[REVIEW]: Parcellating the parcellation issue - a proof of concept for reproducible analyses using Neurolibre

[roboneuro]

Submitting author: !--author-handle-->@pbellec<!--end-author-handle-- (Pierre Bellec) Repository: https://github.com/pbellec/editorial_parcellation Branch with paper.md (empty if default branch): main Version: v1.0.0 Editor: !--editor-->@agahkarakuzu<!--end-editor-- Reviewers: !--reviewers-list-->@agahkarakuzu<!--end-reviewers-list-- Reproducible preprint: https://preprint.neurolibre.org/10.55458/neurolibre.00010 Repository archive: 10.5281/zenodo.10031956 Data archive: 10.5281/zenodo.10031958 Book archive: 10.5281/zenodo.10031954 Docker archive: 10.5281/zenodo.10031960

Status

Status badge code:

HTML: <a href="http://neurolibre.herokuapp.com/papers/e62c9b30f9d1748c1e395c178b74a932"><img src="http://neurolibre.herokuapp.com/papers/e62c9b30f9d1748c1e395c178b74a932/status.svg"></a>
Markdown: [![status](http://neurolibre.herokuapp.com/papers/e62c9b30f9d1748c1e395c178b74a932/status.svg)](http://neurolibre.herokuapp.com/papers/e62c9b30f9d1748c1e395c178b74a932)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@anirudhk686, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @agahkarakuzu know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @anirudhk686

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [x] I confirm that I read and will adhere to the NeuroLibre code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@pbellec) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [ ] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[agahkarakuzu]

@roboneuro add @agahkarakuzu as reviewer

[roboneuro]

Can't add reviewers: There is no editor assigned yet

[agahkarakuzu]

@roboneuro add @agahkarakuzu as editor

[roboneuro]

Assigned! @agahkarakuzu is now the editor

[agahkarakuzu]

@roboneuro add @agahkarakuzu as reviewer

[roboneuro]

Can't add reviewers: There is no editor assigned yet

[agahkarakuzu]

@roboneuro build book

[roboneuro]

:eyes: Looks like the reproducible preprint you requested has been already built:

[{"time_added":"2023-03-01 13:54:52 +0000","book_url":"https://preview.neurolibre.org/book-artifacts/pbellec/github.com/editorial_parcellation/634f774be6fd6df28febdd7eb72bc75fcf025a3a/_build/html/","download_url":null}]

[agahkarakuzu]

@roboneuro build extended pdf

[roboneuro]

🔴 Extended PDF - Build draft

---

Status: Failed 4ac000c5 Last updated: 2023-10-20 09:04:26 PDT

:information_source: See details

'NoneType' object has no attribute 'strip'

[agahkarakuzu]

@roboneuro recommend-accept

[roboneuro]

Attempting dry run of processing paper acceptance...

[roboneuro]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.neuroimage.2017.11.063 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[roboneuro]

:wave: @openjournals/neurolibre-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/neurolibre/preprints/pull/61, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[agahkarakuzu]

@pbellec if you are happy with the PDF above and the reproducible preprint, I'll start the production.

[pbellec]

an ongoing issue with this submission (which I just checked is still present) is that the download gets downloaded again every time.

This is contrary to neurolibre's spirit. Even if the dataset is very small and is not an issue, at least while figshare continues to serve data, as the point of this submission is to have a lightweight example of notebook publishing, it really bugs me.

I'm going to investigate on my end, but if you have a suggestion, I'll take it.

Re the pdf, you're not planning at attempting an extended pdf?

[agahkarakuzu]

I've sent a pull request to deal with redownloading.

Extended PDF supports ipynb files, this is myst markdown, for which extended build is not parsing content yet.

[pbellec]

I've merged your PR.

pdf looks good! Most links are broken, but I think this is normal as reproducibility assets have not yet been published.

[agahkarakuzu]

@roboneuro build book

[roboneuro]

🔴 Binder build has failed 🥀

---

Status: Failed 01aa5664 Last updated: 2023-10-20 09:54:41 PDT

:information_source: See details

The next comment will forward the logs

[roboneuro]

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Waiting for build to start...
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Building wheels for collected packages: wget
  Building wheel for wget (setup.py): started
  Building wheel for wget (setup.py): finished with status 'done'
  Created wheel for wget: filename=wget-3.2-py3-none-any.whl size=9680 sha256=f53db166227fee24cf1a2aa595aca45f54cb8b95c5f7d58847ca3517b3eed5ce
  Stored in directory: /tmp/pip-ephem-wheel-cache-640navg6/wheels/a1/b6/7c/0e63e34eb06634181c63adacca38b79ff8f35c37e3c13e3c02
Successfully built wget
Installing collected packages: typing-extensions, traitlets, importlib-metadata, attrs, packaging, smmap, nbconvert, gitdb, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, snowballstemmer, pyyaml, more-itertools, mdit-py-plugins, markdown-it-py, latexcodec, jupyter-server-mathjax, jmespath, jeepney, imagesize, GitPython, docutils, colorama, alabaster, sphinx, SecretStorage, requests-toolbelt, pybtex, pyasn1, numpy, nbdime, jaraco.classes, importlib-resources, botocore, beautifulsoup4, uc-micro-py, tqdm, toml, tenacity, sphinx-togglebutton, scipy, s3transfer, rsa, python-gitlab, pydata-sphinx-theme, pybtex-docutils, platformdirs, pillow, patsy, patool, pandas, myst-parser, msgpack, looseversion, kiwisolver, keyrings.alt, keyring, jupyter-sphinx, jupyter-cache, iso8601, humanize, fonttools, filelock, fasteners, cycler, click, boto, annexremote, wget, threadpoolctl, statsmodels, sphinxcontrib-bibtex, sphinx-thebe, sphinx-panels, sphinx-external-toc, sphinx-copybutton, sphinx-comments, sphinx-book-theme, plotly, osfclient, myst-nb, matplotlib, linkify-it-py, jupytext, jupyterbook-latex, joblib, gdown, datalad, awscli, wordcloud, traitlet-widgets, seaborn, scikit-learn, repo2data, plotly-express, jupyter-book, imageio
  Attempting uninstall: typing-extensions
    Found existing installation: typing-extensions 3.10.0.0
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  Attempting uninstall: importlib-metadata
    Found existing installation: importlib-metadata 4.6.3
    Uninstalling importlib-metadata-4.6.3:
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  Attempting uninstall: attrs
    Found existing installation: attrs 21.2.0
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  Attempting uninstall: packaging
    Found existing installation: packaging 21.0
    Uninstalling packaging-21.0:
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  Attempting uninstall: nbconvert
    Found existing installation: nbconvert 6.0.7
    Uninstalling nbconvert-6.0.7:
      Successfully uninstalled nbconvert-6.0.7
Successfully installed GitPython-3.1.40 SecretStorage-3.3.3 alabaster-0.7.13 annexremote-1.6.0 attrs-20.3.0 awscli-1.29.67 beautifulsoup4-4.12.2 boto-2.49.0 botocore-1.31.67 click-8.1.7 colorama-0.4.4 cycler-0.11.0 datalad-0.19.3 docutils-0.16 fasteners-0.19 filelock-3.12.2 fonttools-4.38.0 gdown-4.7.1 gitdb-4.0.11 humanize-4.6.0 imageio-2.9.0 imagesize-1.4.1 importlib-metadata-6.7.0 importlib-resources-5.12.0 iso8601-2.1.0 jaraco.classes-3.2.3 jeepney-0.8.0 jmespath-1.0.1 joblib-1.3.2 jupyter-book-0.11.1 jupyter-cache-0.4.3 jupyter-server-mathjax-0.2.6 jupyter-sphinx-0.3.2 jupyterbook-latex-0.3.1 jupytext-1.10.3 keyring-24.1.1 keyrings.alt-4.2.0 kiwisolver-1.4.5 latexcodec-2.0.1 linkify-it-py-1.0.3 looseversion-1.3.0 markdown-it-py-0.6.2 matplotlib-3.5.3 mdit-py-plugins-0.2.6 more-itertools-9.1.0 msgpack-1.0.5 myst-nb-0.12.3 myst-parser-0.13.7 nbconvert-5.6.1 nbdime-3.2.1 numpy-1.21.2 osfclient-0.0.5 packaging-23.2 pandas-1.3.3 patool-1.12 patsy-0.5.3 pillow-9.5.0 platformdirs-3.11.0 plotly-5.17.0 plotly-express-0.4.1 pyasn1-0.5.0 pybtex-0.24.0 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.7.2 python-gitlab-3.15.0 pyyaml-6.0.1 repo2data-2.4.4 requests-toolbelt-1.0.0 rsa-4.7.2 s3transfer-0.7.0 scikit-learn-0.24.2 scipy-1.7.1 seaborn-0.11.2 smmap-5.0.1 snowballstemmer-2.2.0 soupsieve-2.4.1 sphinx-3.5.4 sphinx-book-theme-0.1.10 sphinx-comments-0.0.3 sphinx-copybutton-0.5.2 sphinx-external-toc-0.2.4 sphinx-panels-0.5.2 sphinx-thebe-0.0.10 sphinx-togglebutton-0.2.3 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-bibtex-2.2.1 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 statsmodels-0.13.5 tenacity-8.2.3 threadpoolctl-3.1.0 toml-0.10.2 tqdm-4.66.1 traitlet-widgets-5.5.1 traitlets-5.1.1 typing-extensions-4.7.1 uc-micro-py-1.0.2 wget-3.2 wordcloud-1.8.1
Removing intermediate container 8ec6ad41af0b
 ---> 960c8e453750
Step 42/51 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> 88f5315b06c5
Step 43/51 : LABEL repo2docker.ref="44bf57812cf875be690353e71bdfcaf013d04786"
 ---> Running in f6302985b8e2
Removing intermediate container f6302985b8e2
 ---> 10e455946652
Step 44/51 : LABEL repo2docker.repo="https://github.com/pbellec/editorial_parcellation"
 ---> Running in 6f9d61874c1e
Removing intermediate container 6f9d61874c1e
 ---> 72098379ec97
Step 45/51 : LABEL repo2docker.version="2021.08.0"
 ---> Running in f95063b99195
Removing intermediate container f95063b99195
 ---> 03ef6121b590
Step 46/51 : USER ${NB_USER}
 ---> Running in 6c1a3db81dea
Removing intermediate container 6c1a3db81dea
 ---> f01aaf340230
Step 47/51 : ENV PYTHONUNBUFFERED=1
 ---> Running in 5b53d80c6be7
Removing intermediate container 5b53d80c6be7
 ---> ab1a6663ee19
Step 48/51 : COPY /python3-login /usr/local/bin/python3-login
 ---> 8872149d00e0
Step 49/51 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint
 ---> 8d49509d7ab5
Step 50/51 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]
 ---> Running in 868d775f272e
Removing intermediate container 868d775f272e
 ---> 687ebcfaa344
Step 51/51 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
 ---> Running in 4a95d2d08cf9
Removing intermediate container 4a95d2d08cf9
 ---> 30f469ad6afd
{"aux": {"ID": "sha256:30f469ad6afdf5beaeaabc29e90c962dcc1e76e9b20fc17afd46505fa51a093c"}}Successfully built 30f469ad6afd
Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-pbellec-2deditorial-5fparcellation-e26e81:44bf57812cf875be690353e71bdfcaf013d04786
Pushing image
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Successfully pushed binder-registry.conp.cloud/binder-registry.conp.cloud/binder-pbellec-2deditorial-5fparcellation-e26e81:44bf57812cf875be690353e71bdfcaf013d04786Built image, launching...
Launching server...
Server requested
2023-10-20T16:51:20.478234Z [Normal] Successfully assigned binderhub/jupyter-pbellec-2deditorial-5fparcellation-2d75adkjt0 to neurolibre-master
2023-10-20T16:51:36Z [Normal] Container image "jupyterhub/k8s-network-tools:1.1.2" already present on machine
2023-10-20T16:51:42Z [Normal] Created container block-cloud-metadata
2023-10-20T16:51:49Z [Normal] Started container block-cloud-metadata
2023-10-20T16:51:50Z [Normal] Pulling image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-pbellec-2deditorial-5fparcellation-e26e81:44bf57812cf875be690353e71bdfcaf013d04786"
2023-10-20T16:52:25Z [Normal] Successfully pulled image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-pbellec-2deditorial-5fparcellation-e26e81:44bf57812cf875be690353e71bdfcaf013d04786" in 34.886439791s
2023-10-20T16:52:49Z [Normal] Created container notebook
2023-10-20T16:52:51Z [Normal] Started container notebook
Server ready at /jupyter/user/pbellec-editorial_parcellation-75adkjt0/
server running at https://test.conp.cloud/jupyter/user/pbellec-editorial_parcellation-75adkjt0/

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

Jupyter Book build log

Running Jupyter-Book v0.11.1
Source Folder: /home/jovyan/content
Config Path: /home/jovyan/content/_config.yml
Output Path: /mnt/books/pbellec/github.com/editorial_parcellation/44bf57812cf875be690353e71bdfcaf013d04786/_build/html
Running Sphinx v3.5.4
Adding copy buttons to code blocks...
Adding copy buttons to code blocks...
making output directory... done
[etoc] Changing master_doc to 'intro'
myst v0.13.7: MdParserConfig(renderer='sphinx', commonmark_only=False, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, update_mathjax=True, enable_extensions=['html_image'], disable_syntax=[], url_schemes=['mailto', 'http', 'https'], heading_anchors=None, html_meta=[], footnote_transition=True, substitutions=[], sub_delimiters=['{', '}'])
MyST-NB: Excluded Paths: set()
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 3 source files that are out of date
updating environment: MyST-NB: Potential docnames to execute: ['papers', 'conclusion', 'intro']
executing outdated notebooks... Executing: /home/jovyan/content/papers.md
Executing: /home/jovyan/content/conclusion.md
Execution Succeeded: /home/jovyan/content/conclusion.md
Executing: /home/jovyan/content/intro.md
Execution Succeeded: /home/jovyan/content/intro.md
done
[new config] 3 added, 0 changed, 0 removed
reading sources... [ 33%] conclusion
Merged cached outputs into content/conclusion.md
reading sources... [ 66%] intro
Merged cached outputs into content/intro.md
reading sources... [100%] papers

WARNING: Execution Failed: /home/jovyan/content/papers.md
WARNING: Couldn't find cache key for notebook file content/papers.md. Outputs will not be inserted.
  Last execution failed with traceback saved in /mnt/books/pbellec/github.com/editorial_parcellation/44bf57812cf875be690353e71bdfcaf013d04786/_build/html/reports/papers.log
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [ 33%] conclusion
writing output... [ 66%] intro
writing output... [100%] papers

generating indices... genindex done
writing additional pages... search done
copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 2 warnings.

The HTML pages are in ../../mnt/books/pbellec/github.com/editorial_parcellation/44bf57812cf875be690353e71bdfcaf013d04786/_build/html.
[etoc] missing index.html written as redirect to 'intro.html'

===============================================================================

Finished generating HTML for book.
Your book's HTML pages are here:
    ../../mnt/books/pbellec/github.com/editorial_parcellation/44bf57812cf875be690353e71bdfcaf013d04786/_build/html/
You can look at your book by opening this file in a browser:
    ../../mnt/books/pbellec/github.com/editorial_parcellation/44bf57812cf875be690353e71bdfcaf013d04786/_build/html/index.html
Or paste this line directly into your browser bar:
    file:///mnt/books/pbellec/github.com/editorial_parcellation/44bf57812cf875be690353e71bdfcaf013d04786/_build/html/index.html

===============================================================================

Jupyter-book execution failed!

Execution error log for papers notebook (papers.ipynb) or MyST (papers.md)).

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_cache/executors/utils.py", line 56, in single_nb_execution
    record_timing=False,
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/client.py", line 1112, in execute
    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/util.py", line 74, in wrapped
    return just_run(coro(*args, **kwargs))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/util.py", line 53, in just_run
    return loop.run_until_complete(coro)
  File "/srv/conda/envs/notebook/lib/python3.7/asyncio/base_events.py", line 587, in run_until_complete
    return future.result()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/client.py", line 554, in async_execute
    cell, index, execution_count=self.code_cells_executed + 1
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/client.py", line 857, in async_execute_cell
    self._check_raise_for_error(cell, exec_reply)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/client.py", line 760, in _check_raise_for_error
    raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
# Check where the notebooks are located in the current path
# This is necessary because thebe does not behave like jupyter hub
import os
if os.path.exists('content'):
  os.chdir('content')

# Import data from figshare, using repo2data https://github.com/SIMEXP/Repo2Data
from repo2data import repo2data
dl = repo2data.Repo2Data(os.path.join('..', 'binder', 'data_requirement.json'))
path_data = dl.install()[0]
------------------

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
/srv/conda/envs/notebook/lib/python3.7/shutil.py in move(src, dst, copy_function)
    565     try:
--> 566         os.rename(src, real_dst)
    567     except OSError:

FileNotFoundError: [Errno 2] No such file or directory: '/home/jovyan/content/9843721_7xaae21.tmp' -> '. (1)./data/editorial_parcellation/9843721'

During handling of the above exception, another exception occurred:

FileNotFoundError                         Traceback (most recent call last)
 in 
      8 from repo2data import repo2data
      9 dl = repo2data.Repo2Data(os.path.join('..', 'binder', 'data_requirement.json'))
---> 10 path_data = dl.install()[0]

/srv/conda/envs/notebook/lib/python3.7/site-packages/repo2data/repo2data.py in install(self)
     73         #if not, it is a single assignment
     74         else:
---> 75             ret += [Repo2DataChild(self._data_requirement_file, self._use_server).install()]
     76 
     77         return ret

/srv/conda/envs/notebook/lib/python3.7/site-packages/repo2data/repo2data.py in install(self)
    247                 os.makedirs(self._dst_path)
    248             # Downloading with the right method, depending on the src type
--> 249             self._scan_dl_type()
    250             # If needed, decompression of the data
    251             self._archive_decompress()

/srv/conda/envs/notebook/lib/python3.7/site-packages/repo2data/repo2data.py in _scan_dl_type(self)
    221                 and not re.match(".*?(drive\\.google\\.com).*?", self._data_requirement_file["src"])
    222                 and not re.match(".*?(https://osf\\.io).*?", self._data_requirement_file["src"])):
--> 223             self._wget_download()
    224         # if the source link has a .git, we use datalad
    225         elif re.match(".*?(\\.git)", self._data_requirement_file["src"]):

/srv/conda/envs/notebook/lib/python3.7/site-packages/repo2data/repo2data.py in _wget_download(self)
    149             try:
    150                 wget.download(self._data_requirement_file["src"]
--> 151                              , out=self._dst_path)
    152                 print(" ")
    153                 attempts = 999

/srv/conda/envs/notebook/lib/python3.7/site-packages/wget.py in download(url, out, bar)
    532     if os.path.exists(filename):
    533         filename = filename_fix_existing(filename)
--> 534     shutil.move(tmpfile, filename)
    535 
    536     #print headers

/srv/conda/envs/notebook/lib/python3.7/shutil.py in move(src, dst, copy_function)
    578             rmtree(src)
    579         else:
--> 580             copy_function(src, real_dst)
    581             os.unlink(src)
    582     return real_dst

/srv/conda/envs/notebook/lib/python3.7/shutil.py in copy2(src, dst, follow_symlinks)
    264     if os.path.isdir(dst):
    265         dst = os.path.join(dst, os.path.basename(src))
--> 266     copyfile(src, dst, follow_symlinks=follow_symlinks)
    267     copystat(src, dst, follow_symlinks=follow_symlinks)
    268     return dst

/srv/conda/envs/notebook/lib/python3.7/shutil.py in copyfile(src, dst, follow_symlinks)
    119     else:
    120         with open(src, 'rb') as fsrc:
--> 121             with open(dst, 'wb') as fdst:
    122                 copyfileobj(fsrc, fdst)
    123     return dst

FileNotFoundError: [Errno 2] No such file or directory: '. (1)./data/editorial_parcellation/9843721'
FileNotFoundError: [Errno 2] No such file or directory: '. (1)./data/editorial_parcellation/9843721'

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

[pbellec]

@agahkarakuzu I have updated dependencies, as well as all issues raised by @anirudhk686 . So I think you should be able to recompile the book , and we should be good to go.

[agahkarakuzu]

@roboneuro build book

[roboneuro]

🔴 Binder build has failed 🥀

---

Status: Failed 70c4745b Last updated: 2023-10-20 14:05:12 PDT

:information_source: See details

The next comment will forward the logs

[roboneuro]

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockerl98n2n64'...
HEAD is now at 815964b Merge pull request #10 from pbellec/iss6
Building conda environment for python=3.7Using PythonBuildPack builder
Building conda environment for python=3.7Building conda environment for python=3.7Step 1/51 : FROM buildpack-deps:bionic
 ---> bf89ebf6b3e4
Step 2/51 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> ae378de4f5b9
Step 3/51 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 08a78cfb4049
Step 4/51 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> fbceb2a67733
Step 5/51 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> 3cf70612d1fc
Step 6/51 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 54727b822f5d
Step 7/51 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> dc588c857c02
Step 8/51 : ENV SHELL /bin/bash
 ---> Using cache
 ---> 5e06214b4b44
Step 9/51 : ARG NB_USER
 ---> Using cache
 ---> 42ff2be77138
Step 10/51 : ARG NB_UID
 ---> Using cache
 ---> bd417f3d3dd4
Step 11/51 : ENV USER ${NB_USER}
 ---> Using cache
 ---> b60430c82d10
Step 12/51 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 5e458aff2510
Step 13/51 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> a438632f3dc3
Step 14/51 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> 0942e47ae895
Step 15/51 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> bad1e96f449e
Step 16/51 : EXPOSE 8888
 ---> Using cache
 ---> 73090ab9c46f
Step 17/51 : ENV APP_BASE /srv
 ---> Using cache
 ---> 3a4d18f1d969
Step 18/51 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> 0475c612f284
Step 19/51 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> 4a2d8b0fcc6c
Step 20/51 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> d1a029699546
Step 21/51 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> b14a9e7011ae
Step 22/51 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 7bb964d87d10
Step 23/51 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 56b69ac27d81
Step 24/51 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> 55a865e1b0ca
Step 25/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> d82b4d87d277
Step 26/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e7-2elock-4f1154 /tmp/env/environment.lock
 ---> Using cache
 ---> 175f3c212aac
Step 27/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> Using cache
 ---> c1bcf5d3bbd2
Step 28/51 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 1c2997e02be2
Step 29/51 : USER ${NB_USER}
 ---> Using cache
 ---> 43da6d61d80f
Step 30/51 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> a0eb3d6c7bde
Step 31/51 : USER root
 ---> Using cache
 ---> 3cddb7aebc76
Step 32/51 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> 1031221c3d3e
Step 33/51 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> 6ce4404a9fa0
Step 34/51 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 040b57734c85
Step 35/51 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> a22c4522f25b
Step 36/51 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 487a0e882c0b
Step 37/51 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 942a7191c6f5
Step 38/51 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> a79741aa8269
Step 39/51 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> 413ef46b6dae
Step 40/51 : USER ${NB_USER}
 ---> Running in 0b37084b96ab
Removing intermediate container 0b37084b96ab
 ---> 2a01bfb39e29
Step 41/51 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Running in 33ea7f50906a
Collecting accessible-pygments==0.0.4
  Downloading accessible_pygments-0.0.4-py2.py3-none-any.whl (29 kB)
Collecting alabaster==0.7.13
  Downloading alabaster-0.7.13-py3-none-any.whl (13 kB)
Collecting annexremote==1.6.0
  Downloading annexremote-1.6.0-py3-none-any.whl (25 kB)
Collecting asttokens==2.4.0
  Downloading asttokens-2.4.0-py2.py3-none-any.whl (27 kB)
Collecting attrs==23.1.0
  Downloading attrs-23.1.0-py3-none-any.whl (61 kB)
Collecting awscli==1.29.67
  Downloading awscli-1.29.67-py3-none-any.whl (4.3 MB)
Collecting Babel==2.13.0
  Downloading Babel-2.13.0-py3-none-any.whl (10.1 MB)
Requirement already satisfied: backcall==0.2.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from -r binder/requirements.txt (line 8)) (0.2.0)
Collecting beautifulsoup4==4.12.2
  Downloading beautifulsoup4-4.12.2-py3-none-any.whl (142 kB)
Collecting boto==2.49.0
  Downloading boto-2.49.0-py2.py3-none-any.whl (1.4 MB)
Collecting botocore==1.31.67
  Downloading botocore-1.31.67-py3-none-any.whl (11.3 MB)
Collecting certifi==2023.7.22
  Downloading certifi-2023.7.22-py3-none-any.whl (158 kB)
ERROR: Could not find a version that satisfies the requirement cffi==1.16.0 (from versions: 0.1, 0.2, 0.2.1, 0.3, 0.4, 0.4.1, 0.4.2, 0.5, 0.6, 0.7, 0.7.1, 0.7.2, 0.8, 0.8.1, 0.8.2, 0.8.3, 0.8.4, 0.8.5, 0.8.6, 0.9.0, 0.9.1, 0.9.2, 1.0.0, 1.0.1, 1.0.2.post2, 1.0.3, 1.1.0, 1.1.1, 1.1.2, 1.2.0.post1, 1.2.1, 1.3.0, 1.3.1, 1.4.0, 1.4.1, 1.4.2, 1.5.0, 1.5.1, 1.5.2, 1.6.0, 1.7.0, 1.8.2, 1.8.3, 1.9.0, 1.9.1, 1.10.0, 1.11.0, 1.11.1, 1.11.2, 1.11.3, 1.11.4, 1.11.5, 1.12.0, 1.12.1, 1.12.2, 1.12.3, 1.13.0, 1.13.1, 1.13.2, 1.14.0, 1.14.1, 1.14.2, 1.14.3, 1.14.4, 1.14.5, 1.14.6, 1.15.0rc1, 1.15.0rc2, 1.15.0, 1.15.1)
ERROR: No matching distribution found for cffi==1.16.0
Removing intermediate container 33ea7f50906a
The command '/bin/sh -c ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"' returned a non-zero code: 1Built image, launching...

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

I could not find any book log for pbellec/editorial_parcellation at 815964b747fdfc7ccee49526f5c30ca4c5765054

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

[agahkarakuzu]

@pbellec the new requirements.txt is freezing a lot of versions, and I guess some of them are not compatible with default python version. If these are versions are working for you locally, can you add binder/runtime.txt with the following content:

python-3.8

or some other python version. Another option is to relax the dependencies by reverting to the previous requirements (with repo2data==2.9.1).

[pbellec]

ok so I tried to fix python to my local version: https://github.com/pbellec/editorial_parcellation/blob/main/binder/runtime.txt

I've struggled a bit to get the dependencies to install by simply changing a bit the old versions. That's why I ended up just freezing everything.

But if that does not work, I'll try to remove some of the constraints, or remove them entirely: it should compile just fine with the latest versions of all the libraries.

[agahkarakuzu]

@roboneuro build book

[roboneuro]

🔴 Binder build has failed 🥀

---

Status: Failed 46e8aaac Last updated: 2023-10-20 15:24:44 PDT

:information_source: See details

The next comment will forward the logs

[roboneuro]

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2docker5b5otnzs'...
HEAD is now at 9a6b829 Merge branch 'main' of github.com:pbellec/editorial_parcellation
Building conda environment for python=3.10Using PythonBuildPack builder
Building conda environment for python=3.10Building conda environment for python=3.10Step 1/51 : FROM buildpack-deps:bionic
 ---> bf89ebf6b3e4
Step 2/51 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> ae378de4f5b9
Step 3/51 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 08a78cfb4049
Step 4/51 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> fbceb2a67733
Step 5/51 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> 3cf70612d1fc
Step 6/51 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 54727b822f5d
Step 7/51 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> dc588c857c02
Step 8/51 : ENV SHELL /bin/bash
 ---> Using cache
 ---> 5e06214b4b44
Step 9/51 : ARG NB_USER
 ---> Using cache
 ---> 42ff2be77138
Step 10/51 : ARG NB_UID
 ---> Using cache
 ---> bd417f3d3dd4
Step 11/51 : ENV USER ${NB_USER}
 ---> Using cache
 ---> b60430c82d10
Step 12/51 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 5e458aff2510
Step 13/51 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> a438632f3dc3
Step 14/51 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> 0942e47ae895
Step 15/51 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> bad1e96f449e
Step 16/51 : EXPOSE 8888
 ---> Using cache
 ---> 73090ab9c46f
Step 17/51 : ENV APP_BASE /srv
 ---> Using cache
 ---> 3a4d18f1d969
Step 18/51 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> 0475c612f284
Step 19/51 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> 4a2d8b0fcc6c
Step 20/51 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> d1a029699546
Step 21/51 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> b14a9e7011ae
Step 22/51 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 7bb964d87d10
Step 23/51 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 56b69ac27d81
Step 24/51 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> 55a865e1b0ca
Step 25/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> d82b4d87d277
Step 26/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2elock-1dbdca /tmp/env/environment.lock
 ---> 4e425aa327df
Step 27/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> 2660f52ca882
Step 28/51 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Running in b686f19d0b7c
Removing intermediate container b686f19d0b7c
 ---> 9815e6de0e56
Step 29/51 : USER ${NB_USER}
 ---> Running in f4e56322d9de
Removing intermediate container f4e56322d9de
 ---> 538ce8aedbab
Step 30/51 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Running in cee1b82a94dc
Removing intermediate container cee1b82a94dc
 ---> 0232a91b0abf
Step 31/51 : USER root
 ---> Running in 915bef4b7621
Removing intermediate container 915bef4b7621
 ---> 6476fcc46921
Step 32/51 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Running in 533b57908497
++ dirname /tmp/install-miniforge.bash
+ cd /tmp
+ MINIFORGE_VERSION=4.9.2-2
+ MAMBA_VERSION=0.7.4
+ SHA256SUM=7a7bfaff87680298304a97ba69bcf92f66c810995a7155a2918b99fafb8ca1dc
+ URL=https://github.com/conda-forge/miniforge/releases/download/4.9.2-2/Mambaforge-4.9.2-2-Linux-x86_64.sh
+ INSTALLER_PATH=/tmp/miniforge-installer.sh
+ unset HOME
+ wget --quiet https://github.com/conda-forge/miniforge/releases/download/4.9.2-2/Mambaforge-4.9.2-2-Linux-x86_64.sh -O /tmp/miniforge-installer.sh
time: 2.927
+ chmod +x /tmp/miniforge-installer.sh
+ echo '7a7bfaff87680298304a97ba69bcf92f66c810995a7155a2918b99fafb8ca1dc  /tmp/miniforge-installer.sh'
+ sha256sum --quiet -c -
+ bash /tmp/miniforge-installer.sh -b -p /srv/conda
PREFIX=/srv/conda
Unpacking payload ...

  0%|          | 0/57 [00:00 965e83304b1b
Step 33/51 : ARG REPO_DIR=${HOME}
 ---> Running in 5442c31ae2fe
Removing intermediate container 5442c31ae2fe
 ---> 88cea159489a
Step 34/51 : ENV REPO_DIR ${REPO_DIR}
 ---> Running in 06c303b1233c
Removing intermediate container 06c303b1233c
 ---> ad2557461a2f
Step 35/51 : WORKDIR ${REPO_DIR}
 ---> Running in 94b24d15b190
Removing intermediate container 94b24d15b190
 ---> af93ed8d88fa
Step 36/51 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Running in aa6d3d49a332
Removing intermediate container aa6d3d49a332
 ---> 4972cfb3e4b6
Step 37/51 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Running in 0846170b4f74
Removing intermediate container 0846170b4f74
 ---> 1abfb5f5942c
Step 38/51 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Running in 78f9ea034f52
Removing intermediate container 78f9ea034f52
 ---> 597a06ba7db3
Step 39/51 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> f897c890dfe6
Step 40/51 : USER ${NB_USER}
 ---> Running in 673847476a8b
Removing intermediate container 673847476a8b
 ---> 5b4637216ee2
Step 41/51 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Running in 1c3032b27cff
Collecting accessible-pygments==0.0.4
  Downloading accessible_pygments-0.0.4-py2.py3-none-any.whl (29 kB)
Collecting alabaster==0.7.13
  Downloading alabaster-0.7.13-py3-none-any.whl (13 kB)
Collecting annexremote==1.6.0
  Downloading annexremote-1.6.0-py3-none-any.whl (25 kB)
Collecting asttokens==2.4.0
  Downloading asttokens-2.4.0-py2.py3-none-any.whl (27 kB)
Collecting attrs==23.1.0
  Downloading attrs-23.1.0-py3-none-any.whl (61 kB)
Collecting awscli==1.29.67
  Downloading awscli-1.29.67-py3-none-any.whl (4.3 MB)
Collecting Babel==2.13.0
  Downloading Babel-2.13.0-py3-none-any.whl (10.1 MB)
Requirement already satisfied: backcall==0.2.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from -r binder/requirements.txt (line 8)) (0.2.0)
Collecting beautifulsoup4==4.12.2
  Downloading beautifulsoup4-4.12.2-py3-none-any.whl (142 kB)
Collecting boto==2.49.0
  Downloading boto-2.49.0-py2.py3-none-any.whl (1.4 MB)
Collecting botocore==1.31.67
  Downloading botocore-1.31.67-py3-none-any.whl (11.3 MB)
Collecting certifi==2023.7.22
  Downloading certifi-2023.7.22-py3-none-any.whl (158 kB)
ERROR: Could not find a version that satisfies the requirement cffi==1.16.0 (from versions: 0.1, 0.2, 0.2.1, 0.3, 0.4, 0.4.1, 0.4.2, 0.5, 0.6, 0.7, 0.7.1, 0.7.2, 0.8, 0.8.1, 0.8.2, 0.8.3, 0.8.4, 0.8.5, 0.8.6, 0.9.0, 0.9.1, 0.9.2, 1.0.0, 1.0.1, 1.0.2.post2, 1.0.3, 1.1.0, 1.1.1, 1.1.2, 1.2.0.post1, 1.2.1, 1.3.0, 1.3.1, 1.4.0, 1.4.1, 1.4.2, 1.5.0, 1.5.1, 1.5.2, 1.6.0, 1.7.0, 1.8.2, 1.8.3, 1.9.0, 1.9.1, 1.10.0, 1.11.0, 1.11.1, 1.11.2, 1.11.3, 1.11.4, 1.11.5, 1.12.0, 1.12.1, 1.12.2, 1.12.3, 1.13.0, 1.13.1, 1.13.2, 1.14.0, 1.14.1, 1.14.2, 1.14.3, 1.14.4, 1.14.5, 1.14.6, 1.15.0rc1, 1.15.0rc2, 1.15.0, 1.15.1)
ERROR: No matching distribution found for cffi==1.16.0
Removing intermediate container 1c3032b27cff
The command '/bin/sh -c ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"' returned a non-zero code: 1Built image, launching...

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

I could not find any book log for pbellec/editorial_parcellation at 9a6b8292d6fabe6ab49ca0fa95b4ebf0b3f48ba0

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

[pbellec]

I've pushed the repo with a simplified requirements file. Fingers crossed.

[agahkarakuzu]

@roboneuro build book

[roboneuro]

🔴 Binder build has failed 🥀

---

Status: Failed 1cf72b5c Last updated: 2023-10-21 14:28:58 PDT

:information_source: See details

The next comment will forward the logs

[roboneuro]

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2docker2t7da287'...
HEAD is now at c1435a3 Limiting the number of explicit dependencies.
Building conda environment for python=3.10Using PythonBuildPack builder
Building conda environment for python=3.10Building conda environment for python=3.10Step 1/51 : FROM buildpack-deps:bionic
 ---> bf89ebf6b3e4
Step 2/51 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> ae378de4f5b9
Step 3/51 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 08a78cfb4049
Step 4/51 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> fbceb2a67733
Step 5/51 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> 3cf70612d1fc
Step 6/51 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 54727b822f5d
Step 7/51 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> dc588c857c02
Step 8/51 : ENV SHELL /bin/bash
 ---> Using cache
 ---> 5e06214b4b44
Step 9/51 : ARG NB_USER
 ---> Using cache
 ---> 42ff2be77138
Step 10/51 : ARG NB_UID
 ---> Using cache
 ---> bd417f3d3dd4
Step 11/51 : ENV USER ${NB_USER}
 ---> Using cache
 ---> b60430c82d10
Step 12/51 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 5e458aff2510
Step 13/51 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> a438632f3dc3
Step 14/51 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> 0942e47ae895
Step 15/51 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> bad1e96f449e
Step 16/51 : EXPOSE 8888
 ---> Using cache
 ---> 73090ab9c46f
Step 17/51 : ENV APP_BASE /srv
 ---> Using cache
 ---> 3a4d18f1d969
Step 18/51 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> 0475c612f284
Step 19/51 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> 4a2d8b0fcc6c
Step 20/51 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> d1a029699546
Step 21/51 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> b14a9e7011ae
Step 22/51 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 7bb964d87d10
Step 23/51 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 56b69ac27d81
Step 24/51 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> 55a865e1b0ca
Step 25/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> d82b4d87d277
Step 26/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2elock-1dbdca /tmp/env/environment.lock
 ---> Using cache
 ---> 4e425aa327df
Step 27/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> Using cache
 ---> 2660f52ca882
Step 28/51 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 9815e6de0e56
Step 29/51 : USER ${NB_USER}
 ---> Using cache
 ---> 538ce8aedbab
Step 30/51 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 0232a91b0abf
Step 31/51 : USER root
 ---> Using cache
 ---> 6476fcc46921
Step 32/51 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> 965e83304b1b
Step 33/51 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> 88cea159489a
Step 34/51 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> ad2557461a2f
Step 35/51 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> af93ed8d88fa
Step 36/51 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 4972cfb3e4b6
Step 37/51 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 1abfb5f5942c
Step 38/51 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 597a06ba7db3
Step 39/51 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> 1b21f743cf30
Step 40/51 : USER ${NB_USER}
 ---> Running in 7b89c5b9db9c
Removing intermediate container 7b89c5b9db9c
 ---> 87fb2bc177ca
Step 41/51 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Running in 06eb46ad0838
Collecting jupyter-book==0.15.1
  Downloading jupyter_book-0.15.1-py3-none-any.whl (43 kB)
ERROR: Could not find a version that satisfies the requirement matplotlib==3.8.0 (from versions: 0.86, 0.86.1, 0.86.2, 0.91.0, 0.91.1, 1.0.1, 1.1.0, 1.1.1, 1.2.0, 1.2.1, 1.3.0, 1.3.1, 1.4.0, 1.4.1rc1, 1.4.1, 1.4.2, 1.4.3, 1.5.0, 1.5.1, 1.5.2, 1.5.3, 2.0.0b1, 2.0.0b2, 2.0.0b3, 2.0.0b4, 2.0.0rc1, 2.0.0rc2, 2.0.0, 2.0.1, 2.0.2, 2.1.0rc1, 2.1.0, 2.1.1, 2.1.2, 2.2.0rc1, 2.2.0, 2.2.2, 2.2.3, 2.2.4, 2.2.5, 3.0.0rc2, 3.0.0, 3.0.1, 3.0.2, 3.0.3, 3.1.0rc1, 3.1.0rc2, 3.1.0, 3.1.1, 3.1.2, 3.1.3, 3.2.0rc1, 3.2.0rc3, 3.2.0, 3.2.1, 3.2.2, 3.3.0rc1, 3.3.0, 3.3.1, 3.3.2, 3.3.3, 3.3.4, 3.4.0rc1, 3.4.0rc2, 3.4.0rc3, 3.4.0, 3.4.1, 3.4.2, 3.4.3, 3.5.0b1, 3.5.0rc1, 3.5.0, 3.5.1, 3.5.2, 3.5.3)
ERROR: No matching distribution found for matplotlib==3.8.0
Removing intermediate container 06eb46ad0838
The command '/bin/sh -c ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"' returned a non-zero code: 1Built image, launching...

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

I could not find any book log for pbellec/editorial_parcellation at c1435a3dfa21204e6b9750880182c8ae753d7e4d

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

[agahkarakuzu]

@pbellec the build did not like matplotlib version.

[pbellec]

alright, I pushed a new version without dependencies.

[agahkarakuzu]

@roboneuro build book

[roboneuro]

🟠 Book Build (Preview)

---

Status: In progress 3a044edf Last updated: 2023-10-21 15:51:26 PDT

:information_source: See details

Running for: https://test.conp.cloud/build/gh/pbellec/editorial_parcellation.git/c14de52ad40a3a2a2e30aaaaf9e877ba70f4d9f1

[agahkarakuzu]

@roboneuro build book

[roboneuro]

🔴 Binder build has failed 🥀

---

Status: Failed 4c6d98b9 Last updated: 2023-10-21 17:24:56 PDT

:information_source: See details

The next comment will forward the logs

[roboneuro]

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Found built image, launching...
Launching server...
Server requested
2023-10-22T00:23:14Z [Normal] Successfully assigned binderhub/jupyter-pbellec-2deditorial-5fparcellation-2dur4py6xd to neurolibre-master
2023-10-22T00:23:20Z [Normal] Container image "jupyterhub/k8s-network-tools:1.1.2" already present on machine
2023-10-22T00:23:24Z [Normal] Created container block-cloud-metadata
2023-10-22T00:23:25Z [Normal] Started container block-cloud-metadata
2023-10-22T00:23:26Z [Normal] Pulling image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-pbellec-2deditorial-5fparcellation-e26e81:c14de52ad40a3a2a2e30aaaaf9e877ba70f4d9f1"
2023-10-22T00:24:10Z [Normal] Successfully pulled image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-pbellec-2deditorial-5fparcellation-e26e81:c14de52ad40a3a2a2e30aaaaf9e877ba70f4d9f1" in 43.802037367s
2023-10-22T00:24:37Z [Normal] Created container notebook
2023-10-22T00:24:39Z [Normal] Started container notebook
Server ready at /jupyter/user/pbellec-editorial_parcellation-ur4py6xd/
server running at https://test.conp.cloud/jupyter/user/pbellec-editorial_parcellation-ur4py6xd/

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

Jupyter Book build log

Running Jupyter-Book v0.15.1
Source Folder: /home/jovyan/content
Config Path: /home/jovyan/content/_config.yml
Output Path: /mnt/books/pbellec/github.com/editorial_parcellation/c14de52ad40a3a2a2e30aaaaf9e877ba70f4d9f1/_build/html
Running Sphinx v5.0.2
Adding copy buttons to code blocks...
Adding copy buttons to code blocks...
making output directory... done
[etoc] Changing master_doc to 'intro'
locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['html_image'], disable_syntax=[], all_links_external=False, url_schemes=['mailto', 'http', 'https'], ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area')
myst-nb v0.17.2: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='cache', execution_cache_path='/mnt/books/pbellec/github.com/editorial_parcellation/c14de52ad40a3a2a2e30aaaaf9e877ba70f4d9f1/_build/.jupyter_cache', execution_excludepatterns=[], execution_timeout=-1, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='show', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False)
Using jupyter-cache at: /mnt/books/pbellec/github.com/editorial_parcellation/c14de52ad40a3a2a2e30aaaaf9e877ba70f4d9f1/_build/.jupyter_cache
locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 3 source files that are out of date
updating environment: locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[new config] 3 added, 0 changed, 0 removed
reading sources... [ 33%] conclusion
/home/jovyan/content/conclusion.md: Executing notebook using local CWD [mystnb]
/home/jovyan/content/conclusion.md: Executed notebook in 1.02 seconds [mystnb]
/home/jovyan/content/conclusion.md: Cached executed notebook: ID=1 [mystnb]
reading sources... [ 66%] intro
/home/jovyan/content/intro.md: Using cached notebook: ID=1 [mystnb]
reading sources... [100%] papers
/home/jovyan/content/papers.md: Executing notebook using local CWD [mystnb]

/home/jovyan/content/papers.md: WARNING: Executing notebook failed: CellExecutionError [mystnb.exec]
/home/jovyan/content/papers.md: WARNING: Notebook exception traceback saved in: /mnt/books/pbellec/github.com/editorial_parcellation/c14de52ad40a3a2a2e30aaaaf9e877ba70f4d9f1/_build/html/reports/papers.err.log [mystnb.exec]
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [ 33%] conclusion

Extension error (pydata_sphinx_theme):
Handler  for event 'html-page-context' threw an exception (exception: 'dict object' has no attribute 'image_relative')
Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 94, in emit
    results.append(listener.handler(self.app, *args))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/__init__.py", line 241, in update_and_remove_templates
    context[section] = list(filter(_remove_empty_templates, context[section]))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/__init__.py", line 236, in _remove_empty_templates
    rendered = app.builder.templates.render(tname, context)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/jinja2glue.py", line 189, in render
    return self.environment.get_template(template).render(context)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jinja2/environment.py", line 1304, in render
    self.environment.handle_exception()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jinja2/environment.py", line 925, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/theme/pydata_sphinx_theme/components/navbar-logo.html", line 13, in top-level template code
    {% set is_logo = "light" in theme_logo["image_relative"] %}
jinja2.exceptions.UndefinedError: 'dict object' has no attribute 'image_relative'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/sphinx.py", line 171, in build_sphinx
    app.build(force_all, filenames)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/application.py", line 329, in build
    self.builder.build_update()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 290, in build_update
    len(to_build))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 352, in build
    self.write(docnames, list(updated_docnames), method)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 544, in write
    self._write_serial(sorted(docnames))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 554, in _write_serial
    self.write_doc(docname, doctree)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/html/__init__.py", line 649, in write_doc
    self.handle_page(docname, ctx, event_arg=doctree)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/html/__init__.py", line 1052, in handle_page
    templatename, ctx, event_arg)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/application.py", line 458, in emit_firstresult
    allowed_exceptions=allowed_exceptions)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 112, in emit_firstresult
    for result in self.emit(name, *args, allowed_exceptions=allowed_exceptions):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 103, in emit
    (listener.handler, name), exc, modname=modname) from exc
sphinx.errors.ExtensionError: Handler  for event 'html-page-context' threw an exception (exception: 'dict object' has no attribute 'image_relative')

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/bin/jupyter-book", line 8, in 
    sys.exit(main())
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 318, in build
    result, builder, OUTPUT_PATH, build_type, PAGE_NAME, click.echo
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 525, in builder_specific_actions
    raise RuntimeError(_message_box(msg, color="red", doprint=False)) from result
RuntimeError:
===============================================================================

There was an error in building your book. Look above for the cause.

===============================================================================

Jupyter-book exit code: 1
Jupyter-book build failed!

Execution error log for papers notebook (papers.ipynb) or MyST (papers.md)).

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_cache/executors/utils.py", line 64, in single_nb_execution
    **kwargs,
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/client.py", line 1112, in execute
    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/util.py", line 74, in wrapped
    return just_run(coro(*args, **kwargs))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/util.py", line 53, in just_run
    return loop.run_until_complete(coro)
  File "/srv/conda/envs/notebook/lib/python3.7/asyncio/base_events.py", line 587, in run_until_complete
    return future.result()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/client.py", line 554, in async_execute
    cell, index, execution_count=self.code_cells_executed + 1
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/client.py", line 857, in async_execute_cell
    self._check_raise_for_error(cell, exec_reply)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/client.py", line 760, in _check_raise_for_error
    raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
from sklearn.feature_extraction.text import TfidfVectorizer
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import Normalizer
from sklearn.decomposition import TruncatedSVD

# Prepare a model to extract a bag of words representation
vectorizer = TfidfVectorizer(max_df=0.5, max_features=300,
                                 min_df=2, stop_words='english',
                             use_idf=True)
X = vectorizer.fit_transform(data.Abstract) # apply the TFIDF model to the abstracts of the papers
fts = vectorizer.get_feature_names_out() # Get the most relevant terms selected by the procedure
svd = TruncatedSVD(10, algorithm="arpack") # Prepare the SVD model
normalizer = Normalizer(copy=False) # Normalize the outputs of the svd
lsa = make_pipeline(svd, normalizer) # Put the SVD and normalization in a pipeline
X = lsa.fit_transform(X) # Apply the SVD to the TFIDF features

# Now make a radar plot with all the components
import plotly.express as px
import numpy as np
df_X = pd.DataFrame(data=np.concatenate([data['Author'].to_numpy().reshape([38, 1]), X], axis=1),
                    columns= np.concatenate([['First author'],[f'component {d}' for d in range(10)]]))
df_visu = pd.melt(df_X, id_vars='First author')
fig = px.line_polar(df_visu, r='value', theta='variable', color='First author', line_close=True,
            color_discrete_sequence=px.colors.sequential.Plasma_r)
fig.show()
------------------

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
 in 
     16 
     17 # Now make a radar plot with all the components
---> 18 import plotly.express as px
     19 import numpy as np
     20 df_X = pd.DataFrame(data=np.concatenate([data['Author'].to_numpy().reshape([38, 1]), X], axis=1),

ModuleNotFoundError: No module named 'plotly'
ModuleNotFoundError: No module named 'plotly'

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

[agahkarakuzu]

@pbellec plotly is missing from dependencies

[pbellec]

:/ ok I had removed too much. I've added back plotly (and imageio). Also tested build locally from a fresh venv, and it's working.

[agahkarakuzu]

@roboneuro build book

[roboneuro]

🔴 Binder build has failed 🥀

---

Status: Failed 6c72d6f6 Last updated: 2023-10-21 18:06:47 PDT

:information_source: See details

The next comment will forward the logs

[roboneuro]

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockertdpdxsi6'...
HEAD is now at ba22e6c Adding missing dependencies.
Building conda environment for python=3.10Using PythonBuildPack builder
Building conda environment for python=3.10Building conda environment for python=3.10Step 1/51 : FROM buildpack-deps:bionic
 ---> bf89ebf6b3e4
Step 2/51 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> ae378de4f5b9
Step 3/51 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 08a78cfb4049
Step 4/51 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> fbceb2a67733
Step 5/51 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> 3cf70612d1fc
Step 6/51 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 54727b822f5d
Step 7/51 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> dc588c857c02
Step 8/51 : ENV SHELL /bin/bash
 ---> Using cache
 ---> 5e06214b4b44
Step 9/51 : ARG NB_USER
 ---> Using cache
 ---> 42ff2be77138
Step 10/51 : ARG NB_UID
 ---> Using cache
 ---> bd417f3d3dd4
Step 11/51 : ENV USER ${NB_USER}
 ---> Using cache
 ---> b60430c82d10
Step 12/51 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 5e458aff2510
Step 13/51 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> a438632f3dc3
Step 14/51 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> 0942e47ae895
Step 15/51 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> bad1e96f449e
Step 16/51 : EXPOSE 8888
 ---> Using cache
 ---> 73090ab9c46f
Step 17/51 : ENV APP_BASE /srv
 ---> Using cache
 ---> 3a4d18f1d969
Step 18/51 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> 0475c612f284
Step 19/51 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> 4a2d8b0fcc6c
Step 20/51 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> d1a029699546
Step 21/51 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> b14a9e7011ae
Step 22/51 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 7bb964d87d10
Step 23/51 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 56b69ac27d81
Step 24/51 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> 55a865e1b0ca
Step 25/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> d82b4d87d277
Step 26/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2elock-1dbdca /tmp/env/environment.lock
 ---> Using cache
 ---> 4e425aa327df
Step 27/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> Using cache
 ---> 2660f52ca882
Step 28/51 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 9815e6de0e56
Step 29/51 : USER ${NB_USER}
 ---> Using cache
 ---> 538ce8aedbab
Step 30/51 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 0232a91b0abf
Step 31/51 : USER root
 ---> Using cache
 ---> 6476fcc46921
Step 32/51 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> 965e83304b1b
Step 33/51 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> 88cea159489a
Step 34/51 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> ad2557461a2f
Step 35/51 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> af93ed8d88fa
Step 36/51 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 4972cfb3e4b6
Step 37/51 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 1abfb5f5942c
Step 38/51 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 597a06ba7db3
Step 39/51 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> 1f5b14640afd
Step 40/51 : USER ${NB_USER}
 ---> Running in a93bd56b876e
Removing intermediate container a93bd56b876e
 ---> f940d731750b
Step 41/51 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Running in 637021b47b54
Collecting jupyter-book
  Downloading jupyter_book-0.15.1-py3-none-any.whl (43 kB)
Collecting matplotlib
  Downloading matplotlib-3.5.3-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB)
Collecting numpy
  Downloading numpy-1.21.6-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
Collecting repo2data
  Downloading repo2data-2.9.1-py3-none-any.whl (7.6 kB)
Collecting scikit-learn
  Downloading scikit_learn-1.0.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (24.8 MB)
Collecting scipy
  Downloading scipy-1.7.3-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (38.1 MB)
Collecting seaborn
  Downloading seaborn-0.12.2-py3-none-any.whl (293 kB)
Collecting wordcloud
  Downloading wordcloud-1.9.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (437 kB)
Collecting plotly
  Downloading plotly-5.17.0-py2.py3-none-any.whl (15.6 MB)
Collecting imageio
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Requirement already satisfied: Jinja2 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jupyter-book->-r binder/requirements.txt (line 1)) (3.0.1)
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WARNING: The candidate selected for download or install is a yanked version: 'zenodo-get' candidate (version 1.3.4 at https://files.pythonhosted.org/packages/d8/37/0351ee61eb7eef9e660732da3ba3e1b7d97b9d219c8e250db469e2a33dbc/zenodo_get-1.3.4-py2.py3-none-any.whl#sha256=b71cd784df7877749a7bdb00513964ce0c9f6b62aad3311a8725a3b279d6f4f5 (from https://pypi.org/simple/zenodo-get/) (requires-python:>=3.6))
Reason for being yanked: server side API change made it incompatible
Building wheels for collected packages: wget
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  Stored in directory: /tmp/pip-ephem-wheel-cache-z3zjfzf1/wheels/a1/b6/7c/0e63e34eb06634181c63adacca38b79ff8f35c37e3c13e3c02
Successfully built wget
Installing collected packages: typing-extensions, importlib-metadata, mdurl, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, snowballstemmer, pyyaml, Pygments, more-itertools, markdown-it-py, latexcodec, jmespath, jeepney, imagesize, docutils, alabaster, tabulate, sphinx, SecretStorage, requests-toolbelt, pybtex, pyasn1, mdit-py-plugins, jaraco.classes, importlib-resources, click, botocore, beautifulsoup4, accessible-pygments, wget, uc-micro-py, tqdm, s3transfer, rsa, python-gitlab, pydata-sphinx-theme, pybtex-docutils, platformdirs, pillow, patool, numpy, myst-parser, msgpack, looseversion, kiwisolver, keyrings.alt, keyring, jupyter-cache, iso8601, humanize, fonttools, filelock, fasteners, cycler, colorama, boto, annexremote, zenodo-get, threadpoolctl, tenacity, sphinxcontrib-bibtex, sphinx-togglebutton, sphinx-thebe, sphinx-multitoc-numbering, sphinx-jupyterbook-latex, sphinx-external-toc, sphinx-design, sphinx-copybutton, sphinx-comments, sphinx-book-theme, scipy, pandas, osfclient, myst-nb, matplotlib, linkify-it-py, joblib, gdown, datalad, awscli, wordcloud, seaborn, scikit-learn, repo2data, plotly, jupyter-book, imageio
  Attempting uninstall: typing-extensions
    Found existing installation: typing-extensions 3.10.0.0
    Uninstalling typing-extensions-3.10.0.0:
      Successfully uninstalled typing-extensions-3.10.0.0
  Attempting uninstall: importlib-metadata
    Found existing installation: importlib-metadata 4.6.3
    Uninstalling importlib-metadata-4.6.3:
      Successfully uninstalled importlib-metadata-4.6.3
  Attempting uninstall: Pygments
    Found existing installation: Pygments 2.9.0
    Uninstalling Pygments-2.9.0:
      Successfully uninstalled Pygments-2.9.0
Successfully installed Pygments-2.16.1 SecretStorage-3.3.3 accessible-pygments-0.0.4 alabaster-0.7.13 annexremote-1.6.0 awscli-1.29.68 beautifulsoup4-4.12.2 boto-2.49.0 botocore-1.31.68 click-8.1.7 colorama-0.4.4 cycler-0.11.0 datalad-0.19.3 docutils-0.16 fasteners-0.19 filelock-3.12.2 fonttools-4.38.0 gdown-4.7.1 humanize-4.6.0 imageio-2.31.2 imagesize-1.4.1 importlib-metadata-6.7.0 importlib-resources-5.12.0 iso8601-2.1.0 jaraco.classes-3.2.3 jeepney-0.8.0 jmespath-1.0.1 joblib-1.3.2 jupyter-book-0.15.1 jupyter-cache-0.5.0 keyring-24.1.1 keyrings.alt-4.2.0 kiwisolver-1.4.5 latexcodec-2.0.1 linkify-it-py-2.0.2 looseversion-1.3.0 markdown-it-py-2.2.0 matplotlib-3.5.3 mdit-py-plugins-0.3.5 mdurl-0.1.2 more-itertools-9.1.0 msgpack-1.0.5 myst-nb-0.17.2 myst-parser-0.18.1 numpy-1.21.6 osfclient-0.0.5 pandas-1.3.5 patool-1.12 pillow-9.5.0 platformdirs-3.11.0 plotly-5.17.0 pyasn1-0.5.0 pybtex-0.24.0 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.13.3 python-gitlab-3.15.0 pyyaml-6.0.1 repo2data-2.9.1 requests-toolbelt-1.0.0 rsa-4.7.2 s3transfer-0.7.0 scikit-learn-1.0.2 scipy-1.7.3 seaborn-0.12.2 snowballstemmer-2.2.0 soupsieve-2.4.1 sphinx-5.0.2 sphinx-book-theme-1.0.1 sphinx-comments-0.0.3 sphinx-copybutton-0.5.2 sphinx-design-0.3.0 sphinx-external-toc-0.3.1 sphinx-jupyterbook-latex-0.5.2 sphinx-multitoc-numbering-0.1.3 sphinx-thebe-0.2.1 sphinx-togglebutton-0.3.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-bibtex-2.5.0 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 tabulate-0.9.0 tenacity-8.2.3 threadpoolctl-3.1.0 tqdm-4.66.1 typing-extensions-4.7.1 uc-micro-py-1.0.2 wget-3.2 wordcloud-1.9.2 zenodo-get-1.3.4
Removing intermediate container 637021b47b54
 ---> 5e65fcd7d61c
Step 42/51 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> 61422015095b
Step 43/51 : LABEL repo2docker.ref="ba22e6c1da7f861e89d63d8757cbd0225c610fe8"
 ---> Running in 6e4ce428a281
Removing intermediate container 6e4ce428a281
 ---> 9f807b2a0b8e
Step 44/51 : LABEL repo2docker.repo="https://github.com/pbellec/editorial_parcellation"
 ---> Running in 48982bf4ca23
Removing intermediate container 48982bf4ca23
 ---> edb092714eff
Step 45/51 : LABEL repo2docker.version="2021.08.0"
 ---> Running in a26e931391ae
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 ---> 73efed42ab4d
Step 46/51 : USER ${NB_USER}
 ---> Running in 9ade3bbd12b0
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 ---> 31175ede3da3
Step 47/51 : ENV PYTHONUNBUFFERED=1
 ---> Running in 7c2086189681
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 ---> 697e34de7f24
Step 48/51 : COPY /python3-login /usr/local/bin/python3-login
 ---> ed037e9bdb95
Step 49/51 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint
 ---> 9d1edd2d3829
Step 50/51 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]
 ---> Running in c43c4e9925af
Removing intermediate container c43c4e9925af
 ---> 3908b3582dae
Step 51/51 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
 ---> Running in bb0dc0c25a94
Removing intermediate container bb0dc0c25a94
 ---> f723fca00b6c
{"aux": {"ID": "sha256:f723fca00b6c771ff955aa127de764799d39085dfcfe0967bb30aed7f1592dac"}}Successfully built f723fca00b6c
Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-pbellec-2deditorial-5fparcellation-e26e81:ba22e6c1da7f861e89d63d8757cbd0225c610fe8
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Successfully pushed binder-registry.conp.cloud/binder-registry.conp.cloud/binder-pbellec-2deditorial-5fparcellation-e26e81:ba22e6c1da7f861e89d63d8757cbd0225c610fe8Built image, launching...
Launching server...
Server requested
2023-10-22T01:03:50Z [Normal] Successfully assigned binderhub/jupyter-pbellec-2deditorial-5fparcellation-2dh3n9h4q8 to neurolibre-master
2023-10-22T01:04:10Z [Normal] Container image "jupyterhub/k8s-network-tools:1.1.2" already present on machine
2023-10-22T01:04:17Z [Normal] Created container block-cloud-metadata
2023-10-22T01:04:22Z [Normal] Started container block-cloud-metadata
2023-10-22T01:04:23Z [Normal] Pulling image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-pbellec-2deditorial-5fparcellation-e26e81:ba22e6c1da7f861e89d63d8757cbd0225c610fe8"
2023-10-22T01:04:56Z [Normal] Successfully pulled image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-pbellec-2deditorial-5fparcellation-e26e81:ba22e6c1da7f861e89d63d8757cbd0225c610fe8" in 32.075257678s
2023-10-22T01:05:14Z [Normal] Created container notebook
2023-10-22T01:05:17Z [Normal] Started container notebook
Server ready at /jupyter/user/pbellec-editorial_parcellation-h3n9h4q8/
server running at https://test.conp.cloud/jupyter/user/pbellec-editorial_parcellation-h3n9h4q8/

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

Jupyter Book build log

Running Jupyter-Book v0.15.1
Source Folder: /home/jovyan/content
Config Path: /home/jovyan/content/_config.yml
Output Path: /mnt/books/pbellec/github.com/editorial_parcellation/ba22e6c1da7f861e89d63d8757cbd0225c610fe8/_build/html
Running Sphinx v5.0.2
Adding copy buttons to code blocks...
Adding copy buttons to code blocks...
making output directory... done
[etoc] Changing master_doc to 'intro'
locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['html_image'], disable_syntax=[], all_links_external=False, url_schemes=['mailto', 'http', 'https'], ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area')
myst-nb v0.17.2: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='cache', execution_cache_path='/mnt/books/pbellec/github.com/editorial_parcellation/ba22e6c1da7f861e89d63d8757cbd0225c610fe8/_build/.jupyter_cache', execution_excludepatterns=[], execution_timeout=-1, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='show', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False)
Using jupyter-cache at: /mnt/books/pbellec/github.com/editorial_parcellation/ba22e6c1da7f861e89d63d8757cbd0225c610fe8/_build/.jupyter_cache
locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 3 source files that are out of date
updating environment: locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[new config] 3 added, 0 changed, 0 removed
reading sources... [ 33%] conclusion
/home/jovyan/content/conclusion.md: Executing notebook using local CWD [mystnb]
/home/jovyan/content/conclusion.md: Executed notebook in 1.01 seconds [mystnb]
/home/jovyan/content/conclusion.md: Cached executed notebook: ID=1 [mystnb]
reading sources... [ 66%] intro
/home/jovyan/content/intro.md: Using cached notebook: ID=1 [mystnb]
reading sources... [100%] papers
/home/jovyan/content/papers.md: Executing notebook using local CWD [mystnb]
/home/jovyan/content/papers.md: Executed notebook in 12.54 seconds [mystnb]
/home/jovyan/content/papers.md: Cached executed notebook: ID=2 [mystnb]

/home/jovyan/content/papers.md:48: WARNING: skipping unknown output mime type: application/vnd.plotly.v1+json [mystnb.unknown_mime_type]
/home/jovyan/content/papers.md:229: WARNING: skipping unknown output mime type: application/vnd.plotly.v1+json [mystnb.unknown_mime_type]
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [ 33%] conclusion

Extension error (pydata_sphinx_theme):
Handler  for event 'html-page-context' threw an exception (exception: 'dict object' has no attribute 'image_relative')
Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 94, in emit
    results.append(listener.handler(self.app, *args))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/__init__.py", line 241, in update_and_remove_templates
    context[section] = list(filter(_remove_empty_templates, context[section]))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/__init__.py", line 236, in _remove_empty_templates
    rendered = app.builder.templates.render(tname, context)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/jinja2glue.py", line 189, in render
    return self.environment.get_template(template).render(context)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jinja2/environment.py", line 1304, in render
    self.environment.handle_exception()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jinja2/environment.py", line 925, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/theme/pydata_sphinx_theme/components/navbar-logo.html", line 13, in top-level template code
    {% set is_logo = "light" in theme_logo["image_relative"] %}
jinja2.exceptions.UndefinedError: 'dict object' has no attribute 'image_relative'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/sphinx.py", line 171, in build_sphinx
    app.build(force_all, filenames)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/application.py", line 329, in build
    self.builder.build_update()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 290, in build_update
    len(to_build))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 352, in build
    self.write(docnames, list(updated_docnames), method)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 544, in write
    self._write_serial(sorted(docnames))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 554, in _write_serial
    self.write_doc(docname, doctree)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/html/__init__.py", line 649, in write_doc
    self.handle_page(docname, ctx, event_arg=doctree)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/html/__init__.py", line 1052, in handle_page
    templatename, ctx, event_arg)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/application.py", line 458, in emit_firstresult
    allowed_exceptions=allowed_exceptions)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 112, in emit_firstresult
    for result in self.emit(name, *args, allowed_exceptions=allowed_exceptions):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 103, in emit
    (listener.handler, name), exc, modname=modname) from exc
sphinx.errors.ExtensionError: Handler  for event 'html-page-context' threw an exception (exception: 'dict object' has no attribute 'image_relative')

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/bin/jupyter-book", line 8, in 
    sys.exit(main())
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 318, in build
    result, builder, OUTPUT_PATH, build_type, PAGE_NAME, click.echo
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 525, in builder_specific_actions
    raise RuntimeError(_message_box(msg, color="red", doprint=False)) from result
RuntimeError:
===============================================================================

There was an error in building your book. Look above for the cause.

===============================================================================

Jupyter-book exit code: 1
Jupyter-book build failed!

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

[pbellec]

not sure what's going on here. The link to the binderhub server is broken (and duplicated). And the error message seems to come from the pydata_sphinx_theme sphinx theme, and python 3.7. This is different from what I specified in binder/runtime.txt. Not sure what to do.

[agahkarakuzu]

This is due to jupyter book version, there is a known issue with sphinx version it uses. Switching to jupyter-book==0.13.0 should fix it.

[pbellec]

ok great. I've fixed the version of jupyter-book and successfully ran a local build in a fresh venv.

[agahkarakuzu]

@roboneuro build book