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implemented minimal-mistakes
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+43485
-54
lines changed

‎.jekyll-cache/Jekyll/Cache/Jekyll--Cache/b7/9606fb3afea5bd1609ed40b622142f1c98125abcfe89a76a661b0e8e343910

+1
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I"n{"source"=>"/home/simon/Github/SwissBIAS.github.io", "destination"=>"/home/simon/Github/SwissBIAS.github.io/_site", "collections_dir"=>"", "cache_dir"=>".jekyll-cache", "plugins_dir"=>"_plugins", "layouts_dir"=>"_layouts", "data_dir"=>"_data", "includes_dir"=>"_includes", "collections"=>{"posts"=>{"output"=>true, "permalink"=>"/:categories/:year/:month/:day/:title:output_ext"}, "members"=>{"output"=>true}}, "safe"=>false, "include"=>[".htaccess"], "exclude"=>[".sass-cache", ".jekyll-cache", "gemfiles", "Gemfile", "Gemfile.lock", "node_modules", "vendor/bundle/", "vendor/cache/", "vendor/gems/", "vendor/ruby/"], "keep_files"=>[".git", ".svn"], "encoding"=>"utf-8", "markdown_ext"=>"markdown,mkdown,mkdn,mkd,md", "strict_front_matter"=>false, "show_drafts"=>nil, "limit_posts"=>0, "future"=>false, "unpublished"=>false, "whitelist"=>[], "plugins"=>[], "markdown"=>"kramdown", "highlighter"=>"rouge", "lsi"=>false, "excerpt_separator"=>"\n\n", "incremental"=>false, "detach"=>false, "port"=>"4000", "host"=>"127.0.0.1", "baseurl"=>nil, "show_dir_listing"=>false, "permalink"=>"date", "paginate_path"=>"/page:num", "timezone"=>nil, "quiet"=>false, "verbose"=>false, "defaults"=>[{"scope"=>{"path"=>"", "type"=>"members"}, "values"=>{"layout"=>"member"}}, {"scope"=>{"path"=>"", "type"=>"posts"}, "values"=>{"layout"=>"post"}}, {"scope"=>{"path"=>""}, "values"=>{"layout"=>"default"}}], "liquid"=>{"error_mode"=>"warn", "strict_filters"=>false, "strict_variables"=>false}, "kramdown"=>{"auto_ids"=>true, "toc_levels"=>[1, 2, 3, 4, 5, 6], "entity_output"=>"as_char", "smart_quotes"=>"lsquo,rsquo,ldquo,rdquo", "input"=>"GFM", "hard_wrap"=>false, "guess_lang"=>true, "footnote_nr"=>1, "show_warnings"=>false, "syntax_highlighter"=>"rouge", "syntax_highlighter_opts"=>{:default_lang=>"plaintext", :guess_lang=>true}, "coderay"=>{}}, "livereload_port"=>35729, "serving"=>true, "watch"=>true, "url"=>nil}:ET

‎.jekyll-cache/Jekyll/Cache/Jekyll--Converters--Markdown/19/bc5c12064d6f72ab2f00bdbea21537017ec22e561e10513a8b81827afcfe86

+3
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I"j<p>Simon works at ETH Zurich.
2+
He heads IDA - the Image and Data Analysis group inside of ScopeM.</p>
3+
:ET

‎.jekyll-cache/Jekyll/Cache/Jekyll--Converters--Markdown/2a/bd8888595a22b8d04efa8e4b159a997e7d2d1c693151d4eb93393cc3b33f78

+3
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,3 @@
1+
I"j<p>Simon works at ETH Zurich.
2+
He heads IDA - the Image and Data Analysis group inside of ScopeM.</p>
3+
:ET

‎.jekyll-cache/Jekyll/Cache/Jekyll--Converters--Markdown/3e/54c8d9675c87149f01e7a42f7106c584ab23ef3c27f8564044dca6384db034

+3
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I"T<h2 id="hello-world">Hello world!</h2>
2+
<p>This page is written in markdown</p>
3+
:ET

‎.jekyll-cache/Jekyll/Cache/Jekyll--Converters--Markdown/40/c8434a547d3379912f412d1b997d88128e32d490bfea4330aa7dc882d8c971

+97
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1+
I"H<h1 id="setup-notes">Setup notes</h1>
2+
<p>2021-02-04, sfn</p>
3+
4+
<h3 id="first-steps-hello-world-and-readme">First steps (hello world and README)</h3>
5+
<ul>
6+
<li>Following instructions on https://pages.github.com/</li>
7+
<li>Editing files/repo locally and using a terminal as git client, do
8+
<ul>
9+
<li>git add –all</li>
10+
<li>git commit -m “Initial commit”</li>
11+
<li>git push -u origin main</li>
12+
</ul>
13+
</li>
14+
<li>Editing files/repo locally and using the GitHub desktop git client (mac or win), do
15+
<ul>
16+
<li>click “commit to main”</li>
17+
<li>click “push”</li>
18+
</ul>
19+
</li>
20+
<li>Editing files on GitHub, do
21+
<ul>
22+
<li>click “Commit change” at bottom of change</li>
23+
</ul>
24+
</li>
25+
</ul>
26+
27+
<h3 id="next-steps-jekyll-and-themes">Next steps (Jekyll and themes)</h3>
28+
<ul>
29+
<li>The idea is that Jekyll is installed locally once and used to create the structure of hte site — most edits are done directly in GitHub afterwards, requiring only a browswer</li>
30+
<li>Read here https://docs.github.com/en/github/working-with-github-pages/creating-a-github-pages-site-with-jekyll</li>
31+
<li>It appears to be necessary to install Jekyll on local machine</li>
32+
</ul>
33+
34+
<h3 id="installing-jekyll-on-ubuntu">Installing Jekyll on Ubuntu</h3>
35+
<ul>
36+
<li>I have previously done this on macOS, so that is definitely possible and actually turns out to be easier</li>
37+
<li>https://jekyllrb.com/docs/installation/ubuntu/</li>
38+
<li>In home-dir do
39+
<ul>
40+
<li>$ sudo sed -i ‘/cdrom/d’ /etc/apt/sources.list</li>
41+
<li>$ sudo apt-get install ruby-full build-essential zlib1g-dev</li>
42+
<li>$ echo ‘# Install Ruby Gems to ~/gems’ » ~/.bashrc</li>
43+
<li>$ echo ‘export PATH=”$HOME/gems/bin:$PATH”’ » ~/.bashrc</li>
44+
<li>$ source ~/.bashrc</li>
45+
<li>$ gem install jekyll bundler</li>
46+
<li>$ jekyll –version
47+
<ul>
48+
<li>answer: $ jekyll 4.2.0</li>
49+
</ul>
50+
</li>
51+
<li>$ gem env
52+
<ul>
53+
<li>GEM PATHS tells me I run ruby 2.7.0</li>
54+
</ul>
55+
</li>
56+
<li>$ ruby -v
57+
<ul>
58+
<li>answer: 2.7.0p0</li>
59+
</ul>
60+
</li>
61+
<li>$ gem install jekyll bundler</li>
62+
</ul>
63+
</li>
64+
<li>In ~/Github/SwissBIAS.github.io/ do (has to happen in folder of the project)
65+
<ul>
66+
<li>create file “Gemfile” and add this (more will be added later on)
67+
<ul>
68+
<li>source “https://rubygems.org”</li>
69+
<li>gem “jekyll”</li>
70+
</ul>
71+
</li>
72+
<li>$ gem install bundler</li>
73+
<li>$ bundle install</li>
74+
<li>$ bundle exec jekyll serve
75+
<ul>
76+
<li>then navigate to http://127.0.0.1:4000/ (http://localhost:4000/) to see local version of site</li>
77+
<li>Looks slightly different from on GitHub, because GitHub has some default theme running</li>
78+
<li>Automatically creates the folder /_site/ containing “index.html” generated from “index.md”, etc</li>
79+
</ul>
80+
</li>
81+
<li>create folder /_layouts/ and populate with layout templates</li>
82+
<li>create folder /_members/ and populate with one file per member, e.g. “simon.noerrelykke.md”, “romain.guit.md” etc - one markdown file for each member</li>
83+
<li>etc, basically following this tutoriar: https://jekyllrb.com/docs/step-by-step/01-setup/</li>
84+
</ul>
85+
</li>
86+
</ul>
87+
88+
<h3 id="theme-if-bare-bones-is-too-bland">Theme (if bare-bones is too bland)</h3>
89+
<ul>
90+
<li>Because I already know it, and because it is the most popular <a href="https://github.com/topics/jekyll-theme">theme</a>, I start with <a href="https://github.com/mmistakes/minimal-mistakes">minimal-mistakes</a>
91+
<ul>
92+
<li>Quick-start guide here: https://mmistakes.github.io/minimal-mistakes/docs/quick-start-guide/
93+
https://jekyllrb.com/docs/step-by-step/01-setup/</li>
94+
</ul>
95+
</li>
96+
</ul>
97+
:ET

‎.jekyll-cache/Jekyll/Cache/Jekyll--Converters--Markdown/80/00612652d9b2e52bd6f0ebbff681fc3b9beaf16281d7da08c50e9f5a609c35

+5
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I"�<p>Romain works at EPFL in BIOP.
2+
He is a biologist by training, but has worked with image analysis since ~2010authors.</p>
3+
4+
<p>Create staff.html and itera</p>
5+
:ET

‎.jekyll-cache/Jekyll/Cache/Jekyll--Converters--Markdown/86/092bb629aac2f22f1000de768e2a2a26476ad03c05708709a16f62f4f561c9

+5
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I"�<h1 id="about-page">About page</h1>
2+
3+
<p>SwissBIAS is the Swiss BioImage Analysts’s Society, or network, if you please.<br />
4+
Founded on 2021-01-21 in a kick-off Zoom call between 25 Swiss-based bioimage analyts</p>
5+
:ET

‎.jekyll-cache/Jekyll/Cache/Jekyll--Converters--Markdown/b7/27435ec78b113bfc8e45518f37e576c9b14d3a77c3a32bad64f6e3127e20f4

+3
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@@ -0,0 +1,3 @@
1+
I"{<p>Romain works at EPFL in BIOP.
2+
He is a biologist by training, but has worked with image analysis since ~2010authors.</p>
3+
:ET

‎.jekyll-cache/Jekyll/Cache/Jekyll--Converters--Markdown/d9/569d45bf8417b1688d426d7027839f8fbdb98f35343ce52af0695cbd0094b6

+3
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,3 @@
1+
I"{<p>Romain works at EPFL in BIOP.
2+
He is a biologist by training, but has worked with image analysis since ~2010authors.</p>
3+
:ET

‎.jekyll-cache/Jekyll/Cache/Jekyll--Converters--Markdown/da/690bb865c68893cc0f713ed459302d2665ca26e7c38b6222d11ad4ce2756f9

+2
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@@ -0,0 +1,2 @@
1+
I"-<p>All posts written by all authors</p>
2+
:ET

‎.jekyll-cache/Jekyll/Cache/Jekyll--Converters--Markdown/ea/2a4290ed02ba8bec76e203f8dda3f67066091dc9b5f4a804e863df9af0c71d

+96
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,96 @@
1+
I"�<h1 id="setup-notes">Setup notes</h1>
2+
<p>Some notes from setting up the SwissBIAS website on GitHub, using Jekyll, from Ubuntu</p>
3+
<h3 id="first-steps-hello-world-and-readme">First steps (hello world and README)</h3>
4+
<ul>
5+
<li>Following instructions on https://pages.github.com/</li>
6+
<li>Editing files/repo locally and using a terminal as git client, do
7+
<ul>
8+
<li>git add –all</li>
9+
<li>git commit -m “Initial commit”</li>
10+
<li>git push -u origin main</li>
11+
</ul>
12+
</li>
13+
<li>Editing files/repo locally and using the GitHub desktop git client (mac or win), do
14+
<ul>
15+
<li>click “commit to main”</li>
16+
<li>click “push”</li>
17+
</ul>
18+
</li>
19+
<li>Editing files on GitHub, do
20+
<ul>
21+
<li>click “Commit change” at bottom of change</li>
22+
</ul>
23+
</li>
24+
</ul>
25+
26+
<h3 id="next-steps-jekyll-and-themes">Next steps (Jekyll and themes)</h3>
27+
<ul>
28+
<li>The idea is that Jekyll is installed locally once and used to create the structure of hte site — most edits are done directly in GitHub afterwards, requiring only a browswer</li>
29+
<li>Read here https://docs.github.com/en/github/working-with-github-pages/creating-a-github-pages-site-with-jekyll</li>
30+
<li>It appears to be necessary to install Jekyll on local machine</li>
31+
</ul>
32+
33+
<h3 id="installing-jekyll-on-ubuntu">Installing Jekyll on Ubuntu</h3>
34+
<ul>
35+
<li>I have previously done this on macOS, so that is definitely possible and actually turns out to be easier</li>
36+
<li>https://jekyllrb.com/docs/installation/ubuntu/</li>
37+
<li>In home-dir do
38+
<ul>
39+
<li>$ sudo sed -i ‘/cdrom/d’ /etc/apt/sources.list</li>
40+
<li>$ sudo apt-get install ruby-full build-essential zlib1g-dev</li>
41+
<li>$ echo ‘# Install Ruby Gems to ~/gems’ » ~/.bashrc</li>
42+
<li>$ echo ‘export PATH=”$HOME/gems/bin:$PATH”’ » ~/.bashrc</li>
43+
<li>$ source ~/.bashrc</li>
44+
<li>$ gem install jekyll bundler</li>
45+
<li>$ jekyll –version
46+
<ul>
47+
<li>answer: $ jekyll 4.2.0</li>
48+
</ul>
49+
</li>
50+
<li>$ gem env
51+
<ul>
52+
<li>GEM PATHS tells me I run ruby 2.7.0</li>
53+
</ul>
54+
</li>
55+
<li>$ ruby -v
56+
<ul>
57+
<li>answer: 2.7.0p0</li>
58+
</ul>
59+
</li>
60+
<li>$ gem install jekyll bundler</li>
61+
</ul>
62+
</li>
63+
<li>In ~/Github/SwissBIAS.github.io/ do (has to happen in folder of the project)
64+
<ul>
65+
<li>create file “Gemfile” and add this (more will be added later on)
66+
<ul>
67+
<li>source “https://rubygems.org”</li>
68+
<li>gem “jekyll”</li>
69+
</ul>
70+
</li>
71+
<li>$ gem install bundler</li>
72+
<li>$ bundle install</li>
73+
<li>$ bundle exec jekyll serve
74+
<ul>
75+
<li>then navigate to http://127.0.0.1:4000/ (http://localhost:4000/) to see local version of site</li>
76+
<li>Looks slightly different from on GitHub, because GitHub has some default theme running</li>
77+
<li>Automatically creates the folder /_site/ containing “index.html” generated from “index.md”, etc</li>
78+
</ul>
79+
</li>
80+
<li>create folder /_layouts/ and populate with layout templates</li>
81+
<li>create folder /_members/ and populate with one file per member, e.g. “simon.noerrelykke.md”, “romain.guit.md” etc - one markdown file for each member</li>
82+
<li>etc, basically following this tutorial: https://jekyllrb.com/docs/step-by-step/01-setup/</li>
83+
</ul>
84+
</li>
85+
</ul>
86+
87+
<h3 id="theme-if-bare-bones-is-too-bland">Theme (if bare-bones is too bland)</h3>
88+
<ul>
89+
<li>Because I already know it, and because it is the most popular <a href="https://github.com/topics/jekyll-theme">theme</a>, I start with <a href="https://github.com/mmistakes/minimal-mistakes">minimal-mistakes</a>
90+
<ul>
91+
<li>Quick-start guide here: https://mmistakes.github.io/minimal-mistakes/docs/quick-start-guide/
92+
https://jekyllrb.com/docs/step-by-step/01-setup/</li>
93+
</ul>
94+
</li>
95+
</ul>
96+
:ET

‎.jekyll-cache/Jekyll/Cache/Jekyll--Converters--Markdown/ee/06728c2541205d05fe2e640ae754d6f93dea09c17f4cb902ea4368951ef56f

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
I"�<p>Romain works at EPFL in BIOP.
2+
He is a biologist by training, but has worked with image analysis since ~2010authors.</p>
3+
4+
<p>Create staff.html and itera</p>
5+
:ET

‎.jekyll-cache/Jekyll/Cache/Jekyll--Converters--Markdown/f8/e2e36e309082b10be137080394b382eabf1bb0abc348fc81032708ece4cded

+96
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,96 @@
1+
I"�<h1 id="setup-notes">Setup notes</h1>
2+
<p>Some notes from setting up the SwissBIAS website on GitHub, using Jekyll, from Ubuntu</p>
3+
<h3 id="first-steps-hello-world-and-readme">First steps (hello world and README)</h3>
4+
<ul>
5+
<li>Following instructions on https://pages.github.com/</li>
6+
<li>Editing files/repo locally and using a terminal as git client, do
7+
<ul>
8+
<li>git add –all</li>
9+
<li>git commit -m “Initial commit”</li>
10+
<li>git push -u origin main</li>
11+
</ul>
12+
</li>
13+
<li>Editing files/repo locally and using the GitHub desktop git client (mac or win), do
14+
<ul>
15+
<li>click “commit to main”</li>
16+
<li>click “push”</li>
17+
</ul>
18+
</li>
19+
<li>Editing files on GitHub, do
20+
<ul>
21+
<li>click “Commit change” at bottom of change</li>
22+
</ul>
23+
</li>
24+
</ul>
25+
26+
<h3 id="next-steps-jekyll-and-themes">Next steps (Jekyll and themes)</h3>
27+
<ul>
28+
<li>The idea is that Jekyll is installed locally once and used to create the structure of hte site — most edits are done directly in GitHub afterwards, requiring only a browswer</li>
29+
<li>Read here https://docs.github.com/en/github/working-with-github-pages/creating-a-github-pages-site-with-jekyll</li>
30+
<li>It appears to be necessary to install Jekyll on local machine</li>
31+
</ul>
32+
33+
<h3 id="installing-jekyll-on-ubuntu">Installing Jekyll on Ubuntu</h3>
34+
<ul>
35+
<li>I have previously done this on macOS, so that is definitely possible and actually turns out to be easier</li>
36+
<li>https://jekyllrb.com/docs/installation/ubuntu/</li>
37+
<li>In home-dir do
38+
<ul>
39+
<li>$ sudo sed -i ‘/cdrom/d’ /etc/apt/sources.list</li>
40+
<li>$ sudo apt-get install ruby-full build-essential zlib1g-dev</li>
41+
<li>$ echo ‘# Install Ruby Gems to ~/gems’ » ~/.bashrc</li>
42+
<li>$ echo ‘export PATH=”$HOME/gems/bin:$PATH”’ » ~/.bashrc</li>
43+
<li>$ source ~/.bashrc</li>
44+
<li>$ gem install jekyll bundler</li>
45+
<li>$ jekyll –version
46+
<ul>
47+
<li>answer: $ jekyll 4.2.0</li>
48+
</ul>
49+
</li>
50+
<li>$ gem env
51+
<ul>
52+
<li>GEM PATHS tells me I run ruby 2.7.0</li>
53+
</ul>
54+
</li>
55+
<li>$ ruby -v
56+
<ul>
57+
<li>answer: 2.7.0p0</li>
58+
</ul>
59+
</li>
60+
<li>$ gem install jekyll bundler</li>
61+
</ul>
62+
</li>
63+
<li>In ~/Github/SwissBIAS.github.io/ do (has to happen in folder of the project)
64+
<ul>
65+
<li>create file “Gemfile” and add this (more will be added later on)
66+
<ul>
67+
<li>source “https://rubygems.org”</li>
68+
<li>gem “jekyll”</li>
69+
</ul>
70+
</li>
71+
<li>$ gem install bundler</li>
72+
<li>$ bundle install</li>
73+
<li>$ bundle exec jekyll serve
74+
<ul>
75+
<li>then navigate to http://127.0.0.1:4000/ (http://localhost:4000/) to see local version of site</li>
76+
<li>Looks slightly different from on GitHub, because GitHub has some default theme running</li>
77+
<li>Automatically creates the folder /_site/ containing “index.html” generated from “index.md”, etc</li>
78+
</ul>
79+
</li>
80+
<li>create folder /_layouts/ and populate with layout templates</li>
81+
<li>create folder /_members/ and populate with one file per member, e.g. “simon.noerrelykke.md”, “romain.guit.md” etc - one markdown file for each member</li>
82+
<li>etc, basically following this tutoriar: https://jekyllrb.com/docs/step-by-step/01-setup/</li>
83+
</ul>
84+
</li>
85+
</ul>
86+
87+
<h3 id="theme-if-bare-bones-is-too-bland">Theme (if bare-bones is too bland)</h3>
88+
<ul>
89+
<li>Because I already know it, and because it is the most popular <a href="https://github.com/topics/jekyll-theme">theme</a>, I start with <a href="https://github.com/mmistakes/minimal-mistakes">minimal-mistakes</a>
90+
<ul>
91+
<li>Quick-start guide here: https://mmistakes.github.io/minimal-mistakes/docs/quick-start-guide/
92+
https://jekyllrb.com/docs/step-by-step/01-setup/</li>
93+
</ul>
94+
</li>
95+
</ul>
96+
:ET

‎Gemfile

+12
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@@ -0,0 +1,12 @@
1+
source "https://rubygems.org"
2+
3+
# gem "jekyll"
4+
5+
# group :jekyll_plugins do
6+
# gem "jekyll-feed"
7+
# gem "jekyll-seo-tag"
8+
# end
9+
10+
# 2021-02-04, sfn: for use remote themes (works better with GitHub)
11+
gem "github-pages", group: :jekyll_plugins
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gem "jekyll-include-cache", group: :jekyll_plugins

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