From b0d398bd5e9e5b595da2578d666dcaaff3d460e7 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 13:31:13 -0400 Subject: [PATCH 01/36] install doc link checker --- .github/workflows/build.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 552f93b..04e53c1 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -15,12 +15,15 @@ jobs: uses: actions/checkout@v4.1.1 with: submodules: true - + - name: Setup .NET Core SDK uses: actions/setup-dotnet@v4.0.0 with: dotnet-version: 8.x + - name: Install DocLinkChecker + run: dotnet tool install DocLinkChecker + - name: Setup DocFX run: dotnet tool restore From e9538edf5fec0066fc0b49f7ada4e99dd70dbfb3 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 13:35:35 -0400 Subject: [PATCH 02/36] First test running DocLinkChecker --- .github/workflows/build.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 04e53c1..015c8ea 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -24,6 +24,9 @@ jobs: - name: Install DocLinkChecker run: dotnet tool install DocLinkChecker + - name: Check Documentation Links + run: dotnet DocLinkChecker -d articles -v + - name: Setup DocFX run: dotnet tool restore From 0fda26c867b0a26589972fc787856cfbd516521a Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 13:41:24 -0400 Subject: [PATCH 03/36] Update links to match what DocLinkChecker expects --- articles/getting-started/initialize_oni_context.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/articles/getting-started/initialize_oni_context.md b/articles/getting-started/initialize_oni_context.md index 1b9983a..645b645 100644 --- a/articles/getting-started/initialize_oni_context.md +++ b/articles/getting-started/initialize_oni_context.md @@ -7,11 +7,11 @@ The [`CreateContext`](xref:OpenEphys.Onix.CreateContext) operator initializes th 1. From the Bonsai editor, navigate to the toolbox on the left side of the screen and expand the **Source** section. Next, expand the **OpenEphys.Onix** section, and find the `CreateContext` line. The node can then be added by either double-clicking it, or dragging and dropping the node into the workflow. - ![Search for CreateContext node manually](~/images/bonsai-editor-place-create-context-manually.png){width=700px} + ![Search for CreateContext node manually](../../images/bonsai-editor-place-create-context-manually.png){width=700px} 2. Click on the textbox at the top of the toolbox on the left, or from Ctrl + E to focus on the textbox, and type `CreateContext` to search for the node. Same as (1), the node can be placed by double-clicking or dragging and dropping; additionally, if the `CreateContext` string is highlighted Enter can be pressed to place the node immediately. - ![Search for CreateContext node from textbox](~/images/bonsai-editor-place-create-context-search.png){width=700px} + ![Search for CreateContext node from textbox](../../images/bonsai-editor-place-create-context-search.png){width=700px} 3. Hover over the image of the [`CreateContext`](xref:OpenEphys.Onix.CreateContext) workflow below, and click on the clipboard icon in the top-right corner of the workflow image to copy the workflow to the clipboard. Navigate back to Bonsai, and paste the copied workflow into the active editor. Pasting can be done via Ctrl + V, or right-clicking in the editor and choosing **Paste**. @@ -20,5 +20,5 @@ The [`CreateContext`](xref:OpenEphys.Onix.CreateContext) operator initializes th This is a nominally functional workflow that provides access to the ONI context, from which all nodes can then be linked to and configured, while also demonstrating how a Breakout Board can be configured before finishing the configuration chain by placing a [`StartAcquisition`](xref:OpenEphys.Onix.StartAcquisition) node: :::workflow -![CreateContext](~/workflows/operators/ConfigureBreakoutBoard.bonsai) +![CreateContext](../../workflows/operators/ConfigureBreakoutBoard.bonsai) ::: From 8c8b6826441cab979461ad0c036ed848614aef89 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 13:45:28 -0400 Subject: [PATCH 04/36] Create DocLinkChecker.config --- .github/workflows/DocLinkChecker.config | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 .github/workflows/DocLinkChecker.config diff --git a/.github/workflows/DocLinkChecker.config b/.github/workflows/DocLinkChecker.config new file mode 100644 index 0000000..f1129b3 --- /dev/null +++ b/.github/workflows/DocLinkChecker.config @@ -0,0 +1,25 @@ +{ + "DocumentationFiles": { + "src": "", + "Files": [ + "**/*.md" + ], + "Exclude": [] + }, + "ResourceFolderNames": [ + "images" + ], + "DocLinkChecker": { + "RelativeLinkStrategy": "All", + "CheckForOrphanedResources": true, + "CleanupOrphanedResources": false, + "ValidatePipeTableFormatting": true, + "ValidateExternalLinks": true, + "ConcurrencyLevel": 5, + "MaxHttpRedirects": 20, + "ExternalLinkDurationWarning": 3000, + "WhitelistUrls": [ + "http://localhost" + ] + } +} From ac734d73581812aef2be806bafd7fbf39b96a53c Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 13:46:19 -0400 Subject: [PATCH 05/36] Call DocLinkChecker.config --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 015c8ea..dae1511 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -25,7 +25,7 @@ jobs: run: dotnet tool install DocLinkChecker - name: Check Documentation Links - run: dotnet DocLinkChecker -d articles -v + run: dotnet DocLinkChecker -v -f .github/workflows/DocLinkChecker.config - name: Setup DocFX run: dotnet tool restore From ab4b7efaf1416be4d84c8742dadd9fd859841165 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 13:47:57 -0400 Subject: [PATCH 06/36] Update DocLinkChecker.config --- .github/workflows/DocLinkChecker.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/DocLinkChecker.config b/.github/workflows/DocLinkChecker.config index f1129b3..b7eb2ef 100644 --- a/.github/workflows/DocLinkChecker.config +++ b/.github/workflows/DocLinkChecker.config @@ -1,6 +1,6 @@ { "DocumentationFiles": { - "src": "", + "src": "*", "Files": [ "**/*.md" ], From b5b5b70c4827d531c9f59a634e3733c99f60e907 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 13:50:40 -0400 Subject: [PATCH 07/36] Update DocLinkChecker.config --- .github/workflows/DocLinkChecker.config | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/DocLinkChecker.config b/.github/workflows/DocLinkChecker.config index b7eb2ef..44a4a71 100644 --- a/.github/workflows/DocLinkChecker.config +++ b/.github/workflows/DocLinkChecker.config @@ -1,6 +1,8 @@ { "DocumentationFiles": { - "src": "*", + "src": [ + "articles" + ], "Files": [ "**/*.md" ], From ceca053972b2814c323bea4ce6e080530d5d8e14 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 13:52:56 -0400 Subject: [PATCH 08/36] Update DocLinkChecker.config --- .github/workflows/DocLinkChecker.config | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/DocLinkChecker.config b/.github/workflows/DocLinkChecker.config index 44a4a71..f81bb78 100644 --- a/.github/workflows/DocLinkChecker.config +++ b/.github/workflows/DocLinkChecker.config @@ -1,8 +1,6 @@ { "DocumentationFiles": { - "src": [ - "articles" - ], + "src": "articles", "Files": [ "**/*.md" ], From 8989b9bd307210fbaa04b0c36d8ce18e9c3925d5 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 13:56:11 -0400 Subject: [PATCH 09/36] Update tips_and_tricks.md --- articles/getting-started/tips_and_tricks.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/articles/getting-started/tips_and_tricks.md b/articles/getting-started/tips_and_tricks.md index 8a1ed92..adc77dd 100644 --- a/articles/getting-started/tips_and_tricks.md +++ b/articles/getting-started/tips_and_tricks.md @@ -11,7 +11,7 @@ The order of nodes is also important for which actions can be taken. In the tabl | Goal | Clicks / Keystrokes | Description | | ---- | ------------------- | ----------- | -| Link two nodes | Click and hold the first node, drag the cursor to the second node, and release | While dragging the cursor, it will temporarily change to a red symbol until there is a valid target (e.g., the second node), where it will change to an up arrow | +| Link two nodes | Click and hold the first node, drag the cursor to the second node, and release | While dragging the cursor, it will temporarily change to a red symbol until there is a valid target (e.g., the second node), where it will change to an up arrow | | Link two nodes | Right-click the first node, and select **Create Connection**. Select the second node | While moving the cursor, it will change to an up arrow. A valid node target will change color when hovering over it | | Link two nodes on placement | Click on a node in the editor to select it, then place a node using either method (1) or (2) above | If a node is currently selected in the editor when a new node is added, whether it is added by clicking and dragging, double-clicking, or pressing **Enter**, the newly placed node will be connected to the first node automatically | | Unlink two nodes | Click the first node to select it, hold **Shift**, click and hold the first node, drag to the second node, and release | While dragging the cursor, it will temporarily change to a red symbol until there is a valid target (e.g., the second node), where it will change to an up arrow | From f9408bc097a214cbfd4b880dd3d925af849a5b01 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 13:59:31 -0400 Subject: [PATCH 10/36] Update DocLinkChecker.config --- .github/workflows/DocLinkChecker.config | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/DocLinkChecker.config b/.github/workflows/DocLinkChecker.config index f81bb78..bcd2511 100644 --- a/.github/workflows/DocLinkChecker.config +++ b/.github/workflows/DocLinkChecker.config @@ -7,7 +7,8 @@ "Exclude": [] }, "ResourceFolderNames": [ - "images" + "images", + "workflows" ], "DocLinkChecker": { "RelativeLinkStrategy": "All", From 8395e9de970b82a29701dc9307e2ffc85db6d39d Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 14:10:47 -0400 Subject: [PATCH 11/36] Remove the articles folder; all folders should be specified from CLI --- .github/workflows/DocLinkChecker.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/DocLinkChecker.config b/.github/workflows/DocLinkChecker.config index bcd2511..d142f81 100644 --- a/.github/workflows/DocLinkChecker.config +++ b/.github/workflows/DocLinkChecker.config @@ -1,6 +1,6 @@ { "DocumentationFiles": { - "src": "articles", + "src": "", "Files": [ "**/*.md" ], From cf3384d242d461804b7bc92724282e7f8cb8a789 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 14:11:11 -0400 Subject: [PATCH 12/36] Update build.yml --- .github/workflows/build.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index dae1511..20f5965 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -24,8 +24,8 @@ jobs: - name: Install DocLinkChecker run: dotnet tool install DocLinkChecker - - name: Check Documentation Links - run: dotnet DocLinkChecker -v -f .github/workflows/DocLinkChecker.config + - name: Check Documentation Links in Articles + run: dotnet DocLinkChecker -v -f .github/workflows/DocLinkChecker.config -d articles - name: Setup DocFX run: dotnet tool restore From 584432b4fa2ca8e7b33e4fdb9508e7fecce35422 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 14:13:08 -0400 Subject: [PATCH 13/36] Also check tutorials --- .github/workflows/build.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 20f5965..4716399 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -27,6 +27,9 @@ jobs: - name: Check Documentation Links in Articles run: dotnet DocLinkChecker -v -f .github/workflows/DocLinkChecker.config -d articles + - name: Check Documentation Links in Tutorials + run: dotnet DocLinkChecker -v -f .github/workflows/DocLinkChecker.config -d tutorials + - name: Setup DocFX run: dotnet tool restore From 5e968cae4adfed82737a098c2d8eefa05c2a5900 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 14:16:49 -0400 Subject: [PATCH 14/36] Update headstage64-tut.md --- tutorials/headstage64-tut.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/headstage64-tut.md b/tutorials/headstage64-tut.md index 9bd99bd..f53d300 100644 --- a/tutorials/headstage64-tut.md +++ b/tutorials/headstage64-tut.md @@ -1,5 +1,5 @@ # Headstage 64 Tutorial :::workflow -![Headstage64](~/workflows/examples/Headstage64.bonsai) +![Headstage64](../../workflows/examples/Headstage64.bonsai) ::: From 79230a30990aa18b410a0e313fcec17a89abae0f Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 14:17:01 -0400 Subject: [PATCH 15/36] Update neuropixelsv1e-tut.md --- tutorials/neuropixelsv1e-tut.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/neuropixelsv1e-tut.md b/tutorials/neuropixelsv1e-tut.md index 3ee54b8..3463a53 100644 --- a/tutorials/neuropixelsv1e-tut.md +++ b/tutorials/neuropixelsv1e-tut.md @@ -1,5 +1,5 @@ # NeuropixelsV1e Tutorial :::workflow -![NeuropixelsV1e](~/workflows/examples/NeuropixelsV1e.bonsai) +![NeuropixelsV1e](../../workflows/examples/NeuropixelsV1e.bonsai) ::: From 91d7cc11fcd6f2226cafd1a9661b553a944c7a55 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 14:17:13 -0400 Subject: [PATCH 16/36] Update neuropixelsv2e-tut.md --- tutorials/neuropixelsv2e-tut.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/neuropixelsv2e-tut.md b/tutorials/neuropixelsv2e-tut.md index d7a7406..d13f58a 100644 --- a/tutorials/neuropixelsv2e-tut.md +++ b/tutorials/neuropixelsv2e-tut.md @@ -1,5 +1,5 @@ # NeuropixelsV2e Tutorial :::workflow -![NeuropixelsV2e](~/workflows/examples/NeuropixelsV2e.bonsai) +![NeuropixelsV2e](../../workflows/examples/NeuropixelsV2e.bonsai) ::: From a1b4b769194c83f24677b17e29b443b2d15d3372 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 14:19:57 -0400 Subject: [PATCH 17/36] Update headstage64-tut.md --- tutorials/headstage64-tut.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/headstage64-tut.md b/tutorials/headstage64-tut.md index f53d300..35f362e 100644 --- a/tutorials/headstage64-tut.md +++ b/tutorials/headstage64-tut.md @@ -1,5 +1,5 @@ # Headstage 64 Tutorial :::workflow -![Headstage64](../../workflows/examples/Headstage64.bonsai) +![Headstage64](../workflows/examples/Headstage64.bonsai) ::: From 4e3e53e21e066e13c0b0594a3a6e6f8ca4f1ff27 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 14:20:04 -0400 Subject: [PATCH 18/36] Update neuropixelsv1e-tut.md --- tutorials/neuropixelsv1e-tut.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/neuropixelsv1e-tut.md b/tutorials/neuropixelsv1e-tut.md index 3463a53..92c40fb 100644 --- a/tutorials/neuropixelsv1e-tut.md +++ b/tutorials/neuropixelsv1e-tut.md @@ -1,5 +1,5 @@ # NeuropixelsV1e Tutorial :::workflow -![NeuropixelsV1e](../../workflows/examples/NeuropixelsV1e.bonsai) +![NeuropixelsV1e](../workflows/examples/NeuropixelsV1e.bonsai) ::: From f3e8bee3474ddb0098e12adb8e6cf934c5e4ae43 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 14:20:12 -0400 Subject: [PATCH 19/36] Update neuropixelsv2e-tut.md --- tutorials/neuropixelsv2e-tut.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/neuropixelsv2e-tut.md b/tutorials/neuropixelsv2e-tut.md index d13f58a..534ee9d 100644 --- a/tutorials/neuropixelsv2e-tut.md +++ b/tutorials/neuropixelsv2e-tut.md @@ -1,5 +1,5 @@ # NeuropixelsV2e Tutorial :::workflow -![NeuropixelsV2e](../../workflows/examples/NeuropixelsV2e.bonsai) +![NeuropixelsV2e](../workflows/examples/NeuropixelsV2e.bonsai) ::: From 0cb913f7c830e39df8bb0dd5040a182b5cd63d00 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 15:59:13 -0400 Subject: [PATCH 20/36] Add lychee check for broken links in HTML pages --- .github/workflows/build.yml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 4716399..6d9d7dc 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -24,9 +24,11 @@ jobs: - name: Install DocLinkChecker run: dotnet tool install DocLinkChecker + # This checks for missing / broken links in the *.md files directly prior to building the website - name: Check Documentation Links in Articles run: dotnet DocLinkChecker -v -f .github/workflows/DocLinkChecker.config -d articles + # This checks for missing / broken links in the *.md files directly prior to building the website - name: Check Documentation Links in Tutorials run: dotnet DocLinkChecker -v -f .github/workflows/DocLinkChecker.config -d tutorials @@ -39,6 +41,14 @@ jobs: - name: Build Documentation run: .\build.ps1 + + # This checks for missing / broken links in the *.html files after building the website. + # We need to run this step here to check that all auto-generated API pages have valid links too. + - name: Check HTML Links After Building + uses: lycheeverse/lychee-action@v1.10.0 + with: + args: --base . --verbose --no-progress './_site/**/*.html' + fail: true - name: Checkout gh-pages uses: actions/checkout@v4.1.1 From 061463687655a74ad6bdd315ef569fc26ea25117 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 16:07:28 -0400 Subject: [PATCH 21/36] test ubuntu --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 6d9d7dc..fd44635 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -9,7 +9,7 @@ on: jobs: build: - runs-on: windows-latest + runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@v4.1.1 From 58ee261be68ae456e837fc243ec1bc78cd166f62 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 16:13:05 -0400 Subject: [PATCH 22/36] Update build.yml --- .github/workflows/build.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index fd44635..469d3fc 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -9,7 +9,7 @@ on: jobs: build: - runs-on: ubuntu-latest + runs-on: windows-latest steps: - name: Checkout uses: actions/checkout@v4.1.1 @@ -45,9 +45,9 @@ jobs: # This checks for missing / broken links in the *.html files after building the website. # We need to run this step here to check that all auto-generated API pages have valid links too. - name: Check HTML Links After Building - uses: lycheeverse/lychee-action@v1.10.0 + uses: lycheeverse/lychee-action@v1 with: - args: --base . --verbose --no-progress './_site/**/*.html' + args: --base . --verbose --no-progress '_site/**/*.html' fail: true - name: Checkout gh-pages From 385e597c9d15bc14dd53b9fd60ac90c52b4217a1 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 16:15:25 -0400 Subject: [PATCH 23/36] Update build.yml --- .github/workflows/build.yml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 469d3fc..27f753e 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -16,6 +16,14 @@ jobs: with: submodules: true + # This checks for missing / broken links in the *.html files after building the website. + # We need to run this step here to check that all auto-generated API pages have valid links too. + - name: Check HTML Links (TESTING) + uses: lycheeverse/lychee-action@v1 + with: + args: --base _site --verbose --no-progress '_site/**/*.md' # '_site/**/*.html' + fail: true + - name: Setup .NET Core SDK uses: actions/setup-dotnet@v4.0.0 with: From c719962666edfef99c75ef37a767a49f62be8b82 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 16:18:59 -0400 Subject: [PATCH 24/36] test ubuntu v2 --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 27f753e..0226637 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -9,7 +9,7 @@ on: jobs: build: - runs-on: windows-latest + runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@v4.1.1 From 64c973209fe452c4dcb332ac337ac929ce19db37 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 16:26:12 -0400 Subject: [PATCH 25/36] Testing multiple jobs --- .github/workflows/build.yml | 21 ++++++++++----------- 1 file changed, 10 insertions(+), 11 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 0226637..27c6787 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -9,21 +9,13 @@ on: jobs: build: - runs-on: ubuntu-latest + runs-on: windows-latest steps: - name: Checkout uses: actions/checkout@v4.1.1 with: submodules: true - # This checks for missing / broken links in the *.html files after building the website. - # We need to run this step here to check that all auto-generated API pages have valid links too. - - name: Check HTML Links (TESTING) - uses: lycheeverse/lychee-action@v1 - with: - args: --base _site --verbose --no-progress '_site/**/*.md' # '_site/**/*.html' - fail: true - - name: Setup .NET Core SDK uses: actions/setup-dotnet@v4.0.0 with: @@ -50,14 +42,21 @@ jobs: - name: Build Documentation run: .\build.ps1 + check: + runs-on: ubuntu-latest + needs: build + steps: # This checks for missing / broken links in the *.html files after building the website. # We need to run this step here to check that all auto-generated API pages have valid links too. - name: Check HTML Links After Building uses: lycheeverse/lychee-action@v1 with: - args: --base . --verbose --no-progress '_site/**/*.html' + args: --base _site --verbose --no-progress '_site/**/*.html' fail: true - + + deploy: + runs-on: ubuntu-latest + steps: - name: Checkout gh-pages uses: actions/checkout@v4.1.1 with: From 6ba1bfa623588ea1da322cddbf83df881f85f0be Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 16:41:43 -0400 Subject: [PATCH 26/36] Update build.yml --- .github/workflows/build.yml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 27c6787..87bdf61 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -49,13 +49,14 @@ jobs: # This checks for missing / broken links in the *.html files after building the website. # We need to run this step here to check that all auto-generated API pages have valid links too. - name: Check HTML Links After Building - uses: lycheeverse/lychee-action@v1 + uses: lycheeverse/lychee-action@v1.10.0 with: - args: --base _site --verbose --no-progress '_site/**/*.html' + args: --verbose --no-progress _site/**/*.html fail: true deploy: runs-on: ubuntu-latest + needs: [build, check] steps: - name: Checkout gh-pages uses: actions/checkout@v4.1.1 @@ -64,7 +65,7 @@ jobs: path: gh-pages - name: Publish to github pages - uses: peaceiris/actions-gh-pages@v3.9.3 + uses: peaceiris/actions-gh-pages@v4.0.0 with: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: _site From e28654d4243a3488397b4cb0718150fd5a6b2c3d Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 16:51:00 -0400 Subject: [PATCH 27/36] Update build.yml --- .github/workflows/build.yml | 22 ++++++++++++++++------ 1 file changed, 16 insertions(+), 6 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 87bdf61..95d4bcd 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -42,10 +42,24 @@ jobs: - name: Build Documentation run: .\build.ps1 - check: + - name: Upload Artifact + uses: actions/upload-artifact@v4 + with: + name: _site + path: _site + if-no-files-found: error + + check_and_deploy: + name: Check and Deply runs-on: ubuntu-latest needs: build steps: + - name: Download Artifact + uses: actions/download-artifact@v4 + with: + name: _site + path: _site + # This checks for missing / broken links in the *.html files after building the website. # We need to run this step here to check that all auto-generated API pages have valid links too. - name: Check HTML Links After Building @@ -53,11 +67,7 @@ jobs: with: args: --verbose --no-progress _site/**/*.html fail: true - - deploy: - runs-on: ubuntu-latest - needs: [build, check] - steps: + - name: Checkout gh-pages uses: actions/checkout@v4.1.1 with: From c649624afdc019a3f8fcdf597453d1fe629db549 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 17:01:16 -0400 Subject: [PATCH 28/36] Update build.yml --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 95d4bcd..9d0f85d 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -50,7 +50,7 @@ jobs: if-no-files-found: error check_and_deploy: - name: Check and Deply + name: Check and Deploy runs-on: ubuntu-latest needs: build steps: From e9e6ccf7db3be0f410028415fa8ce131de917fcc Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 17:10:09 -0400 Subject: [PATCH 29/36] Create .lycheeignore --- .github/workflows/.lycheeignore | 1 + 1 file changed, 1 insertion(+) create mode 100644 .github/workflows/.lycheeignore diff --git a/.github/workflows/.lycheeignore b/.github/workflows/.lycheeignore new file mode 100644 index 0000000..875f1d4 --- /dev/null +++ b/.github/workflows/.lycheeignore @@ -0,0 +1 @@ +/^.*DataFrame.*/gm From 0c20ad3b3172c9c55f2c17bdfcf2cf422229d479 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 17:16:51 -0400 Subject: [PATCH 30/36] Delete .github/workflows/.lycheeignore --- .github/workflows/.lycheeignore | 1 - 1 file changed, 1 deletion(-) delete mode 100644 .github/workflows/.lycheeignore diff --git a/.github/workflows/.lycheeignore b/.github/workflows/.lycheeignore deleted file mode 100644 index 875f1d4..0000000 --- a/.github/workflows/.lycheeignore +++ /dev/null @@ -1 +0,0 @@ -/^.*DataFrame.*/gm From ef67e362b0fa32691736b1b912202f30b308b849 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 17:28:02 -0400 Subject: [PATCH 31/36] Update build.yml --- .github/workflows/build.yml | 17 ++--------------- 1 file changed, 2 insertions(+), 15 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 9d0f85d..c5f4f8b 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -49,8 +49,8 @@ jobs: path: _site if-no-files-found: error - check_and_deploy: - name: Check and Deploy + check: + name: Check Links runs-on: ubuntu-latest needs: build steps: @@ -67,16 +67,3 @@ jobs: with: args: --verbose --no-progress _site/**/*.html fail: true - - - name: Checkout gh-pages - uses: actions/checkout@v4.1.1 - with: - ref: gh-pages - path: gh-pages - - - name: Publish to github pages - uses: peaceiris/actions-gh-pages@v4.0.0 - with: - github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: _site - force_orphan: true From 816dfa5a1e2a6c1dc203a7fe93decebb180b5f3a Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 17:32:56 -0400 Subject: [PATCH 32/36] Create deploy.yml --- .github/workflows/deploy.yml | 39 ++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 .github/workflows/deploy.yml diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml new file mode 100644 index 0000000..012f4a3 --- /dev/null +++ b/.github/workflows/deploy.yml @@ -0,0 +1,39 @@ +# Downloads and publishes the documentation website to gh-pages branch +name: Deploy docs + +on: + push: + branches: + main + +jobs: + build: + runs-on: ubuntu-latest + steps: + # This will download the artifact from the most recent run of the given workflow. + # Assumes that the stated workflow was run during a PR check, and then that PR was subsequently approved, triggering this workflow. + # If there are multiple PRs open, and a new commit is added to a different PR it could lead to a conflict in which artifact is downloaded. + - name: Download Artifact + run: | + repo="${{ github.repository }}" + workflow="build.yml" + artifact="_site" + run_id=`gh run --repo ${repo} list --workflow ${workflow} --json databaseId --jq .[0].databaseId` + mkdir html + cd html + gh run --repo ${repo} download ${run_id} -n ${artifact} + env: + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + + - name: Checkout gh-pages + uses: actions/checkout@v4.1.1 + with: + ref: gh-pages + path: gh-pages + + - name: Publish to github pages + uses: peaceiris/actions-gh-pages@v4.0.0 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: _site + force_orphan: true From 3c68ad0b0ccff2e2848636f85bffbaca4cbc0621 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Thu, 1 Aug 2024 17:33:26 -0400 Subject: [PATCH 33/36] Update build.yml --- .github/workflows/build.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index c5f4f8b..44994b5 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -2,8 +2,7 @@ name: Build docs on: - workflow_dispatch: - push: + pull_request: branches: main From 93670922074040b594bcba0a27f56917c9aeb0d5 Mon Sep 17 00:00:00 2001 From: Brandon Parks Date: Fri, 2 Aug 2024 15:59:23 -0400 Subject: [PATCH 34/36] Testing github actions (#1) Add link checking both before and after building documentation --- .config/dotnet-tools.json | 6 +++ .github/workflows/DocLinkChecker.config | 13 +++--- .github/workflows/build.yml | 45 ++++++++++++++----- .github/workflows/deploy.yml | 39 ---------------- .../OpenEphys.Onix.ConfigureBreakoutBoard.md | 2 +- apidoc/OpenEphys.Onix.ConfigureHeadstage64.md | 2 +- ...s.Onix.ConfigureNeuropixelsV1eHeadstage.md | 2 +- ...ix.ConfigureNeuropixelsV2eBetaHeadstage.md | 2 +- ...s.Onix.ConfigureNeuropixelsV2eHeadstage.md | 2 +- apidoc/OpenEphys_Onix_Bno055Data.md | 3 -- apidoc/OpenEphys_Onix_ConfigureBno055.md | 3 -- .../getting-started/initialize_oni_context.md | 6 +-- articles/getting-started/next_steps.md | 2 +- articles/getting-started/node_types.md | 6 +-- articles/getting-started/tips_and_tricks.md | 6 +-- articles/hubs/breakoutboard.md | 2 +- articles/hubs/headstage64.md | 2 +- articles/hubs/neuropixelsv1e.md | 2 +- articles/hubs/neuropixelsv2e.md | 2 +- articles/hubs/neuropixelsv2ebeta.md | 2 +- build.ps1 | 2 +- filter.yml | 6 +-- index.md | 8 ++-- src/onix-bonsai-onix1 | 2 +- template/conceptual.html.primary.tmpl | 4 +- 25 files changed, 77 insertions(+), 94 deletions(-) delete mode 100644 .github/workflows/deploy.yml delete mode 100644 apidoc/OpenEphys_Onix_Bno055Data.md delete mode 100644 apidoc/OpenEphys_Onix_ConfigureBno055.md diff --git a/.config/dotnet-tools.json b/.config/dotnet-tools.json index 278b6c7..4211169 100644 --- a/.config/dotnet-tools.json +++ b/.config/dotnet-tools.json @@ -7,6 +7,12 @@ "commands": [ "docfx" ] + }, + "doclinkchecker": { + "version": "1.19.0", + "commands": [ + "DocLinkChecker" + ] } } } \ No newline at end of file diff --git a/.github/workflows/DocLinkChecker.config b/.github/workflows/DocLinkChecker.config index d142f81..1c30fc1 100644 --- a/.github/workflows/DocLinkChecker.config +++ b/.github/workflows/DocLinkChecker.config @@ -1,14 +1,17 @@ { "DocumentationFiles": { - "src": "", + "src": ".", "Files": [ - "**/*.md" + "**/*.md", + "*.md" ], - "Exclude": [] + "Exclude": [ + "_site/*", + ".bonsai/*", + "src/*" + ] }, "ResourceFolderNames": [ - "images", - "workflows" ], "DocLinkChecker": { "RelativeLinkStrategy": "All", diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 44994b5..be2532f 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -2,9 +2,10 @@ name: Build docs on: + push: + branches: [ main ] pull_request: - branches: - main + branches: [ main ] jobs: build: @@ -23,13 +24,9 @@ jobs: - name: Install DocLinkChecker run: dotnet tool install DocLinkChecker - # This checks for missing / broken links in the *.md files directly prior to building the website - - name: Check Documentation Links in Articles - run: dotnet DocLinkChecker -v -f .github/workflows/DocLinkChecker.config -d articles - - # This checks for missing / broken links in the *.md files directly prior to building the website - - name: Check Documentation Links in Tutorials - run: dotnet DocLinkChecker -v -f .github/workflows/DocLinkChecker.config -d tutorials + # Check for missing / broken links in the *.md files prior to building the website + - name: Check Documentation Links + run: dotnet DocLinkChecker -v -f .github/workflows/DocLinkChecker.config - name: Setup DocFX run: dotnet tool restore @@ -39,7 +36,7 @@ jobs: run: .\Setup.ps1 - name: Build Documentation - run: .\build.ps1 + run: .\build.ps1 --logLevel Warning --warningsAsErrors - name: Upload Artifact uses: actions/upload-artifact@v4 @@ -64,5 +61,31 @@ jobs: - name: Check HTML Links After Building uses: lycheeverse/lychee-action@v1.10.0 with: - args: --verbose --no-progress _site/**/*.html + args: --verbose --no-progress --base _site --exclude ^https://github\.com.*merge.* '_site/**/*.html' fail: true + + deploy: + name: Deploy docs to gh-pages + runs-on: ubuntu-latest + needs: [ build, check ] + if: github.event_name == 'push' + steps: + - name: Download Artifact + uses: actions/download-artifact@v4 + with: + name: _site + path: _site + + - name: Checkout gh-pages + uses: actions/checkout@v4.1.1 + with: + ref: gh-pages + path: gh-pages + + - name: Publish to github pages + uses: peaceiris/actions-gh-pages@v4.0.0 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: _site + force_orphan: true + diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml deleted file mode 100644 index 012f4a3..0000000 --- a/.github/workflows/deploy.yml +++ /dev/null @@ -1,39 +0,0 @@ -# Downloads and publishes the documentation website to gh-pages branch -name: Deploy docs - -on: - push: - branches: - main - -jobs: - build: - runs-on: ubuntu-latest - steps: - # This will download the artifact from the most recent run of the given workflow. - # Assumes that the stated workflow was run during a PR check, and then that PR was subsequently approved, triggering this workflow. - # If there are multiple PRs open, and a new commit is added to a different PR it could lead to a conflict in which artifact is downloaded. - - name: Download Artifact - run: | - repo="${{ github.repository }}" - workflow="build.yml" - artifact="_site" - run_id=`gh run --repo ${repo} list --workflow ${workflow} --json databaseId --jq .[0].databaseId` - mkdir html - cd html - gh run --repo ${repo} download ${run_id} -n ${artifact} - env: - GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} - - - name: Checkout gh-pages - uses: actions/checkout@v4.1.1 - with: - ref: gh-pages - path: gh-pages - - - name: Publish to github pages - uses: peaceiris/actions-gh-pages@v4.0.0 - with: - github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: _site - force_orphan: true diff --git a/apidoc/OpenEphys.Onix.ConfigureBreakoutBoard.md b/apidoc/OpenEphys.Onix.ConfigureBreakoutBoard.md index 8677647..fc6cc39 100644 --- a/apidoc/OpenEphys.Onix.ConfigureBreakoutBoard.md +++ b/apidoc/OpenEphys.Onix.ConfigureBreakoutBoard.md @@ -1,5 +1,5 @@ --- -uid: OpenEphys.Onix.ConfigureBreakoutBoard +uid: OpenEphys.Onix1.ConfigureBreakoutBoard --- [!INCLUDE [Hub Template](hub_template.md)] \ No newline at end of file diff --git a/apidoc/OpenEphys.Onix.ConfigureHeadstage64.md b/apidoc/OpenEphys.Onix.ConfigureHeadstage64.md index 36d1720..22bcd1a 100644 --- a/apidoc/OpenEphys.Onix.ConfigureHeadstage64.md +++ b/apidoc/OpenEphys.Onix.ConfigureHeadstage64.md @@ -1,5 +1,5 @@ --- -uid: OpenEphys.Onix.ConfigureHeadstage64 +uid: OpenEphys.Onix1.ConfigureHeadstage64 --- [!INCLUDE [Hub Template](hub_template.md)] \ No newline at end of file diff --git a/apidoc/OpenEphys.Onix.ConfigureNeuropixelsV1eHeadstage.md b/apidoc/OpenEphys.Onix.ConfigureNeuropixelsV1eHeadstage.md index c1a6b25..14a4ced 100644 --- a/apidoc/OpenEphys.Onix.ConfigureNeuropixelsV1eHeadstage.md +++ b/apidoc/OpenEphys.Onix.ConfigureNeuropixelsV1eHeadstage.md @@ -1,5 +1,5 @@ --- -uid: OpenEphys.Onix.ConfigureNeuropixelsV1eHeadstage +uid: OpenEphys.Onix1.ConfigureNeuropixelsV1eHeadstage --- [!INCLUDE [Hub Template](hub_template.md)] \ No newline at end of file diff --git a/apidoc/OpenEphys.Onix.ConfigureNeuropixelsV2eBetaHeadstage.md b/apidoc/OpenEphys.Onix.ConfigureNeuropixelsV2eBetaHeadstage.md index 998fe13..235fa3f 100644 --- a/apidoc/OpenEphys.Onix.ConfigureNeuropixelsV2eBetaHeadstage.md +++ b/apidoc/OpenEphys.Onix.ConfigureNeuropixelsV2eBetaHeadstage.md @@ -1,5 +1,5 @@ --- -uid: OpenEphys.Onix.ConfigureNeuropixelsV2eBetaHeadstage +uid: OpenEphys.Onix1.ConfigureNeuropixelsV2eBetaHeadstage --- [!INCLUDE [Hub Template](hub_template.md)] \ No newline at end of file diff --git a/apidoc/OpenEphys.Onix.ConfigureNeuropixelsV2eHeadstage.md b/apidoc/OpenEphys.Onix.ConfigureNeuropixelsV2eHeadstage.md index 85340d2..a947648 100644 --- a/apidoc/OpenEphys.Onix.ConfigureNeuropixelsV2eHeadstage.md +++ b/apidoc/OpenEphys.Onix.ConfigureNeuropixelsV2eHeadstage.md @@ -1,5 +1,5 @@ --- -uid: OpenEphys.Onix.ConfigureNeuropixelsV2eHeadstage +uid: OpenEphys.Onix1.ConfigureNeuropixelsV2eHeadstage --- [!INCLUDE [Hub Template](hub_template.md)] \ No newline at end of file diff --git a/apidoc/OpenEphys_Onix_Bno055Data.md b/apidoc/OpenEphys_Onix_Bno055Data.md deleted file mode 100644 index 5c92613..0000000 --- a/apidoc/OpenEphys_Onix_Bno055Data.md +++ /dev/null @@ -1,3 +0,0 @@ ---- -uid: OpenEphys.Onix.Bno055Data ---- diff --git a/apidoc/OpenEphys_Onix_ConfigureBno055.md b/apidoc/OpenEphys_Onix_ConfigureBno055.md deleted file mode 100644 index 1495311..0000000 --- a/apidoc/OpenEphys_Onix_ConfigureBno055.md +++ /dev/null @@ -1,3 +0,0 @@ ---- -uid: OpenEphys.Onix.ConfigureBno055 ---- diff --git a/articles/getting-started/initialize_oni_context.md b/articles/getting-started/initialize_oni_context.md index 645b645..84958c9 100644 --- a/articles/getting-started/initialize_oni_context.md +++ b/articles/getting-started/initialize_oni_context.md @@ -3,7 +3,7 @@ uid: InitializeOniContext title: Initialize the ONI Context --- -The [`CreateContext`](xref:OpenEphys.Onix.CreateContext) operator initializes the acquisition context, and it should be the first node you add to your workflow as it provides access to the hardware device table for all other configuration operators. There are several different ways to find this node and add it to the workflow: +The [`CreateContext`](xref:OpenEphys.Onix1.CreateContext) operator initializes the acquisition context, and it should be the first node you add to your workflow as it provides access to the hardware device table for all other configuration operators. There are several different ways to find this node and add it to the workflow: 1. From the Bonsai editor, navigate to the toolbox on the left side of the screen and expand the **Source** section. Next, expand the **OpenEphys.Onix** section, and find the `CreateContext` line. The node can then be added by either double-clicking it, or dragging and dropping the node into the workflow. @@ -13,11 +13,11 @@ The [`CreateContext`](xref:OpenEphys.Onix.CreateContext) operator initializes th ![Search for CreateContext node from textbox](../../images/bonsai-editor-place-create-context-search.png){width=700px} -3. Hover over the image of the [`CreateContext`](xref:OpenEphys.Onix.CreateContext) workflow below, and click on the clipboard icon in the top-right corner of the workflow image to copy the workflow to the clipboard. Navigate back to Bonsai, and paste the copied workflow into the active editor. Pasting can be done via Ctrl + V, or right-clicking in the editor and choosing **Paste**. +3. Hover over the image of the [`CreateContext`](xref:OpenEphys.Onix1.CreateContext) workflow below, and click on the clipboard icon in the top-right corner of the workflow image to copy the workflow to the clipboard. Navigate back to Bonsai, and paste the copied workflow into the active editor. Pasting can be done via Ctrl + V, or right-clicking in the editor and choosing **Paste**. ## CreateContext Workflow -This is a nominally functional workflow that provides access to the ONI context, from which all nodes can then be linked to and configured, while also demonstrating how a Breakout Board can be configured before finishing the configuration chain by placing a [`StartAcquisition`](xref:OpenEphys.Onix.StartAcquisition) node: +This is a nominally functional workflow that provides access to the ONI context, from which all nodes can then be linked to and configured, while also demonstrating how a Breakout Board can be configured before finishing the configuration chain by placing a [`StartAcquisition`](xref:OpenEphys.Onix1.StartAcquisition) node: :::workflow ![CreateContext](../../workflows/operators/ConfigureBreakoutBoard.bonsai) diff --git a/articles/getting-started/next_steps.md b/articles/getting-started/next_steps.md index 0bec522..a18c0df 100644 --- a/articles/getting-started/next_steps.md +++ b/articles/getting-started/next_steps.md @@ -5,6 +5,6 @@ title: Next Steps Continue browsing and check out specific nodes on the left to see how to configure each node, as well as some ways to visualize data. Each page will have a fully functional workflow that can be copied into Bonsai to provide an easy starting point for generating data. -For more technical information on each node, head to the to see a more developer-focused view of each node. +For more technical information on each node, head to the to see a more developer-focused view of each node. More complex and in-depth tutorials for placing multiple nodes and moving towards generating data in an experimental setting can be found in the . diff --git a/articles/getting-started/node_types.md b/articles/getting-started/node_types.md index 0790cb2..bc3f82c 100644 --- a/articles/getting-started/node_types.md +++ b/articles/getting-started/node_types.md @@ -7,8 +7,8 @@ In Bonsai, all objects are called "nodes", and have a specific function associat | Node Type | Description | Example ONIX nodes | | --------- | ----------- | ------------------ | -| Source | Generate event streams from devices or files | [`CreateContext`](xref:OpenEphys.Onix.CreateContext), [`Bno055Data`](xref:OpenEphys.Onix.Bno055Data), [`NeuropixelsV1eData`](xref:OpenEphys.Onix.NeuropixelsV1eData) | -| Sink | Save data or trigger external outputs | [`ConfigureHeadstage64`](xref:OpenEphys.Onix.ConfigureHeadstage64), [`ConfigureNeuropixelsV1eHeadstage`](xref:OpenEphys.Onix.ConfigureNeuropixelsV1eHeadstage) | -| Combinator | Manage control flow or synchronize parallel inputs | [`StartAcquisition`](xref:OpenEphys.Onix.StartAcquisition) | +| Source | Generate event streams from devices or files | [`CreateContext`](xref:OpenEphys.Onix1.CreateContext), [`Bno055Data`](xref:OpenEphys.Onix1.Bno055Data), [`NeuropixelsV1eData`](xref:OpenEphys.Onix1.NeuropixelsV1eData) | +| Sink | Save data or trigger external outputs | [`ConfigureHeadstage64`](xref:OpenEphys.Onix1.ConfigureHeadstage64), [`ConfigureNeuropixelsV1eHeadstage`](xref:OpenEphys.Onix1.ConfigureNeuropixelsV1eHeadstage) | +| Combinator | Manage control flow or synchronize parallel inputs | [`StartAcquisition`](xref:OpenEphys.Onix1.StartAcquisition) | Nodes are placed in the Bonsai editor and can be saved into a "workflow", which is a grouping of nodes and saved settings. This workflow can then be run to perform some task, depending on what nodes are placed. diff --git a/articles/getting-started/tips_and_tricks.md b/articles/getting-started/tips_and_tricks.md index adc77dd..1f7a085 100644 --- a/articles/getting-started/tips_and_tricks.md +++ b/articles/getting-started/tips_and_tricks.md @@ -20,7 +20,7 @@ The order of nodes is also important for which actions can be taken. In the tabl | Change order of nodes in a row | Hold **Ctrl**, click and hold the first node, drag to the right to the second node, and release | This action does not require that the node be selected prior to performing the action. This can change the order of any two nodes that are a part of the same row; it is not constrained to adjacent nodes. Note that if the new placement of the nodes is not valid (such as giving a `Source` node an input), it will knock the node of the current row and remove any connections | > [!Note] -> In the context of `OpenEphys.Onix`, almost all workflows should have the top row containing a [`CreateContext`](xref:OpenEphys.Onix.CreateContext) node connected to an arbitrary number of `Configure*` nodes, finished with a [`StartAcquisition`](xref:OpenEphys.Onix.StartAcquisition) node. Subsequent rows can contain the corresponding `*Data` nodes configured above, and any processing / visualizing nodes needed. +> In the context of `OpenEphys.Onix1`, almost all workflows should have the top row containing a [`CreateContext`](xref:OpenEphys.Onix1.CreateContext) node connected to an arbitrary number of `Configure*` nodes, finished with a [`StartAcquisition`](xref:OpenEphys.Onix1.StartAcquisition) node. Subsequent rows can contain the corresponding `*Data` nodes configured above, and any processing / visualizing nodes needed.
@@ -29,6 +29,6 @@ The order of nodes is also important for which actions can be taken. In the tabl Some nodes, specifically many of the `Configure*` nodes, can have a GUI attached to the node that allows for easy manipulation of **Configuration** properties in a graphical environment. These GUIs can be accessed by double-clicking on a node; if there is a GUI assigned to it, then it will be opened up in a new window. Please note that not all nodes have GUIs, but if you think that a node would benefit from having this functionality added please reach out to us. > [!Note] -> GUIs are not part of the base `OpenEphys.Onix` library. To take advantage of this added functionality, you must install the accompanying `OpenEphys.Onix.Design` library using the Bonsai package manager. +> GUIs are not part of the base `OpenEphys.Onix1` library. To take advantage of this added functionality, you must install the accompanying `OpenEphys.Onix1.Design` library using the Bonsai package manager. -A number of Bonsai nodes also come shipped with GUIs, but similar to `OpenEphys.Onix`, the corresponding `*.Design` library must be installed before it can be leveraged. +A number of Bonsai nodes also come shipped with GUIs, but similar to `OpenEphys.Onix1`, the corresponding `*.Design` library must be installed before it can be leveraged. diff --git a/articles/hubs/breakoutboard.md b/articles/hubs/breakoutboard.md index c73c988..c4da2db 100644 --- a/articles/hubs/breakoutboard.md +++ b/articles/hubs/breakoutboard.md @@ -4,7 +4,7 @@ title: BreakoutBoard isGuide: true isHeadstage: true headstage: BreakoutBoard -devices: [ { id: MemoryMonitor, file: device-memorymonitor }, { id: Heartbeat, file: device-heartbeat }, { id: DigitalIO, file: device-digitalio } , { id: AnalogIO, file: device-analogio } ] +devices: [ { id: MemoryMonitor, file: ~/articles/devices/memorymonitor }, { id: Heartbeat, file: ~/articles/devices/heartbeat }, { id: DigitalIO, file: ~/articles/devices/breakoutdigitalio } , { id: AnalogIO, file: ~/articles/devices/breakoutanalogio } ] workflow: true workflow_file: ~/workflows/hubs/BreakoutBoard.bonsai --- diff --git a/articles/hubs/headstage64.md b/articles/hubs/headstage64.md index 08f7296..23c04a8 100644 --- a/articles/hubs/headstage64.md +++ b/articles/hubs/headstage64.md @@ -4,7 +4,7 @@ title: Headstage64 isGuide: true isHeadstage: true headstage: Headstage64 -devices: [ { id: TS4231, file: device-ts4231 }, { id: RHD2164, file: device-rhd2164 }, { id: BNO055, file: device-bno055 } ] +devices: [ { id: TS4231, file: ~/articles/devices/ts4231 }, { id: RHD2164, file: ~/articles/devices/rhd2164 }, { id: BNO055, file: ~/articles/devices/bno055 } ] workflow: true workflow_file: ~/workflows/hubs/Headstage64.bonsai --- diff --git a/articles/hubs/neuropixelsv1e.md b/articles/hubs/neuropixelsv1e.md index bae0a03..e99eb1a 100644 --- a/articles/hubs/neuropixelsv1e.md +++ b/articles/hubs/neuropixelsv1e.md @@ -4,7 +4,7 @@ title: NeuropixelsV1eHeadstage isGuide: true isHeadstage: true headstage: NeuropixelsV1e -devices: [ { id: NeuropixelsV1e, file: device-neuropixelsv1e }, { id: BNO055, file: device-bno055_neuropixelsv1e } ] +devices: [ { id: NeuropixelsV1e, file: ~/articles/devices/neuropixelsv1e }, { id: BNO055, file: ~/articles/devices/bno055_neuropixelsv1e } ] workflow: true workflow_file: ~/workflows/hubs/NeuropixelsV1e.bonsai --- diff --git a/articles/hubs/neuropixelsv2e.md b/articles/hubs/neuropixelsv2e.md index 71f9ac3..22ef191 100644 --- a/articles/hubs/neuropixelsv2e.md +++ b/articles/hubs/neuropixelsv2e.md @@ -4,7 +4,7 @@ title: NeuropixelsV2eHeadstage isGuide: true isHeadstage: true headstage: NeuropixelsV2e -devices: [ { id: NeuropixelsV2e, file: device-neuropixelsv2e }, { id: BNO055, file: device-bno055_neuropixelsv2e } ] +devices: [ { id: NeuropixelsV2e, file: ~/articles/devices/neuropixelsv2e }, { id: BNO055, file: ~/articles/devices/bno055_neuropixelsv2e } ] workflow: true workflow_file: ~/workflows/hubs/NeuropixelsV2e.bonsai --- diff --git a/articles/hubs/neuropixelsv2ebeta.md b/articles/hubs/neuropixelsv2ebeta.md index 9abbe0e..db876b3 100644 --- a/articles/hubs/neuropixelsv2ebeta.md +++ b/articles/hubs/neuropixelsv2ebeta.md @@ -4,7 +4,7 @@ title: NeuropixelsV2eBetaHeadstage isGuide: true isHeadstage: true headstage: NeuropixelsV2eBeta -devices: [ { id: NeuropixelsV2eBeta, file: device-neuropixelsv2ebeta }, { id: BNO055, file: device-bno055_neuropixelsv2e } ] +devices: [ { id: NeuropixelsV2eBeta, file: ~/articles/devices/neuropixelsv2ebeta }, { id: BNO055, file: ~/articles/devices/bno055_neuropixelsv2e } ] workflow: true workflow_file: ~/workflows/hubs/NeuropixelsV2eBeta.bonsai --- diff --git a/build.ps1 b/build.ps1 index 05eb599..c8b834c 100644 --- a/build.ps1 +++ b/build.ps1 @@ -3,6 +3,6 @@ $libPath = ".\src\onix-bonsai-onix1\" dotnet build $libPath --configuration Release # Export workflow vectors -$libPath = Join-Path $libPath "artifacts\bin\OpenEphys.Onix\release" +$libPath = Join-Path $libPath "artifacts\bin\OpenEphys.Onix1\release" .\docfx-tools\modules\Export-Image.ps1 -bootstrapperPath .\.bonsai\Bonsai.exe $libPath dotnet docfx @args \ No newline at end of file diff --git a/filter.yml b/filter.yml index feaf080..f6264b2 100644 --- a/filter.yml +++ b/filter.yml @@ -12,11 +12,7 @@ apiRules: uidRegex: OpenEphys.Onix.DeviceContext - exclude: uidRegex: ^.*DeviceFactory -- exclude: - uidRegex: ^.*DataFrame -- exclude: - type: Enum - exclude: uidRegex: OpenEphys.Onix.ConfigureFmcLinkController - exclude: - uidRegex: OpenEphys.Onix.ConfigureDS90UB9x \ No newline at end of file + uidRegex: OpenEphys.Onix.ConfigureDS90UB9x diff --git a/index.md b/index.md index ae030bb..5c5ac2d 100644 --- a/index.md +++ b/index.md @@ -24,9 +24,9 @@ Other major advantages include:
-| | | | -|:--------------:|:-------------------:|:---------:|:---:| -| [![User Guide](images/macbook.svg){width=200}](xref:GettingStarted) | [![Operator Guide](images/books.svg){width=200}](xref:OpenEphys.Onix) | [![Tutorials](images/running.svg){width=200}](xref:TutorialsLandingPage) | -| [New to Bonsai or
OpenEphys.Onix? Start here!](xref:GettingStarted) | [Operator references here](xref:OpenEphys.Onix) | [Check out our tutorials
for useful workflows](xref:TutorialsLandingPage) | +| | | | +|:--------------:|:-------------------:|:---------:| +| [![User Guide](images/macbook.svg){width=200}](xref:GettingStarted) | [![Operator Guide](images/books.svg){width=200}](xref:OpenEphys.Onix1) | [![Tutorials](images/running.svg){width=200}](xref:TutorialsLandingPage) | +| [New to Bonsai or
OpenEphys.Onix? Start here!](xref:GettingStarted) | [Operator references here](xref:OpenEphys.Onix1) | [Check out our tutorials
for useful workflows](xref:TutorialsLandingPage) |
\ No newline at end of file diff --git a/src/onix-bonsai-onix1 b/src/onix-bonsai-onix1 index 9347ce3..5dc8fb8 160000 --- a/src/onix-bonsai-onix1 +++ b/src/onix-bonsai-onix1 @@ -1 +1 @@ -Subproject commit 9347ce3c0d71dddf7b8dc8cb87c31d151032d824 +Subproject commit 5dc8fb8a0fd42549ba143fd91bc12292c57fb35b diff --git a/template/conceptual.html.primary.tmpl b/template/conceptual.html.primary.tmpl index a67dd37..921fadb 100644 --- a/template/conceptual.html.primary.tmpl +++ b/template/conceptual.html.primary.tmpl @@ -31,8 +31,8 @@ {{>partials/device.visualize_text}} {{/visualize_text}} -

Refer to Visualizing Data for more information on visualizers and how to download them.

-

Note that data will not be shown until a workflow is running. Check out Running a Workflow to see how to run a workflow.

+

Refer to Visualizing Data for more information on visualizers and how to download them.

+

Note that data will not be shown until a workflow is running. Check out Running a Workflow to see how to run a workflow.

{{/visualize}} {{/isGuide}} From 30628ee815a3cb2fe37e78bb7c7bdd0d8e592856 Mon Sep 17 00:00:00 2001 From: bparks13 Date: Fri, 2 Aug 2024 16:23:43 -0400 Subject: [PATCH 35/36] Add regex filter for published pages --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index be2532f..d09e393 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -61,7 +61,7 @@ jobs: - name: Check HTML Links After Building uses: lycheeverse/lychee-action@v1.10.0 with: - args: --verbose --no-progress --base _site --exclude ^https://github\.com.*merge.* '_site/**/*.html' + args: --verbose --no-progress --base _site --exclude ^https://github\.com.*(merge|apiSpec).* '_site/**/*.html' fail: true deploy: From 0330d01db1aba814e192fe9b33418b64b6591d4e Mon Sep 17 00:00:00 2001 From: bparks13 Date: Fri, 2 Aug 2024 16:32:34 -0400 Subject: [PATCH 36/36] Fix regex --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index d09e393..78c60d4 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -61,7 +61,7 @@ jobs: - name: Check HTML Links After Building uses: lycheeverse/lychee-action@v1.10.0 with: - args: --verbose --no-progress --base _site --exclude ^https://github\.com.*(merge|apiSpec).* '_site/**/*.html' + args: --verbose --no-progress --base _site --exclude ^https://github\.com.*merge.* --exclude ^https://github\.com.*apiSpec.* '_site/**/*.html' fail: true deploy: