{"id":22007063,"url":"https://github.com/exabyte-io/documentation","last_synced_at":"2026-05-16T04:19:03.460Z","repository":{"id":30587916,"uuid":"34143020","full_name":"Exabyte-io/documentation","owner":"Exabyte-io","description":"Exabyte.io platform documentation containing a detailed explanation of the entities, and their relationship, as well as a list of hands-on video tutorials.","archived":false,"fork":false,"pushed_at":"2026-04-01T11:27:44.000Z","size":14909,"stargazers_count":10,"open_issues_count":6,"forks_count":3,"subscribers_count":11,"default_branch":"main","last_synced_at":"2026-04-01T13:24:25.873Z","etag":null,"topics":["chemistry","cloud-computing","exabyte-io","materials","materials-genome","materials-informatics","materials-science","simulation-modeling"],"latest_commit_sha":null,"homepage":"https://docs.mat3ra.com","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"jessegavin/jQuery-Chord-Transposer","license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Exabyte-io.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2015-04-17T22:30:03.000Z","updated_at":"2026-03-25T08:27:59.000Z","dependencies_parsed_at":"2024-01-17T18:57:26.115Z","dependency_job_id":"0a169493-6697-4ca9-b5d7-89f1afbabdad","html_url":"https://github.com/Exabyte-io/documentation","commit_stats":null,"previous_names":[],"tags_count":64,"template":false,"template_full_name":null,"purl":"pkg:github/Exabyte-io/documentation","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Exabyte-io%2Fdocumentation","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Exabyte-io%2Fdocumentation/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Exabyte-io%2Fdocumentation/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Exabyte-io%2Fdocumentation/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Exabyte-io","download_url":"https://codeload.github.com/Exabyte-io/documentation/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Exabyte-io%2Fdocumentation/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31291071,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-01T13:12:26.723Z","status":"ssl_error","status_checked_at":"2026-04-01T13:12:25.102Z","response_time":53,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["chemistry","cloud-computing","exabyte-io","materials","materials-genome","materials-informatics","materials-science","simulation-modeling"],"created_at":"2024-11-30T01:16:49.399Z","updated_at":"2026-05-16T04:19:03.437Z","avatar_url":"https://github.com/Exabyte-io.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Mat3ra Documentation\n\n[Mat3ra](https://www.mat3ra.com) is a computational platform for the development of new materials and chemicals. The present documentation explains how the [platform](https://platform.mat3ra.com/) works in details. Currently deployed version of the documentation is available at [this link](http://docs.mat3ra.com).\n\n## Setup\n\nFor a quick installation:\n\n1. Install dependencies: python 3 (tested on Python `3.10`-`3.13`), `pip`, `curl`, [`virtualenv`](https://virtualenv.pypa.io/en/latest/installation/), git, [git-lfs](https://git-lfs.github.com/).\n\n2. Clone this repository:\n\n    ```bash\n    git clone https://github.com/Exabyte-io/documentation.git\n    ```\n\n3. Setup virtual environment\n\n    ```bash\n    cd documentation\n    virtualenv venv\n    source venv/bin/activate\n    pip install --no-deps -r requirements.txt\n    ```\n\n4. Init git submodules:\n\n    ```bash\n    git submodule update --recursive --init\n    ```\n\n5. (Optional) Set the documentation directory, if plan to use other languages than English:\n\n    ```bash\n    export DOCS_dir=\"lang/ja/docs\"\n    ```\n\n6. Start mkdocs server (after sourcing virtual environment):\n\n    ```bash\n    mkdocs serve\n    ```\n\nYou should have the documentation up and running at `http://localhost:8000`\n\n## Development\n\n[MkDocs](http://www.mkdocs.org/#getting-started) is used to convert Markdown files (*.md) into static html and [is configured](mkdocs.yml) to use [Mkdocs-material](https://squidfunk.github.io/mkdocs-material/) theme.\n\n### Tutorial Video Formats\n\nGenerally, text-based tutorials should have a video tutorial published alongside them. A few notes about the video\ntutorials:\n- Resolution should be kept such that users can read the text that's on the screen without needing to zoom in. A good\n  resolution to record in is 720p (1152 x 720 on a macbook, or 1280 x 720 elsewhere).\n\n### Formatting Styles\n\n#### Headers\n\nWrite the main header (title) of the page as the first line, using top-level markdown notation (`#`). After adopting [\"Material\"](https://squidfunk.github.io/mkdocs-material/) mkdocs theme, the Table of contents (on the right, containing the current page structure) is not operational when more than one top-level header is present (h1). Therefore, we shall limit each and every page to only use **one** top-level header, and all the rest should be entered as sub-headers.\n\nAll other sub-headers contained throughout the remainder of the page should then be entered as second, third or even fourth degree headers, like in the following example:\n\n```text\n# Main Header (only one allowed, to be put in first line of page)\n## Second-degree Sub-header\n### Third-degree Sub-Header\n#### Fourth-degree Sub-header\n```\n\nFor long doc pages, we may enumerate sections and sub-sections (helpful to\ndetermine scroll/reading position).\n\n```text\n# 1. Section One\n## 1.1 Subsection One\n## 1.2 Subsection Two\n# 2. Section Two\n```\n\n#### New Lines\n\nLeave a newline after the heading elements:\n\n```text\n## Job\n\nYou can create a new job by clicking the appropriate icon.\n```\n\n#### Empty Spaces\n\nLeave ONLY one empty line at the bottom of the page, and between paragraphs. Minimize the presence of unnecessary empty spaces within the main text of the page.\n\nLeave more than one empty line (2-3) when \"coming back\" to higher-level header from nested level, as below:\n\n```text\n## Job\n\n...\n\n### Job Parameters\n\n...\n\n#### Job Sub-parameters\n\n...\n\n\n## Workflow\n\n...\n```\n\n#### Admonition Styles\n\nThere are multiple [admonition](https://squidfunk.github.io/mkdocs-material/reference/admonitions/) classes available in MKDocs: tip (green), warning (orange), error (red), note (blue), and many others. To insert them in documentation pages, enter them with the following style:\n\n```text\n!!!tip \"Unused credits\"\n    All unused credits automatically roll over into the next validity period.\n```\n\nis rendered into:\n\n!!!tip \"Unused credits\"\n    All unused credits automatically roll over into the next validity period.\n\n#### Expandable Sections\n\nExpandable section can be added using:\n\n```text\n\u003cdetails markdown=\"1\"\u003e\n  \u003csummary\u003e**INCAR**\u003c/summary\u003e\n    ```\n    ALGO = Normal\n    EDIFF = 0.0001\n    ...\n    ```\n\u003c/details\u003e\n```\n\nis rendered into:\n\n\u003cdetails markdown=\"1\"\u003e\n  \u003csummary\u003e**INCAR**\u003c/summary\u003e\n    ```\n    ALGO = Normal\u003cbr\u003e\n    EDIFF = 0.0001\n    ...\n    ```\n\u003c/details\u003e\n\nPlease note the `markdown=1` tag, without it the content of the `\u003cdetails\u003e` tag will not be processed appropriately. Also, the two spaces before `\u003csummary\u003e` seem mandatory for the same purpose.\n\n#### ZMDI Icons\n\nUse [zmdi](http://zavoloklom.github.io/material-design-iconic-font/cheatsheet.html) icons instead of saying \"click\" the button with 3 stripes:\n\n```text\nclick the \u003ci class=\"zmdi zmdi-check zmdi-hc-border\"\u003e\u003c/i\u003e icon\n```\n\nwill be rendered as: \"click the \u003ci class=\"zmdi zmdi-check zmdi-hc-border\"\u003e\u003c/i\u003e icon\".\n\nWe use the same ZMDI icon set for the main application. To find the correct ZMDI tag for an icon present on the Mat3ra user interface, right click on it within your web browser and click on \"Inspect Element\". The ZMDI tag should be mentioned within the resulting HTML code describing the user interface.\n\n### Links\n\n#### External Links\n\nIncluding an external link is best done via a dedicated \"Links\" footnote section at the bottom of the page, through the `[^1]`, `[^2]`, `[^3]` etc... linking notation (this feature is implemented via the Footnotes [pymdwown extension package](https://squidfunk.github.io/mkdocs-material/extensions/footnotes)). For example (note the different style of citation for Websites, PDF documents, Wikipedia articles etc....):\n\n```text\nApple is the main competitor to Microsoft [^1].\n\nMac OS [^2] is the main Operating System developed by Apple.\n\nMac OS can run VASP, a type of ab-initio simulation code [^3].\n\nFull instructions on how to use VASP can be found in Ref. [^4].\n\n## Links\n\n[^1]: [Microsoft, Official Website](www.microsoft.com)\n[^2]: [Mac OS, Official Website](www.apple.com/mac-os.html)\n[^3]: [Wikipedia Ab-initio, Website](www.wikipedia.org/ab-initio-simulations.html)\n[^4]: [VASP manual, Document](www.vasp.com/user-manual.pdf)\n\n///FOOTNOTES GO HERE///\n```\n\nBy default, footnotes are included at the bottom of the page. `///FOOTNOTES GO HERE///` statement is necessary to include them elsewhere.\n\n#### Links to Other Documentation Pages\n\nIncluding a local link to another page in the documentation, or a specific sub-header section within that page, is done with the following notations respectively.\n\n```text\nWe explain service levels [in this page](../../pricing/service-levels.md)\n```\n\n```text\nThe particular information can be found [here](../../pricing/service-levels.md#pricing)\n```\n\nUse **ONLY RELATIVE** paths starting from the current page, not the absolute ones.\n\n### Images and Animations\n\nImages (.png, .webp, .gif) are stored inside [images](images) directory and are automatically hosted on Git LFS.\nThis is an acceptable way to contribute images, as long as the size is kept small (below 1Mb each) in order to avoid exceeding Github LFS quota.\n\n\u003e Note: Do NOT put videos inside this directory! Upload the video into your preferred online storage system such as Google Drive, DropBox, or YouTube, and share its link with us to review and put it up online.\n\nPut images in separate folders within the main \"images\" directory, one for each top level section of the documentation.\nAlso in this case it is essential to use **RELATIVE** and not absolute paths to the image, starting from the current page.\n\nA few conventions to use when naming images:\n\n1. Try to use hyphen-case for naming the images. for example, `this-is-a-good-image-name.png`; this makes it easy for a\nsearch engine to understand what the image is, and keeps the words neatly separated.\n\n2. Avoid \"keyword-stuffing,\" which search engines penalize. For example, in an image of copper nanoparticles, a\ngood image title might be \"icosahedral-copper-nanoparticle-blue-background.\" A \"keyword-stuffed\" version of this\nmight be \"copper-cu-nanoparticle-np-icosahedron-chemistry-nanomaterials-chemical-engineering-catalysis.png.\" A good rule of\nthumb for whether an image title is keyword-stuffed or not is to ask: \"Is this a natural way of describing the\nimage that would actually be used in a spoken conversation?\"\n\n#### Preferred Image Format `.webp`\n\nThe .webp format is preferred due to its size-effectiveness on the web.\nTo convert images to .webp format, make sure you have the `webp` package installed on your system. On MacOS, it can be done using Homebrew:\n\n```bash\nbrew install webp\n```\n\nThen convert .png images to .webp using the following command in the target folder:\n```bash\nfor file in $( ls *.png); do cwebp \"${file}\" -o \"${file%*.png}.webp\"; done\n```\n\nFor more details about webp, please refer to https://developers.google.com/speed/webp\n\n#### Including Images\n\nIncluding an image/screenshot is done as follows, in MKDocs notation (don't use HTML tags).\n\n```markdown\n![Alt-Text](../path/to/the/image.png \"Optional Title\")\n```\n\nFor example:\n\n```markdown\n![Simulation Diagram](../../images/simulation-job-wokflow-unit-explained.png \"Simulation Diagram\")\n```\n\nAlt-text is a [short description](https://en.wikipedia.org/wiki/Alt_attribute)\nof the image being used. This is generally intended to provide an accessible description of the image for those who are\nusing screen readers. A few guidelines for the alt-text:\n\n- Try to keep the image descriptions under 100 characters, since some screen readers will limit the number of characters\n  it uses when describing an image to someone.\n- Don't begin with redundant phrases such as \"This is an image of...\", \"This picture shows...\", etc. Just describe what's in\nthe image. For example, instead of \"This picture shows a plate of spam and eggs,\" instead write \"Plate of spam and eggs\"\n\nNote that alt-text generally used as part of search indexing in addition to the image title, so try to think about keywords for the image and the page,\nand weave them (organically) into the alt-text.\n\nThe Optional Title (quotes after the path to the image) is the mouseover text that is generated. Generally, it should be\nsimple and human-readable.\n\n\n#### Including GIFs\n\nGIFs should be stored in the same image folders as normal images (see above) with a suggested frame rate of 15 (fps). Including a GIF image is done as follows.\n\n```text\n\u003cimg data-gifffer=\"/images/AddCredit.gif\" /\u003e\n```\n\nIn this case, absolute paths to the GIF need to be used, since we insert GIFs directly with HTML and relative paths don't work with HTML commands.\n\nWe use a third-party plugin, embedded into the source of this repository (\"giffer\") in order to make gif images clickable like videos.\n\n#### Embedding Youtube Videos\n\nYoutube videos can be embedded within documentation page through the following block of commands, linking to the video's identifier present in its URL:\n\n```text\n\u003cdiv class=\"video-wrapper\"\u003e\n\u003ciframe class=\"gifffer\" width=\"100%\" height=\"100%\" src=\"https://www.youtube.com/embed/MBpd-yKUCM4\" frameborder=\"0\" allow=\"accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen\u003e\u003c/iframe\u003e\n\u003c/div\u003e\n```\n\n#### Clickable Image Maps\n\nIncluding a clickable image map is done as follows. Note that absolute paths to the image are required in this case, since we have to use HTML commands which don't work with relative paths.\n\n\n```text\n\u003cimg src=\"/images/workflow-designer-initial.png\" usemap=\"#mapname\"\u003e\n\n\u003cmap name=\"mapname\"\u003e\n    \u003carea shape=\"rect\" coords=\"0,91,190,512\" href=\"/workflow-designer/sidebar-items/\"\u003e\n    \u003carea shape=\"rect\" coords=\"190,91,754,512\" href=\"/workflow-designer/source-editor/\"\u003e\n    \u003carea shape=\"rect\" coords=\"0,28,754,91\" href=\"/workflow-designer/header-menu-actions\"\u003e\n\u003c/map\u003e\n\n\u003c!--\n    coords=\"x1,y1,x2,y2\"\n    x1=top left X coordinate\n    y1=top left Y coordinate\n    x2=bottom right X coordinate\n    y2=bottom right Y coordinate\n--\u003e\n```\n\n### Code Blocks\n\n#### JSON Schemas and Examples\n\nIncluding resolved JSON schemas and associated examples should be done within dedicated `data.md` pages for each concept being explained.\n\nThe [markdown_include](https://github.com/Exabyte-io/markdown-include) package is used to include JSON content into markdown documents, by putting direct links to pages inside the [ESSE repository](https://github.com/Exabyte-io/exabyte-esse) instead of copying their contents in the main documentation.\n\n```text\n    === \"Schema\"\n\n        ```json\n        --8\u003c-- \"data/esse/schema/material.json\"\n        ```\n\n    === \"Example\"\n\n        ```json\n        --8\u003c-- \"data/esse/example/material.json\"\n        ```\n```\n\n#### Code Snippets\n\nUse the following conventions: \"object\" to quote object or concept, or `button` (between ` ticks as opposed to \" quotes) to cite user interface icons or command-line statements in-line.\n\nExtended code blocks should be enclosed between pairs of triple ticks with name of interpreter for the language being shown, like so:\n\n    ```bash\n    exec something\n    VARIABLE = \"Example\"\n    print \"Hello World\"\n    ```\n\n#### Latex Math Equations\n\nMath equations written in Latex can be inserted within documentation pages (after installing requirements - see instructions at the top of this page) both in-line and as separate blocks, using the dollar notation as shown in the following example:\n\n```text\nWe define the Average Pressure $p_{avg}$ of a Material according to the following conventional formula.\n\n$$\np_{avg}=-\\frac{1}{3} \\mathrm{Tr} \\hspace{1pt} {\\boldsymbol{\\sigma}}\n$$\n```\n\n## Contribution\n\nThis repository is an [open-source](LICENSE.md) work-in-progress and we welcome contributions. We suggest forking this repository and introducing the adjustments there, the changes in the fork can further be considered for merging into this repository as explained in [GitHub Standard Fork and Pull Request Workflow](https://gist.github.com/Chaser324/ce0505fbed06b947d962).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fexabyte-io%2Fdocumentation","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fexabyte-io%2Fdocumentation","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fexabyte-io%2Fdocumentation/lists"}