Bump jinja2 from 3.1.5 to 3.1.6, update GitHub Pages deployment (#92)

* Bump jinja2 from 3.1.5 to 3.1.6
- See security tab for more information regarding the security update

* Update ONI links

* Update to modern GitHub pages deployment

* Ignore timeout for white-matter.com

Author: bparks13

.github/workflows/build_and_test.yml .github/workflows/build_docs_publish_pages.yml

@@ -1,19 +1,21 @@
-name: Build and Test Documentation
+name: Build Documentation
 
 on:
+  push:
+    branches: [ main ]
   pull_request:
-    branches:
-      - main
+    branches: [ main ]
 
 jobs:
-  build_and_test:
-    name: Build and Test
+  build:
+    name: Build
     runs-on: ubuntu-22.04
-    environment: Testing
 
     steps:
       - name: Check out repository code
         uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
       - name: Setup Python
         uses: actions/setup-python@v5
@@ -33,11 +35,24 @@ jobs:
       - name: Check all external links
         id: make_linkcheck
         run: |
-          pipenv run make linkcheck SPHINXOPTS="-W --keep-going -n" # -n: nit-picky mode, generates warnings for all missing references
+          pipenv run make linkcheck SPHINXOPTS="-W --keep-going"
 
-      - name: Upload docs
-        uses: actions/upload-artifact@v4
+      - name: Upload GitHub Pages Artifact
+        uses: actions/upload-pages-artifact@v3
         with:
-          name: html
-          if-no-files-found: error
-          path: docs/html/*
+          path: docs/html/
+
+  deploy:
+    name: Deploy docs
+    runs-on: ubuntu-22.04
+    needs: build
+    if: github.event_name == 'push' && always() && !failure() && !cancelled()
+    
+    permissions:
+      # Both required by actions/deploy-pages
+      pages: write
+      id-token: write
+      
+    steps:
+      - name: Deploy to GitHub Pages
+        uses: actions/deploy-pages@v4

.github/workflows/deploy_docs.yml

@@ -10,3 +10,5 @@ make = "*"
 pytz = "*"
 sphinxcontrib-wavedrom = "*"
 jinja2 = "*"
+
+[dev-packages]

Pipfile

@@ -22,10 +22,10 @@ Understanding the System
 - See the :ref:`hardware_guide` for a description of each ONIX hardware component and decide which you will need.
 
 .. note::
-    To understand the underlying hardware specifications, check out the `ONI Hardware Specification <https://open-ephys.github.io/ONI/hw-spec/index.html>`_.
+    To understand the underlying hardware specifications, check out the `ONI Hardware Specification <https://open-ephys.github.io/ONI/v1.0/hw-spec/index.html>`_.
 
 .. note::
-    For developers who want to dig into the API, check out the `ONI API Documentation <https://open-ephys.github.io/ONI/api/index.html>`_.
+    For developers who want to dig into the API, check out the `ONI API Documentation <https://open-ephys.github.io/ONI/v1.0/api/index.html>`_.
 
 Usage Warnings
 --------------------------------

Pipfile.lock

@@ -48,12 +48,12 @@ FAQ
     I have existing acquisition hardware. Can I can use your API and software to acquire data from it?
         Yes. We tried to design our API so that it decouples hardware details
         from software in a generic way. Have a look at the
-        `Driver Translators <https://open-ephys.github.io/ONI/api/liboni/driver-translators/index.html>`_ page
+        `Driver Translators <https://open-ephys.github.io/ONI/v1.0/api/liboni/driver-translators/index.html>`_ page
         for more information on how to use the ONIX API with your hardware.
         Depending on how your device communicates with the computer it may only
         take 10's of lines of C.
 
     I have existing acquisition software. Can I integrate support for ONIX hardware using your API?
-        Yes. Have a look at the `ONI API Documentation <https://open-ephys.github.io/ONI/api/index.html>`_
+        Yes. Have a look at the `ONI API Documentation <https://open-ephys.github.io/ONI/v1.0/api/index.html>`_
         to get started. Also let us know if you want help.
 

source/Getting Started/index.rst

@@ -29,7 +29,7 @@
     debugging and basic streaming IO with ONIX hardware.
 
 .. tip:: ONIX uses an `ONI-compliant API
-   <https://open-ephys.github.io/ONI/api/index.html>`__ that is software
+   <https://open-ephys.github.io/ONI/v1.0/api/index.html>`__ that is software
    agnostic. If you want to use ONIX hardware with your acquisition software,
    please :ref:`get in touch <support>`.
 

source/Resources/faq.rst

@@ -11,7 +11,7 @@ Command Line Application
 
 ``oni-repl`` is a simple `read-eval-print loop (REPL)
 <https://en.wikipedia.org/wiki/Read%E2%80%93eval%E2%80%93print_loop>`__ for
-`liboni <https://open-ephys.github.io/ONI/api/liboni/index.html>`__. 
+`liboni <https://open-ephys.github.io/ONI/v1.0/api/liboni/index.html>`__. 
 
 :Code: https://github.com/open-ephys/liboni/tree/main/api/liboni/oni-repl
 :Compatibility: Any ONI-compliant hardware
@@ -34,10 +34,10 @@ hardware to perform the following:
 - Bulk initialize device register state
 
 .. note:: ``oni-repl`` was created for hardware debugging and as a test program
-   for `liboni <https://open-ephys.github.io/ONI/api/liboni/index.html>`__.
+   for `liboni <https://open-ephys.github.io/ONI/v1.0/api/liboni/index.html>`__.
    However, its simplicity and lack of abstraction compared to
    :ref:`bonsai_onixref` make it useful as an example of how to use `liboni
-   <https://open-ephys.github.io/ONI/api/liboni/index.html>`__ and for quickly
+   <https://open-ephys.github.io/ONI/v1.0/api/liboni/index.html>`__ and for quickly
    examining hardware state and hub firmware versions.
 
 .. code-block:: none

source/Software Guide/index.rst

@@ -153,7 +153,8 @@
     'https://multimedia.3m.com/mws/media/*', 
     'https://www.intel.com/*',
     'https://www.analog.com/*',
-    'https://www.xilinx.com/*'
+    'https://www.xilinx.com/*',
+    'https://white-matter.com/*'
 ]
 
 # NB: Allow this permanent redirect for a Visual Studio package