add doxygen documentation #946
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📝 WalkthroughWalkthroughThis pull request introduces documentation improvements for the project. It adds a new Doxygen configuration file with comprehensive settings for generating project documentation. The Makefile is updated with two new targets: one for cleaning build artifacts and another for running the Doxygen build. Additionally, a new "Developer documentation" section is added to an existing markdown file. The Sphinx configuration now supports Markdown files by including the Changes
Sequence Diagram(s)sequenceDiagram
participant Dev as Developer
participant Make as Makefile
participant Sphinx as Sphinx Build System
Dev->>Make: Run "make clean"
Make->>Sphinx: Execute Sphinx clean command (remove build directory)
Sphinx-->>Make: Build directory removed
Make-->>Dev: Clean complete
sequenceDiagram
participant Dev as Developer
participant Make as Makefile
participant Doxygen as Doxygen Tool
Dev->>Make: Run "make Doxygen-build"
Make->>Doxygen: Invoke Doxygen using Doxyfile
Doxygen-->>Make: Documentation generated
Make-->>Dev: Doxygen build complete
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Actionable comments posted: 3
🧹 Nitpick comments (1)
doc/Makefile (1)
25-26: Enhance the Doxygen-build target.Consider adding error handling and making the target phony.
+.PHONY: help Makefile clean Doxygen-build + Doxygen-build: - doxygen Doxyfile + @command -v doxygen >/dev/null 2>&1 || { echo >&2 "doxygen not found. Please install it."; exit 1; } + @doxygen Doxyfile || { echo >&2 "Doxygen documentation generation failed"; exit 1; }
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📒 Files selected for processing (5)
doc/Doxyfile.in(1 hunks)doc/Makefile(1 hunks)doc/doxypages/main.md(1 hunks)doc/source/conf.py(2 hunks)doc/source/requirements.txt(1 hunks)
✅ Files skipped from review due to trivial changes (1)
- doc/source/requirements.txt
🧰 Additional context used
🪛 LanguageTool
doc/doxypages/main.md
[uncategorized] ~4-~4: “were” seems less likely than “where”.
Context: # Developer documentation This is were all dark secrets are revealed.
(AI_HYDRA_LEO_CPT_WERE_WHERE)
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🔇 Additional comments (1)
doc/source/conf.py (1)
53-53: LGTM! Good addition of Markdown support.The addition of the
myst_parserextension and.mdfile support enhances documentation capabilities by allowing both reStructuredText and Markdown files.Also applies to: 87-88
| PROJECT_BRIEF = "adaptive mesh refinement hybrid kinetic code" | ||
| PROJECT_LOGO = | ||
| PROJECT_ICON = | ||
| OUTPUT_DIRECTORY = /home/aunai/Documents/code/phare/PHARE/doc/build |
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Replace hardcoded output directory path.
The output directory is hardcoded to a specific user's path which will not work for other developers.
Replace with a relative path:
-OUTPUT_DIRECTORY = /home/aunai/Documents/code/phare/PHARE/doc/build
+OUTPUT_DIRECTORY = @CMAKE_CURRENT_BINARY_DIR@📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| OUTPUT_DIRECTORY = /home/aunai/Documents/code/phare/PHARE/doc/build | |
| OUTPUT_DIRECTORY = @CMAKE_CURRENT_BINARY_DIR@ |
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| # Developer documentation | ||
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| This is were all dark secrets are revealed. |
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🛠️ Refactor suggestion
Enhance the developer documentation content.
The current content is too informal and lacks substance. Consider adding:
- Purpose of the developer documentation
- Overview of the codebase structure
- Setup instructions
- Contribution guidelines
Would you like me to help generate a more comprehensive template for the developer documentation?
🧰 Tools
🪛 LanguageTool
[uncategorized] ~4-~4: “were” seems less likely than “where”.
Context: # Developer documentation This is were all dark secrets are revealed.
(AI_HYDRA_LEO_CPT_WERE_WHERE)
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| # Developer documentation | ||
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| This is were all dark secrets are revealed. |
There was a problem hiding this comment.
Fix grammatical error.
There's a typo in the sentence.
-This is were all dark secrets are revealed.
+This is where all dark secrets are revealed.📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| This is were all dark secrets are revealed. | |
| This is where all dark secrets are revealed. |
🧰 Tools
🪛 LanguageTool
[uncategorized] ~4-~4: “were” seems less likely than “where”.
Context: # Developer documentation This is were all dark secrets are revealed.
(AI_HYDRA_LEO_CPT_WERE_WHERE)
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limits sphinx version, see #955 |
This adds the doxygen configuration for generating developer's documentation.
I'm not sure we want the doxygen html outputs generated somewhere (where? how automatically?) or we want to use
breatheextention to sphinx to couple our sphinx documentation published on readthedoc to doxygen comments in our code.TBD together
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