From 3a7cd6948a99aef2361015ead861bb21051d57bb Mon Sep 17 00:00:00 2001 From: Josh Siegle Date: Sun, 2 Jul 2023 13:01:22 -0700 Subject: [PATCH 1/5] Standardize documentation sites --- LICENSE | 427 +++++++++++++++++++ Pipfile | 4 +- Pipfile.lock | 383 +++++++++++------ README.rst | 111 ++--- source/_static/images/oe_logo_name.png | Bin 6568 -> 0 bytes source/_static/images/oe_logo_name.svg | 216 +--------- source/_static/images/oe_logo_name_light.png | Bin 12128 -> 0 bytes source/_static/images/oe_logo_template.svg | 60 --- source/_static/theme_overrides.css | 121 ++++-- source/conf.py | 31 +- source/index.rst | 86 +--- 11 files changed, 825 insertions(+), 614 deletions(-) create mode 100644 LICENSE delete mode 100644 source/_static/images/oe_logo_name.png delete mode 100644 source/_static/images/oe_logo_name_light.png delete mode 100644 source/_static/images/oe_logo_template.svg diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..e04b480 --- /dev/null +++ b/LICENSE @@ -0,0 +1,427 @@ +Attribution-ShareAlike 4.0 International + +======================================================================= + +Creative Commons Corporation ("Creative Commons") is not a law firm and +does not provide legal services or legal advice. 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Except for the limited purpose of indicating that +material is shared under a Creative Commons public license or as +otherwise permitted by the Creative Commons policies published at +creativecommons.org/policies, Creative Commons does not authorize the +use of the trademark "Creative Commons" or any other trademark or logo +of Creative Commons without its prior written consent including, +without limitation, in connection with any unauthorized modifications +to any of its public licenses or any other arrangements, +understandings, or agreements concerning use of licensed material. For +the avoidance of doubt, this paragraph does not form part of the +public licenses. + +Creative Commons may be contacted at creativecommons.org. diff --git a/Pipfile b/Pipfile index af72b98..0c92cb5 100644 --- a/Pipfile +++ b/Pipfile @@ -5,4 +5,6 @@ verify_ssl = true [packages] sphinx = "*" -pydata-sphinx-theme = "0.3.1" +pydata-sphinx-theme = "0.13.3" +sphinx-tabs = "*" +make = "*" \ No newline at end of file diff --git a/Pipfile.lock b/Pipfile.lock index b4dda5f..3d2ae6d 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "0aa2888709cd8cb4742790f09b8ea9b06b53b4c78697429df10546cda32dbe77" + "sha256": "17dd2856de93f29781feadfdf8df0119417ea5c39ffe32c829b3ba590ce845a5" }, "pipfile-spec": 6, "requires": {}, @@ -14,184 +14,291 @@ ] }, "default": { + "accessible-pygments": { + "hashes": [ + "sha256:416c6d8c1ea1c5ad8701903a20fcedf953c6e720d64f33dc47bfb2d3f2fa4e8d", + "sha256:e7b57a9b15958e9601c7e9eb07a440c813283545a20973f2574a5f453d0e953e" + ], 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Documentation -************************************************* -This template is for building documentation of Open Ephys devices or software. +========= +Documentation for the Open Ephys Commutators +========= -What is this template -#################################### -The documentation files are written in reStructuredText and saved in the 'source' folder. Sphinx is a documentation generator that converts these .rst files to HTML, so that browsers can display them. This sphinx 'build' can be performed locally so that you can preview pages in a browser, or it can be done by github remotely (see below for build instructions). - -Sphinx is a Python project, and each sphinx site relies on a specific list of python packages. These are listed in the Pipfile so that local or remote builds know which packages to install. This project uses pipenv, allowing the user to create a virtual environment in which the correct version of all required packages is installed (see 'local build'). - -How to use this template -#################################### - -- Click the green 'use this template' button to make a new repo. Keep in mind Github pages can only be built from public repos. - -- You probably want to clone this new repository to your local computer. - -- Make the changes described below under 'What to customize' and commit these changes to GitHub. - -- This will trigger the remote build, and the generation of the branch 'gh-pages'. - -- Once the 'gh-pages' branch exists, on the Github repo, navigate to Settings/ Pages. Select Source: Deploy from a branch and select the branch gh=pages / root. Save! - -- Your page should start building; once it's done check it looks as expected. - -What to customize -#################################### -Each documentation page is saved as an individual .rst file in the 'source' folder. Docs are written primarily in reStructuredText, and HTML can be used within the .rst file. Images are saved under _static. Assuming you are making a new Open Ephys Doc site, besides obviously customizing the content of the pages, you will need to make sure to update: - -* source/index.rst - * Change License text at the end as appropriate -* conf.py: - * project = "OE docs" # change to your project name - * "github_user": "open-ephys", # change to the GitHub username from which the page will be deployed - * "github_repo": "doc-template", # change to new repo - * html_logo = "_static/images/oe_logo_template.svg" # change to svg with your logo - - Change the device name on the logo "oe_logo_name.svg" - Miso, Bold, 36 pt, Kerning: Optical - Be sure to expand text before saving as .svg as Miso will not load as font. -* source_static/theme_overrides.css - * Change overhead navigation bar colour (.navbar { background: yourfavecolour }) -* .github/workflows/sphinx-build.yml - * git clone https://github.com/open-ephys/doc-template.git # change to your repo +This documentation's source template was taken from the `Spinal HDL `_ project. -If you are using this template for your own device outside of Open Ephys you will need to edit more of the conf.py file. +The theme is based on the `PyData Sphinx Theme `_ -Building remotely -************************************************* -Pushing to the main branch of the repo triggers GitHub Actions. Gh-actions will generate a virtual environment, build the HTML pages, and then commit and push these to the 'gh-pages' branch, by following the instructions under .github/workflows/sphinx-build. Finally, if under repo settings gh pages is enabled and is set to be deployed from the 'gh-pages' branch, the docs site will be generated at https://username.github.io/reponame. To activate gh pages, go to your repo settings, Pages menu, and under "Build and Deployment", choose gh-pages in the dropdown menu. It should say "Your GitHub Pages sites is currently being built from the gh-pages branch". +For more detailed usage instructions, see the `Open Ephys Doc Template `_ -Building locally -************************************************* -Building HTML files locally allows you to preview changes before updating the live site. We recommend working with 'virtual environments' in which you can install the (versions of the) python packages that the site needs, without messing up your own installs. Here's how: +How to build this documentation +=============================== With pipenv (recommended) -------------------------------------------------- - -Requirements (system) - -* make +----------- Requirements (Python 3): @@ -71,7 +24,14 @@ Create a virtual environment with pipenv (will use the Pipfile for installing th pipenv install -You can then spawn a subshell with +then you can build the documentation + +.. code:: shell + + pipenv run make html + +if you want run ``make`` multiple times, prepend ``pipenv run`` on each command can be annoying, +you can spawn a subshell with .. code:: shell @@ -88,34 +48,23 @@ and then you can use ``make`` the usual way all the outputs will be in docs folder (for html: docs/html) -Exit the virtualenv with - -.. code:: exit +without pipenv/virtualenv +------------------------- +Requirements (system): - exit - - -Troubleshooting -###################################### - -No gh-pages branch? -If the gh-pages branch is not automatically made, the build will fail and complain that there is no such branch. In that case, make an empty branch as follows: +* make -.. code:: empty +Requirements (Python 3): - git checkout --orphan gh-pages - git reset --hard - git commit --allow-empty -m "Initialising gh-pages branch" - git push origin gh-pages - git checkout main - -Error while building? -By default github pages `will use Jekyll `_ to generate a static site. To override this, check that there is a .nojekyll file in the gh-pages branch (just an empty file called '.nojekyll'). +* sphinx +* pydata-sphinx-theme=="0.13.3" +After installing the requirements you can run -Acknowledgements -#################################### +.. code:: shell -This documentation's source template was taken from the `Spinal HDL `_ project. + make html # for html + make latex # for latex + make latexpdf # for latex (will require latexpdf installed) + make # list all the available output format -The theme is based on the `PyData Sphinx Theme `_ diff --git a/source/_static/images/oe_logo_name.png b/source/_static/images/oe_logo_name.png deleted file mode 100644 index 6a4373da404bc921296c6760ab7b62f4cf5554a1..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6568 zcmV;Z8CT|sP)pF8FWQhbW?9;ba!ELWdL_~cP?peYja~^aAhuUa%Y?FJQ@H188t~n zK~#90?VWd+TvhqUKX=;pmTXBjyXn1=1_}vMLT@U9QbeW614Kcpiik>4kO(S26dNF# 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navigation bar*/ .navbar { background: #723D46 !important; - font-size: 1rem; + font-size: 1em; } /* navigation bar: text*/ @@ -48,6 +48,12 @@ margin-right: 10px; } +.search-button { + color: white !important; + margin-right: 30px; +} + + /* navigation bar: text color of page titles when hovered*/ .navbar a:hover { color: #2f401f !important; @@ -62,7 +68,7 @@ transition-duration: 0.4s; /* how quickly to change*/ } -/* left side links */ +/* left side links .bd-links > .active a { color: #3c81be !important; transition-duration: 0.4s; @@ -72,15 +78,15 @@ color: #5fb5dc !important; transition-duration: 0.4s; transform: translate(2px, 0px); -} +} */ -/* right side links */ +/* right side links .toc-entry > .nav-link.active { font-weight: 600; color: #344b39; background-color: transparent; border-left: 2px solid #da714a; -} +} */ /* body text*/ a { @@ -92,23 +98,6 @@ a:hover { text-decoration: none; } -/* body links (external, add link icon) */ -a.reference.external:after { - font-family: 'Font Awesome 5 Free'; - font-weight: 900; - content: ' \f35d'; - font-size: 0.5rem; - vertical-align: super; -} - -a.external-link:after { - font-family: 'Font Awesome 5 Free'; - font-weight: 900; - content: ' \f35d'; - font-size: 0.5rem; - vertical-align: super; -} - p.card-reference { margin: 0 0 0rem; font-family: "Bitter", sans-serif; @@ -141,7 +130,6 @@ body { background-color: white; margin-bottom: 1.15rem; font-size: 1rem; - padding-top: 100px; color: #242c16; font-family: "Source Sans", sans-serif; } @@ -151,7 +139,6 @@ h1 { font-family: "Bitter", sans-serif; font-weight: 400; line-height: 1.15; - text-align: center; margin-top: 0; color: #242c16; font-size: 2.2em; @@ -271,18 +258,11 @@ p { margin: 0.3rem 0; } -/* change color of Twitter logo */ -i.fa-twitter-square:before { - color: #333; -} - - - /* logo */ .navbar-brand { position: relative; - height: 60px; + height: 70px; width: auto; } @@ -291,20 +271,6 @@ i.fa-twitter-square:before { display: none } -/* Make top level nav bar links a bit bigger */ -.navbar { - font-size: 1.1em; -} - - - - - - - - - - /* Bonsai workflows & copy button */ .download-copy-img @@ -452,3 +418,66 @@ i.fa-twitter-square:before { img { max-width: 100%; } + + +/* Landing page cards */ +.card-columns { + column-count: 4 !important; +} + +.card-title { + margin: 1rem; +} + +.intro-card .card-text { + margin:20px 0px; + color: var(--onix-txt-color) !important; +} + +.card-img-top { + margin-top: 2em; +} + +.card { + border: 0; +} + +.intro-card { + transition: transform 0.2s ease; + border: 0; +} + +.intro-card:hover { + transform: scale(1.05); +} + +.col-lg-6 { + margin-top: 2em; +} + +/* Gallery cards */ + +.gallery-card .card-header { + height: 100%; + margin-top: 0rem; + align-items: center; + justify-content: center; + text-align: center; +} /* example of the default height for title */ + +.bd-content { + flex-grow: 1; + max-width: 100%; +} + +.bd-page-width { + max-width: 100rem; +} + +.bd-sidebar-primary { + width: 20%; +} + +strong { + font-weight: bold; +} diff --git a/source/conf.py b/source/conf.py index 8248d19..5463a23 100644 --- a/source/conf.py +++ b/source/conf.py @@ -21,7 +21,7 @@ # -- Project information ----------------------------------------------------- -project = "Open Ephys Documentation" +project = "Open Ephys Commutator Docs" copyright = "2010-{}, Open Ephys & Contributors".format(datetime.now(timezone.utc).year) author = "Open Ephys & Contributors" @@ -88,8 +88,9 @@ # a list of builtin themes. # html_theme = "pydata_sphinx_theme" -html_logo = "_static/images/oe_logo_name.png" +html_logo = "_static/images/oe_logo_commutators.svg" html_scaled_image_link = True +html_title = project # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, @@ -106,9 +107,10 @@ html_sidebars = { 'index': ['search-field.html'], - "**": ["search-field.html", "sidebar-nav-bs.html"] + "**": ["sidebar-nav-bs.html"] } + # -- Options for HTMLHelp output --------------------------------------------- # Output file base name for HTML help builder. @@ -184,14 +186,15 @@ # documentation. html_theme = "pydata_sphinx_theme" -html_logo = "_static/images/oe_logo_name.png" +html_logo = "_static/images/oe_logo_name.svg" html_scaled_image_link = True html_theme_options = { - 'external_links': [{'name': 'Open Ephys', 'url': 'https://open-ephys.org'}, ], - 'navigation_with_keys': True, - 'use_edit_page_button': False, - 'show_toc_level': 1, + 'use_edit_page_button': True, + "navigation_with_keys": True, + "navbar_end": ["navbar-icon-links"], + "navbar_align": "content", + "footer_start": ["copyright"], 'icon_links': [ dict(name='GitHub', url='https://github.com/open-ephys/commutator-docs', @@ -203,6 +206,18 @@ url='https://discord.gg/WXAx2URNQU', icon='fab fa-discord') ], + #'canonical_url': '', + #'analytics_id': '', + #'logo_only': False, + # + #'prev_next_buttons_location': 'bottom', + #'style_external_links': False, + # Toc options + #'collapse_navigation': False, + #'sticky_navigation': True, + # 'navigation_depth': 4, + #'includehidden': True, + #'titles_only': False } html_favicon = "_static/images/favicon.png" diff --git a/source/index.rst b/source/index.rst index 0eb33b1..d12142b 100644 --- a/source/index.rst +++ b/source/index.rst @@ -1,82 +1,22 @@ .. _oec: -Open Ephys Commutators -************************************************* +.. title:: Home -.. toctree:: - :hidden: +.. image:: _static/images/commutator-front-thin.jpg + :alt: Commutator front image + +| - coax-commutator/index - spi-commutator/index +**Open Ephys Commutators** provide nearly torque-free tether management for freely moving recordings. Inertial-measurement units (IMUs) or video-based pose-estimation methods (e.g. `DeepLabCut `_ or `SLEAP `_) provide real-time measurements of animal orientation. Therefore, these technologies can be used to drive active commutation instead of relying on tether torque measurement, which is used in conventional active commutators. This permits the use of exceptionally thin tethers that promote natural animal behavior but are too flexible to be used with conventional commutators. -.. raw:: html +The **Coax Commutator** is compatible with `UCLA Miniscopes `__ and `ONIX Headstages `__. -
-
-
- Commutator front image -
-
-
-

- Open-ephys commutators provide nearly torque-free - tether management for freely moving recordings. - Inertial-measurement units (IMUs) or video-based - pose-estimation methods (e.g. - DeepLabCut or SLEAP - ) provide real-time measurements of animal orientation. Therefore, these technologies can be - used to drive active commutation instead of - relying on tether torque measurement, which is - used in conventional active commutators. This - permits the use of exceptionally thin tethers (such as these - micro coaxial cables ) that promote natural - animal behavior but are to flexible to be used with - conventional commutators. -
-
- Currently available Open Ephys Commutators include: -

- -

- To start using your your Open Ephys Commutator, please - refer to the guide that corresponds with your - device: -

-
-
-
-
+A commutator compatible with SPI cables is under active development. -.. raw:: html -
-
-
- - -
-

Coax Commutator User Guide

-
- -
-
-
-
- - -
-

SPI Commutator User Guide

-
- -
-
-
+.. toctree:: + :hidden: + :maxdepth: 2 + :titlesonly: + coax-commutator/index \ No newline at end of file From 26d703ff08fa423a8ccc6e92f6fe2982547c04ae Mon Sep 17 00:00:00 2001 From: Josh Siegle Date: Sat, 8 Jul 2023 17:19:07 -0700 Subject: [PATCH 2/5] Update logo SVG --- source/_static/images/oe_logo_name.svg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/source/_static/images/oe_logo_name.svg b/source/_static/images/oe_logo_name.svg index 53dff0f..d40bde3 100644 --- a/source/_static/images/oe_logo_name.svg +++ b/source/_static/images/oe_logo_name.svg @@ -1 +1 @@ -Commutators \ No newline at end of file + \ No newline at end of file From 2d7bea8dab5f6d98fc99710c0fcff134ee304c8f Mon Sep 17 00:00:00 2001 From: Josh Siegle Date: Fri, 14 Jul 2023 20:31:37 -0700 Subject: [PATCH 3/5] Add purchase link --- source/coax-commutator/developer-guide/index.rst | 3 +-- source/conf.py | 1 + 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/source/coax-commutator/developer-guide/index.rst b/source/coax-commutator/developer-guide/index.rst index edccf5f..f8595ec 100644 --- a/source/coax-commutator/developer-guide/index.rst +++ b/source/coax-commutator/developer-guide/index.rst @@ -4,8 +4,7 @@ Developer Guide ------------------------------------------------- .. attention:: This section provides information on hacking a commutator or - building your own. For an overview of Open Ephys Commutators, visit the - :ref:`oec`. For instructions on how to use the Coaxial Commutator, visit + building your own. For instructions on how to use the Coaxial Commutator, visit the Coaxial Commutator :ref:`quick_start` Guide and :ref:`user_guide`. Design Files diff --git a/source/conf.py b/source/conf.py index 5463a23..46b29c5 100644 --- a/source/conf.py +++ b/source/conf.py @@ -195,6 +195,7 @@ "navbar_end": ["navbar-icon-links"], "navbar_align": "content", "footer_start": ["copyright"], + "external_links": [{"name": "Purchase", "url": "https://open-ephys.org/commutators/coaxial-commutator"},], 'icon_links': [ dict(name='GitHub', url='https://github.com/open-ephys/commutator-docs', From 636369492e433c6aca096bfcf83456ece18d892a Mon Sep 17 00:00:00 2001 From: Josh Siegle Date: Fri, 14 Jul 2023 20:40:55 -0700 Subject: [PATCH 4/5] Update GitHub link --- source/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/source/conf.py b/source/conf.py index 46b29c5..1d5dcb9 100644 --- a/source/conf.py +++ b/source/conf.py @@ -198,7 +198,7 @@ "external_links": [{"name": "Purchase", "url": "https://open-ephys.org/commutators/coaxial-commutator"},], 'icon_links': [ dict(name='GitHub', - url='https://github.com/open-ephys/commutator-docs', + url='https://github.com/open-ephys/onix-commutator', icon='fab fa-github'), dict(name='Twitter', url='https://twitter.com/openephys', From 1ea5dc44d45b113c69afc65583043a5ff6c23d15 Mon Sep 17 00:00:00 2001 From: Josh Siegle Date: Sun, 16 Jul 2023 13:39:58 -0700 Subject: [PATCH 5/5] Update theme_overrides --- source/_static/theme_overrides.css | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/source/_static/theme_overrides.css b/source/_static/theme_overrides.css index 8ae0369..2c3c521 100644 --- a/source/_static/theme_overrides.css +++ b/source/_static/theme_overrides.css @@ -249,16 +249,18 @@ h4, h5, h6 { line-height: 1.5; + margin-bottom: 0.7em; } /* List items in main area, but not in side bars */ body > li, p { line-height: 1.5; - margin: 0.3rem 0; + margin: 0.7rem 0; } + /* logo */ .navbar-brand { position: relative;