[Install error] cannot import name 'soft_unicode' from 'markupsafe'

[andrevitorelli]

On candide, I'm trying to install mccd on the shapepipe environment. I get the following otuput:

(shapepipe) [<username>@c03 ~/github]$ pip pip install mccd
Collecting mccd
  Using cached mccd-1.1.1-py3-none-any.whl (74 kB)
Collecting modopt==1.5.1
  Using cached modopt-1.5.1-py3-none-any.whl (59 kB)
Requirement already satisfied: scipy>=1.5.4 in /home/<username>/.conda/envs/shapepipe/lib/python3.9/site-packages (from mccd) (1.8.0)
Requirement already satisfied: numpy>=1.19.5 in /home/<username>/.conda/envs/shapepipe/lib/python3.9/site-packages (from mccd) (1.22.3)
Collecting python-pysap==0.0.5
  Using cached python-pySAP-0.0.5.tar.gz (656 kB)
  Preparing metadata (setup.py) ... done
Requirement already satisfied: astropy>=4.0.2 in /home/<username>/.conda/envs/shapepipe/lib/python3.9/site-packages (from mccd) (5.0)
Collecting scipy>=1.5.4
  Downloading scipy-1.5.4-cp39-cp39-manylinux1_x86_64.whl (25.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 25.8/25.8 MB 22.1 MB/s eta 0:00:00
Collecting importlib-metadata==3.7.0
  Using cached importlib_metadata-3.7.0-py3-none-any.whl (11 kB)
Collecting numpy>=1.19.5
  Downloading numpy-1.19.5-cp39-cp39-manylinux2010_x86_64.whl (14.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.9/14.9 MB 23.8 MB/s eta 0:00:00
Collecting progressbar2==3.53.1
  Using cached progressbar2-3.53.1-py2.py3-none-any.whl (25 kB)
Collecting matplotlib==3.3.4
  Downloading matplotlib-3.3.4-cp39-cp39-manylinux1_x86_64.whl (11.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.5/11.5 MB 26.7 MB/s eta 0:00:00
Collecting astropy>=4.0.2
  Downloading astropy-4.1.tar.gz (7.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.8/7.8 MB 24.3 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [28 lines of output]
      Traceback (most recent call last):
        File "/home/<username>/.conda/envs/shapepipe/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
          main()
        File "/home/<username>/.conda/envs/shapepipe/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/home/<username>/.conda/envs/shapepipe/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 130, in get_requires_for_build_wheel
          return hook(config_settings)
        File "/tmp/pip-build-env-uvwtpde6/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 177, in get_requires_for_build_wheel
          return self._get_build_requires(
        File "/tmp/pip-build-env-uvwtpde6/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 159, in _get_build_requires
          self.run_setup()
        File "/tmp/pip-build-env-uvwtpde6/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 174, in run_setup
          exec(compile(code, __file__, 'exec'), locals())
        File "setup.py", line 70, in <module>
          ext_modules=get_extensions())
        File "/tmp/pip-build-env-uvwtpde6/overlay/lib/python3.9/site-packages/extension_helpers/_setup_helpers.py", line 67, in get_extensions
          ext_modules.extend(setuppkg.get_extensions())
        File "./astropy/modeling/setup_package.py", line 59, in get_extensions
          from jinja2 import Environment, FileSystemLoader
        File "/tmp/pip-build-env-uvwtpde6/overlay/lib/python3.9/site-packages/jinja2/__init__.py", line 33, in <module>
          from jinja2.environment import Environment, Template
        File "/tmp/pip-build-env-uvwtpde6/overlay/lib/python3.9/site-packages/jinja2/environment.py", line 15, in <module>
          from jinja2 import nodes
        File "/tmp/pip-build-env-uvwtpde6/overlay/lib/python3.9/site-packages/jinja2/nodes.py", line 19, in <module>
          from jinja2.utils import Markup
        File "/tmp/pip-build-env-uvwtpde6/overlay/lib/python3.9/site-packages/jinja2/utils.py", line 642, in <module>
          from markupsafe import Markup, escape, soft_unicode
      ImportError: cannot import name 'soft_unicode' from 'markupsafe' (/tmp/pip-build-env-uvwtpde6/overlay/lib/python3.9/site-packages/markupsafe/__init__.py)
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

Any suggestions?

[tobias-liaudat]

Oh I've never seen that error before.

@andrevitorelli Could you list which modules you have load in candide before installing mccd?

Could you also confirm where you are installing it? I mean, you are trying to install it in the conda environment generated by shapepipe? Normally, mccd is installed by default in the shapepipe conda environment.

I also see that you are trying to install the version 1.1.1 of mccd, but the current version is 1.2.3. Is there a specific reason for that?

[andrevitorelli]

Could you also confirm where you are installing it?

Inside the shapepipe environment on candide

you are trying to install it in the conda environment generated by shapepipe?

Yes

I also see that you are trying to install the version 1.1.1 of mccd, but the current version is 1.2.3. Is there a specific reason for that?

So, I noticed that after installing ShapePipe, mccd wasn't installed and I couldn't find any error message. (but the ShapePipe installer displays it as not installed at the end). I then pip install mccd --user it, and didn't choose version, so there is no specific reason for that.

[tobias-liaudat]

Ok you can try using the version specified in shapepipe's environment.yml file. You can do pip install mccd==1.2.3, as you are already inside the conda environment I think there's no need for the user flag.

[martinkilbinger]

Hi @andrevitorelli we had problems with astropy v 4.1 in the past, maybe it's related to that. This was fixed with 4.2, try to force astropy to this version, or, as in shapepipe now, 5.0.

[andrevitorelli]

When trying to install with pip install mccd==1.2.3 I get a pysap installation error. Still looking into it...

[andrevitorelli]

Pointing out to the root cause of the install fail here: CEA-COSMIOC/pysap/#178

[andrevitorelli]

Issue above solves this.