mimic phb docs formatting

docs/inputs/inputs.md

@@ -15,7 +15,7 @@ The JSON file contains information about the mutations detected in the sample: t
 | input_json | The path to the JSON file that was produced by `TB-Profiler` |
 | input_bam  | The path to the BAM file that was produced by `TB-Profiler` |
 
-!!! info
+!!! dna "Remember the `bam.bai` file"
     The BAM file must have the accompanying BAI file in the same directory. It must also be named exactly the same as the BAM file but ending with a `.bai` suffix.
 
 ## Optional Inputs

docs/inputs/theiaprok.md

@@ -2,11 +2,11 @@
 title: TheiaProk Inputs on Terra
 ---
 
-When running `tbp-parser` as part of the TheiaProk workflow series ([find documentation for TheiaProk here](https://theiagen.notion.site/Theiagen-Public-Health-Resources-a4bd134b0c5c4fe39870e21029a30566?pvs=4)) on [Terra.bio](https://terra.bio), an optional input must be activated to instruct TheiaProk to run `tbp-parser`.
+When running `tbp-parser` as part of the TheiaProk workflow series ([find documentation for TheiaProk here](https://theiagen.github.io/public_health_bioinformatics/v2.2.0/workflows/genomic_characterization/theiaprok/)) on [Terra.bio](https://terra.bio), an optional input must be activated to instruct TheiaProk to run `tbp-parser`.
 
 `tbp-parser` is not on by default due to the nature of this tool and its outputs.
 
-!!! info annotate "TheiaProk Version"
+!!! dna annotate "TheiaProk Version"
     This information only corresponds to PHB v2.2.0. These inputs and outputs may not be applicable to other versions of TheiaProk.
 
 *[PHB]: Public Health Bioinformatics is the GitHub repository that contains the TheiaProk workflows.

docs/outputs/theiaprok.md

@@ -3,9 +3,9 @@ title: TheiaProk Outputs on Terra
 ---
 
 
-When running `tbp-parser` as part of the TheiaProk workflow series ([find documentation for TheiaProk here](https://theiagen.notion.site/Theiagen-Public-Health-Resources-a4bd134b0c5c4fe39870e21029a30566?pvs=4)) on [Terra.bio](https://terra.bio), you will find the following outputs in your data table.
+When running `tbp-parser` as part of the TheiaProk workflow series ([find documentation for TheiaProk here](https://theiagen.github.io/public_health_bioinformatics/v2.2.0/workflows/genomic_characterization/theiaprok/)) on [Terra.bio](https://terra.bio), you will find the following outputs in your data table.
 
-!!! info annotate "TheiaProk Version"
+!!! dna annotate "TheiaProk Version"
     This information only corresponds to PHB v2.2.0. These inputs and outputs may not be applicable to other versions of TheiaProk.
 
 *[PHB]: Public Health Bioinformatics is the GitHub repository that contains the TheiaProk workflows.

docs/stylesheets/extra.css

@@ -0,0 +1,188 @@
+/* color scheme */
+[data-md-color-scheme="light"] {
+  --md-primary-bg-color: #ffffff;
+  --md-primary-fg-color: #116eb7;
+  --md-accent-bg-color: #ffffff;
+  --md-accent-fg-color: #1da74a;
+  th {
+    background: #ffffff;
+    color: #262626;
+  }
+}
+[data-md-color-scheme="light"] img[src$="#only-dark"],
+[data-md-color-scheme="light"] img[src$="#gh-dark-mode-only"] {
+  display: none; /* Hide dark images in light mode */
+}
+[data-md-color-scheme="slate"] img[src$="#only-light"],
+[data-md-color-scheme="slate"] img[src$="#gh-light-mode-only"] {
+  display: none; /* Hide light images in dark mode */
+}
+[data-md-color-scheme="slate"] {
+  --md-primary-bg-color: #1da74a;
+  --md-primary-fg-color: #262626;
+  --md-accent-bg-color: #ffffff;
+  --md-accent-fg-color: #1da74a;
+  th {
+    background: #1F2029;
+    color: #ffffff;
+  }
+}
+
+/* dna admonition */
+:root {
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+
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+:root {
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+}
+.md-typeset .techdetails > .admonition-title::before,
+.md-typeset .techdetails > summary::before {
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+          mask-image: var(--md-admonition-icon--techdetails);
+}
+
+/* text toggle admonition */
+:root {
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+}
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+  background-color: rgba(255, 255, 255, 0);
+}
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+.md-typeset .task > summary::before {
+  background-color: rgb(125, 125, 125);
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+          mask-image: var(--md-admonition-icon--task);
+}
+.md-typeset .task > h5 {
+  /* this renders the heading readable by screen readers but does not display it */
+  margin: -1px; padding: 0; border: 0; 
+  visibility: hidden;
+  margin-top: -15px; /* this makes the header in the TOC jump to the top of the admonition box */
+  position: relative;
+}
+
+/* caption admonition */
+:root {
+  --md-admonition-icon--caption: url('data:image/svg+xml;charset=utf-8,<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M10 14.29 6.5 19h10.96l-2.71-3.54-1.97 2.34L10 14.29M5 21V7h13.96v14H5m7-18.6 2.61 2.63H9.37L12 2.4M5 5.03c-.5 0-1 .19-1.39.58C3.2 6 3 6.46 3 7v14c0 .5.2 1 .61 1.39C4 22.8 4.5 23 5 23h13.96c.54 0 1-.2 1.41-.61.4-.39.63-.89.63-1.39V7c0-.54-.23-1-.63-1.39-.41-.39-.87-.58-1.41-.58H16L12 1 7.96 5.03H5Z"/></svg>')
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+.md-typeset .caption > summary::before {
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+          mask-image: var(--md-admonition-icon--caption);
+}
+.md-typeset .caption > h5 {
+  /* this renders the heading readable by screen readers but does not display it */
+  margin: -1px; padding: 0; border: 0; 
+  visibility: hidden;
+  margin-top: -15px; /* this makes the header in the TOC jump to the top of the admonition box */
+  position: relative;
+}
+
+/* edit the tip admonition */
+.md-typeset .tip > h5 {
+  /* this renders the heading readable by screen readers but does not display it */
+  margin: -1px; padding: 0; border: 0; 
+  visibility: hidden;
+  margin-top: -15px; /* this makes the header in the TOC jump to the top of the admonition box */
+  position: relative;
+}
+
+/* content width */
+.md-grid {
+  max-width: initial;
+}
+
+/* scrollbar and resizable columns in tables */
+table {
+  overflow-y: scroll;
+  max-height: 500px;
+  display: block;
+}
+th {
+  position: sticky;
+  top: 0;
+  resize: horizontal;
+  overflow: auto;
+}
+td {
+  word-break: break-all;
+}
+
+

interpretation_docs/index.md

@@ -0,0 +1,6 @@
+---
+title: Interpretation Documents
+---
+
+
+![Interpretation Documents](v1.2.3_interpretation_logic.pdf){ type=application/pdf }

mkdocs.yml

@@ -2,6 +2,7 @@ site_name: tbp-parser
 site_author: Sage Wright
 site_description: A TBProfiler output parser
 
+site_url: https://theiagen.github.io/tbp-parser/
 repo_url: https://github.com/theiagen/tbp-parser
 
 theme: 
@@ -12,54 +13,54 @@ theme:
     - content.code.copy
     - content.tabs.link
     - content.tooltips
-    - navigation.expand
+    #- navigation.expand
     - navigation.instant
-    - navigation.instant.preview
+    #- navigation.instant.preview
     - navigation.path
-    - navigation.sections
     - navigation.tabs
     - navigation.top
     - navigation.tracking
     - search.highlight
     - search.suggest
     - toc.follow
-    - toc.integrate
   language: en
   palette:
-    - scheme: default
-      toggle: 
+    - media: "(prefers-color-scheme: light)"
+      scheme: light 
+      toggle:
         icon: material/weather-night
-        title: Switch to Dark Mode
-      primary: teal
-      accent: light blue
-    - scheme: slate
+        name: Switch to Dark Mode
+    - media: "(prefers-color-scheme: dark)"
+      scheme: slate
+      accent: indigo
+      primary: black
       toggle:
         icon: material/white-balance-sunny
-        title: Switch to Light Mode
-      primary: teal
-      accent: deep purple
+        name: Switch to Light Mode
 
 nav:
-  - Home: index.md
-  - Getting Started: usage.md
-  - Inputs: 
-      - inputs/inputs.md
-      - TheiaProk Inputs on Terra: inputs/theiaprok.md
-  - Outputs:
-      - outputs/index.md
-      - Laboratorian report: outputs/laboratorian.md
-      - LIMS report: outputs/lims.md
-      - Looker report: outputs/looker.md
-      - Coverage report: outputs/coverage.md
-      - TheiaProk Outputs on Terra: outputs/theiaprok.md
+  - tbp-parser:
+      - Home: index.md
+      - Getting Started: usage.md
+      - Inputs:
+          - inputs/inputs.md
+          - TheiaProk Inputs on Terra: inputs/theiaprok.md
+      - Outputs: 
+          - outputs/index.md
+          - Laboratorian report: outputs/laboratorian.md
+          - LIMS report: outputs/lims.md
+          - Looker report: outputs/looker.md
+          - Coverage report: outputs/coverage.md
+          - TheiaProk Outputs on Terra: outputs/theiaprok.md
   - Versioning: 
-     - versioning/index.md
-     - Brief Description of Versions: versioning/brief.md
-     - Exhaustive List of Versions: versioning/exhaustive.md
+    - versioning/index.md
+    - Brief Description of Versions: versioning/brief.md
+    - Exhaustive List of Versions: versioning/exhaustive.md
   - Algorithm:
       - algorithm/index.md
       - Technical Code Breakdown: algorithm/technical.md
-      - Interpretation Document: algorithm/interpretation.md
+      - Interpretation Document: algorithm/interpretation.md`
+
 
 markdown_extensions: 
   - abbr
@@ -76,6 +77,7 @@ markdown_extensions:
   - pymdownx.inlinehilite
   - pymdownx.keys
   - pymdownx.mark
+  - pymdownx.caret
   - pymdownx.snippets
   - pymdownx.superfences
   - pymdownx.tasklist:
@@ -88,11 +90,17 @@ plugins:
       enable_creation_date: true
       type: iso_date
   - search
+  - glightbox
+  - mike
 
 extra_javascript:
   - https://unpkg.com/[email protected]/dist/tablesort.min.js
   - javascripts/tablesort.js
 
+
+extra_css:
+  - stylesheets/extra.css
+
 extra:
   social:
     - icon: fontawesome/brands/github-alt
@@ -103,6 +111,8 @@ extra:
       link: https://www.linkedin.com/company/theiagen
   version:
     provider: mike
+    default: latest
+    alias: true
 
 copyright: |
   &copy; 2024 <a href="https://www.theiagen.com" target="_blank" rel="noopener">Theiagen Genomics</a>