Merge pull request #90 from CLIMB-TRE/development

Fixed breaking change from Typer, updated documentation site styles

.github/workflows/docs.yml

@@ -27,9 +27,7 @@ jobs:
       - name: Install dependencies
         run: |
           pip install .
-          pip install mkdocs-material
-          pip install mkdocstrings[python]
-          pip install mkdocs-with-pdf
+          pip install mkdocs-material mkdocstrings-python mkdocs-with-pdf
       - name: Deploy site
         run: |
           typer onyx.cli utils docs --output docs/cli/documentation.md

docs/cli/getting-started.md

@@ -1,6 +1,7 @@
+[](){#cli-getting-started}
 # Getting started
 
-This guide walks through getting started with the Onyx-client CLI.
+This guide walks through getting started with the Onyx-client command-line interface.
 
 The guide assumes an environment where authentication credentials are pre-configured.
 
@@ -50,7 +51,7 @@ Filtering on the CLI uses a `field=value` syntax, where `field` is the name of a
 
 Multiple filters can be provided, and only the records that satisfy *all* these filters will be returned.
 
-### Lookups
+### Advanced filtering using lookups
 
 The data can be filtered in more complex ways using [lookups][lookups]. These use a `field.lookup=value` syntax (or alternatively, `field__lookup=value`), and different ones are available depending on a field's [data type][types] (e.g. [`text`][text], [`integer`][integer]). There are lookups for searching between a range of values on a field ([`range`][range]), whether a field's value is empty ([`isnull`][isnull]), whether a field case-insensitively contains some text ([`icontains`][icontains]), and [more][lookups]. 
 

docs/index.md

@@ -7,11 +7,11 @@ hide:
 
 ## Introduction
 
-This site documents usage of [Onyx-client](https://github.com/CLIMB-TRE/onyx-client), a program designed for interacting with the [Onyx](https://github.com/CLIMB-TRE/onyx/) database. 
+This site documents [Onyx-client](https://github.com/CLIMB-TRE/onyx-client), a program that provides a command-line interface and Python API for interacting with the [Onyx](https://github.com/CLIMB-TRE/onyx/) database.
 
-Onyx-client and Onyx are being developed as part of the [CLIMB-TRE](https://climb-tre.github.io/) project. 
+Onyx is being developed as part of the [CLIMB-TRE](https://climb-tre.github.io/) project. 
 
-![Onyx](img/onyx.png)
+![Image of the Onyx command-line interface](img/cli.png)
 
 ## Installation
 
@@ -48,14 +48,16 @@ $ pip install .
 
 ## Accessibility
 
-### Enable/disable colours
+### Enable/disable colours in the command-line interface
 
-Colours are enabled by default in the output of the Onyx-Client. To disable them, create an environment variable `ONYX_COLOURS` with the value `NONE`:
+Colours are enabled by default in the output of the command-line interface. To disable them, create an environment variable `ONYX_COLOURS` with the value `NONE`:
 
 ```
 $ export ONYX_COLOURS=NONE
 ```
 
+![Image of the Onyx command-line interface without colours](img/cli-no-colours.png)
+
 To re-enable colours, unset the environment variable:
 
 ```

docs/stylesheets/extra.css

@@ -1,9 +1,9 @@
 [data-md-color-scheme="slate"][data-md-color-primary="black"] {
-    --md-typeset-a-color: rgb(171, 71, 189);
-    /* or any other hex value */
+    --md-typeset-a-color: #d63384;
+    --md-accent-fg-color: #d63384;
 }
 
 [data-md-color-primary="black"] {
-    --md-typeset-a-color: rgb(171, 71, 189);
-    /* or any other hex value */
+    --md-typeset-a-color: #d63384;
+    --md-accent-fg-color: #d63384;
 }

mkdocs.yml

@@ -6,14 +6,15 @@ site_author: CLIMB-TRE
 
 theme:
   name: material
+  logo: assets/logo.svg
   icon:
     repo: fontawesome/brands/github
   palette:
     # Palette toggle for light mode
     - media: "(prefers-color-scheme: light)"
       scheme: default
       primary: black
-      accent: purple
+      accent: custom
       toggle:
         icon: material/weather-sunny
         name: Switch to dark mode
@@ -22,7 +23,7 @@ theme:
     - media: "(prefers-color-scheme: dark)"
       scheme: slate
       primary: black
-      accent: purple
+      accent: custom
       toggle:
         icon: material/weather-night
         name: Switch to light mode
@@ -56,6 +57,7 @@ plugins:
       cover_subtitle: ""
 
 markdown_extensions:
+  - attr_list
   - pymdownx.highlight:
       anchor_linenums: true
       line_spans: __span
@@ -75,14 +77,15 @@ nav:
   - Command-line interface: 
     - Getting started: cli/getting-started.md
     - Documentation: cli/documentation.md
-  - Python API: 
+  - Python API:
+    # - Getting started: api/getting-started.md
     - Documentation:
       - OnyxClient: api/documentation/client.md
       - OnyxConfig: api/documentation/config.md
       - OnyxEnv: api/documentation/env.md
       - OnyxField: api/documentation/field.md
       - Exceptions: api/documentation/exceptions.md
-  - Fields Reference: 
+  - Types & Lookups:
       - Types: fields/types.md
       - Lookups: fields/lookups.md
   - CLIMB-TRE: https://climb-tre.github.io

onyx/cli.py

@@ -34,6 +34,8 @@ def list_commands(self, ctx):
 
 
 app = typer.Typer(
+    name="onyx",
+    help="API for pathogen metadata.",
     cls=DefinedOrderGroup,
     no_args_is_help=True,
     pretty_exceptions_show_locals=False,
@@ -1484,7 +1486,7 @@ def version_callback(value: bool):
         raise typer.Exit()
 
 
-@app.callback(name="onyx", help=f"API for pathogen metadata.")
+@app.callback()
 def common(
     context: typer.Context,
     domain: Optional[str] = typer.Option(

onyx/version.py

@@ -1 +1 @@
-__version__ = "4.6.0"
+__version__ = "4.6.1"