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BUG: Fix bug with rst_prolog/rst_epilog in NB #1204

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BUG: Fix bug with rst_prolog/rst_epilog in NB #1204

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20 changes: 17 additions & 3 deletions sphinx_gallery/gen_rst.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1125,6 +1125,7 @@ def generate_file_rst(fname, target_dir, src_dir, gallery_conf, seen_backrefs=No
src_file = os.path.normpath(os.path.join(src_dir, fname))
target_file = os.path.join(target_dir, fname)
_replace_md5(src_file, target_file, "copy", mode="t")
fname_nice = os.path.relpath(src_file, gallery_conf["src_dir"])

file_conf, script_blocks, node = split_code_and_text_blocks(
src_file, return_node=True
Expand All @@ -1134,14 +1135,18 @@ def generate_file_rst(fname, target_dir, src_dir, gallery_conf, seen_backrefs=No

executable = executable_script(src_file, gallery_conf)

reason = "md5sum not current"
if md5sum_is_current(target_file, mode="t"):
do_return = True
if executable:
if gallery_conf["run_stale_examples"]:
do_return = False
do_return, reason = False, "run_stale_examples=True"
else:
gallery_conf["stale_examples"].append(target_file)
do_return, reason = True, "stale"
else:
do_return, reason = True, "not executable"
if do_return:
logger.debug("%s: not running, %s", fname_nice, reason)
return intro, title, (0, 0)

image_dir = os.path.join(target_dir, "images")
Expand All @@ -1160,12 +1165,14 @@ def generate_file_rst(fname, target_dir, src_dir, gallery_conf, seen_backrefs=No
}

if executable and gallery_conf["reset_modules_order"] in ["before", "both"]:
logger.debug("%s: clean modules before", fname_nice)
clean_modules(gallery_conf, fname, "before")
logger.debug("%s: running, %s", fname_nice, reason)
output_blocks, time_elapsed = execute_script(
script_blocks, script_vars, gallery_conf, file_conf
)

logger.debug("%s ran in : %.2g seconds\n", src_file, time_elapsed)
logger.debug("%s ran in : %.2g seconds", fname_nice, time_elapsed)

# Create dummy images
if not executable:
Expand Down Expand Up @@ -1202,20 +1209,24 @@ def generate_file_rst(fname, target_dir, src_dir, gallery_conf, seen_backrefs=No
script_blocks = script_blocks[:-1]
output_blocks = output_blocks[:-1]

logger.debug("%s: create rst blocks", fname_nice)
example_rst = rst_blocks(script_blocks, output_blocks, file_conf, gallery_conf)
memory_used = gallery_conf["memory_base"] + script_vars["memory_delta"]
if not executable:
time_elapsed = memory_used = 0.0 # don't let the output change
logger.debug("%s: saving rst", fname_nice)
save_rst_example(example_rst, target_file, time_elapsed, memory_used, gallery_conf)

save_thumbnail(image_path_template, src_file, script_vars, file_conf, gallery_conf)

logger.debug("%s: writing notebook", fname_nice)
example_nb = jupyter_notebook(script_blocks, gallery_conf, target_dir)
ipy_fname = replace_py_ipynb(target_file) + ".new"
save_notebook(example_nb, ipy_fname)
_replace_md5(ipy_fname, mode="t")

# Write names
logger.debug("%s: resolve backrefs", fname_nice)
if gallery_conf["inspect_global_variables"]:
global_variables = script_vars["example_globals"]
else:
Expand All @@ -1241,6 +1252,7 @@ def generate_file_rst(fname, target_dir, src_dir, gallery_conf, seen_backrefs=No
}

# Write backreferences
logger.debug("%s: write backrefs", fname_nice)
_write_backreferences(
backrefs, seen_backrefs, gallery_conf, target_dir, fname, intro, title
)
Expand All @@ -1250,8 +1262,10 @@ def generate_file_rst(fname, target_dir, src_dir, gallery_conf, seen_backrefs=No
del global_variables["___"]
del script_vars, global_variables # don't keep these during reset
if executable and gallery_conf["reset_modules_order"] in ["after", "both"]:
logger.debug("%s: clean modules after", fname_nice)
clean_modules(gallery_conf, fname, "after")

logger.debug("%s: done", fname_nice)
return intro, title, (time_elapsed, memory_used)


Expand Down
4 changes: 4 additions & 0 deletions sphinx_gallery/tests/tinybuild/doc/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -101,6 +101,10 @@ def notebook_modification_function(notebook_content, notebook_filename):
notebook_content["cells"] = [markdown_cell] + notebook_content["cells"]


rst_prolog = """
.. _mylink: https://example.com
"""

sphinx_gallery_conf = {
"doc_module": ("sphinx_gallery",),
"reference_url": {
Expand Down
2 changes: 1 addition & 1 deletion sphinx_gallery/tests/tinybuild/examples/plot_animation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
Animation support
=================

Show an animation, which should end up nicely embedded below.
Show an animation, which should end up nicely embedded below. See `mylink`_.
"""

import numpy as np
Expand Down
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