Conda install requirements succeeds, but import module later fails

[physicsmonk]

Details

• Read the Docs project URL: https://readthedocs.org/projects/medypt/
• Build URL (if applicable): https://readthedocs.org/projects/medypt/builds/30438721/
• Read the Docs username (if applicable): https://readthedocs.org/profiles/physicsmonk/

Expected Result

Import all required modules and properly build the docs

Actual Result

Conda installing requirements succeeds, but importing module gmsh later fails. The build succeeds, but leads to blank pages.

Raw log:

Read the Docs build information
Build id: 30438721
Project: medypt
Version: latest
Commit: 20f9754311e204b58e8a1295f3389d0c1fc6717e
Date: 2025-11-24T14:53:43.560140Z
State: finished
Success: True


[rtd-command-info] start-time: 2025-11-24T14:53:44.102834Z, end-time: 2025-11-24T14:53:44.303789Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/physicsmonk/medypt.git .
Cloning into '.'...

[rtd-command-info] start-time: 2025-11-24T14:53:44.361659Z, end-time: 2025-11-24T14:53:44.556346Z, duration: 0, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main


[rtd-command-info] start-time: 2025-11-24T14:53:44.634796Z, end-time: 2025-11-24T14:53:44.671873Z, duration: 0, exit-code: 0
git checkout --force origin/main
Note: switching to 'origin/main'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 20f9754 Remove version requirement for sphinx in environment.yml

[rtd-command-info] start-time: 2025-11-24T14:53:44.724850Z, end-time: 2025-11-24T14:53:44.764973Z, duration: 0, exit-code: 0
cat .readthedocs.yaml
# Read the Docs configuration file
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details

# Required
version: 2

# Set the OS, Python version, and other tools you might need
build:
  os: ubuntu-24.04
  tools:
    python: "miniconda3-3.12-24.9"

# Build documentation in the "docs/" directory with Sphinx
sphinx:
   configuration: docs/source/conf.py

# Optionally, but recommended,
# declare the Python requirements required to build your documentation
# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
# python:
#    install:
#    - requirements: docs/requirements.txt
conda:
  environment: docs/environment.yml

[rtd-command-info] start-time: 2025-11-24T14:53:55.748613Z, end-time: 2025-11-24T14:53:55.836840Z, duration: 0, exit-code: 0
asdf global python miniconda3-3.12-24.9.2-0


[rtd-command-info] start-time: 2025-11-24T14:53:58.062951Z, end-time: 2025-11-24T14:53:58.100299Z, duration: 0, exit-code: 0
cat docs/environment.yml
channels:
- conda-forge
- nodefaults
dependencies:
- python=3.13.7
- fenics-dolfinx==0.10.0
- gmsh==4.15.0
- mpi4py==4.1.1
- numpy==2.3.5
- petsc4py==3.24.1
- scifem==0.14.0
- sphinx
- sphinx_rtd_theme
- pip: []
- sphinx
name: medypt-docs
prefix: /home/docs/.conda/envs/medypt-docs

[rtd-command-info] start-time: 2025-11-24T14:53:58.137889Z, end-time: 2025-11-24T14:56:18.878724Z, duration: 140, exit-code: 0
conda env create --quiet --name latest --file docs/environment.yml
/home/docs/.asdf/installs/python/miniconda3-3.12-24.9.2-0/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
  action(self, namespace, argument_values, option_string)
Warning: you have pip-installed dependencies in your environment file, but you do not list pip itself as one of your conda dependencies.  Conda may not use the correct pip to install your packages, and they may end up in the wrong place.  Please add an explicit pip dependency.  I'm adding one for you, but still nagging you.
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... 

To enable CUDA support, UCX requires the CUDA Runtime library (libcudart).
The library can be installed with the appropriate command below:

* For CUDA 12, run:    conda install cuda-cudart cuda-version=12
* For CUDA 13, run:    conda install cuda-cudart cuda-version=13

If any of the packages you requested use CUDA then CUDA should already
have been installed for you.



To enable CUDA support, please follow UCX's instruction above.

To additionally enable NCCL support, run:    conda install nccl



On Linux, Open MPI is built with CUDA awareness but it is disabled by default.
To enable it, please set the environment variable
OMPI_MCA_opal_cuda_support=true
before launching your MPI processes.
Equivalently, you can set the MCA parameter in the command line:
mpiexec --mca opal_cuda_support 1 ...
Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via
UCX. Please consult UCX documentation for further details.



done

[rtd-command-info] start-time: 2025-11-24T14:56:18.987774Z, end-time: 2025-11-24T14:56:19.029450Z, duration: 0, exit-code: 0
cat docs/source/conf.py
# Configuration file for the Sphinx documentation builder.
#
# For the full list of built-in configuration values, see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html

# -- Project information -----------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information

import os
import sys
sys.path.insert(0, os.path.abspath('../../src'))

project = 'MEDYPT'
copyright = '2025, Yin Shi'
author = 'Yin Shi'

# -- General configuration ---------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

extensions = [
    'sphinx.ext.autodoc',
    'sphinx_rtd_theme'
]

templates_path = ['_templates']
exclude_patterns = []



# -- Options for HTML output -------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output

html_theme = 'sphinx_rtd_theme'
html_static_path = ['_static']

[rtd-command-info] start-time: 2025-11-24T14:56:19.073832Z, end-time: 2025-11-24T14:56:21.970042Z, duration: 2, exit-code: 0
python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v8.2.3
loading translations [en]... done
WARNING: html_static_path entry '_static' does not exist
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 6 source files that are out of date
updating environment: [new config] 6 added, 0 changed, 0 removed
reading sources... [ 17%] imt
reading sources... [ 33%] index
reading sources... [ 50%] maters
reading sources... [ 67%] model
reading sources... [ 83%] modules
reading sources... [100%] utils

WARNING: autodoc: failed to import module 'imt'; the following exception was raised:
['Traceback (most recent call last):\n', '  File "/home/docs/checkouts/readthedocs.org/user_builds/medypt/conda/latest/lib/python3.13/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n    module = import_module(modname, try_reload=True)\n', '  File "/home/docs/checkouts/readthedocs.org/user_builds/medypt/conda/latest/lib/python3.13/site-packages/sphinx/ext/autodoc/importer.py", line 175, in import_module\n    module = importlib.import_module(modname)\n', '  File "/home/docs/checkouts/readthedocs.org/user_builds/medypt/conda/latest/lib/python3.13/importlib/__init__.py", line 88, in import_module\n    return _bootstrap._gcd_import(name[level:], package, level)\n           ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', '  File "<frozen importlib._bootstrap>", line 1387, in _gcd_import\n', '  File "<frozen importlib._bootstrap>", line 1360, in _find_and_load\n', '  File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked\n', '  File "<frozen importlib._bootstrap>", line 935, in _load_unlocked\n', '  File "<frozen importlib._bootstrap_external>", line 1026, in exec_module\n', '  File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed\n', '  File "/home/docs/checkouts/readthedocs.org/user_builds/medypt/checkouts/latest/src/imt.py", line 5, in <module>\n    import gmsh\n', "ModuleNotFoundError: No module named 'gmsh'\n"] [autodoc.import_object]
WARNING: autodoc: failed to import module 'model'; the following exception was raised:
['Traceback (most recent call last):\n', '  File "/home/docs/checkouts/readthedocs.org/user_builds/medypt/conda/latest/lib/python3.13/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n    module = import_module(modname, try_reload=True)\n', '  File "/home/docs/checkouts/readthedocs.org/user_builds/medypt/conda/latest/lib/python3.13/site-packages/sphinx/ext/autodoc/importer.py", line 175, in import_module\n    module = importlib.import_module(modname)\n', '  File "/home/docs/checkouts/readthedocs.org/user_builds/medypt/conda/latest/lib/python3.13/importlib/__init__.py", line 88, in import_module\n    return _bootstrap._gcd_import(name[level:], package, level)\n           ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', '  File "<frozen importlib._bootstrap>", line 1387, in _gcd_import\n', '  File "<frozen importlib._bootstrap>", line 1360, in _find_and_load\n', '  File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked\n', '  File "<frozen importlib._bootstrap>", line 935, in _load_unlocked\n', '  File "<frozen importlib._bootstrap_external>", line 1026, in exec_module\n', '  File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed\n', '  File "/home/docs/checkouts/readthedocs.org/user_builds/medypt/checkouts/latest/src/model.py", line 17, in <module>\n    from utils import relativeL2error, TMat, gen_therm_noise\n', '  File "/home/docs/checkouts/readthedocs.org/user_builds/medypt/checkouts/latest/src/utils.py", line 8, in <module>\n    import gmsh  # type: ignore\n    ^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'gmsh'\n"] [autodoc.import_object]
WARNING: autodoc: failed to import module 'utils'; the following exception was raised:
['Traceback (most recent call last):\n', '  File "/home/docs/checkouts/readthedocs.org/user_builds/medypt/conda/latest/lib/python3.13/site-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n    module = import_module(modname, try_reload=True)\n', '  File "/home/docs/checkouts/readthedocs.org/user_builds/medypt/conda/latest/lib/python3.13/site-packages/sphinx/ext/autodoc/importer.py", line 175, in import_module\n    module = importlib.import_module(modname)\n', '  File "/home/docs/checkouts/readthedocs.org/user_builds/medypt/conda/latest/lib/python3.13/importlib/__init__.py", line 88, in import_module\n    return _bootstrap._gcd_import(name[level:], package, level)\n           ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', '  File "<frozen importlib._bootstrap>", line 1387, in _gcd_import\n', '  File "<frozen importlib._bootstrap>", line 1360, in _find_and_load\n', '  File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked\n', '  File "<frozen importlib._bootstrap>", line 935, in _load_unlocked\n', '  File "<frozen importlib._bootstrap_external>", line 1026, in exec_module\n', '  File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed\n', '  File "/home/docs/checkouts/readthedocs.org/user_builds/medypt/checkouts/latest/src/utils.py", line 8, in <module>\n    import gmsh  # type: ignore\n    ^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'gmsh'\n"] [autodoc.import_object]
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
copying assets... 
copying static files... 
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/medypt/checkouts/latest/_readthedocs/html/_static/documentation_options.js
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/medypt/checkouts/latest/_readthedocs/html/_static/language_data.js
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/medypt/checkouts/latest/_readthedocs/html/_static/basic.css
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/medypt/checkouts/latest/_readthedocs/html/_static/js/versions.js
copying static files: done
copying extra files... 
copying extra files: done
copying assets: done
writing output... [ 17%] imt
writing output... [ 33%] index
writing output... [ 50%] maters
writing output... [ 67%] model
writing output... [ 83%] modules
writing output... [100%] utils

generating indices... genindex py-modindex done
writing additional pages... search done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 4 warnings.

The HTML pages are in ../../_readthedocs/html.

[physicsmonk]

Another weird thing is that RTD automatically added pip and sphinx in my environment.yml and warns me that I used pip to install some requirements while I didn't.

[physicsmonk]

Forgot to mention that the docs were built without any problem locally.

[humitos]

The build URL that you linked looks successful https://app.readthedocs.org/projects/medypt/builds/30438721/. Can you expand on the issue you are experimenting here?

[physicsmonk]

Thanks for helping me. The problem is that there are some blank pages in the documentation. For these blank pages, the log reported ModuleNotFoundError for importing gmsh, which should've been installed successfully because the conda-environment building stage generated no error.