{"id":18524292,"url":"https://github.com/mdanalysis/mdanalysis.github.io","last_synced_at":"2025-04-10T01:09:49.950Z","repository":{"id":29541464,"uuid":"33080483","full_name":"MDAnalysis/MDAnalysis.github.io","owner":"MDAnalysis","description":"MDAnalysis home page mdanalysis.org as GitHub pages.","archived":false,"fork":false,"pushed_at":"2025-04-06T00:14:49.000Z","size":95173,"stargazers_count":14,"open_issues_count":19,"forks_count":43,"subscribers_count":13,"default_branch":"master","last_synced_at":"2025-04-10T01:09:43.672Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://mdanalysis.org","language":"CSS","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MDAnalysis.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2015-03-29T16:39:09.000Z","updated_at":"2025-04-06T00:14:53.000Z","dependencies_parsed_at":"2024-11-06T17:55:11.995Z","dependency_job_id":null,"html_url":"https://github.com/MDAnalysis/MDAnalysis.github.io","commit_stats":{"total_commits":747,"total_committers":46,"mean_commits":16.23913043478261,"dds":0.6305220883534137,"last_synced_commit":"b0f858f4c7a7d4a9a1eedebb44ab3ae7dc7c8858"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FMDAnalysis.github.io","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FMDAnalysis.github.io/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FMDAnalysis.github.io/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2FMDAnalysis.github.io/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MDAnalysis","download_url":"https://codeload.github.com/MDAnalysis/MDAnalysis.github.io/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248137886,"owners_count":21053775,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-06T17:40:28.811Z","updated_at":"2025-04-10T01:09:49.925Z","avatar_url":"https://github.com/MDAnalysis.png","language":"CSS","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MDAnalysis Web Site #\n\nThe home page [www.mdanalysis.org](https://www.mdanalysis.org) is maintained as\na [GitHub pages](https://pages.github.com) site. The home page is also\naccessible as [mdanalysis.github.io](https://mdanalysis.github.io).\n\nPages are generated from markdown files using the static site\ngenerator\n[Jekyll](https://help.github.com/articles/using-jekyll-with-pages/).\n\n## General page authoring guide ##\n\n- use [GitHub-flavored Markdown](https://github.github.com/gfm/)\n- use utf-8 encoding\n- The top-level heading (h1) is set by the *title:* attribute in the\n  front matter of each page.\n- In-text headings start at h2, i.e., `## heading title ##` in\n  Markdown. There should *not be any h1 headings inside the page*.\n  \nFor further notes see [Web development](#web-development) below.\n\n\n## Blog [mdanalysis.org/blog](https://www.mdanalysis.org/blog) ##\n\nCheck out the repository, edit the pages under `_posts`, and push\ncommits. The published pages are on the *master* branch.\n\n### File name \n\nBlog posts should be placed under `_posts`. These should have names\naccording to:\n\n    YEAR-MONTH-DAY-title.md\n\nwhere `YEAR` is a four-digit number, and `MONTH` and `DAY` are both two-digit\nnumbers. \n\n### Meta data header of markdown files\n\nEach post should have a header with:\n\n    ---\n    layout: post\n    title: \"The title of this post\"\n    ---\n\nin order for it to be picked up by the paginator. You *must* put the title in\nquotation marks if it contains special characters.\n\nOther keys can be in the header (such as *date* (overrides file name date) or\n*order* (for [static pages](#static-pages))).\n\n\n### Section headers\n\n* Do not put a title at the start of the post. The title from the metadata will\n  create the level 1 header.\n* Do not use level 1 (`# ... #`) headers, level 1 is reserved for the overall\n  title.\n* Use level 2 (`## ... ##`) or higher level headers.\n\n\n### Good to know\n\nThe `blog` directory should not be touched, as this is only here to set the paginator.\n\n* The `_site` directory is generated by Jekyll on the GitHub server side and\n  should not be included in commits.\n* You can sign posts with your\n  [@mention](https://help.github.com/articles/mentions-on-github-pages/)\n  and it will link to your GitHub profile.\n* If the date on a post is in in the future at the time of the commit,\n  it will not be built *and will not appear* (until the next commit on\n  or after the time of the post).\n\n\n## Web development ##\n\nWe are using the minimalist [Hyde](https://github.com/poole/hyde) theme for\n[Jekyll](https://jekyllrb.com/docs/).\n\n### Static pages\nAdditional static pages go under `pages`. If they have the layout type\n\"page\" they will be automatically included in the *sidebar*. The static\n\"about\" page is left at the top level.\n\nTo customize the *order of pages in the sidebar*, add the attribute\n`order: \u003cINTEGER\u003e` to the front-matter. Pages will be sorted lowest to\nhighest. Note that some entries in the sidebar are hardcoded in\n`_includes/sidebar.html`.\n\nIf a page should *not show up in the sidebar*, use `layout:\notherpage`.\n\n\n\n\n### Creating content ###\n\nThere are two ways to add and edit files:\n\n* Check out the repository, edit the pages, and push commits. The\n  published pages are on the *master* branch.\n* Use the *add file*/*upload file* and *edit file* functionality in\n  the https://github.com/MDAnalysis/MDAnalysis.github.io repository\n  web frontend.\n  \n\n### Mark-up format: Markdown ###\n\nThe GitHub pages can either use HTML or\n[markdown](http://daringfireball.net/projects/markdown/) as processed by\n[Jekyll](https://help.github.com/articles/using-jekyll-with-pages/).\n\nThe actual markdown processor is\n[kramdown](http://kramdown.gettalong.org) so it parses more than basic\nmarkdown --- see the\n[kramdown syntax](http://kramdown.gettalong.org/syntax.html),\nincluding MathJax.\n\n### Images ###\n\nDrop images into the `public/images` directory and include them like\n\n```html\n  \u003cimg src=\"{{ site.images }}/imagename.png\"\n   style=\"float: right\" alt=\"alternative text\" width=\"30%\"/\u003e\n   ```\n\nor use Markdown\n```markdown\n![alternative text]({{ site.images }}/imagename.png)\n```\n\n\n### Notes on using Jekyll ###\n\n#### Absolute site links\n\nFor links between pages to work, generate absolute links with `site.baseurl`\nliquid tag:\n\n```\n[see citations]({{ site.baseurl }}/pages/citations)\n```\n\nThe example will link to the file `/pages/citations`.\n\n**Note**: Always put a slash `/` *after* `{{ site.baseurl }}`.\n\nWe define additional variables in `_config.yml` and use them with liquid tags.\nIn particular, the sidebar `_includes/sidebar.html` is configured with\nadditional links that are all stored in the config file.\n\n#### Links to blog posts\nUse the\n[post_url](https://jekyllrb.com/docs/liquid/tags/#linking-to-posts)\nliquid tag `{% post_url FILENAME_NO_SUFFIX %}`. *FILENAME_NO_SUFFIX*\nis something like \"2025-02-11-GSOC2024-final-blog\" to reference the\nfile `_posts/2025-02-11-GSOC2024-final-blog.md`. Note that the `.md`\nsuffix is *not* included.\n\nPrefix with the baseurl so you use it something like\n```markdown\nSee the [GSOC 2024 blog post]({{ site.baseurl }}/{% post_url 2025-02-11-GSOC2024-final-blog %}) \nfor more details.\n```\n\n#### Liquid tags\n\nOne does not need spaces between the configuration variable and the\ncurly braces (i.e.  `{{ site.baseurl }}/` as typical seen). If you\nfind that your editor breaks the line inside the curly braces\n(which upsets Jekyll greatly) then omit the space.\n\n\n\n### Local testing ###\n\nTo locally test that your edits look ok before pushing them, run\n*Jekyll* from a docker container (always works if you can get docker\nto run) or install\n[Jekyll](https://help.github.com/articles/using-jekyll-with-pages/) as\ndescribed in the docs (can be frustrating because of broken dependencies).\n\n\n#### Using docker container for local builds ####\n\nRunning Jekyll from a docker image:\n\n* on Linux you should be able to start/run docker after installing the\n  appropriate docker package through your package manager\n* on MacOS\n  - install Docker Desktop\n    https://docs.docker.com/desktop/install/mac-install/ and let it\n    install all kind of startup items\n  - start Docker\n\nFollow the solution from https://stackoverflow.com/a/58850151/ as\ndescribed next:\n\nTo **build the static site**, run `jekyll build` inside docker:\n```bash\nexport JEKYLL_VERSION=4.0\ndocker run --rm \\\n  --volume=\"$PWD:/srv/jekyll\" \\\n  -it jekyll/jekyll:$JEKYLL_VERSION \\\n  jekyll build\n```\nThe static site files are stored in the `_site` directory.\n\nThen you must **serve the site** so you can view them in a web browser\n```bash\npython -m http.server --directory _site 4444\n```\n(You can leave out the port number and then it defaults to 8000.)\n\nPoint your browser to http://localhost:4444\n\nWhen you make changes, you need to re-build the site.\n\n*Note that the CSS is only rendered correctly when the pages are\nserved. Just directly browsing the files will not show the site as it\nwill appear on the web.*\n\t\n\n#### Build site locally ####\n\nTo run Jekyll in a way that matches the GitHub Pages build server, run `Jekyll`\nwith `Bundler`. See [INSTALL](INSTALL.md) for notes on how to install Jekyll\nlocally.\n\nUse the command\n\n    bundle exec jekyll serve --watch --livereload --future --incremental\n\nin the root of your repository (after switching to the gh-pages branch for\nproject repositories), and your site should be available at\n\u003chttp://localhost:4000\u003e. \n\nRunning Jekyll locally has the advantage that you can have it update\nthe site continuously while you're editing files.\n\n(See the [serve commandline\noptions](https://jekyllrb.com/docs/configuration/options/#serve-command-options)\nfor more details.)\n\nFor a full list of Jekyll commands, see the [Jekyll\ndocumentation](https://jekyllrb.com/docs/).\n\n\n\n\n##### Updating the github-pages plugin #####\n\nIf you try out new functionality or plugins locally and you get error\nmessages then try to\n[update the github-pages plugin](https://help.github.com/articles/setting-up-your-pages-site-locally-with-jekyll/#keeping-your-site-up-to-date-with-the-github-pages-gem)\nwith\n\n    bundle update github-pages\n\n##### Problems with jekyll and required packages? #####\n\n* See [INSTALL](INSTALL.md) and if in doubt, follow the latest instructions from\n  [GitHub: Testing your GitHub Pages site locally with\n  Jekyll](https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll/testing-your-github-pages-site-locally-with-jekyll)\n  and in particular [Jekyll's installation\n  instructions](https://jekyllrb.com/docs/installation/)\n\n* **Problems with installing jekyll/github-pages?** If the standard\n  installation for jekyll does not work for you (many people complain,\n  for instance, *commonmarker* does not install\n  https://stackoverflow.com/questions/58849651/bundler-cannot-install-commonmarker)\n  try a **docker container**, as described above.\n\n* In case the you get an error that a **javascript environment is\n  missing**, install a javascript environment like `nodejs` from your\n  distribution repositories.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmdanalysis%2Fmdanalysis.github.io","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmdanalysis%2Fmdanalysis.github.io","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmdanalysis%2Fmdanalysis.github.io/lists"}