diff --git a/doc/HOWTO_build_the_doc b/doc/HOWTO_build_the_doc deleted file mode 100644 index fedfd92..0000000 --- a/doc/HOWTO_build_the_doc +++ /dev/null @@ -1,18 +0,0 @@ -If needed create the environment:: - - conda env create -name env_fluidfft_doc --file environment.yml - -Run in a terminal from this directory:: - - make html - -Also useful:: - - make clean - make cleanall - -Dependencies to build the documentation: - -- sphinx -- numpydoc - diff --git a/doc/conf.py b/doc/conf.py index 9f2ce8c..a62be31 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -26,16 +26,12 @@ plt.ioff() -from fluiddoc.ipynb_maker import execute_notebooks from fluiddyn.util import modification_date import fluidfft import fluidfft.bench_analysis from fluidfft.bench_analysis import plot_scaling -execute_notebooks("ipynb") -nbsphinx_execute = "never" - here = os.path.dirname(__file__) here_tmp = os.path.join(here, "tmp") html = os.path.join(here, "_build/html") @@ -70,9 +66,9 @@ def save_fig_scaling(dir_name, dim, n0, n1, n2=None): path_dir = os.path.join(path_fluidfft_bench_results, dir_name) path_fig = os.path.join(here_tmp, "fig_" + dir_name + ".png") - if not os.path.exists(path_fig) or modification_date( - path_dir - ) > modification_date(path_fig): + if not os.path.exists(path_fig) or modification_date(path_dir) > modification_date( + path_fig + ): print("make fig", path_fig) fig = plot_scaling(path_dir, None, dim, n0, n1, n2, show=False) fig.savefig(path_fig) @@ -113,13 +109,12 @@ def save_fig_scaling(dir_name, dim, n0, n1, n2=None): "sphinx.ext.autodoc", "sphinx.ext.doctest", "sphinx.ext.todo", - # 'sphinx.ext.pngmath', "sphinx.ext.mathjax", "sphinx.ext.viewcode", "sphinx.ext.autosummary", "numpydoc", - "nbsphinx", "sphinx_copybutton", + "myst_nb", # 'fluiddoc.mathmacro', # 'breathe' ] @@ -168,13 +163,6 @@ def save_fig_scaling(dir_name, dim, n0, n1, n2=None): # directories to ignore when looking for source files. exclude_patterns = ["_build", "install/blas_libs.rst"] paths_notebooks = Path("ipynb").glob("*.ipynb") -exclude_patterns.extend( - [ - f"ipynb/{path.name}" - for path in paths_notebooks - if not path.name.endswith(".executed.ipynb") - ] -) # The reST default role (used for this markup: `text`) to use for all # documents. @@ -328,9 +316,7 @@ def save_fig_scaling(dir_name, dim, n0, n1, n2=None): # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). -man_pages = [ - ("index", "FluidFFT", "FluidFFT Documentation", ["Pierre Augier"], 1) -] +man_pages = [("index", "FluidFFT", "FluidFFT Documentation", ["Pierre Augier"], 1)] # If true, show URL addresses after external links. # man_show_urls = False @@ -373,3 +359,31 @@ def save_fig_scaling(dir_name, dim, n0, n1, n2=None): autodoc_member_order = "bysource" todo_include_todos = True + +# Execute ipynb files into with a cache ... +nb_execution_mode = "cache" +nb_execution_cache_path = "./_build/jupyter_cache" +os.makedirs(nb_execution_cache_path, exist_ok=True) +# ... except these ipynb files +nb_execution_excludepatterns = ["ipynb/executed/*"] + +nb_execution_raise_on_error = True +nb_execution_show_tb = True +nb_merge_streams = True + +myst_enable_extensions = [ + "amsmath", + # "attrs_inline", + "colon_fence", + # "deflist", + "dollarmath", + # "fieldlist", + # "linkify", + # "replacements", + # "smartquotes", + # "strikethrough", + "substitution", + # "tasklist", +] + +suppress_warnings = ["mystnb.unknown_mime_type"] diff --git a/doc/tutorials.rst b/doc/tutorials.rst index 62a0af7..172c6b4 100644 --- a/doc/tutorials.rst +++ b/doc/tutorials.rst @@ -12,9 +12,9 @@ simpler to use directly the "operators" classes .. toctree:: :maxdepth: 1 - ipynb/tuto_fft2d_seq.executed + ipynb/tuto_fft2d_seq.ipynb ipynb/executed/tuto_fft2d_mpi ipynb/executed/tuto_fft2d_mpi_domain_decomp - ipynb/tuto_fft3d_seq.executed + ipynb/tuto_fft3d_seq.ipynb ipynb/executed/tuto_fft3d_mpi ipynb/executed/tuto_fft3d_mpi_domain_decomp diff --git a/pdm.lock b/pdm.lock index 4e8ba5c..6bd63c5 100644 --- a/pdm.lock +++ b/pdm.lock @@ -5,7 +5,7 @@ groups = ["default", "build", "dev", "doc", "lint", "mpi", "pyfftw", "test"] strategy = ["cross_platform", "inherit_metadata"] lock_version = "4.4.1" -content_hash = "sha256:3e8d44e8664b93bf198cfefaeae4dae6a6551f5d436d6118c060340f5a447a75" +content_hash = 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