Remove Zenodo badge, patch Doxygen's cookie.js to store in session storage. (#373)

Resolves #370 but might break certain browsers.

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Author: samcunliffe

.github/workflows/doxygen-gh-pages.yml

@@ -18,58 +18,60 @@ jobs:
   doxygen:
     runs-on: macos-latest
     steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+        with:
+          submodules: "true"
 
-    - name: Checkout repository
-      uses: actions/checkout@v5
-      with:
-        submodules: "true"
+      - name: Install Doxygen
+        run: brew install doxygen graphviz
+        shell: bash
 
-    - name: Install Doxygen
-      run: brew install doxygen graphviz
-      shell: bash
+      - name: Run Doxygen
+        run: doxygen doc/Doxyfile
+        shell: bash
 
-    - name: Run Doxygen
-      run: doxygen doc/Doxyfile
-      shell: bash
+      # Disabling jekyll ensures pages with underscores work on gh pages.
+      - name: Create .nojekyll
+        run: touch html/.nojekyll
+        shell: bash
 
-    # Disabling jekyll ensures pages with underscores work on gh pages.
-    - name: Create .nojekyll
-      run: touch html/.nojekyll
-      shell: bash
+      - name: Manually copy over assets
+        # Preserve the directory structure to keep README's image references!
+        run: |
+          mkdir -p html/doc/assets
+          cp -R doc/assets/*.png html/doc/assets
+        shell: bash
 
-    - name: Manually copy over assets
-      # Preserve the directory structure to keep README's image references!
-      run: |
-        mkdir -p html/doc/assets
-        cp -R doc/assets/*.png html/doc/assets
-      shell: bash
+      - name: Manually patch cookie.js
+        run: cp doc/js/cookie.js html/cookie.js
+        shell: bash
 
-    - name: Upload the website
-      uses: actions/upload-artifact@v4
-      with:
-        name: tdms_website
-        path: html/*
-        retention-days: 1
+      - name: Upload the website
+        uses: actions/upload-artifact@v4
+        with:
+          name: tdms_website
+          path: html/*
+          retention-days: 1
 
   publish:
     runs-on: ubuntu-latest
     needs: doxygen
     if: github.event_name == 'push' && github.ref_name == 'main'
     steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
 
-    - name: Checkout repository
-      uses: actions/checkout@v5
+      - name: Download the content for deployment
+        uses: actions/download-artifact@v5
+        with:
+          name: tdms_website
+          path: html
+          # Recreate and download to the html directory just for tidiness sake.
 
-    - name: Download the content for deployment
-      uses: actions/download-artifact@v5
-      with:
-        name: tdms_website
-        path: html
-        # Recreate and download to the html directory just for tidiness sake.
-
-    - name: Commit to GitHub Pages
-      uses: JamesIves/github-pages-deploy-action@v4
-      with:
-        token: ${{ secrets.GITHUB_TOKEN }}
-        branch: gh-pages
-        folder: html
+      - name: Commit to GitHub Pages
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          branch: gh-pages
+          folder: html

README.md

@@ -4,7 +4,7 @@
 and title at the top of README.md when building the project page (the title
 would be duplicated) everything else in README.md is also the project homepage. -->
 
-# TDMS · [![latest release](https://badgen.net/github/release/UCL/TDMS)](https://github.com/UCL/TDMS/releases)  [![license](https://badgen.net/badge/license/GPL-3.0/blue)](https://github.com/UCL/TDMS/blob/main/LICENSE) [![Build and test](https://github.com/UCL/TDMS/actions/workflows/ci.yml/badge.svg)](https://github.com/UCL/TDMS/actions/workflows/ci.yml) [![MATLAB tests](https://github.com/UCL/TDMS/actions/workflows/matlab_tests.yml/badge.svg)](https://github.com/UCL/TDMS/actions/workflows/matlab_tests.yml) [![codecov](https://codecov.io/gh/UCL/TDMS/branch/main/graph/badge.svg?token=3kqP14kslL)](https://codecov.io/gh/UCL/TDMS) [![DOI](https://zenodo.org/badge/448864310.svg)](https://zenodo.org/badge/latestdoi/448864310)
+# TDMS · [![latest release](https://badgen.net/github/release/UCL/TDMS)](https://github.com/UCL/TDMS/releases) [![license](https://badgen.net/badge/license/GPL-3.0/blue)](https://github.com/UCL/TDMS/blob/main/LICENSE) [![Build and test](https://github.com/UCL/TDMS/actions/workflows/ci.yml/badge.svg)](https://github.com/UCL/TDMS/actions/workflows/ci.yml) [![MATLAB tests](https://github.com/UCL/TDMS/actions/workflows/matlab_tests.yml/badge.svg)](https://github.com/UCL/TDMS/actions/workflows/matlab_tests.yml) [![codecov](https://codecov.io/gh/UCL/TDMS/branch/main/graph/badge.svg?token=3kqP14kslL)](https://codecov.io/gh/UCL/TDMS) [![DOI:10.5281/zenodo.7950603](doc/assets/doi-badge.svg)](https://zenodo.org/badge/latestdoi/448864310)
 
 <!-- \endcond -->
 
@@ -26,6 +26,7 @@ It needs to be built against [FFTW](https://www.fftw.org/) and [MATLAB](https://
 Assuming you don't already have them, you'll need a C++ compiler, CMake, OpenMP and FFTW.
 
 For Debian-based distributions this should be as simple as
+
 ```{sh}
 $ sudo apt install git gcc cmake libfftw3-dev libgomp1
 ```
@@ -61,10 +62,11 @@ Assuming you don't already have them, you'll need to download and install:
 <!-- when updating to version 1.1+, uncomment
 
 * [HDF5](https://portal.hdfgroup.org/display/HDF5/HDF5+CPP+Reference+Manuals) -->
-* [MATLAB](https://www.mathworks.com/products/matlab.html),
-* [Visual Studio](https://visualstudio.microsoft.com/vs/community/) and **be sure to select the C++ developer kit**,
-* [CMake](https://cmake.org/download/),
-* and [FFTW](https://www.fftw.org/install/windows.html).
+
+- [MATLAB](https://www.mathworks.com/products/matlab.html),
+- [Visual Studio](https://visualstudio.microsoft.com/vs/community/) and **be sure to select the C++ developer kit**,
+- [CMake](https://cmake.org/download/),
+- and [FFTW](https://www.fftw.org/install/windows.html).
 
 You can check that the Visual Studio compiler was installed with:
 
@@ -74,7 +76,6 @@ PS> MSBuild.exe -h
 
 Potentially the simplest way to get FFTW is via [conda](https://anaconda.org/conda-forge/fftw):
 
-
 ```{pwsh}
 PS> conda install -c conda-forge fftw --yes
 ```
@@ -84,10 +85,12 @@ PS> conda install -c conda-forge fftw --yes
 You'll need to ensure the paths to FFTW and MATLAB (the locations of `fftw3.dll` and `libmex.dll` respectively) are in the `env:Path`.
 
 These can be found, e.g. by
+
 ```{pwsh}
 PS> conda list fftw # assuming you installed via conda
 PS> which.exe MATLAB
 ```
+
 Which should return something like `C:\Program Files (x86)\MATLAB\R20XXx\bin\matlab` and maybe `C:\ProgramData\envs\base\bin`.
 If you downloaded FFTW and created `fftw3.dll` with `lib.exe`, you just need to know where you saved it.
 
@@ -98,22 +101,23 @@ PS> $env:Path += ";C:\Program Files (x86)\MATLAB\R20XXx\bin\;C:\ < wherever fftw
 ```
 
 Which will help Windows locate `.dll` files later.
-For all following instructions, you'll have to substitute our mentions of ``tdms`` with ``tdms.exe`` and ``$`` is used to denote a command prompt which, in PowerShell, would look like ``PS>``
+For all following instructions, you'll have to substitute our mentions of `tdms` with `tdms.exe` and `$` is used to denote a command prompt which, in PowerShell, would look like `PS>`
 
 <details>
 <summary>Even more Windows troubleshooting</summary>
 
-We've seen that in a fresh PowerShell window, Windows does not remember the location of the ``.dll`` files, so you may have to re-add them to the path, or copy them into the directory where TDMS was installed.
+We've seen that in a fresh PowerShell window, Windows does not remember the location of the `.dll` files, so you may have to re-add them to the path, or copy them into the directory where TDMS was installed.
 
-TDMS typically installs to ``"C:\Program Files (x86)\tdms\bin\tdms.exe"``.
+TDMS typically installs to `"C:\Program Files (x86)\tdms\bin\tdms.exe"`.
 
 </details>
 
 </details>
 
-------
+---
 
 You'll need to download and install [MATLAB](https://www.mathworks.com/products/matlab.html), and take note where the headers are installed.
+
 </details>
 
 ## Installation
@@ -137,10 +141,12 @@ If CMake cannot find MATLAB, FFTW, or install to the default installation prefix
 <!-- TODO: add HDF5 when updating to v1.1+ -->
 
 You can check that `tdms` was installed correctly and is in your `PATH` by running:
+
 ```{sh}
 $ tdms --help
 $ tdms --version
 ```
+
 in a new terminal.
 
 ## How to run
@@ -177,7 +183,7 @@ In a terminal run
 $ which tdms
 ```
 
-Copy the full path (something like `/usr/local/bin/tdms`) into [`run_pstd_bscan.m`](https://github.com/UCL/TDMS/blob/main/examples/arc_01/run_pstd_bscan.m), replacing the ` 'tdms' ` text in the calls to the ``system()`` function.
+Copy the full path (something like `/usr/local/bin/tdms`) into [`run_pstd_bscan.m`](https://github.com/UCL/TDMS/blob/main/examples/arc_01/run_pstd_bscan.m), replacing the `'tdms'` text in the calls to the `system()` function.
 
 </details>
 
@@ -205,6 +211,7 @@ These options can be selected by setting the corresponding flag variables in the
 When `tdms` reads the input, it will verify if the input file contains a dataset that matches the names of these flags.
 
 There are two flags available for configuration in the input file.
+
 <details>
 <summary> `use_pstd` </summary>
 - If not provided, or provided as `false`, then the default timestepping method of finite-differences (FDTD) will be used.
@@ -217,10 +224,12 @@ There are two flags available for configuration in the input file.
 
 \note Typically bandlimited interpolation is superior to cubic interpolation when the extent of the Yee cell is of approximately the same order as, but slightly less than, one-sixth of the shortest wavelength of interest.
 Otherwise, cubic interpolation typically enjoys superior accuracy.
+
 </details>
 
 TDMS is parallelised with [OpenMP](https://en.wikipedia.org/wiki/OpenMP).
 You can set the maximum number of threads using the `OMP_NUM_THREADS` environment variable before calling the TDMS executable.
+
 ```{sh}
 $ export OMP_NUM_THREADS=4 # for example
 ```

doc/assets/doi-badge.svg

@@ -0,0 +1,25 @@
+/*!
+This is a patched 'Cookie helper functions' from Doxygen that overrides all
+cookie setting and places everything in sessionStorage. It might break some browsers but works in Firefox and Chrome.
+
+Original header:
+ Copyright (c) 2023 Dimitri van Heesch
+ Released under MIT license.
+*/
+let Cookie = {
+  cookie_namespace: 'doxygen_',
+
+  readSetting(cookie,defVal) {
+    const val = sessionStorage.getItem(this.cookie_namespace+cookie);
+    if (val) return val;
+    return defVal;
+  },
+
+  writeSetting(cookie,val,days=0) { // default days='session', 0=session cookie, -1=delete
+    sessionStorage.setItem(this.cookie_namespace+cookie,val);
+  },
+
+  eraseSetting(cookie) {
+    sessionStorage.removeItem(this.cookie_namespace+cookie);
+  },
+}