Revamp the software section #19
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@@ -4,3 +4,5 @@ _build/ | |
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| .DS_Store | ||
| Thumbs.db | ||
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| gallery.txt | ||
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@@ -34,6 +34,7 @@ | |
| extensions = [ | ||
| 'myst_parser', # there's also myst_nb, which supports embedding Jupyter notebooks, but is heavier. | ||
| 'sphinx_panels', | ||
| 'sphinx_design', | ||
| ] | ||
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| myst_heading_anchors = 4 # enable #section links: https://myst-parser.readthedocs.io/en/latest/syntax/optional.html#syntax-header-anchors | ||
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@@ -103,3 +104,94 @@ | |
| "README.html")): # don't create dangling symlinks; | ||
| # it annoyes Github Pages. | ||
| os.symlink("README.html", z) | ||
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| # -- Custom scripts ---------------------------------------------------------- | ||
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| import os | ||
| from pathlib import Path | ||
| import random | ||
| import requests | ||
| from subprocess import run | ||
| from textwrap import dedent | ||
| from urllib.parse import urlparse | ||
| from ghapi.all import GhApi | ||
| import pandas as pd | ||
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| import yaml | ||
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| from sphinx.application import Sphinx | ||
| from sphinx.util import logging | ||
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| LOGGER = logging.getLogger("conf") | ||
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| def build_gallery(app: Sphinx): | ||
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There was a problem hiding this comment. It's inelegant to do all this in the conf.py file, running it on every parse like this. It would be significantly cleaner to package this script as a custom directive, stick it up on pypi, and then instead of do There was a problem hiding this comment. and those images should be inlined There was a problem hiding this comment. agreed-- but i don't have the time to do it, so #47 |
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| # Build the gallery file | ||
| LOGGER.info("building gallery...") | ||
| grid_items = [] | ||
| projects = yaml.safe_load((Path(app.srcdir) / "gallery_software.yml").read_text()) | ||
| for item in projects: | ||
| if not item.get("image"): | ||
| item["image"] = "https://jupyterbook.org/_images/logo-square.svg" | ||
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| repo_text = "" | ||
| star_text = "" | ||
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| if item["repository"]: | ||
| repo_text = f'{{bdg-link-secondary}}`repo <{item["repository"]}>`' | ||
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| try: | ||
| url = urlparse(item["repository"]) | ||
| if url.netloc == "github.com": | ||
| _, org, repo = url.path.rstrip("/").split("/") | ||
| star_text = f"[]({item['repository']})" | ||
| except Exception as error: | ||
| pass | ||
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| grid_items.append( | ||
| f"""\ | ||
| `````{{grid-item-card}} | ||
| :text-align: center | ||
| <img src="{item["image"]}" alt="logo" loading="lazy" style="max-width: 100%; max-height: 100px; margin: auto" /> | ||
| +++ | ||
| {" ".join(item["name"].split())} | ||
| ````{{grid}} 2 2 2 2 | ||
| :margin: 0 0 0 0 | ||
| :padding: 0 0 0 0 | ||
| :gutter: 1 | ||
| ```{{grid-item}} | ||
| :child-direction: row | ||
| :child-align: start | ||
| :class: sd-fs-5 | ||
| {{bdg-link-secondary}}`website <{item["website"]}>` | ||
| {repo_text} | ||
| ``` | ||
| ```{{grid-item}} | ||
| :child-direction: row | ||
| :child-align: end | ||
| {star_text} | ||
| ``` | ||
| ```` | ||
| ````` | ||
| """ | ||
| ) | ||
| grid_items = "\n".join(grid_items) | ||
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| # :column: text-center col-6 col-lg-4 | ||
| # :card: +my-2 | ||
| # :img-top-cls: w-75 m-auto p-2 | ||
| # :body: d-none | ||
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| panels = f""" | ||
| ``````{{grid}} 1 2 3 3 | ||
| :gutter: 1 1 2 2 | ||
| :class-container: full-width | ||
| {dedent(grid_items)} | ||
| `````` | ||
| """ | ||
| (Path(app.srcdir) / "gallery_software.txt").write_text(panels) | ||
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| def setup(app: Sphinx): | ||
| app.add_css_file("_static/theme.css") | ||
| app.connect("builder-inited", build_gallery) | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
| - name: Comprehensive library of analysis tools for multi-parametric MRI of the spinal cord | ||
| website: https://spinalcordtoolbox.com/ | ||
| repository: https://github.com/spinalcordtoolbox/spinalcordtoolbox | ||
| image: https://raw.githubusercontent.com/spinalcordtoolbox/spinalcordtoolbox/master/documentation/source/_static/img/logo_sct.png | ||
| - name: Integrated framework for medical image analysis with deep learning | ||
| website: https://ivadomed.org | ||
| repository: https://github.com/ivadomed/ivadomed | ||
| image: https://raw.githubusercontent.com/ivadomed/ivadomed/master/images/ivadomed_logo.png | ||
| - name: Simulation, analysis, and visualization of qMRI data (Magnetization Transfer, Diffusion, etc.) | ||
| website: https://qmrlab.readthedocs.io | ||
| repository: https://github.com/qMRLab/qMRLab | ||
| image: https://raw.githubusercontent.com/qMRLab/documentation/master/logo/qMR_logo_orig.png | ||
| - name: Software tools to perform advanced static and real-time shimming experiments with MRI. | ||
| website: https://shimming-toolbox.org | ||
| repository: https://github.com/shimming-toolbox/shimming-toolbox | ||
| image: https://raw.githubusercontent.com/shimming-toolbox/shimming-toolbox/master/docs/source/_static/img/shimming_toolbox_logo.png | ||
| - name: Segmentation of axon and myelin on microscopy data. | ||
| website: https://axondeepseg.readthedocs.io/ | ||
| repository: https://github.com/neuropoly/axondeepseg | ||
| image: https://raw.githubusercontent.com/neuropoly/axondeepseg/master/docs/source/_static/logo_ads-alpha.png |
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,31 +1,37 @@ | ||
| # `🖥` Software | ||
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| Below is a list of software projects created at **NeuroPoly** or at collaborative institutions. These projects are open source and freely available. | ||
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| ## Image analysis | ||
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| ```{include} gallery_software.txt | ||
| ``` | ||
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| <!-- ## Pipeline and template | ||
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| TODO: Add this section | ||
| This section contains projects --> | ||
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| <!-- Deprecated software: | ||
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| | | Multiclass Segmentation | Code related to the NIH marmoset longitudinal segmentation project | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/multiclass-segmentation) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/multiclass-segmentation/blob/master/README.md) | | ||
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| | | AxonSeg | Automatic segmentation of axon and myelin from microscopy data | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axonseg) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/axonseg/blob/master/README.md) | | ||
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| | | AxonPacking | Simulation software for arrangements of axons in white matter | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/axonpacking) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/axonpacking/blob/master/README.md) | | ||
| --> | ||
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| <!-- Data / Atlas to add in another section | ||
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| | | Template | A framework for creating unbiased MRI templates of the spinal cord | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/template) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/template/blob/master/README.md) | | ||
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| | | Atlas Rat | Scripts to generate a microstructure atlas of the rat spinal cord | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/atlas-rat) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/atlas-rat/blob/master/README.md) | | ||
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| | | Tract Clustering | Data-driven approach for tracts in rat histology | [<i class="fab fa-github" title="Source" aria-hidden="true"></i><span>Source</span>](https://github.com/neuropoly/tract-clustering) | [<i class="fa fa-book" title="Documentation" aria-hidden="true"></i><span>Documentation</span>](https://github.com/neuropoly/tract-clustering/blob/master/README.md) | | ||
| --> | ||
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| ## Contributing | ||
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| **NeuroPoly** welcomes and appreciates contributions. To get started, please check out [**NeuroPoly**'s contributing guidelines](https://intranet.neuro.polymtl.ca/geek-tips/contributing). |
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This is a strange dependency. It pulls in bootstrap? But bootstrap has already been deprecated for several years by the existence of https://developer.mozilla.org/en-US/docs/Learn/CSS/CSS_layout/Grids. If I look at the web debugger in https://sphinx-design.readthedocs.io/en/sbt-theme/grids.html#grid-options I see they're not using that at all though:
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this is needed, otherwise on compilation i get: