>>>> >><br>
>>>>>>> >> conda --version && python --version<br>
>>>>>>> >> conda 4.3.30<br>
>>>>>>> >> Python 3.8.5<br>
>>>>>>> >><br>
>>>>>>> >> Here is the contents of my environment.yml file:<br>
>>>>>>> >><br>
>>>>>>> >> name: mne<br>
>>>>>>> >> channels:<br>
>>>>>>> >> - defaults<br>
>>>>>>> >> dependencies:<br>
>>>>>>> >> - python>=3.8<br>
>>>>>>> >> - pip<br>
>>>>>>> >> - numpy<br>
>>>>>>> >> - scipy<br>
>>>>>>> >> - matplotlib<br>
>>>>>>> >> - numba<br>
>>>>>>> >> - pandas<br>
>>>>>>> >> - xlrd<br>
>>>>>>> >> - scikit-learn<br>
>>>>>>> >> - h5py<br>
>>>>>>> >> - pillow<br>
>>>>>>> >> - statsmodels<br>
>>>>>>> >> - jupyter<br>
>>>>>>> >> - joblib<br>
>>>>>>> >> - psutil<br>
>>>>>>> >> - numexpr<br>
>>>>>>> >> - traits<br>
>>>>>>> >> - pyface<br>
>>>>>>> >> - traitsui<br>
>>>>>>> >> - imageio<br>
>>>>>>> >> - tqdm<br>
>>>>>>> >> - spyder-kernels<br>
>>>>>>> >> - pip:<br>
>>>>>>> >> - mne<br>
>>>>>>> >> - imageio-ffmpeg>=0.4.1<br>
>>>>>>> >> - vtk>=9.0.1<br>
>>>>>>> >> - pyvista>=0.24<br>
>>>>>>> >> - pyvistaqt<br>
>>>>>>> >> - mayavi<br>
>>>>>>> >> - PySurfer[save_movie]<br>
>>>>>>> >> - dipy --only-binary dipy<br>
>>>>>>> >> - nibabel<br>
>>>>>>> >> - nilearn<br>
>>>>>>> >> - neo<br>
>>>>>>> >> - python-picard<br>
>>>>>>> >> - PyQt5>=5.10,<5.14; platform_system == "Darwin"<br>
>>>>>>> >> - PyQt5>=5.10; platform_system != "Darwin"<br>
>>>>>>> >><br>
>>>>>>> >> MEG Technician<br>
>>>>>>> >> The Mind Research Network<br>
>>>>>>> >> 1101 Yale Blvd. NE<br>
>>>>>>> >> Albuquerque, New Mexico 87106<br>
>>>>>>> >><br>
>>>>>>> > _______________________________________________<br>
>>>>>>> > Mne_analysis mailing list<br>
>>>>>>> > <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>
>>>>>>> > <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
>>>>>>><br>
>>>>>>> _______________________________________________<br>
>>>>>>> Mne_analysis mailing list<br>
>>>>>>> <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>
>>>>>>> <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
>>>>>><br>
>>>>>> _______________________________________________<br>
>>>>>> Mne_analysis mailing list<br>
>>>>>> <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>
>>>>>> <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
>>>>><br>
>>>>> _______________________________________________<br>
>>>>> Mne_analysis mailing list<br>
>>>>> <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>
>>>>> <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
>>>><br>
>>>><br>
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