diff --git a/.github/workflows/doc.yml b/.github/workflows/doc.yml new file mode 100644 index 0000000..65f545d --- /dev/null +++ b/.github/workflows/doc.yml @@ -0,0 +1,35 @@ +name: Documentation + +on: + push: + branches: + - master + pull_request: + branches: + - master + +jobs: + build-manual: + runs-on: ubuntu-20.04 + steps: + - uses: actions/checkout@v2 + - uses: conda-incubator/setup-miniconda@v2 + with: + mamba-version: "*" + activate-environment: pari-jupyter-doc + environment-file: doc/environment.yml + python-version: 3.9 + auto-activate-base: false + - name: Conda list + shell: bash -l {0} + run: | + conda info + conda list + - name: Install pari-jupyter + shell: bash -l {0} + run: pip install --verbose --no-index . + - name: Build documentation + shell: bash -l {0} + run: | + cd doc + make html SPHINXOPTS="-W" diff --git a/doc/.gitignore b/doc/.gitignore new file mode 100644 index 0000000..69fa449 --- /dev/null +++ b/doc/.gitignore @@ -0,0 +1 @@ +_build/ diff --git a/doc/Makefile b/doc/Makefile new file mode 100644 index 0000000..b559116 --- /dev/null +++ b/doc/Makefile @@ -0,0 +1,177 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = _build + +# User-friendly check for sphinx-build +ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) +$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) +endif + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext + +help: + @echo "Please use \`make ' where is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " xml to make Docutils-native XML files" + @echo " pseudoxml to make pseudoxml-XML files for display purposes" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/pari-jupyter.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pari-jupyter.qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/pari-jupyter" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pari-jupyter" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +latexpdfja: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through platex and dvipdfmx..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. 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The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." + +xml: + $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml + @echo + @echo "Build finished. The XML files are in $(BUILDDIR)/xml." + +pseudoxml: + $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml + @echo + @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." diff --git a/doc/conf.py b/doc/conf.py new file mode 100644 index 0000000..e0b84bd --- /dev/null +++ b/doc/conf.py @@ -0,0 +1,257 @@ +# -*- coding: utf-8 -*- +# +# pari-jupyter documentation build configuration file + +import sys +import os + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +#sys.path.insert(0, os.path.abspath('.')) +sys.path.insert(0, os.path.abspath('..')) + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +#needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + 'sphinx.ext.autodoc', + 'sphinx.ext.todo', + 'sphinx.ext.mathjax', + 'sphinx.ext.viewcode', + 'myst_nb', +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix of source filenames. +source_suffix = '.rst' + +# The encoding of source files. +#source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'pari-jupyter' +copyright = u'2015-2021, Vincent Delecroix and Jeroen Demeyer' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +# version = 'X.Y' +# The full version, including alpha/beta/rc tags. +# release = 'X.Y' +import PARIKernel +version = release = PARIKernel.__version__ + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +#language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +#today = '' +# Else, today_fmt is used as the format for a strftime call. +#today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ['_build', 'news'] + +# The reST default role (used for this markup: `text`) to use for all +# documents. +#default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +#add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +#add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +#show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +#modindex_common_prefix = [] + +# If true, keep warnings as "system message" paragraphs in the built documents. +#keep_warnings = False + + +# -- Options for HTML output ---------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = 'default' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +#html_theme_options = {} + +# Add any paths that contain custom themes here, relative to this directory. +#html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v documentation". +#html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +#html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +#html_logo = None + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +#html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = [] + +# Add any extra paths that contain custom files (such as robots.txt or +# .htaccess) here, relative to this directory. These files are copied +# directly to the root of the documentation. +#html_extra_path = [] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +#html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +#html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +#html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +#html_additional_pages = {} + +# If false, no module index is generated. +#html_domain_indices = True + +# If false, no index is generated. +#html_use_index = True + +# If true, the index is split into individual pages for each letter. +#html_split_index = False + +# If true, links to the reST sources are added to the pages. +#html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +#html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +#html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +#html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +#html_file_suffix = None + +# Output file base name for HTML help builder. +htmlhelp_basename = 'pari-jupyterdoc' + + +# -- Options for LaTeX output --------------------------------------------- + +latex_elements = { +# The paper size ('letterpaper' or 'a4paper'). +#'papersize': 'letterpaper', + +# The font size ('10pt', '11pt' or '12pt'). +#'pointsize': '10pt', + +# Additional stuff for the LaTeX preamble. +#'preamble': '', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, +# author, documentclass [howto, manual, or own class]). +latex_documents = [ + ('index', 'pari-jupyter.tex', u'pari-jupyter documentation', + u'Vincent Delecroix and Jeroen Demeyer', 'manual'), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +#latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +#latex_use_parts = False + +# If true, show page references after internal links. +#latex_show_pagerefs = False + +# If true, show URL addresses after external links. +#latex_show_urls = False + +# Documents to append as an appendix to all manuals. +#latex_appendices = [] + +# If false, no module index is generated. +#latex_domain_indices = True + + +# -- Options for manual page output --------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ('index', 'pari-jupyter', u'pari-jupyter documentation', + [u'Vincent Delecroix and Jeroen Demeyer'], 1) +] + +# If true, show URL addresses after external links. +#man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------- + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ('index', 'pari-jupyter', u'pari-jupyter documentation', + u'Vincent Delecroix and Jeroen Demeyer', 'pari-jupyter', 'A jupyter kernel for PARI/GP', + 'Miscellaneous'), +] + +# Documents to append as an appendix to all manuals. +#texinfo_appendices = [] + +# If false, no module index is generated. +#texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +#texinfo_show_urls = 'footnote' + +# If true, do not generate a @detailmenu in the "Top" node's menu. +#texinfo_no_detailmenu = False diff --git a/doc/environment.yml b/doc/environment.yml new file mode 100644 index 0000000..154cfad --- /dev/null +++ b/doc/environment.yml @@ -0,0 +1,21 @@ +# This file lists the minimial dependencies needed to build the documentation +# for pari-jupyter. Create a conda environment with these dependencies +# preinstalled with: +# conda env create -f environment.yml +name: pari-jupyter-doc +channels: + - conda-forge + - defaults +dependencies: + - python=3.9 # NOTE: does not work with 3.10, see https://github.com/jupyter/jupyter_console/issues/245 + - cython + - jupyter + - pip + - ipykernel + - pari + - sphinx + - jupytext + - myst-nb + - tachyon + - pip: + - jupyter_kernel_test # NOTE: not recent enough in conda, see https://github.com/jupyter/jupyter_kernel_test/issues/70 diff --git a/doc/examples.rst b/doc/examples.rst new file mode 100644 index 0000000..423bae6 --- /dev/null +++ b/doc/examples.rst @@ -0,0 +1,7 @@ +Examples +******** + +.. toctree:: + :maxdepth: 1 + + examples/init diff --git a/doc/examples/init.md b/doc/examples/init.md new file mode 100644 index 0000000..974a40c --- /dev/null +++ b/doc/examples/init.md @@ -0,0 +1,153 @@ +--- +jupytext: + formats: ipynb,md:myst + text_representation: + extension: .md + format_name: myst + format_version: 0.13 + jupytext_version: 1.13.0 +kernelspec: + display_name: PARI/GP 12.3 + name: pari_jupyter +--- + +# Introduction to PARI/GP + +Based on B. Allombert pdf presentation available at http://pari.math.u-bordeaux.fr/Events/PARI2019b/talks/init.pdf + +## Introduction + +- PARI is a C library, allowing fast computations +- gp is an easy-touse interactive shell giving access to the PARI functions +- GP is the name of gp's scripting language +- gp2c is the gp GP to PARI compiler allows to convert GP scripts to C + +# Basic objects + +`I` is the imaginary unit and `x` a symbolic variable +```{code-cell} gp +57! +2 / 6 +(1+I)^2 +(x+1)^(-2) +``` +Modular computations +```{code-cell} +Mod(2,5)^3 +Mod(x, x^2+x+1)^3 +w = ffgen([3,5],'w); w^12 \\ in F_3^5 +``` +Usual constants and functions (`%` is the value of the last command while `%12` is the value of the 12-th command) +```{code-cell} gp +Pi +log(2) +\p100 +log(2) +exp(%) +log(1+x) +exp(%12) +``` + +## Help + +To access documentation, use the question mark `?` followed by +```{code-cell} gp +?4 +?atan +``` + +With two question marks `??` you access ? +```{code-cell} gp +??atan +??refcard +??refcard-nf +??tutorial +``` +And what about 3 +```{code-cell} gp +???determinant +``` + +## Vectors and matrices + +```{code-cell} gp +V = [1,2,3]; +W = [4,5,6]~; +M = [1,2,3;4,5,6]; +``` +and products +```{code-cell} gp +V*W +M*W +``` +What is the name for this +```{code-cell} gp +U = [1..10] +``` + +## Components + +Can be used to extract subvector or submatrix +```{code-cell} gp +V[2] +W[1..2] +M[2,2] +M[1,] +M[,2] +M[1..2,1..2] +``` + +## Polymorphism + +```{code-cell} gp +\o0 +``` +Then can factor +```{code-cell} gp +factor(91) +factor(x^4+4) +factor((x^4+1)*Mod(1,a^2-2)) +factor((x^4+4)*Mod(1,13)) +factor(x^4+1,Mod(1,a^2-2)) +factor(x^4+1,Mod(1,13)) +``` + +## Numerical summation +```{code-cell} gp +intnum(x=0,1,1/(1+x^2))/Pi +sumnum(n=1,1/n^2)/Pi^2 +sumalt(n=0,(-1)^n/(2*n+1))*4 +sumalt(n=1,(-1)^n*log(n)) \\ diverging! +2*exp(2*%) +``` + +## Comprehension +```{code-cell} gp +[n^2|n<-[1..10]] +[n^2|n<-[1..10],isprime(n)] +[n^2|n<-primes([1,10])] +[a,b] = [1,2]; +print("a=",a," b=",b) +``` + +## Control structures + +- `if(cond, expr_true{, expr_false})` +- `while(cond, expr)` +- `for(var=start, end, expr(var))` +- `forstep(var=start, end, step, expr(var))` +- `forprime(var=start, end, expr(var))` +- `fordiv(N, var, expr(var))` + +## Memory + +To configure the memory used by PARI, in the file `.gprc` (or +`gprc.txt` under Windows) add the line + + parisizemax=1G + +or do + +```{code-cell} gp +default(parisizemax,"1G"); +``` diff --git a/doc/index.rst b/doc/index.rst new file mode 100644 index 0000000..4cbcfc4 --- /dev/null +++ b/doc/index.rst @@ -0,0 +1,18 @@ +.. pari-jupyter documentation master file + +pari-jupyter documentation +************************** + +Contents: + +.. toctree:: + :maxdepth: 2 + + examples + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search`