diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index 7a55772f..00000000 --- a/docs/Makefile +++ /dev/null @@ -1,177 +0,0 @@ -# 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/Mesa-Geo.qhcp" - @echo "To view the help file:" - @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Mesa-Geo.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/Mesa-Geo" - @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Mesa-Geo" - @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. The text files are in $(BUILDDIR)/text." - -man: - $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man - @echo - @echo "Build finished. The manual pages are in $(BUILDDIR)/man." - -texinfo: - $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo - @echo - @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." - @echo "Run \`make' in that directory to run these through makeinfo" \ - "(use \`make info' here to do that automatically)." - -info: - $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo - @echo "Running Texinfo files through makeinfo..." - make -C $(BUILDDIR)/texinfo info - @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." - -gettext: - $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale - @echo - @echo "Build finished. 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/docs/conf.py b/docs/conf.py index a7cb42f3..31262485 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -115,12 +115,7 @@ # keep_warnings = False # --- Options for nbsphinx ----------------------------------------------- -# prevents cell run time taking too long -nb_execution_timeout = 60 -# uses cached information -nb_execution_mode = "cache" -# ensures there is not a conflict if user has multiple kernels -nbsphinx_kernel_name = 'python-upstream-dev' +nbsphinc_execute = 'never' # -- Options for HTML output ---------------------------------------------- diff --git a/docs/tutorials/intro_tutorial.ipynb b/docs/tutorials/intro_tutorial.ipynb index 32945151..e749c803 100644 --- a/docs/tutorials/intro_tutorial.ipynb +++ b/docs/tutorials/intro_tutorial.ipynb @@ -25,7 +25,7 @@ "- Recovery Rate (time infection lasts)\n", "- Mobility (distance agent moves)\n", "\n", - "### The tutorial then proceeds in three parts: \n", + "**The tutorial then proceeds in three parts:** \n", "- Part 1 Create the Basic Model \n", "- Part 2 Add Agent Behaviors and Model Complexity \n", "- Part 3 Add Visualizations and Interface\n", @@ -39,22 +39,20 @@ ] }, { - "cell_type": "code", - "execution_count": null, - "id": "c0c702b3-c307-4f00-9530-468e29f53184", + "cell_type": "raw", + "id": "0b098d27-39cd-41a3-b171-f525c6035d94", "metadata": {}, - "outputs": [], "source": [ - "#Run this if in colab\n", - "!pip install mesa\n", - "!pip install mesa-geo\n", + "#Run this if in colab (make it is a code cell) \n", + "!pip install mesa --quiet\n", + "!pip install mesa-geo --quiet\n", "!mkdir -p data\n", "!wget -P data https://raw.githubusercontent.com/projectmesa/mesa-geo/tree/main/docs/tutorials/data/TorontoNeighbourhoods.geojson" ] }, { "cell_type": "markdown", - "id": "3f1b8324-9849-4992-b13a-db9a94372d0a", + "id": "163711a0-3d78-4fdd-964d-07f9dd88b9d4", "metadata": {}, "source": [ "## Part 1 Create the Basic Model\n", @@ -1111,9 +1109,9 @@ ], "metadata": { "kernelspec": { - "display_name": "Xeus-Python (Python 3.10)", + "display_name": "Python 3 (ipykernel)", "language": "python", - "name": "mesa_geo" + "name": "python3" }, "language_info": { "codemirror_mode": { diff --git a/pyproject.toml b/pyproject.toml index fae1bb52..79018045 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -64,6 +64,7 @@ dev = [ docs = [ "sphinx", "ipython", + "ipykernel", # necessary to ensure python3 kernel "pydata_sphinx_theme", "seaborn", "myst-nb",