remove document not included in any toctree

[RignonNoel]

fix #7

As proposed by @kousu I ran sphinx locally and I checked the warnings about toctree. It gives me all the dead pages and I deleted them.

I did some search for every files, it seems correct and it seems to work well in local.

[kousu]

To measure this, I first estimated the baseline noise level:

p115628@joplin:~/src/intranet.neuro.polymtl.ca$ git checkout master
Switched to branch 'master'
Your branch is up to date with 'origin/master'.

_build1

``` p115628@joplin:~/src/intranet.neuro.polymtl.ca$ make html Running Sphinx v4.2.0 myst v0.18.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=[], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=4, 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mathjax_classes='tex2jax_process|mathjax_process|math|output_area') building [mo]: targets for 0 po files that are out of date building [html]: targets for 113 source files that are out of date updating environment: [new config] 113 added, 0 changed, 0 removed reading sources... [100%] writing-articles /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/neuropoly/gpus.md:1038: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/printer.md:10: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/courses.md:10: WARNING: Disallowed nested header found, converting to rubric [myst.nested_header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/courses.md:14: WARNING: Disallowed nested header found, converting to rubric [myst.nested_header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/courses.md:28: WARNING: Disallowed nested header found, converting to rubric [myst.nested_header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/courses.md:32: WARNING: Disallowed nested header found, converting to rubric [myst.nested_header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/deep-learning/README.md:22: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/deep-learning/tensorflow.md:15: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/deep-learning/tensorflow.md:75: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/deep-learning/tensorflow.md:83: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/deep-learning/tensorflow.md:90: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/image-processing-software/diffusion-simulator.md:17: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/image-processing-software/itk-snap.md:5: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/docker/README.md:20: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/docker/README.md:28: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/docker/README.md:36: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/docker/README.md:42: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/docker/README.md:52: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/docker/README.md:60: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/docker/README.md:78: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/docker/README.md:108: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/docker/README.md:120: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/git-and-github.md:377: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/git-and-github.md:395: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/git-and-github.md:504: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/git-and-github.md:514: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/git-and-github.md:535: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/git-and-github.md:555: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/git-and-github.md:571: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/git-and-github.md:579: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/git-and-github.md:666: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/git-and-github.md:730: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/git-and-github.md:734: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/microsoft-word.md:3: WARNING: Non-consecutive header level increase; H1 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/microsoft-word.md:10: WARNING: Non-consecutive header level increase; H1 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/virtual-machines/vagrant.md:7: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/virtual-machines/vagrant.md:12: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/virtual-machines/virtualbox.md:3: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/virtual-machines/virtualbox.md:13: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/virtual-machines/virtualbox.md:47: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/virtual-machines/virtualbox.md:55: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/misc/virtual-machines/virtualbox.md:105: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/os-guides/macosx.md:97: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/campus-access.md:9: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/campus-access.md:11: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/campus-access.md:15: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/campus-access.md:24: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/campus-access.md:30: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/campus-access.md:34: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/infrastructure.md:3: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/infrastructure.md:8: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/infrastructure.md:16: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] looking for now-outdated files... none found pickling environment... done checking consistency... /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computer-setup.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/dropbox-google-drive.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/learning-and-resources/deep-learning.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/learning-and-resources/histology.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/learning-and-resources/shared-paperpile-folder.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/learning-and-resources/untitled.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/purchasing-hardware-and-lab-supplies.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/rf-lab/3d-printing/octoprint.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/tips-and-tricks/README.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/tips-and-tricks/programming/README.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/tips-and-tricks/programming/c++.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/tips-and-tricks/programming/matlab.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/tips-and-tricks/programming/python.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/tips-and-tricks/programming/unix-shell-bash.md: WARNING: document isn't included in any toctree done preparing documents... done writing output... [100%] writing-articles /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/bibliography/mri.md:33: WARNING: 'myst' reference target not found: /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/duke.md:23: WARNING: 'myst' reference target not found: ../../#ssh-command-line /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/duke.md:39: WARNING: 'myst' reference target not found: ../../#vpn /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:7: WARNING: 'myst' reference target not found: git-annex.branchable.com/ /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:7: WARNING: 'myst' reference target not found: ../../#vpn /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:16: WARNING: 'myst' reference target not found: ./git-annex.md#installation /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:53: WARNING: 'myst' reference target not found: dge.informatique@polymtl.ca /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:81: WARNING: 'myst' reference target not found: ./git-annex.md#global-git-config /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:162: WARNING: 'myst' reference target not found: #Reviewing-Pull-Requests /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:235: WARNING: 'myst' reference target not found: ./git-annex.md#new-repo /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/neuropoly/README.md:28: WARNING: 'myst' reference target not found: ../#poly-grames /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/neuropoly/README.md:255: WARNING: 'myst' reference target not found: [url](https://github.com/neuropoly/intranet.neuro.polymtl.ca/issues/57) /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/neuropoly/cpus.md:7: WARNING: 'myst' reference target not found: ./computing-resources-neuropoly.md#TODO /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/neuropoly/gpus.md:19: WARNING: 'myst' reference target not found: ./#connect /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/contributing.md:10: WARNING: 'myst' reference target not found: #developing /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/git-annex.md:3: WARNING: 'myst' reference target not found: git-annex.branchable.com/ /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/git-annex.md:75: WARNING: 'myst' reference target not found: #hardlinks /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/git-annex.md:121: WARNING: 'myst' reference target not found: ./internal-server.md#new-repository /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/mri-scanning/mni-mcgill-7t-terra.md:15: WARNING: 'myst' reference target not found: ./ /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/mri-scanning/unf-3t-prisma.md:11: WARNING: 'myst' reference target not found: [url](https://unf-montreal.ca/en/documentation/facility/reservation/) /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/mri-scanning/unf-3t-prisma.md:14: WARNING: 'myst' reference target not found: [url](https://github.com/UNFmontreal/bids_configs/blob/master/studies.json) generating indices... genindex done writing additional pages... search done copying images... [100%] .gitbook/assets/phd101212s.gif copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 87 warnings. The HTML pages are in _build/html. p115628@joplin:~/src/intranet.neuro.polymtl.ca$ mv _build/ _build1 ```

_build2

``` p115628@joplin:~/src/intranet.neuro.polymtl.ca$ make html Running Sphinx v4.2.0 myst v0.18.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=[], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=4, 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') building [mo]: targets for 0 po files that are out of date building [html]: targets for 113 source files that are out of date updating environment: [new config] 113 added, 0 changed, 0 removed reading sources... [100%] writing-articles /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/neuropoly/gpus.md:1038: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/printer.md:10: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/courses.md:10: WARNING: Disallowed nested header found, converting to rubric [myst.nested_header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/courses.md:14: WARNING: Disallowed nested header found, converting to rubric [myst.nested_header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/courses.md:28: WARNING: Disallowed nested header found, converting to rubric [myst.nested_header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/courses.md:32: WARNING: Disallowed nested header found, converting to rubric [myst.nested_header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/deep-learning/README.md:22: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/deep-learning/tensorflow.md:15: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/deep-learning/tensorflow.md:75: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/deep-learning/tensorflow.md:83: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/deep-learning/tensorflow.md:90: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/image-processing-software/diffusion-simulator.md:17: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/image-processing-software/itk-snap.md:5: WARNING: Non-consecutive header level increase; 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H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/campus-access.md:9: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/campus-access.md:11: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/campus-access.md:15: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/campus-access.md:24: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/campus-access.md:30: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/campus-access.md:34: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/infrastructure.md:3: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/infrastructure.md:8: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/infrastructure.md:16: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] looking for now-outdated files... none found pickling environment... done checking consistency... /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computer-setup.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/dropbox-google-drive.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/learning-and-resources/deep-learning.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/learning-and-resources/histology.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/learning-and-resources/shared-paperpile-folder.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/learning-and-resources/untitled.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/purchasing-hardware-and-lab-supplies.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/rf-lab/3d-printing/octoprint.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/tips-and-tricks/README.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/tips-and-tricks/programming/README.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/tips-and-tricks/programming/c++.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/tips-and-tricks/programming/matlab.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/tips-and-tricks/programming/python.md: WARNING: document isn't included in any toctree /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/tips-and-tricks/programming/unix-shell-bash.md: WARNING: document isn't included in any toctree done preparing documents... done writing output... [100%] writing-articles /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/bibliography/mri.md:33: WARNING: 'myst' reference target not found: /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/duke.md:23: WARNING: 'myst' reference target not found: ../../#ssh-command-line /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/duke.md:39: WARNING: 'myst' reference target not found: ../../#vpn /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:7: WARNING: 'myst' reference target not found: git-annex.branchable.com/ /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:7: WARNING: 'myst' reference target not found: ../../#vpn /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:16: WARNING: 'myst' reference target not found: ./git-annex.md#installation /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:53: WARNING: 'myst' reference target not found: dge.informatique@polymtl.ca /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:81: WARNING: 'myst' reference target not found: ./git-annex.md#global-git-config /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:162: WARNING: 'myst' reference target not found: #Reviewing-Pull-Requests /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:235: WARNING: 'myst' reference target not found: ./git-annex.md#new-repo /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/neuropoly/README.md:28: WARNING: 'myst' reference target not found: ../#poly-grames /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/neuropoly/README.md:255: WARNING: 'myst' reference target not found: [url](https://github.com/neuropoly/intranet.neuro.polymtl.ca/issues/57) /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/neuropoly/cpus.md:7: WARNING: 'myst' reference target not found: ./computing-resources-neuropoly.md#TODO /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/neuropoly/gpus.md:19: WARNING: 'myst' reference target not found: ./#connect /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/contributing.md:10: WARNING: 'myst' reference target not found: #developing /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/git-annex.md:3: WARNING: 'myst' reference target not found: git-annex.branchable.com/ /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/git-annex.md:75: WARNING: 'myst' reference target not found: #hardlinks /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/git-annex.md:121: WARNING: 'myst' reference target not found: ./internal-server.md#new-repository /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/mri-scanning/mni-mcgill-7t-terra.md:15: WARNING: 'myst' reference target not found: ./ /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/mri-scanning/unf-3t-prisma.md:11: WARNING: 'myst' reference target not found: [url](https://unf-montreal.ca/en/documentation/facility/reservation/) /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/mri-scanning/unf-3t-prisma.md:14: WARNING: 'myst' reference target not found: [url](https://github.com/UNFmontreal/bids_configs/blob/master/studies.json) generating indices... genindex done writing additional pages... search done copying images... [100%] .gitbook/assets/phd101212s.gif copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 87 warnings. The HTML pages are in _build/html. p115628@joplin:~/src/intranet.neuro.polymtl.ca$ mv _build _build2

diff

```diff p115628@joplin:~/src/intranet.neuro.polymtl.ca$ diff -ru _build1/ _build2/ Binary files _build1/doctrees/environment.pickle and _build2/doctrees/environment.pickle differ Only in _build2/html: _build1 diff -ru _build1/html/computer-setup.html _build2/html/computer-setup.html --- _build1/html/computer-setup.html 2022-07-20 21:30:27.836199683 -0400 +++ _build2/html/computer-setup.html 2022-07-20 21:30:56.423764730 -0400 @@ -1016,8 +1016,8 @@

Shell Profile #

You can edit your shell profile (usually called .bash_profile, but some newer versions of Mac use .zsh_profile ) to create custom commands and make the colours in your terminal look nice.

- - + + .bash_profile

To edit, navigate to $HOME/.bash_profile

# Nice .bash_profile
@@ -1076,8 +1076,8 @@
 

- - + + .zsh_profile

To edit, navigate to $HOME/.zsh_profile

# COLOR
diff -ru _build1/html/computing-resources/data/duke.html _build2/html/computing-resources/data/duke.html
--- _build1/html/computing-resources/data/duke.html 2022-07-20 21:30:28.560188668 -0400
+++ _build2/html/computing-resources/data/duke.html 2022-07-20 21:30:57.159753533 -0400
@@ -990,8 +990,8 @@
 
Mount with GUI#
 
When working on campus or over the VPN, you can connect your computer to duke:
 

-
-
+
+
 macOS

 

 
Open Finder
@@ -999,8 +999,8 @@
 
afp://duke.neuro.polymtl.ca/
 
 
-
-
+
+
 Linux

 

 
Open File Browser
@@ -1008,8 +1008,8 @@
 
smb://duke.neuro.polymtl.ca/
 
 
-
-
+
+
 Windows 10

 

 
Open Windows explorer
@@ -1035,8 +1035,8 @@
 
Mount with Terminal#
 
You can also connect your computer from the CLI, or with a script, which might be more efficient in the long run:
 

-
-
+
+
 Mac OSX

 
Create folder for the mount point on a location (your home directory) where you have read and write access:
 
mkdir <FOLDER_NAME> # (e.g. <FOLDER_NAME>=sct_testing)
@@ -1047,8 +1047,8 @@
 
 
 
-
-
+
+
 Linux

 
To mount:
 
sudo mount -t cifs //duke.neuro.polymtl.ca/<FOLDER_NAME> /mnt/duke/<FOLDER_NAME> -o username=<GRAMES_USERNAME>,noexec
diff -ru _build1/html/computing-resources/neuropoly/gpus.html _build2/html/computing-resources/neuropoly/gpus.html
--- _build1/html/computing-resources/neuropoly/gpus.html    2022-07-20 21:30:29.316177166 -0400
+++ _build2/html/computing-resources/neuropoly/gpus.html    2022-07-20 21:30:57.919741969 -0400
@@ -2154,15 +2154,15 @@
 
SSH tunnelling#
 
If you want to run a Jupyter notebook from a remote server, or monitor a model training using tensorboard, you will need to do an SSH tunnelling to be able to pass the display from the remote cluster to your local station.
 

-
-
+
+
 Secure pipes

 
Install secure pipes and configure it as follows:
 with port_rosenber as the “Port” of the screen session and port_local is a random number (see screenshot below):
 

 
-
-
+
+
 Terminal

 
ssh -N -f -L localhost:8080:localhost:PORTNUMBER username@CLUSTER.neuro.polymtl.ca
 
diff -ru _build1/html/computing-resources/neuropoly/index.html _build2/html/computing-resources/neuropoly/index.html
--- _build1/html/computing-resources/neuropoly/index.html   2022-07-20 21:30:28.980182278 -0400
+++ _build2/html/computing-resources/neuropoly/index.html   2022-07-20 21:30:57.583747081 -0400
@@ -1311,8 +1311,8 @@
 
Home folder#
 
Every GRAMES account has a school-wide personal home folder. It is backed-up nightly.
 

-
-
+
+
 macOS

 

 
Open Finder
@@ -1355,8 +1355,8 @@
 
You can change your password at Gestion des Codes. Also, you can double-check you have VPN access by looking for VPN_* = Actif here.
 
The VPN is a Cisco AnyConnect server. For Linux and macOS you can reach it by first installing a VPN client such as openconnect (recommended) or Cisco AnyConnect Secure Mobility Client (if openconnect is not available for your OS/distro):
 

-
-
+
+
 MacOS

 
brew install openconnect
 
@@ -1384,8 +1384,8 @@
 
 
 
-
-
+
+
 Linux

 
apt install openconnect
 
@@ -1407,8 +1407,8 @@
 

- - + + Windows

Please follow the official steps from PolyMTL (French or English.

In case the above links ever break, the steps are:

@@ -1489,15 +1489,15 @@

The best way to do this is sshfs, which makes them appear as if they were a drive on your computer:

Install sshfs, if not yet installed:

- - + + Linux

sudo apt install -y sshfs
 

- - + + mac

brew install --cask osxfuse
 brew install sshfs
@@ -1532,8 +1532,8 @@
 

 
VNC (graphical interface)#
 

-
-
+
+
 macOS

 

 
Open Finder
@@ -1542,8 +1542,8 @@
 
You can use your local/network account information or the shared account credentials
 
 
-
-
+
+
 PC/Linux

 

 
Establish a VNC connection using vinaigre.
diff -ru _build1/html/computing-resources/neuropoly/README.html _build2/html/computing-resources/neuropoly/README.html
--- _build1/html/computing-resources/neuropoly/README.html  2022-07-20 21:30:28.980182278 -0400
+++ _build2/html/computing-resources/neuropoly/README.html  2022-07-20 21:30:57.583747081 -0400
@@ -1311,8 +1311,8 @@
 
Home folder#
 
Every GRAMES account has a school-wide personal home folder. It is backed-up nightly.
 

-
-
+
+
 macOS

 

 
Open Finder
@@ -1355,8 +1355,8 @@
 
You can change your password at Gestion des Codes. Also, you can double-check you have VPN access by looking for VPN_* = Actif here.
 
The VPN is a Cisco AnyConnect server. For Linux and macOS you can reach it by first installing a VPN client such as openconnect (recommended) or Cisco AnyConnect Secure Mobility Client (if openconnect is not available for your OS/distro):
 

-
-
+
+
 MacOS

 
brew install openconnect
 
@@ -1384,8 +1384,8 @@
 

- - + + Linux

apt install openconnect
 

@@ -1407,8 +1407,8 @@

- - + + Windows

Please follow the official steps from PolyMTL (French or English.

In case the above links ever break, the steps are:

@@ -1489,15 +1489,15 @@

The best way to do this is sshfs, which makes them appear as if they were a drive on your computer:

Install sshfs, if not yet installed:

- - + + Linux

sudo apt install -y sshfs
 

- - + + mac

brew install --cask osxfuse
 brew install sshfs
@@ -1532,8 +1532,8 @@
 

 
VNC (graphical interface)#
 

-
-
+
+
 macOS

 

 
Open Finder
@@ -1542,8 +1542,8 @@
 
You can use your local/network account information or the shared account credentials
 
 
-
-
+
+
 PC/Linux

 

 
Establish a VNC connection using vinaigre.
diff -ru _build1/html/courses.html _build2/html/courses.html
--- _build1/html/courses.html   2022-07-20 21:30:29.960167368 -0400
+++ _build2/html/courses.html   2022-07-20 21:30:58.563732171 -0400
@@ -1182,8 +1182,8 @@
 

 
Requirements for Polytechnique#
 

-
-
+
+
 MSc

 

 
Details of the program on the Polymtl website.
@@ -1195,8 +1195,8 @@
 
Jury
 
Please refer to the Règlements généraux des études supérieures  (53.4 COMPOSITION ET NOMINATION DU JURY).
 
-
-
+
+
 PhD

 

 
Details of the program on the Polymtl website.
diff -ru _build1/html/geek-tips/bash-shell/index.html _build2/html/geek-tips/bash-shell/index.html
--- _build1/html/geek-tips/bash-shell/index.html    2022-07-20 21:30:30.400160674 -0400
+++ _build2/html/geek-tips/bash-shell/index.html    2022-07-20 21:30:58.987725720 -0400
@@ -1667,15 +1667,15 @@
 
Checksum #
 
This procedure creates a unique signature for your files and folders. It enables to check for integrity when you share data.
 

-
-
+
+
 Linux

 
find FOLDER -type f -exec md5sum {} \; | md5sum
 
 
 
-
-
+
+
 Mac

 
find -s FOLDER -type f -exec shasum {} \; | shasum
 find -s FOLDER -type f -exec md5 {} \; | md5
diff -ru _build1/html/geek-tips/bash-shell/README.html _build2/html/geek-tips/bash-shell/README.html
--- _build1/html/geek-tips/bash-shell/README.html   2022-07-20 21:30:30.400160674 -0400
+++ _build2/html/geek-tips/bash-shell/README.html   2022-07-20 21:30:58.987725720 -0400
@@ -1667,15 +1667,15 @@
 
Checksum #
 
This procedure creates a unique signature for your files and folders. It enables to check for integrity when you share data.
 

-
-
+
+
 Linux

 
find FOLDER -type f -exec md5sum {} \; | md5sum
 
 
 
-
-
+
+
 Mac

 
find -s FOLDER -type f -exec shasum {} \; | shasum
 find -s FOLDER -type f -exec md5 {} \; | md5
diff -ru _build1/html/geek-tips/git-annex.html _build2/html/geek-tips/git-annex.html
--- _build1/html/geek-tips/git-annex.html   2022-07-20 21:30:31.768139860 -0400
+++ _build2/html/geek-tips/git-annex.html   2022-07-20 21:31:00.363704784 -0400
@@ -1093,8 +1093,8 @@
 
Installation#
 
You must have a unix OS. git-annex is simply not compatible with anything else.
 

-
-
+
+
 Linux

 

 
Arch: pacman -Sy git-annex
@@ -1104,15 +1104,15 @@
 
if on an older system and can’t upgrade, you can try installing conda (or miniforge and then using conda install -f conda-forge git-annex.
 
 
-
-
+
+
 macOS

 
brew install git-annex
 
 
 
-
-
+
+
 Windows 10 (via WSL)

 
Install WSL, pick a distro, and then run one of:
 

@@ -1121,8 +1121,8 @@
 
The other distros are supported.
 
 
-
-
+
+
 Windows 10 (via VirtualBox)

 
Install VirtualBox, install a Linux distro inside of it, and then follow the Linux instructions.
 
diff -ru _build1/html/geek-tips/misc/git-and-github.html _build2/html/geek-tips/misc/git-and-github.html
--- _build1/html/geek-tips/misc/git-and-github.html 2022-07-20 21:30:33.952106632 -0400
+++ _build2/html/geek-tips/misc/git-and-github.html 2022-07-20 21:31:02.543671617 -0400
@@ -1696,24 +1696,24 @@
 
Installation#
 
Full instructions to install git here. We have a quick-start below:
 

-
-
+
+
 Linux

 
sudo apt-get update
 apt-get install git-all
 
 
 
-
-
+
+
 MacOSX

 
Probably the easiest way to install on MacOSX is to install via XCode Command Line Tools. To check if git is installed:
 
git --version
 
 
 
-
-
+
+
 Windows

 
Recommended install: Go to https://git-scm.com/download/win and the download will start automatically.
 
diff -ru _build1/html/geek-tips/misc/openneuro.html _build2/html/geek-tips/misc/openneuro.html
--- _build1/html/geek-tips/misc/openneuro.html  2022-07-20 21:30:34.264101885 -0400
+++ _build2/html/geek-tips/misc/openneuro.html  2022-07-20 21:31:02.859666809 -0400
@@ -1014,8 +1014,8 @@
 

 
Installation#
 

-
-
+
+
 Debian/Ubuntu

 
Install datalad using conda :
 
source miniconda3/etc/profile.d/conda.sh
@@ -1035,8 +1035,8 @@
 
 
 
-
-
+
+
 MacOS

 
Install datalad using conda :
 
source miniconda3/etc/profile.d/conda.sh
@@ -1083,18 +1083,18 @@
 

 
Installation#
 

-
-
+
+
 Linux

 
Follow the AWS Installation Instructions for Linux.
 
-
-
+
+
 MacOS

 
Follow the AWS Installation Instructions for MacOS.
 
-
-
+
+
 Windows

 
Follow the AWS Installation Instructions for Windows.
 
diff -ru _build1/html/geek-tips/os-guides/linux.html _build2/html/geek-tips/os-guides/linux.html
--- _build1/html/geek-tips/os-guides/linux.html 2022-07-20 21:30:35.180087948 -0400
+++ _build2/html/geek-tips/os-guides/linux.html 2022-07-20 21:31:03.779652812 -0400
@@ -1004,8 +1004,8 @@
 
2. Edit mount table, type : sudo nano /etc/fstab
 
3. For the following operating systems:
 

-
-
+
+
 Ubuntu 14.04 LTS

 
Add the following lines at the bottom of the file:
 
#data_processing @SERVER
@@ -1016,8 +1016,8 @@
 
 
 
-
-
+
+
 Debian Wheezy 8

 
Add the following lines at the bottom of the file:
 
#data_processing @SERVER
diff -ru _build1/html/onboarding/computer-setup.html _build2/html/onboarding/computer-setup.html
--- _build1/html/onboarding/computer-setup.html 2022-07-20 21:30:37.672050034 -0400
+++ _build2/html/onboarding/computer-setup.html 2022-07-20 21:31:06.319614166 -0400
@@ -1018,8 +1018,8 @@
 
Shell Profile #
 
You can edit your shell profile (usually called .bash_profile, but some newer versions of Mac use .zsh_profile ) to create custom commands and make the colours in your terminal look nice.
 

-
-
+
+
 .bash_profile

 
To edit, navigate to $HOME/.bash_profile
 
# Nice .bash_profile
@@ -1078,8 +1078,8 @@
 
 
 
-
-
+
+
 .zsh_profile

 
To edit, navigate to $HOME/.zsh_profile
 
# COLOR
```

There's a bit of noise that looks like it's due to the tabs plugin -- it generates UUIDs for each tab, so those are necessarily non-deterministic. I think I can deal with eye-balling those issues.

[kousu]

Next I did the build on this branch:

_build-cleaner

``` p115628@joplin:~/src/intranet.neuro.polymtl.ca$ git checkout nr/clean-up-warnings Switched to branch 'nr/clean-up-warnings' Your branch and 'origin/nr/clean-up-warnings' have diverged, and have 18 and 1 different commits each, respectively. (use "git pull" to merge the remote branch into yours) p115628@joplin:~/src/intranet.neuro.polymtl.ca$ git rebase master Current branch nr/clean-up-warnings is up to date. p115628@joplin:~/src/intranet.neuro.polymtl.ca$ make html Running Sphinx v4.2.0 myst v0.18.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=[], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=4, 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') building [mo]: targets for 0 po files that are out of date building [html]: targets for 99 source files that are out of date updating environment: [new config] 99 added, 0 changed, 0 removed reading sources... [100%] writing-articles /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/neuropoly/gpus.md:1038: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/printer.md:10: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/courses.md:10: WARNING: Disallowed nested header found, converting to rubric [myst.nested_header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/courses.md:14: WARNING: Disallowed nested header found, converting to rubric [myst.nested_header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/courses.md:28: WARNING: Disallowed nested header found, converting to rubric [myst.nested_header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/courses.md:32: WARNING: Disallowed nested header found, converting to rubric [myst.nested_header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/deep-learning/README.md:22: WARNING: Non-consecutive header level increase; 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H2 to H4 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/campus-access.md:9: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/campus-access.md:11: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/campus-access.md:15: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/campus-access.md:24: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/campus-access.md:30: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/campus-access.md:34: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/infrastructure.md:3: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/infrastructure.md:8: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/onboarding/infrastructure.md:16: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header] looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [100%] writing-articles /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/bibliography/mri.md:33: WARNING: 'myst' reference target not found: /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/duke.md:23: WARNING: 'myst' reference target not found: ../../#ssh-command-line /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/duke.md:39: WARNING: 'myst' reference target not found: ../../#vpn /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:7: WARNING: 'myst' reference target not found: git-annex.branchable.com/ /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:7: WARNING: 'myst' reference target not found: ../../#vpn /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:16: WARNING: 'myst' reference target not found: ./git-annex.md#installation /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:53: WARNING: 'myst' reference target not found: dge.informatique@polymtl.ca /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:81: WARNING: 'myst' reference target not found: ./git-annex.md#global-git-config /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:162: WARNING: 'myst' reference target not found: #Reviewing-Pull-Requests /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.md:235: WARNING: 'myst' reference target not found: ./git-annex.md#new-repo /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/neuropoly/README.md:28: WARNING: 'myst' reference target not found: ../#poly-grames /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/neuropoly/README.md:255: WARNING: 'myst' reference target not found: [url](https://github.com/neuropoly/intranet.neuro.polymtl.ca/issues/57) /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/neuropoly/cpus.md:7: WARNING: 'myst' reference target not found: ./computing-resources-neuropoly.md#TODO /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/computing-resources/neuropoly/gpus.md:19: WARNING: 'myst' reference target not found: ./#connect /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/contributing.md:10: WARNING: 'myst' reference target not found: #developing /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/git-annex.md:3: WARNING: 'myst' reference target not found: git-annex.branchable.com/ /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/git-annex.md:75: WARNING: 'myst' reference target not found: #hardlinks /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/geek-tips/git-annex.md:121: WARNING: 'myst' reference target not found: ./internal-server.md#new-repository /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/mri-scanning/mni-mcgill-7t-terra.md:15: WARNING: 'myst' reference target not found: ./ /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/mri-scanning/unf-3t-prisma.md:11: WARNING: 'myst' reference target not found: [url](https://unf-montreal.ca/en/documentation/facility/reservation/) /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/mri-scanning/unf-3t-prisma.md:14: WARNING: 'myst' reference target not found: [url](https://github.com/UNFmontreal/bids_configs/blob/master/studies.json) /home/GRAMES.POLYMTL.CA/p115628/src/intranet.neuro.polymtl.ca/rf-lab/3d-printing/README.md:32: WARNING: unknown document: octoprint generating indices... genindex done writing additional pages... search done copying images... [100%] .gitbook/assets/phd101212s.gif copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 74 warnings. The HTML pages are in _build/html. p115628@joplin:~/src/intranet.neuro.polymtl.ca$ mv _build _build-cleaner ```

[kousu]

And diff'd again:

```diff p115628@joplin:~/src/intranet.neuro.polymtl.ca$ diff -ru _build1 _build-cleaner/ Only in _build1/doctrees: computer-setup.doctree Only in _build1/doctrees: dropbox-google-drive.doctree Binary files _build1/doctrees/environment.pickle and _build-cleaner/doctrees/environment.pickle differ Only in _build1/doctrees: learning-and-resources Only in _build1/doctrees: purchasing-hardware-and-lab-supplies.doctree Only in _build1/doctrees/rf-lab/3d-printing: octoprint.doctree Only in _build1/doctrees: tips-and-tricks Only in _build-cleaner/html: _build1 Only in _build-cleaner/html: _build2 Only in _build1/html: computer-setup.html diff -ru _build1/html/computing-resources/data/duke.html _build-cleaner/html/computing-resources/data/duke.html --- _build1/html/computing-resources/data/duke.html 2022-07-20 21:30:28.560188668 -0400 +++ _build-cleaner/html/computing-resources/data/duke.html 2022-07-20 23:41:45.476556841 -0400 @@ -990,8 +990,8 @@

Mount with GUI#

When working on campus or over the VPN, you can connect your computer to duke:

- - + + macOS

1. Open Finder

@@ -999,8 +999,8 @@

2. afp://duke.neuro.polymtl.ca/

- - + + Linux

1. Open File Browser

@@ -1008,8 +1008,8 @@

2. smb://duke.neuro.polymtl.ca/

- - + + Windows 10

1. Open Windows explorer

@@ -1035,8 +1035,8 @@

Mount with Terminal#

You can also connect your computer from the CLI, or with a script, which might be more efficient in the long run:

- - + + Mac OSX
Create folder for the mount point on a location (your home directory) where you have read and write access:
mkdir <FOLDER_NAME> # (e.g. <FOLDER_NAME>=sct_testing)
@@ -1047,8 +1047,8 @@
 
- - + + Linux
To mount:
sudo mount -t cifs //duke.neuro.polymtl.ca/<FOLDER_NAME> /mnt/duke/<FOLDER_NAME> -o username=<GRAMES_USERNAME>,noexec
diff -ru _build1/html/computing-resources/neuropoly/gpus.html _build-cleaner/html/computing-resources/neuropoly/gpus.html
--- _build1/html/computing-resources/neuropoly/gpus.html    2022-07-20 21:30:29.316177166 -0400
+++ _build-cleaner/html/computing-resources/neuropoly/gpus.html 2022-07-20 23:41:46.196545888 -0400
@@ -2154,15 +2154,15 @@
 
SSH tunnelling#
 
If you want to run a Jupyter notebook from a remote server, or monitor a model training using tensorboard, you will need to do an SSH tunnelling to be able to pass the display from the remote cluster to your local station.
 

-
-
+
+
 Secure pipes

 
Install secure pipes and configure it as follows:
 with port_rosenber as the “Port” of the screen session and port_local is a random number (see screenshot below):
 

 
-
-
+
+
 Terminal

 
ssh -N -f -L localhost:8080:localhost:PORTNUMBER username@CLUSTER.neuro.polymtl.ca
 
diff -ru _build1/html/computing-resources/neuropoly/index.html _build-cleaner/html/computing-resources/neuropoly/index.html
--- _build1/html/computing-resources/neuropoly/index.html   2022-07-20 21:30:28.980182278 -0400
+++ _build-cleaner/html/computing-resources/neuropoly/index.html    2022-07-20 23:41:45.876550756 -0400
@@ -1311,8 +1311,8 @@
 
Home folder#
 
Every GRAMES account has a school-wide personal home folder. It is backed-up nightly.
 

-
-
+
+
 macOS

 

 
Open Finder
@@ -1355,8 +1355,8 @@
 
You can change your password at Gestion des Codes. Also, you can double-check you have VPN access by looking for VPN_* = Actif here.
 
The VPN is a Cisco AnyConnect server. For Linux and macOS you can reach it by first installing a VPN client such as openconnect (recommended) or Cisco AnyConnect Secure Mobility Client (if openconnect is not available for your OS/distro):
 

-
-
+
+
 MacOS

 
brew install openconnect
 
@@ -1384,8 +1384,8 @@
 
- - + + Linux
apt install openconnect
 
@@ -1407,8 +1407,8 @@
- - + + Windows

Please follow the official steps from PolyMTL (French or English.

In case the above links ever break, the steps are:

@@ -1489,15 +1489,15 @@

The best way to do this is sshfs, which makes them appear as if they were a drive on your computer:

Install sshfs, if not yet installed:

- - + + Linux

sudo apt install -y sshfs
 

- - + + mac

brew install --cask osxfuse
 brew install sshfs
@@ -1532,8 +1532,8 @@
 

 
VNC (graphical interface)#
 

-
-
+
+
 macOS

 

 
Open Finder
@@ -1542,8 +1542,8 @@
 
You can use your local/network account information or the shared account credentials
 
 
-
-
+
+
 PC/Linux

 

 
Establish a VNC connection using vinaigre.
diff -ru _build1/html/computing-resources/neuropoly/README.html _build-cleaner/html/computing-resources/neuropoly/README.html
--- _build1/html/computing-resources/neuropoly/README.html  2022-07-20 21:30:28.980182278 -0400
+++ _build-cleaner/html/computing-resources/neuropoly/README.html   2022-07-20 23:41:45.876550756 -0400
@@ -1311,8 +1311,8 @@
 
Home folder#
 
Every GRAMES account has a school-wide personal home folder. It is backed-up nightly.
 

-
-
+
+
 macOS

 

 
Open Finder
@@ -1355,8 +1355,8 @@
 
You can change your password at Gestion des Codes. Also, you can double-check you have VPN access by looking for VPN_* = Actif here.
 
The VPN is a Cisco AnyConnect server. For Linux and macOS you can reach it by first installing a VPN client such as openconnect (recommended) or Cisco AnyConnect Secure Mobility Client (if openconnect is not available for your OS/distro):
 

-
-
+
+
 MacOS

 
brew install openconnect
 
@@ -1384,8 +1384,8 @@
 

- - + + Linux

apt install openconnect
 

@@ -1407,8 +1407,8 @@

- - + + Windows

Please follow the official steps from PolyMTL (French or English.

In case the above links ever break, the steps are:

@@ -1489,15 +1489,15 @@

The best way to do this is sshfs, which makes them appear as if they were a drive on your computer:

Install sshfs, if not yet installed:

- - + + Linux

sudo apt install -y sshfs
 

- - + + mac

brew install --cask osxfuse
 brew install sshfs
@@ -1532,8 +1532,8 @@
 

 
VNC (graphical interface)#
 

-
-
+
+
 macOS

 

 
Open Finder
@@ -1542,8 +1542,8 @@
 
You can use your local/network account information or the shared account credentials
 
 
-
-
+
+
 PC/Linux

 

 
Establish a VNC connection using vinaigre.
diff -ru _build1/html/courses.html _build-cleaner/html/courses.html
--- _build1/html/courses.html   2022-07-20 21:30:29.960167368 -0400
+++ _build-cleaner/html/courses.html    2022-07-20 23:41:46.816536456 -0400
@@ -1182,8 +1182,8 @@
 

 
Requirements for Polytechnique#
 

-
-
+
+
 MSc

 

 
Details of the program on the Polymtl website.
@@ -1195,8 +1195,8 @@
 
Jury
 
Please refer to the Règlements généraux des études supérieures  (53.4 COMPOSITION ET NOMINATION DU JURY).
 
-
-
+
+
 PhD

 

 
Details of the program on the Polymtl website.
Only in _build1/html: dropbox-google-drive.html
diff -ru _build1/html/geek-tips/bash-shell/index.html _build-cleaner/html/geek-tips/bash-shell/index.html
--- _build1/html/geek-tips/bash-shell/index.html    2022-07-20 21:30:30.400160674 -0400
+++ _build-cleaner/html/geek-tips/bash-shell/index.html 2022-07-20 23:41:47.140531527 -0400
@@ -1667,15 +1667,15 @@
 
Checksum #
 
This procedure creates a unique signature for your files and folders. It enables to check for integrity when you share data.
 

-
-
+
+
 Linux

 
find FOLDER -type f -exec md5sum {} \; | md5sum
 
 
 
-
-
+
+
 Mac

 
find -s FOLDER -type f -exec shasum {} \; | shasum
 find -s FOLDER -type f -exec md5 {} \; | md5
diff -ru _build1/html/geek-tips/bash-shell/README.html _build-cleaner/html/geek-tips/bash-shell/README.html
--- _build1/html/geek-tips/bash-shell/README.html   2022-07-20 21:30:30.400160674 -0400
+++ _build-cleaner/html/geek-tips/bash-shell/README.html    2022-07-20 23:41:47.140531527 -0400
@@ -1667,15 +1667,15 @@
 
Checksum #
 
This procedure creates a unique signature for your files and folders. It enables to check for integrity when you share data.
 

-
-
+
+
 Linux

 
find FOLDER -type f -exec md5sum {} \; | md5sum
 
 
 
-
-
+
+
 Mac

 
find -s FOLDER -type f -exec shasum {} \; | shasum
 find -s FOLDER -type f -exec md5 {} \; | md5
diff -ru _build1/html/geek-tips/git-annex.html _build-cleaner/html/geek-tips/git-annex.html
--- _build1/html/geek-tips/git-annex.html   2022-07-20 21:30:31.768139860 -0400
+++ _build-cleaner/html/geek-tips/git-annex.html    2022-07-20 23:41:48.476511203 -0400
@@ -1093,8 +1093,8 @@
 
Installation#
 
You must have a unix OS. git-annex is simply not compatible with anything else.
 

-
-
+
+
 Linux

 

 
Arch: pacman -Sy git-annex
@@ -1104,15 +1104,15 @@
 
if on an older system and can’t upgrade, you can try installing conda (or miniforge and then using conda install -f conda-forge git-annex.
 
 
-
-
+
+
 macOS

 
brew install git-annex
 
 
 
-
-
+
+
 Windows 10 (via WSL)

 
Install WSL, pick a distro, and then run one of:
 

@@ -1121,8 +1121,8 @@
 
The other distros are supported.
 
 
-
-
+
+
 Windows 10 (via VirtualBox)

 
Install VirtualBox, install a Linux distro inside of it, and then follow the Linux instructions.
 
diff -ru _build1/html/geek-tips/misc/git-and-github.html _build-cleaner/html/geek-tips/misc/git-and-github.html
--- _build1/html/geek-tips/misc/git-and-github.html 2022-07-20 21:30:33.952106632 -0400
+++ _build-cleaner/html/geek-tips/misc/git-and-github.html  2022-07-20 23:41:50.516480169 -0400
@@ -1696,24 +1696,24 @@
 
Installation#
 
Full instructions to install git here. We have a quick-start below:
 

-
-
+
+
 Linux

 
sudo apt-get update
 apt-get install git-all
 
 
 
-
-
+
+
 MacOSX

 
Probably the easiest way to install on MacOSX is to install via XCode Command Line Tools. To check if git is installed:
 
git --version
 
 
 
-
-
+
+
 Windows

 
Recommended install: Go to https://git-scm.com/download/win and the download will start automatically.
 
diff -ru _build1/html/geek-tips/misc/openneuro.html _build-cleaner/html/geek-tips/misc/openneuro.html
--- _build1/html/geek-tips/misc/openneuro.html  2022-07-20 21:30:34.264101885 -0400
+++ _build-cleaner/html/geek-tips/misc/openneuro.html   2022-07-20 23:41:50.888474509 -0400
@@ -1014,8 +1014,8 @@
 

 
Installation#
 

-
-
+
+
 Debian/Ubuntu

 
Install datalad using conda :
 
source miniconda3/etc/profile.d/conda.sh
@@ -1035,8 +1035,8 @@
 
 
 
-
-
+
+
 MacOS

 
Install datalad using conda :
 
source miniconda3/etc/profile.d/conda.sh
@@ -1083,18 +1083,18 @@
 

 
Installation#
 

-
-
+
+
 Linux

 
Follow the AWS Installation Instructions for Linux.
 
-
-
+
+
 MacOS

 
Follow the AWS Installation Instructions for MacOS.
 
-
-
+
+
 Windows

 
Follow the AWS Installation Instructions for Windows.
 
diff -ru _build1/html/geek-tips/os-guides/linux.html _build-cleaner/html/geek-tips/os-guides/linux.html
--- _build1/html/geek-tips/os-guides/linux.html 2022-07-20 21:30:35.180087948 -0400
+++ _build-cleaner/html/geek-tips/os-guides/linux.html  2022-07-20 23:41:51.696462218 -0400
@@ -1004,8 +1004,8 @@
 
2. Edit mount table, type : sudo nano /etc/fstab
 
3. For the following operating systems:
 

-
-
+
+
 Ubuntu 14.04 LTS

 
Add the following lines at the bottom of the file:
 
#data_processing @SERVER
@@ -1016,8 +1016,8 @@
 
 
 
-
-
+
+
 Debian Wheezy 8

 
Add the following lines at the bottom of the file:
 
#data_processing @SERVER
Only in _build1/html: learning-and-resources
Binary files _build1/html/objects.inv and _build-cleaner/html/objects.inv differ
diff -ru _build1/html/onboarding/computer-setup.html _build-cleaner/html/onboarding/computer-setup.html
--- _build1/html/onboarding/computer-setup.html 2022-07-20 21:30:37.672050034 -0400
+++ _build-cleaner/html/onboarding/computer-setup.html  2022-07-20 23:41:53.728431306 -0400
@@ -1018,8 +1018,8 @@
 
Shell Profile #
 
You can edit your shell profile (usually called .bash_profile, but some newer versions of Mac use .zsh_profile ) to create custom commands and make the colours in your terminal look nice.
 

-
-
+
+
 .bash_profile

 
To edit, navigate to $HOME/.bash_profile
 
# Nice .bash_profile
@@ -1078,8 +1078,8 @@
 
 
 
-
-
+
+
 .zsh_profile

 
To edit, navigate to $HOME/.zsh_profile
 
# COLOR
Only in _build1/html: purchasing-hardware-and-lab-supplies.html
diff -ru _build1/html/rf-lab/3d-printing/index.html _build-cleaner/html/rf-lab/3d-printing/index.html
--- _build1/html/rf-lab/3d-printing/index.html  2022-07-20 21:30:39.268025751 -0400
+++ _build-cleaner/html/rf-lab/3d-printing/index.html   2022-07-20 23:41:55.180409217 -0400
@@ -1014,7 +1014,7 @@
 
The Modix 3D printer is remotely controlled using OctoPrint. To access the control interface go to the hostname and use the credentials provided above.
 

 
SOP Modix
-
OctoPrint configuration
+
octoprint configuration
 
Modix adjustments
 
 
Only in _build1/html/rf-lab/3d-printing: octoprint.html
diff -ru _build1/html/rf-lab/3d-printing/README.html _build-cleaner/html/rf-lab/3d-printing/README.html
--- _build1/html/rf-lab/3d-printing/README.html 2022-07-20 21:30:39.268025751 -0400
+++ _build-cleaner/html/rf-lab/3d-printing/README.html  2022-07-20 23:41:55.180409217 -0400
@@ -1014,7 +1014,7 @@
 
The Modix 3D printer is remotely controlled using OctoPrint. To access the control interface go to the hostname and use the credentials provided above.
 

 
SOP Modix
-
OctoPrint configuration
+
octoprint configuration
 
Modix adjustments
 
 
```

(continued:)

[kousu]

```diff diff -ru _build1/html/searchindex.js _build-cleaner/html/searchindex.js --- _build1/html/searchindex.js 2022-07-20 21:30:41.239995749 -0400 +++ _build-cleaner/html/searchindex.js 2022-07-20 23:41:56.304392118 -0400 @@ -1 +1 @@ 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\ No newline at end of file Only in _build1/html/_sources: computer-setup.md Only in _build1/html/_sources: dropbox-google-drive.md Only in _build1/html/_sources: learning-and-resources Only in _build1/html/_sources: purchasing-hardware-and-lab-supplies.md Only in _build1/html/_sources/rf-lab/3d-printing: octoprint.md Only in _build1/html/_sources: tips-and-tricks Only in _build1/html: tips-and-tricks ```

[RignonNoel]

Good catch @kousu ! Fixed and added to rf-lab toctree just after the already existing README from the same folder.

[kousu]

Okay I've rebuilt the docs a couple times and diff'd them again. This looks for now. I'm merging.