Comments (9)
Ok, so it seems a problem with outputs containing an advancement bar from tqdm
. Probably a good idea to ignore that carriage return, or to transform it in a new line maybe? Thanks for tracking this down!
from nbconvert.
Hi @matteobachetti, to be clear, it works with 7.13.1? I don't see anything in the 7.14 release itself that looks relevant.
from nbconvert.
Yep, you can see here that nbconvert fixed to <7.14 (it uses 7.13.1) does not produce the issue. But I'm not sure there are no other dependencies that are influenced by this.
https://github.com/StingraySoftware/stingray/actions/runs/7388419796/job/20099216748
from nbconvert.
@blink1073 is there a way to debug this? If I could access the rst files produced by nbconvert, for example, I could look at exactly what lines are producing the raw directive.
from nbconvert.
Unfortunately not, based on looking at spatialaudio/nbsphinx#620.
What you can do is test the specific commits:
nbconvert: git+https://github.com/jupyter/nbconvert.git@a3a069c9a10bb011911166c0f84b9edb1fef305d
The commits we're interested in are:
15625319f6bd7917df8ec891795411554e0015bd
a3a069c9a10bb011911166c0f84b9edb1fef305d
ece13fd22d96fda9cde06534e265bc5fe3fc4c80
0f17b3069d320565af12a4a12da7d9ce3c18dac4
b1715cdae9b4b51c1797a63a7045660145d36aac
from nbconvert.
We ran into this as well. I can't seem to replicate on my Mac, it only occurs in Linux containers in our CI system. We pin the requirements, so, modulo OS differences, I should have the same packages as the CI system.
Example failing notebook: https://github.com/danking/hail/blob/update-deps/hail/python/hail/docs/tutorials/06-joins.ipynb
Our pinned-requirements: https://github.com/danking/hail/blob/update-deps/hail/python/dev/pinned-requirements.txt
The code we run follows, but I've updated the paths to make sense from the root of the Hail repository. The Makefile in hail/python/hail/docs is here.
set -o pipefail
export SPHINXOPTS='-tgenerate_notebook_outputs'
make -C hail install python/hail/docs/change_log.rst
make -C hail/python/hail/docs BUILDDIR=_build clean html
I ran the code from #620 to generate RST from the ipynb and then copied that RST file into my docs and built the docs (on my Mac, which hasn't failed yet) and it seems to have built fine. The generated RST is here.
I'm a bit at a loss about how to move forward.
The log from a CI build showing the errors
+ set -o pipefail
+ export HAIL_SHORT_VERSION=0.2
+ HAIL_SHORT_VERSION=0.2
+ export SPHINXOPTS=-tgenerate_notebook_outputs
+ SPHINXOPTS=-tgenerate_notebook_outputs
+ python3 -m pip install --no-dependencies /io/wheel/hail-0.2.127-py3-none-any.whl
Processing /io/wheel/hail-0.2.127-py3-none-any.whl
Installing collected packages: hail
Successfully installed hail-0.2.127
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
[notice] A new release of pip is available: 23.3.1 -> 23.3.2
[notice] To update, run: python3 -m pip install --upgrade pip
+ cd /io/hail
+ export HAIL_WEBSITE_DIR=/io/website/website/
+ HAIL_WEBSITE_DIR=/io/website/website/
+ sed -E 's/\(hail\#([0-9]+)\)/(\[#\1](https:\/\/github.com\/hail-is\/hail\/pull\/\1))/g'
+ pandoc -o python/hail/docs/change_log.rst --fail-if-warnings --verbose
[INFO] Not rendering RawInline (Format "html") "<NON_REF>"
+ make -C python/hail/docs BUILDDIR=_build clean html
make: Entering directory '/io/hail/python/hail/docs'
rm -rf _build
python3 -msphinx -T -b html -d _build/doctrees -tgenerate_notebook_outputs -W --keep-going . _build/html
Running Sphinx v6.2.1
[autosummary] generating autosummary for: aggregators.rst, annotation_database_ui.rst, api.rst, batch_api.rst, change_log.rst, cheatsheets.rst, cloud/amazon_web_services.rst, cloud/azure.rst, cloud/databricks.rst, cloud/general_advice.rst, ..., tutorials/03-tables.ipynb, tutorials/04-aggregation.ipynb, tutorials/05-filter-annotate.ipynb, tutorials/06-joins.ipynb, tutorials/07-matrixtable.ipynb, tutorials/08-plotting.ipynb, tutorials/09-ggplot.ipynb, types.rst, utils/index.rst, vds/index.rst
[autosummary] generating autosummary for: /io/hail/python/hail/docs/experimental/hail.experimental.DB.rst, /io/hail/python/hail/docs/functions/hail.expr.builders.CaseBuilder.rst, /io/hail/python/hail/docs/functions/hail.expr.builders.SwitchBuilder.rst, /io/hail/python/hail/docs/genetics/hail.genetics.Call.rst, /io/hail/python/hail/docs/genetics/hail.genetics.Locus.rst, /io/hail/python/hail/docs/genetics/hail.genetics.Pedigree.rst, /io/hail/python/hail/docs/genetics/hail.genetics.ReferenceGenome.rst, /io/hail/python/hail/docs/genetics/hail.genetics.Trio.rst, /io/hail/python/hail/docs/hail.GroupedMatrixTable.rst, /io/hail/python/hail/docs/hail.GroupedTable.rst, ..., /io/hail/python/hail/docs/vds/hail.vds.lgt_to_gt.rst, /io/hail/python/hail/docs/vds/hail.vds.local_to_global.rst, /io/hail/python/hail/docs/vds/hail.vds.merge_reference_blocks.rst, /io/hail/python/hail/docs/vds/hail.vds.read_vds.rst, /io/hail/python/hail/docs/vds/hail.vds.sample_qc.rst, /io/hail/python/hail/docs/vds/hail.vds.split_multi.rst, /io/hail/python/hail/docs/vds/hail.vds.store_ref_block_max_length.rst, /io/hail/python/hail/docs/vds/hail.vds.to_dense_mt.rst, /io/hail/python/hail/docs/vds/hail.vds.to_merged_sparse_mt.rst, /io/hail/python/hail/docs/vds/hail.vds.truncate_reference_blocks.rst
loading intersphinx inventory from https://docs.python.org/3.9/objects.inv...
loading intersphinx inventory from https://spark.apache.org/docs/latest/api/python/objects.inv...
loading intersphinx inventory from https://docs.bokeh.org/en/3.1.0/objects.inv...
loading intersphinx inventory from https://numpy.org/doc/stable/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/scipy-1.9.3/objects.inv...
loading intersphinx inventory from https://pandas.pydata.org/docs/objects.inv...
building [mo]: targets for 0 po files that are out of date
writing output...
building [html]: targets for 290 source files that are out of date
updating environment: [new config] 346 added, 0 changed, 0 removed
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writing additional pages... search done
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build finished with problems, 80 warnings.
make: *** [Makefile:52: html] Error 1
make: Leaving directory '/io/hail/python/hail/docs'
from nbconvert.
Could things like this be an issue? I'd have expected the text to be indented.
from nbconvert.
We had a similar problem come up over at XRTpy on this notebook and this other notebook, neither of which have any raw cells.
The error happened on both ubuntu-latest
and macos-latest
, but I was able to get rid of it by setting nbconvert < 7.14
in HinodeXRT/xrtpy#215.
This was the specific error that started showing up a bunch of times:
/Users/runner/work/xrtpy/xrtpy/docs/notebooks/data_analysis/Deconvolving_XRT_images.ipynb:129: ERROR: Content block expected for the "raw" directive; none found.
Thank you!
from nbconvert.
spatialaudio/nbsphinx#620 (comment) shows how to get the intermediate reST representation.
With an older nbconvert
it looks something like this:
.. raw:: text
0%| | 0/6 [00:00<?, ?it/s]
With a newer nbconvert
, the status line starts with a '\x0d'
character, a.k.a. "carriage return".
This seems to confuse the reST parser, because it messes up the indentation.
When copy-pasting it here, it get's messed up in a similar way (but apparently the actual carriage return character doesn't survive copy-pasting):
.. raw:: text
0%| | 0/6 [00:00<?, ?it/s]
I'm not sure if nbconvert
should remove that character from its output, but if not, I guess this has to be ignored in nbsphinx
.
Note that I have not executed the notebook, I have used the pre-executed Check dead time model in Stingray.ipynb
, which looks like this:
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
" 0%| | 0/6 [00:00<?, ?it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"INFO: Calculating PDS model (update) [stingray.deadtime.model]\n"
]
},
from nbconvert.
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from nbconvert.