IPyPublish and Pandoc-Filters

[boisgera]

make in notebooks generates:

Exception occurred:
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/ipypublish/filters_pandoc/prepare_cites.py", line 62, in process_citations
    for subel in initial_content:
TypeError: 'Caption' object is not iterable

Full traceback:

# Sphinx version: 3.5.4
# Python version: 3.9.5 (CPython)
# Docutils version: 0.16 release
# Jinja2 version: 2.11.0
# Last messages:
#   ipypublish: converting /home/boisgera/tmp/python-numerique/notebooks/0-98-checklist.md
#   ipypublish: successful conversion
#   reading sources... [ 13%] 0-99-consignes-rendus
#   ipypublish: converting /home/boisgera/tmp/python-numerique/notebooks/0-99-consignes-rendus.md
#   ipypublish: successful conversion
#   reading sources... [ 16%] 1-01-environnement
#   ipypublish: converting /home/boisgera/tmp/python-numerique/notebooks/1-01-environnement.md
#   ipypublish: successful conversion
#   reading sources... [ 18%] 1-02-rudiments
#   ipypublish: converting /home/boisgera/tmp/python-numerique/notebooks/1-02-rudiments.md
# Loaded extensions:
#   sphinx.ext.mathjax (3.5.4) from /home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/sphinx/ext/mathjax.py
#   sphinxcontrib.applehelp (1.0.2) from /home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/sphinxcontrib/applehelp/__init__.py
#   sphinxcontrib.devhelp (1.0.2) from /home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/sphinxcontrib/devhelp/__init__.py
#   sphinxcontrib.htmlhelp (2.0.0) from /home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/sphinxcontrib/htmlhelp/__init__.py
#   sphinxcontrib.serializinghtml (1.1.5) from /home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/sphinxcontrib/serializinghtml/__init__.py
#   sphinxcontrib.qthelp (1.0.3) from /home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/sphinxcontrib/qthelp/__init__.py
#   alabaster (0.7.12) from /home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/alabaster/__init__.py
#   ipypublish.sphinx.notebook (0.10.12) from /home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/ipypublish/sphinx/notebook/__init__.py
#   ipypublish.sphinx.gls (0.10.12) from /home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/ipypublish/sphinx/gls/__init__.py
#   sphinxcontrib.bibtex (unknown version) from /home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/sphinxcontrib/bibtex/__init__.py
#   sphinx.ext.todo (3.5.4) from /home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/sphinx/ext/todo.py
Traceback (most recent call last):
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/sphinx/cmd/build.py", line 280, in build_main
    app.build(args.force_all, filenames)
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/sphinx/application.py", line 352, in build
    self.builder.build_update()
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 296, in build_update
    self.build(to_build,
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 310, in build
    updated_docnames = set(self.read())
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 417, in read
    self._read_serial(docnames)
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 438, in _read_serial
    self.read_doc(docname)
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 478, in read_doc
    doctree = read_doc(self.app, self.env, self.env.doc2path(docname))
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/sphinx/io.py", line 221, in read_doc
    pub.publish()
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/docutils/core.py", line 217, in publish
    self.document = self.reader.read(self.source, self.parser,
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/sphinx/io.py", line 126, in read
    self.parse()
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/docutils/readers/__init__.py", line 77, in parse
    self.parser.parse(self.input, document)
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/ipypublish/sphinx/notebook/parser.py", line 90, in parse
    outdata = publish(filepath)
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/ipypublish/convert/main.py", line 354, in __call__
    return self.publish(ipynb_path, nb_node)
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/ipypublish/convert/main.py", line 486, in publish
    exporter, stream, resources = self.export_notebook(
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/ipypublish/convert/main.py", line 615, in export_notebook
    body, resources = exporter.from_notebook_node(final_nb)
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/nbconvert/exporters/templateexporter.py", line 384, in from_notebook_node
    output = self.template.render(nb=nb_copy, resources=resources)
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/jinja2/environment.py", line 1090, in render
    self.environment.handle_exception()
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/jinja2/environment.py", line 832, in handle_exception
    reraise(*rewrite_traceback_stack(source=source))
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/jinja2/_compat.py", line 28, in reraise
    raise value.with_traceback(tb)
  File "<template>", line 474, in top-level template code
  File "/home/boisgera/miniconda3/envs/UE12/share/jupyter/nbconvert/templates/compatibility/display_priority.tpl", line 1, in top-level template code
    {{ resources.deprecated("This template is deprecated, please use base/display_priority.j2") }}
  File "/home/boisgera/miniconda3/envs/UE12/share/jupyter/nbconvert/templates/base/display_priority.j2", line 1, in top-level template code
    {%- extends 'base/null.j2' -%}
  File "/home/boisgera/miniconda3/envs/UE12/share/jupyter/nbconvert/templates/base/null.j2", line 25, in top-level template code
    {%- endblock header -%}
  File "/home/boisgera/miniconda3/envs/UE12/share/jupyter/nbconvert/templates/base/null.j2", line 28, in block "body"
    {%- endblock body_header -%}
  File "/home/boisgera/miniconda3/envs/UE12/share/jupyter/nbconvert/templates/base/null.j2", line 30, in block "body_loop"
    {%- for cell in nb.cells -%}
  File "<template>", line 92, in block "any_cell"
  File "/home/boisgera/miniconda3/envs/UE12/share/jupyter/nbconvert/templates/base/null.j2", line 83, in block "any_cell"
    {%- if resources.global_content_filter.include_markdown and not cell.get("transient",{}).get("remove_source", false) -%}
  File "<template>", line 139, in block "markdowncell"
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/ipypublish/filters_pandoc/main.py", line 209, in jinja_filter
    out_str = apply_filter(
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/ipypublish/filters_pandoc/utils.py", line 114, in apply_filter
    out_doc = func(out_doc, **kwargs)  # type: Doc
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/ipypublish/filters_pandoc/prepare_cites.py", line 131, in main
    return pf.run_filter(process_citations, prepare, finalize, doc=doc)
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/panflute/io.py", line 224, in run_filter
    return run_filters([action], *args, **kwargs)
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/panflute/io.py", line 205, in run_filters
    doc = doc.walk(action, doc)
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/panflute/base.py", line 264, in walk
    ans = list(chain.from_iterable(ans))
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/panflute/base.py", line 262, in <genexpr>
    ans = ((item,) if type(item) != list else item for item in ans)
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/panflute/base.py", line 259, in <genexpr>
    ans = (item.walk(action, doc) for item in obj)
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/panflute/base.py", line 275, in walk
    altered = action(self, doc)
  File "/home/boisgera/miniconda3/envs/UE12/lib/python3.9/site-packages/ipypublish/filters_pandoc/prepare_cites.py", line 62, in process_citations
    for subel in initial_content:
TypeError: 'Caption' object is not iterable

[boisgera]

Found chrisjsewell/ipypublish#147.

Tried with panflute 1.12 and pandoc 2.9 (see supported pandoc versions for panflute here.

Now, it seems to work. Pin down these versions (see also: #5).

[parmentelat]

closing as a leftover of the migration to jupyter-book
see also #3 for more details