From cb5e9e9404798eaf61a611bfb7ff354b9965ee7b Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 17:24:14 -0700
Subject: [PATCH 01/26] Add action to deploy docs via GitHub pages

---
 .github/workflows/doxygen-gh-pages.yml | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 .github/workflows/doxygen-gh-pages.yml

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
new file mode 100644
index 00000000..53d06b25
--- /dev/null
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -0,0 +1,17 @@
+name: Doxygen GitHub Pages Deploy Action
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: DenverCoder1/doxygen-github-pages-action@v1.3.1
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: gh-pages
+          folder: docs/html
+          config_file: Doxyfile

From 9769d272f38baaf96c67dd4bb30234cffaaed61e Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 17:34:28 -0700
Subject: [PATCH 02/26] Test running the action on this branch

---
 .github/workflows/doxygen-gh-pages.yml | 3 ++-
 README.md                              | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index 53d06b25..8fa20a2d 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - main
+  pull_request:
 
 jobs:
   deploy:
@@ -12,6 +13,6 @@ jobs:
       - uses: DenverCoder1/doxygen-github-pages-action@v1.3.1
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          branch: gh-pages
+          branch: add/docs_actions
           folder: docs/html
           config_file: Doxyfile
diff --git a/README.md b/README.md
index 42de8837..b77d5d3b 100644
--- a/README.md
+++ b/README.md
@@ -27,7 +27,7 @@ cmake -S . -B build
 cmake --build build --config Release
 ```
 
-Note, if you are using custom installs of HDF5 or BOOST that are not being detected 
+Note, if you are using custom installations of HDF5 or BOOST that are not being detected 
 automatically by cmake, you can specify `HDF5_ROOT` and `BOOST_ROOT` environment variables to 
 point to install directories of HDF5 and BOOST respectively. 
 

From 0dd371c46ebcfae50c3fd0d6493ff40c1b8a42c7 Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 17:38:19 -0700
Subject: [PATCH 03/26] Updated Doxyfile path

---
 .github/workflows/doxygen-gh-pages.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index 8fa20a2d..126b31b9 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -15,4 +15,4 @@ jobs:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           branch: add/docs_actions
           folder: docs/html
-          config_file: Doxyfile
+          config_file: docs/Doxyfile.in

From 7e567e6cdeaba1249c82e2b8373870a3e86c1273 Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 17:57:34 -0700
Subject: [PATCH 04/26] Update the docs action to use cmake for the docs build

---
 .github/workflows/doxygen-gh-pages.yml | 42 +++++++++++++++++++++++---
 1 file changed, 37 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index 126b31b9..d1fee904 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -10,9 +10,41 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: DenverCoder1/doxygen-github-pages-action@v1.3.1
+      - name: Checkout repository
+        uses: actions/checkout@v4
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          branch: add/docs_actions
-          folder: docs/html
-          config_file: docs/Doxyfile.in
+          submodules: "true"
+      - name: Install dependencies - ubuntu
+        run: |
+          sudo apt-get update
+          sudo apt-get install doxygen graphviz -y
+          sudo apt-get install -y libhdf5-dev libboost-all-dev
+          git clone https://github.com/catchorg/Catch2.git
+          cd Catch2
+          git checkout "v3.5.3"
+          cmake -Bbuild -H. -DBUILD_TESTING=OFF
+          sudo cmake --build build/ --target install
+        shell: bash
+
+      - name: Configure and build API
+        run: |
+          cmake -S . -B build -Daq-nwb_DEVELOPER_MODE=ON
+          cmake --preset=dev
+          cmake --build --preset=dev
+        shell: bash
+
+      - name: Build the docs
+        run : |
+          cmake --build --preset=dev --target=docs
+        shell: bash
+
+      - name: Create .nojekyll to ensure pages with underscores work on gh pages
+        run: touch build/dev/docs/html/.nojekyll
+        shell: bash
+
+      - name: Deploy to GitHub Pages
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          branch: test_gh_pages_action
+          folder: build/dev/docs/html

From d1a95a77c3af8efff8411c94acd4c6eed0f93d18 Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 18:00:41 -0700
Subject: [PATCH 05/26] Update preset target

---
 .github/workflows/doxygen-gh-pages.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index d1fee904..6b4550f0 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -29,8 +29,8 @@ jobs:
       - name: Configure and build API
         run: |
           cmake -S . -B build -Daq-nwb_DEVELOPER_MODE=ON
-          cmake --preset=dev
-          cmake --build --preset=dev
+          cmake --preset=ci-ubuntu
+          cmake --build --preset=ci-ubuntu
         shell: bash
 
       - name: Build the docs

From c27dd98cbb0e6b9ed585a3c7e96c67d2860ae73a Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 18:03:37 -0700
Subject: [PATCH 06/26] Remove preset builds

---
 .github/workflows/doxygen-gh-pages.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index 6b4550f0..2a8eebf6 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -26,11 +26,9 @@ jobs:
           sudo cmake --build build/ --target install
         shell: bash
 
-      - name: Configure and build API
+      - name: Configure and build the API
         run: |
           cmake -S . -B build -Daq-nwb_DEVELOPER_MODE=ON
-          cmake --preset=ci-ubuntu
-          cmake --build --preset=ci-ubuntu
         shell: bash
 
       - name: Build the docs

From 1b2607a416962de27ca372aca5972b2af8e8e53c Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 18:08:00 -0700
Subject: [PATCH 07/26] Change preset

---
 .github/workflows/doxygen-gh-pages.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index 2a8eebf6..da5770d5 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -28,12 +28,13 @@ jobs:
 
       - name: Configure and build the API
         run: |
-          cmake -S . -B build -Daq-nwb_DEVELOPER_MODE=ON
+          cmake --preset=dev
+          cmake --build --preset=dev -Daq-nwb_DEVELOPER_MODE=ON
         shell: bash
 
       - name: Build the docs
         run : |
-          cmake --build --preset=dev --target=docs
+          cmake --build --target=docs
         shell: bash
 
       - name: Create .nojekyll to ensure pages with underscores work on gh pages

From 431413c06c1030472829ba94fd0a62a912d1c259 Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 18:11:02 -0700
Subject: [PATCH 08/26] Switch preset

---
 .github/workflows/doxygen-gh-pages.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index da5770d5..446b6064 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -28,13 +28,13 @@ jobs:
 
       - name: Configure and build the API
         run: |
-          cmake --preset=dev
-          cmake --build --preset=dev -Daq-nwb_DEVELOPER_MODE=ON
+          cmake --preset=ci-ubuntu
+          cmake --build --preset=ci-ubuntu -Daq-nwb_DEVELOPER_MODE=ON -j 2
         shell: bash
 
       - name: Build the docs
         run : |
-          cmake --build --target=docs
+          cmake --build --preset=ci-ubuntu --target=docs
         shell: bash
 
       - name: Create .nojekyll to ensure pages with underscores work on gh pages

From 4de612c97c4b16c20fa0145a45ed54a58bff68f6 Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 18:13:19 -0700
Subject: [PATCH 09/26] Remove dev option

---
 .github/workflows/doxygen-gh-pages.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index 446b6064..cc79f196 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -29,7 +29,7 @@ jobs:
       - name: Configure and build the API
         run: |
           cmake --preset=ci-ubuntu
-          cmake --build --preset=ci-ubuntu -Daq-nwb_DEVELOPER_MODE=ON -j 2
+          cmake --build --preset=ci-ubuntu -j 2
         shell: bash
 
       - name: Build the docs

From 0833fd337a50c01a156c458e1b71c2cfdae40a02 Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 18:20:54 -0700
Subject: [PATCH 10/26] test without preset

---
 .github/workflows/doxygen-gh-pages.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index cc79f196..db437dee 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -29,12 +29,12 @@ jobs:
       - name: Configure and build the API
         run: |
           cmake --preset=ci-ubuntu
-          cmake --build --preset=ci-ubuntu -j 2
+          cmake --build
         shell: bash
 
       - name: Build the docs
         run : |
-          cmake --build --preset=ci-ubuntu --target=docs
+          cmake --build --target=docs
         shell: bash
 
       - name: Create .nojekyll to ensure pages with underscores work on gh pages

From 04d7718afb4f469d077be0b56f349edfdd66c9db Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 18:25:17 -0700
Subject: [PATCH 11/26] Add ls commands for testing

---
 .github/workflows/doxygen-gh-pages.yml | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index db437dee..d1654e10 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -29,7 +29,11 @@ jobs:
       - name: Configure and build the API
         run: |
           cmake --preset=ci-ubuntu
-          cmake --build
+          cmake --build build
+        shell: bash
+
+      - name: ls to check
+        run: ls -la build
         shell: bash
 
       - name: Build the docs
@@ -37,8 +41,12 @@ jobs:
           cmake --build --target=docs
         shell: bash
 
+      - name: ls to check
+        run: ls -la build/docs
+        shell: bash
+
       - name: Create .nojekyll to ensure pages with underscores work on gh pages
-        run: touch build/dev/docs/html/.nojekyll
+        run: touch build/docs/html/.nojekyll
         shell: bash
 
       - name: Deploy to GitHub Pages
@@ -46,4 +54,4 @@ jobs:
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           branch: test_gh_pages_action
-          folder: build/dev/docs/html
+          folder: build/docs/html

From fae90768db5081b058528e84026f6bf7235faed3 Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 18:29:32 -0700
Subject: [PATCH 12/26] Adds docs build target

---
 .github/workflows/doxygen-gh-pages.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index d1654e10..98e9d1cf 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -38,7 +38,7 @@ jobs:
 
       - name: Build the docs
         run : |
-          cmake --build --target=docs
+          cmake --build build --target=docs
         shell: bash
 
       - name: ls to check

From b7d087a797de85ee09e7bd9a1853d280f872b16f Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 18:40:21 -0700
Subject: [PATCH 13/26] Enable developer mode

---
 .github/workflows/doxygen-gh-pages.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index 98e9d1cf..05cbff21 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -29,7 +29,7 @@ jobs:
       - name: Configure and build the API
         run: |
           cmake --preset=ci-ubuntu
-          cmake --build build
+          cmake --build build -Daq-nwb_DEVELOPER_MODE=ON
         shell: bash
 
       - name: ls to check

From a8878ebf73d8e1efe49ecff0b0779ef462cf8a93 Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 18:43:32 -0700
Subject: [PATCH 14/26] Use dev-mode preset

---
 .github/workflows/doxygen-gh-pages.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index 05cbff21..2c0fefd2 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -28,8 +28,8 @@ jobs:
 
       - name: Configure and build the API
         run: |
-          cmake --preset=ci-ubuntu
-          cmake --build build -Daq-nwb_DEVELOPER_MODE=ON
+          cmake --preset=dev-mode
+          cmake --build --preset=dev-mode
         shell: bash
 
       - name: ls to check
@@ -38,7 +38,7 @@ jobs:
 
       - name: Build the docs
         run : |
-          cmake --build build --target=docs
+          cmake --build --preset=dev-mode --target=docs
         shell: bash
 
       - name: ls to check

From 24fee47ec2410defd17affe12e5bc77d0fec22ae Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 18:48:13 -0700
Subject: [PATCH 15/26] Update preset

---
 .github/workflows/doxygen-gh-pages.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index 2c0fefd2..d4d90e82 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -28,8 +28,8 @@ jobs:
 
       - name: Configure and build the API
         run: |
-          cmake --preset=dev-mode
-          cmake --build --preset=dev-mode
+          cmake --preset=ci-ubuntu
+          cmake --build build
         shell: bash
 
       - name: ls to check
@@ -38,7 +38,7 @@ jobs:
 
       - name: Build the docs
         run : |
-          cmake --build --preset=dev-mode --target=docs
+          cmake --build --preset=ci-ubuntu --target=docs
         shell: bash
 
       - name: ls to check

From d9730390f40a08845ee0a6a07990ada38b0f774c Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 18:53:59 -0700
Subject: [PATCH 16/26] Try again

---
 .github/workflows/doxygen-gh-pages.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index d4d90e82..ae354372 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -37,8 +37,7 @@ jobs:
         shell: bash
 
       - name: Build the docs
-        run : |
-          cmake --build --preset=ci-ubuntu --target=docs
+        run : cmake --build --preset=ci-ubuntu --target=docs
         shell: bash
 
       - name: ls to check

From fac692562ba9ce3fb43d0312301f5fd454fbb5c9 Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 18:58:49 -0700
Subject: [PATCH 17/26] Try again

---
 .github/workflows/doxygen-gh-pages.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index ae354372..9ed97f99 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -29,7 +29,7 @@ jobs:
       - name: Configure and build the API
         run: |
           cmake --preset=ci-ubuntu
-          cmake --build build
+          cmake --build --preset=ci-ubuntu
         shell: bash
 
       - name: ls to check

From 9c3b38db406dc6241973cd6270e16f67ddee6618 Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 19:01:01 -0700
Subject: [PATCH 18/26] Try again

---
 .github/workflows/doxygen-gh-pages.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index 9ed97f99..2cc20c23 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -29,7 +29,7 @@ jobs:
       - name: Configure and build the API
         run: |
           cmake --preset=ci-ubuntu
-          cmake --build --preset=ci-ubuntu
+          cmake --build build
         shell: bash
 
       - name: ls to check
@@ -37,7 +37,7 @@ jobs:
         shell: bash
 
       - name: Build the docs
-        run : cmake --build --preset=ci-ubuntu --target=docs
+        run : cmake --build build/docs --target=docs
         shell: bash
 
       - name: ls to check

From 1fcef9fe0739ec6a616c4bf2b10882c65383ba5e Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 19:04:47 -0700
Subject: [PATCH 19/26] Try again

---
 .github/workflows/doxygen-gh-pages.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index 2cc20c23..2ca30162 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -37,7 +37,7 @@ jobs:
         shell: bash
 
       - name: Build the docs
-        run : cmake --build build/docs --target=docs
+        run : cmake --build build --target=docs
         shell: bash
 
       - name: ls to check

From 300f7b6e7d5e84fab0963c3bd013ca2620198f35 Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 19:28:24 -0700
Subject: [PATCH 20/26] Try again

---
 .github/workflows/doxygen-gh-pages.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index 2ca30162..53ed813d 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -37,7 +37,7 @@ jobs:
         shell: bash
 
       - name: Build the docs
-        run : cmake --build build --target=docs
+        run : cmake --build --preset=ci-ubuntu --target=docs
         shell: bash
 
       - name: ls to check
@@ -52,5 +52,5 @@ jobs:
         uses: JamesIves/github-pages-deploy-action@v4
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          branch: test_gh_pages_action
+          branch: gh_pages
           folder: build/docs/html

From 32e8b7d82c0462c527792061fde1f3fca9095979 Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 19:29:07 -0700
Subject: [PATCH 21/26] Remove debug ls

---
 .github/workflows/doxygen-gh-pages.yml | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index 53ed813d..67390135 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -32,18 +32,10 @@ jobs:
           cmake --build build
         shell: bash
 
-      - name: ls to check
-        run: ls -la build
-        shell: bash
-
       - name: Build the docs
         run : cmake --build --preset=ci-ubuntu --target=docs
         shell: bash
 
-      - name: ls to check
-        run: ls -la build/docs
-        shell: bash
-
       - name: Create .nojekyll to ensure pages with underscores work on gh pages
         run: touch build/docs/html/.nojekyll
         shell: bash

From b05beebd565245bacecec254db39106608808702 Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Sat, 3 Aug 2024 19:46:32 -0700
Subject: [PATCH 22/26] Add test target

---
 .github/workflows/doxygen-gh-pages.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index 67390135..5206f582 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -44,5 +44,5 @@ jobs:
         uses: JamesIves/github-pages-deploy-action@v4
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          branch: gh_pages
+          branch: test_gh_pages
           folder: build/docs/html

From b32debd2040475d56b76ca7ff09b842381e545f3 Mon Sep 17 00:00:00 2001
From: Steph Prince <40640337+stephprince@users.noreply.github.com>
Date: Sun, 4 Aug 2024 23:53:32 -0700
Subject: [PATCH 23/26] update docs ci build

---
 .github/workflows/doxygen-gh-pages.yml |  2 +-
 cmake/docs-ci.cmake                    | 14 +++++++-------
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index 5206f582..f41a20dd 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -33,7 +33,7 @@ jobs:
         shell: bash
 
       - name: Build the docs
-        run : cmake --build --preset=ci-ubuntu --target=docs
+        run : cmake "-DPROJECT_SOURCE_DIR=$PWD" "-DPROJECT_BINARY_DIR=$PWD/build" -P cmake/docs-ci.cmake
         shell: bash
 
       - name: Create .nojekyll to ensure pages with underscores work on gh pages
diff --git a/cmake/docs-ci.cmake b/cmake/docs-ci.cmake
index 9d2c8ed5..46ced8c5 100644
--- a/cmake/docs-ci.cmake
+++ b/cmake/docs-ci.cmake
@@ -8,13 +8,6 @@ endforeach()
 set(bin "${PROJECT_BINARY_DIR}")
 set(src "${PROJECT_SOURCE_DIR}")
 
-# ---- Dependencies ----
-
-find_program(Python3_EXECUTABLE NAMES python3 python)
-if(NOT Python3_EXECUTABLE)
-  message(FATAL_ERROR "Python executable was not found")
-endif()
-
 # ---- Process project() call in CMakeLists.txt ----
 
 file(READ "${src}/CMakeLists.txt" content)
@@ -76,3 +69,10 @@ endforeach()
 set(config "${bin}/docs/conf.py")
 
 file(REMOVE_RECURSE "${out}/html" "${out}/xml")
+
+execute_process(
+    COMMAND doxygen "${bin}/docs/Doxyfile"
+    COMMENT "Building documentation using Doxygen"
+    VERBATIM
+    RESULT_VARIABLE result
+)

From e910f239a5de02f36c41c51095a4b088aad00b7f Mon Sep 17 00:00:00 2001
From: Steph Prince <40640337+stephprince@users.noreply.github.com>
Date: Mon, 5 Aug 2024 09:26:24 -0700
Subject: [PATCH 24/26] update README to include dev preset info

---
 README.md | 44 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/README.md b/README.md
index 5010e4b4..789ecf65 100644
--- a/README.md
+++ b/README.md
@@ -57,6 +57,50 @@ the option when configuring the build by adding ``-Daq-nwb_DEVELOPER_MODE=ON``,
 ```sh
 cmake -S . -B build -Daq-nwb_DEVELOPER_MODE=ON
 ```
+### Presets
+
+As a developer, you can create your own dev preset by making a `CMakeUserPresets.json` file at the root of
+the project:
+
+```json
+{
+  "version": 2,
+  "cmakeMinimumRequired": {
+    "major": 3,
+    "minor": 15,
+    "patch": 0
+  },
+  "configurePresets": [
+    {
+      "name": "dev",
+      "binaryDir": "${sourceDir}/build/dev",
+      "inherits": ["dev-mode", "ci-<os>"],
+      "cacheVariables": {
+        "CMAKE_BUILD_TYPE": "Debug"
+      }
+    }
+  ],
+  "buildPresets": [
+    {
+      "name": "dev",
+      "configurePreset": "dev",
+      "configuration": "Debug"
+    }
+  ],
+  "testPresets": [
+    {
+      "name": "dev",
+      "configurePreset": "dev",
+      "configuration": "Debug",
+      "output": {
+        "outputOnFailure": true
+      }
+    }
+  ]
+}
+```
+Replace `<os>` in the `CmakeUserPresets.json` file with the name of
+the operating system you have (`win64`, `linux` or `darwin`).
 
 ### Configure, build and test
 

From ede215ab53b4d9fc25f4916355ca103920d16a47 Mon Sep 17 00:00:00 2001
From: Steph Prince <40640337+stephprince@users.noreply.github.com>
Date: Tue, 6 Aug 2024 13:27:48 -0700
Subject: [PATCH 25/26] update workflows

---
 .github/workflows/doxygen-build.yml    | 37 ++++++++++++++++++++++++++
 .github/workflows/doxygen-gh-pages.yml |  3 +--
 docs/Doxyfile.in                       |  5 +++-
 3 files changed, 42 insertions(+), 3 deletions(-)
 create mode 100644 .github/workflows/doxygen-build.yml

diff --git a/.github/workflows/doxygen-build.yml b/.github/workflows/doxygen-build.yml
new file mode 100644
index 00000000..e63cfbbe
--- /dev/null
+++ b/.github/workflows/doxygen-build.yml
@@ -0,0 +1,37 @@
+name: Doxygen Build Test
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: "true"
+      - name: Install dependencies - ubuntu
+        run: |
+          sudo apt-get update
+          sudo apt-get install doxygen graphviz -y
+          sudo apt-get install -y libhdf5-dev libboost-all-dev
+          git clone https://github.com/catchorg/Catch2.git
+          cd Catch2
+          git checkout "v3.5.3"
+          cmake -Bbuild -H. -DBUILD_TESTING=OFF
+          sudo cmake --build build/ --target install
+        shell: bash
+
+      - name: Configure and build the API
+        run: |
+          cmake --preset=ci-ubuntu
+          cmake --build build
+        shell: bash
+
+      - name: Build the docs
+        run : cmake "-DPROJECT_SOURCE_DIR=$PWD" "-DPROJECT_BINARY_DIR=$PWD/build" -P cmake/docs-ci.cmake
+        shell: bash
diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index f41a20dd..b2ec1f18 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - main
-  pull_request:
 
 jobs:
   deploy:
@@ -44,5 +43,5 @@ jobs:
         uses: JamesIves/github-pages-deploy-action@v4
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          branch: test_gh_pages
+          branch: gh_pages
           folder: build/docs/html
diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in
index 4df7bf14..63a2726c 100644
--- a/docs/Doxyfile.in
+++ b/docs/Doxyfile.in
@@ -48,4 +48,7 @@ INTERACTIVE_SVG = YES  # Enable highlighting by hovering on elements
 
 # Add header customization
 HTML_HEADER            = "@PROJECT_SOURCE_DIR@/docs/layout/header.html"
-PROJECT_LOGO           = "@PROJECT_SOURCE_DIR@/resources/logo/aqnwb-logo.png"
\ No newline at end of file
+PROJECT_LOGO           = "@PROJECT_SOURCE_DIR@/resources/logo/aqnwb-logo.png"
+
+# Fail on warnings
+WARN_AS_ERROR = FAIL_ON_WARNINGS_PRINT
\ No newline at end of file

From 70b094aa1836a03f4c671ee0e2ab407262af0fa9 Mon Sep 17 00:00:00 2001
From: Steph Prince <40640337+stephprince@users.noreply.github.com>
Date: Tue, 6 Aug 2024 13:41:02 -0700
Subject: [PATCH 26/26] remove doxygen build test workflow

---
 .github/workflows/doxygen-build.yml | 37 -----------------------------
 1 file changed, 37 deletions(-)
 delete mode 100644 .github/workflows/doxygen-build.yml

diff --git a/.github/workflows/doxygen-build.yml b/.github/workflows/doxygen-build.yml
deleted file mode 100644
index e63cfbbe..00000000
--- a/.github/workflows/doxygen-build.yml
+++ /dev/null
@@ -1,37 +0,0 @@
-name: Doxygen Build Test
-
-on:
-  push:
-    branches:
-      - main
-  pull_request:
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-        with:
-          submodules: "true"
-      - name: Install dependencies - ubuntu
-        run: |
-          sudo apt-get update
-          sudo apt-get install doxygen graphviz -y
-          sudo apt-get install -y libhdf5-dev libboost-all-dev
-          git clone https://github.com/catchorg/Catch2.git
-          cd Catch2
-          git checkout "v3.5.3"
-          cmake -Bbuild -H. -DBUILD_TESTING=OFF
-          sudo cmake --build build/ --target install
-        shell: bash
-
-      - name: Configure and build the API
-        run: |
-          cmake --preset=ci-ubuntu
-          cmake --build build
-        shell: bash
-
-      - name: Build the docs
-        run : cmake "-DPROJECT_SOURCE_DIR=$PWD" "-DPROJECT_BINARY_DIR=$PWD/build" -P cmake/docs-ci.cmake
-        shell: bash