Added structure and style for mkdocs page

JosePizarro3 · JosePizarro3 · commit 79fe1119dc8f · 2024-12-11T11:13:53.000+01:00
Added tutorial md file for create masterdata
diff --git a/docs/assets/datastore-logo-white.png b/docs/assets/datastore-logo-white.png
diff --git a/docs/explanations/data-store.md b/docs/explanations/data-store.md
@@ -0,0 +1,3 @@
+
+!!! warning
+    This page is still under construction.
diff --git a/docs/explanations/openbis.md b/docs/explanations/openbis.md
@@ -0,0 +1,3 @@
+
+!!! warning
+    This page is still under construction.
diff --git a/docs/explanations/pybis.md b/docs/explanations/pybis.md
@@ -0,0 +1,3 @@
+
+!!! warning
+    This page is still under construction.
diff --git a/docs/howtos/overview.md b/docs/howtos/overview.md
@@ -0,0 +1,3 @@
+
+!!! warning
+    This page is still under construction.
diff --git a/docs/howtos/pybis/collections.md b/docs/howtos/pybis/collections.md
@@ -0,0 +1,3 @@
+
+!!! warning
+    This page is still under construction.
diff --git a/docs/howtos/pybis/datasets.md b/docs/howtos/pybis/datasets.md
@@ -0,0 +1,3 @@
+
+!!! warning
+    This page is still under construction.
diff --git a/docs/howtos/pybis/objects.md b/docs/howtos/pybis/objects.md
@@ -0,0 +1,3 @@
+
+!!! warning
+    This page is still under construction.
diff --git a/docs/howtos/pybis/objects_props.md b/docs/howtos/pybis/objects_props.md
@@ -0,0 +1,3 @@
+
+!!! warning
+    This page is still under construction.
diff --git a/docs/howtos/pybis/parent_child.md b/docs/howtos/pybis/parent_child.md
@@ -0,0 +1,3 @@
+
+!!! warning
+    This page is still under construction.
diff --git a/docs/howtos/pybis/projects.md b/docs/howtos/pybis/projects.md
@@ -0,0 +1,3 @@
+
+!!! warning
+    This page is still under construction.
diff --git a/docs/howtos/pybis/searches.md b/docs/howtos/pybis/searches.md
@@ -0,0 +1,3 @@
+
+!!! warning
+    This page is still under construction.
diff --git a/docs/howtos/pybis/setup.md b/docs/howtos/pybis/setup.md
@@ -0,0 +1,3 @@
+
+!!! warning
+    This page is still under construction.
diff --git a/docs/howtos/pybis/spaces.md b/docs/howtos/pybis/spaces.md
@@ -0,0 +1,3 @@
+
+!!! warning
+    This page is still under construction.
diff --git a/docs/index.md b/docs/index.md
@@ -1 +1,60 @@
-Hi!
+---
+hide: toc
+---
+
+# Welcome to the BAM Data Store documentation page.
+
+The BAM **Data Store** is a central system for digital Research Data Management at the Bundesanstalt für Materialforschung und -prüfung (BAM). It is a modified instance of [openBIS](https://openbis.ch/), so this documentation page does not intend to replace the openBIS documentation, but rather serve as an additional source of information for BAM employees who use the Data Store.
+
+<!-- This documentation page is divided according to the [diataxis method](https://www.diataxis.fr/). -->
+
+
+<div markdown="block" class="home-grid">
+
+<div markdown="block">
+
+<h3>Tutorials</h3>
+
+The **Tutorials** are designed to guide you through the general and basic understanding of the functionalities of the Data Store. These are intended for learning the software in a first approach.
+
+- [Creating Masterdata](tutorials/create-masterdata.md)
+- [pyBIS tutorial](tutorials/pybis.md)
+
+</div>
+
+<div markdown="block">
+
+<h3>How-to guides</h3>
+
+The **How-to guides** provide step-by-step instructions for a wide range of tasks. These are oriented for a practical application so you can use them as a fast entry point when searching for specific information.
+
+- Using pyBIS
+- other titles here...
+
+ADD BUTTON HERE TO OPEN HOW-TO GUIDES
+
+
+</div>
+
+<div markdown="block">
+
+<h3>Explanations</h3>
+
+The **Explanations** give you a theoretical background about the main concepts used in the Data Store. These are overlapping with openBIS and pyBIS concepts, but also some specific Data Store ones, as well as on Research Data Management and Good Scientific Practices.
+
+</div>
+
+<div markdown="block">
+
+<h3>References</h3>
+
+The **References** include the glossary of used terms and API documentation.
+
+</div>
+
+</div>
+
+
+## Contact
+Many parts of this documentation are currently under construction. If you have further questions that are not yet answered here, please contact [datastore@bam.de](mailto:datastore@bam.de).
+
diff --git a/docs/references/collection.md b/docs/references/collection.md
@@ -0,0 +1,3 @@
+
+!!! warning
+    This page is still under construction.
diff --git a/docs/references/controlled-vocabulary.md b/docs/references/controlled-vocabulary.md
@@ -0,0 +1,3 @@
+
+!!! warning
+    This page is still under construction.
diff --git a/docs/references/dataset.md b/docs/references/dataset.md
@@ -0,0 +1,3 @@
+
+!!! warning
+    This page is still under construction.
diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css
@@ -1,32 +1,154 @@
 @font-face {
     font-family: "BAM Klavika-Light";
-    src: url("../assets/fonts/BAM_Klavika-Light.ttf");
+    src: url("../assets/fonts/BAMKlavika-Light.ttf");
     font-weight: normal;
     font-style: normal;
 }
 
 @font-face {
     font-family: "BAM Klavika-LightItalic";
-    src: url("../assets/fonts/BAM_Klavika-LightItalic.ttf");
+    src: url("../assets/fonts/BAMKlavika-LightItalic.ttf");
     font-weight: normal;
     font-style: normal;
 }
 
 @font-face {
     font-family: "BAM Klavika-Medium";
-    src: url("../assets/fonts/BAM_Klavika-Medium.ttf");
+    src: url("../assets/fonts/BAMKlavika-Medium.ttf");
     font-weight: normal;
     font-style: normal;
 }
 
 @font-face {
     font-family: "BAM Klavika-MediumItalic";
-    src: url("../assets/fonts/BAM_Klavika-MediumItalic.ttf");
+    src: url("../assets/fonts/BAMKlavika-MediumItalic.ttf");
     font-weight: normal;
     font-style: normal;
 }
 
 :root {
     --md-text-font: "BAM Klavika-Light";
+    --titles-font: "BAM Klavika-Medium";
     --md-code-font: "Noto Mono";
+
+    /* BAM colors */
+    --bam-weiss: rgb(243, 243, 243);
+    --bam-weiss-dark: rgb(238, 241, 243);
+    --bam-schwarz-100: rgb(0, 40, 50);
+    --bam-schwarz-80: rgb(50, 84, 99);
+    --bam-schwarz-60: rgb(95, 123, 137);
+    --bam-schwarz-45: rgb(125, 149, 163);
+    --bam-schwarz-30: rgb(163, 184, 195);
+    --bam-schwarz-15: rgb(204, 216, 223);
+    --bam-rot: rgb(210, 0, 30);
+    --bam-rot-dark: rgb(180, 15, 30);
+    --bam-rot-darker: rgb(140, 20, 25);
+    --bam-rot-darkest: rgb(80, 25, 25);
+    --bam-blau: rgb(0, 175, 240);
+    --bam-blau-dark: rgb(0, 137, 186);
+    --bam-blau-darker: rgb(0, 117, 153);
+    --bam-blau-darkest: rgb(0, 85, 110);
+    --bam-grun: rgb(140, 180, 15);
+    --bam-grun-dark: rgb(130, 165, 50);
+    --bam-grun-darker: rgb(90, 140, 50);
+    --bam-grun-darkest: rgb(55, 120, 50);
+    --bam-gelb: rgb(255, 220, 0);
+    --bam-gelb-dark: rgb(250, 185, 0);
+    --bam-gelb-darker: rgb(230, 155, 0);
+    --bam-gelb-darkest: rgb(205, 125, 0);
+
+    /* Backgrounds, primaries, and secondaries */
+    --background-light: var(--bam-weiss);
+    --color-light: var(--bam-schwarz-100);
+    --background-dark: var(--bam-schwarz-100);
+    --color-dark: var(--bam-weiss);
+
+    --code-color-light: var(--bam-grun-darkest);
+    --code-background-light: rgb(204, 216, 223, 0.3);  /* similar to bam-schwarz-15 */
+    --code-color-dark: var(--bam-grun);
+    --code-background-dark: rgb(27, 72, 83, 0.3);
+
+    --grid-background-light: rgb(238, 229, 174, 0.5);
+
+    --md-primary-fg-color: var(--bam-rot-dark);  /* for hrefs */
+    --md-accent-fg-color: var(--bam-rot);  /* when hovering hrefs */
+    --md-primary-bg-color: var(--bam-rot);  /* for search icon */
+    --md-default-bg-color: var(--bam-weiss);
+}
+
+.md-header__button.md-logo :where(img,svg) {
+    width: 100%;
+    height: 30px;
+}
+
+.md-header, .md-header__inner {
+    background-color: var(--bam-weiss-dark);
+    color: var(--bam-schwarz-100);
+}
+
+.md-header--shadow {
+    box-shadow: 0px 2px 4px -1px rgba(0, 0, 0, 0.2), 0px 4px 5px 0px rgba(0, 0, 0, 0.14), 0px 1px 10px 0px rgba(0, 0, 0, .12);
+    transition: box-shadow 200ms linear;
+}
+
+.md-header__inner {
+    height: 72px;
+}
+
+.md-header__topic {
+    font-size: 24px;
+    font-family: var(--titles-font);
+}
+
+.md-search__form:hover {
+    background-color: rgba(0,0,0,.13);
+}
+
+.md-main {
+    background-color: var(--bam-weiss);
+}
+
+.md-content__inner, .md-typeset {
+    font-size: 0.8rem;
+    font-weight: 500;
+}
+
+.md-typeset h1 {
+    color: var(--bam-schwarz-100);
+    font-family: var(--titles-font)
+}
+
+.home-grid {
+    display: grid;
+    grid-template-columns: 1fr 1fr;
+    grid-column-gap: 24px;
+    row-gap: 24px;
+}
+
+.home-grid div {
+    border-radius: 16px;
+    padding: 24px;
+    background-color: var(--grid-background-light);
+}
+
+.home-grid h3 {
+    margin-top: 0;
+    font-weight: 700;
+}
+
+.md-nav {
+    font-size: 0.8rem;
+}
+
+.md-nav__title {
+    color: var(--bam-schwarz-60)
+}
+
+.md-nav--primary .md-nav__title {
+    background: var(--bam-weiss);
+    box-shadow: 0 0 0 0;
+}
+
+.md-footer {
+    background-color: var(--bam-blau-darkest);
 }
diff --git a/docs/tutorials/create-masterdata.md b/docs/tutorials/create-masterdata.md
@@ -0,0 +1,3 @@
+
+!!! warning
+    This page is still under construction.
diff --git a/docs/tutorials/pybis.md b/docs/tutorials/pybis.md
@@ -0,0 +1,3 @@
+
+!!! warning
+    This page is still under construction.
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -1,32 +1,54 @@
 site_name: BAM Data Store Wiki
 site_description: Documentation page for the BAM Data Store.
 site_author: BAM Data Store
-repo_url: https://git.bam.de/bam-data-store/bam-data-store
+repo_url: https://github.com/BAMresearch/bam-data-store
+nav:
+  - Home: index.md
+  - Tutorial:
+    - Create Masterdata: tutorials/create-masterdata.md
+    - Basic pyBIS usage: tutorials/pybis.md
+  - How-to guides:
+    - Overview: howtos/overview.md
+    - pyBIS:
+      - Initial setup: howtos/pybis/setup.md
+      - Create spaces: howtos/pybis/spaces.md
+      - Create projects: howtos/pybis/projects.md
+      - Create collections: howtos/pybis/collections.md
+      - Create objects: howtos/pybis/objects.md
+      - Modify objects properties: howtos/pybis/objects_props.md
+      - Define parent-child relationships: howtos/pybis/parent_child.md
+      - Create datasets: howtos/pybis/datasets.md
+      - Searches and filters: howtos/pybis/searches.md
+  - Explanations:
+    - Data Store: explanations/data-store.md
+    - OpenBIS : explanations/openbis.md
+    - pyBIS : explanations/pybis.md
+  - References:
+    - Collection: references/collection.md
+    - Controlled Vocabulary: references/controlled-vocabulary.md
+    - Dataset: references/dataset.md
 theme:
   name: material
   palette:
-    # primary: "#00aff0"
-    # accent: "#d2001e"
-    - scheme: default
+    primary: custom
+    accent: custom
+    # - scheme: default
     # - media: "(prefers-color-scheme: light)"
-      toggle:
-        icon: material/weather-sunny
-        name: Switch to light mode
-    - scheme: slate
+    #   toggle:
+    #     icon: material/weather-sunny
+    #     name: Switch to light mode
+    # - scheme: slate
     # - media: "(prefers-color-scheme: dark)"
-      toggle:
-        icon: material/weather-night
-        name: Switch to dark mode
+      # toggle:
+      #   icon: material/weather-night
+      #   name: Switch to dark mode
   logo: assets/datastore-logo.png
-  favicon: assets/datastore-logo.png
+  favicon: assets/datastore-logo-white.png
   features:
     - navigation.path
     - navigation.footer
     - navigation.top
     - content.code.copy
-  # font:
-  #   text: "Klavika"
-  # font: false
 plugins:
   - search
 markdown_extensions:
@@ -47,6 +69,8 @@ markdown_extensions:
       toc_depth: 3
   - pymdownx.arithmatex:
       generic: true
-# extra_css:
-#   - stylesheets/extra.css
-#   - https://fonts.cdnfonts.com/css/noto-mono
+extra_css:
+  - stylesheets/extra.css
+extra_javascript:
+  - 'https://cdnjs.cloudflare.com/ajax/libs/js-yaml/4.1.0/js-yaml.min.js'
+  - 'https://unpkg.com/cytoscape@3.19.1/dist/cytoscape.min.js'

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	`1`	`+`
	`2`	`+!!! warning`
	`3`	`+ This page is still under construction.`