From 3d32da6ea10021b50d29a737969e1ece2f30bb91 Mon Sep 17 00:00:00 2001 From: bennibbelink <79653949+bennibbelink@users.noreply.github.com> Date: Mon, 1 Apr 2024 12:51:51 -0500 Subject: [PATCH 01/22] Adds our custom sidebar to the sphinx build --- source/atemplates/layout.html | 7 ++----- source/conf.py | 4 +++- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/source/atemplates/layout.html b/source/atemplates/layout.html index cfd6ae8e..bf579019 100644 --- a/source/atemplates/layout.html +++ b/source/atemplates/layout.html @@ -1,6 +1,4 @@ -{% extends "!layout.html" %} - -{% block sidebarsearch %} +

{{ _('Useful Pages') }}

- {{ super() }}

Get Cyclus


Current version: 1.5.5 @@ -53,4 +50,4 @@

Acknowledgements

-{% endblock %} +
diff --git a/source/conf.py b/source/conf.py index bf1630d1..c8a5fccf 100644 --- a/source/conf.py +++ b/source/conf.py @@ -186,7 +186,9 @@ #html_use_smartypants = True # Custom sidebar templates, maps document names to template names. -#html_sidebars = {} +html_sidebars = { + '**': [ 'searchbox.html', 'sidebar.html'] +} # Additional templates that should be rendered to pages, maps page names to # template names. From 9a1f7821e3b637bfa9f2afc4dc41fc99405d6cde Mon Sep 17 00:00:00 2001 From: bennibbelink <79653949+bennibbelink@users.noreply.github.com> Date: Mon, 1 Apr 2024 12:56:45 -0500 Subject: [PATCH 02/22] rename layout.html to sidebar.html for clarity --- source/atemplates/{layout.html => sidebar.html} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename source/atemplates/{layout.html => sidebar.html} (100%) diff --git a/source/atemplates/layout.html b/source/atemplates/sidebar.html similarity index 100% rename from source/atemplates/layout.html rename to source/atemplates/sidebar.html From eba35f91c534295e5bee9e3e1d5b77587c47a8e9 Mon Sep 17 00:00:00 2001 From: abachmann Date: Mon, 1 Apr 2024 16:12:26 -0500 Subject: [PATCH 03/22] add newsletters .bib files to config --- source/conf.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/source/conf.py b/source/conf.py index 998fa5a7..6d668117 100644 --- a/source/conf.py +++ b/source/conf.py @@ -57,7 +57,9 @@ 'cep/cep-0004-1.bib', 'cep/cep-0018-1.bib', 'cep/cep-0020-1.bib', - 'cite/citecyc.bib'] + 'cite/citecyc.bib', + 'newsletters/pubsmay2018.bib', + 'newsletters/pubsoct2017.bib'] numpydoc_show_class_members = False From c1d98e1bb5250cd12efe2cfeb30db50f0b4c8c81 Mon Sep 17 00:00:00 2001 From: bennibbelink <79653949+bennibbelink@users.noreply.github.com> Date: Tue, 2 Apr 2024 12:27:13 -0500 Subject: [PATCH 04/22] Update Makefile and README to reflect publishing changes --- Makefile | 25 -------------- README.rst | 83 +++++++++-------------------------------------- docker/README.rst | 7 ++-- 3 files changed, 18 insertions(+), 97 deletions(-) diff --git a/Makefile b/Makefile index 3e51bdf7..62dfea57 100644 --- a/Makefile +++ b/Makefile @@ -30,10 +30,7 @@ help: @echo "Please use \`make ' where is one of" @echo " gh-preview to build HTML in directory $BUILDDIR for testing" @echo " gh-revert to cleanup HTML build in directory $BUILDDIR after testing" - @echo " gh-publish to build final version and push from source branch to main branch" - @echo " gh-publish-only to push from source branch to main branch, assuming already built" @echo " docker-html to use docker to build HTML in directory $BUILDDIR for testing" - @echo " docker-gh-publish to use docker to build final version and push from source branch to main branch" @echo " serve build+serve html files using Python's SimpleHTTPServer" @echo " serve-only serve pre-built html files using Python's SimpleHTTPServer" @echo " dirhtml to make HTML files named index.html in directories" @@ -77,32 +74,10 @@ gh-preview html: @echo @echo "Build finished. The HTML pages are in $(BUILDDIR)." -gh-publish-only: - git fetch $(GH_UPSTREAM_REPO) - git checkout -B $(GH_PUBLISH_BRANCH) $(GH_UPSTREAM_REPO)/$(GH_PUBLISH_BRANCH) - git checkout $(GH_SOURCE_BRANCH) -- $(GH_SOURCE_DIR) - git reset HEAD - rsync -a $(BUILDDIR)/* . - rsync -a $(BUILDDIR)/.* . - git add -f `(cd $(BUILDDIR); find . -type f; cd ..)` - rm -rf $(GH_SOURCE_DIR) $(BUILDDIR) - git commit -m "Generated $(GH_PUBLISH_BRANCH) for `git log $(GH_SOURCE_BRANCH) -1 --pretty=short --abbrev-commit`" && git push --force $(GH_UPSTREAM_REPO) $(GH_PUBLISH_BRANCH) - git checkout $(GH_SOURCE_BRANCH) - -gh-publish: - make clean - make html - make gh-publish-only - docker-gh-preview docker-html: docker build -f docker/fuelcycle.org-deps/Dockerfile -t fuelcycle.org-deps . docker run -w /cyclus.github.com -v $(PWD):/cyclus.github.com fuelcycle.org-deps bash -c "make gh-preview && chmod -R 777 $(BUILDDIR)" -docker-gh-publish: - make clean - make docker-html - make gh-publish-only - serve: html cd $(BUILDDIR) && python -m http.server diff --git a/README.rst b/README.rst index 3e4ba984..191b281a 100644 --- a/README.rst +++ b/README.rst @@ -3,9 +3,9 @@ Dependencies Building the Cyclus website requires: -1. `Sphinx`_ v1.1.2 or higher +1. `Sphinx`_ v7.2.6 or higher -2. `sphinxcontrib-bibtex`_ v0.3.0 or higher +2. `sphinxcontrib-bibtex`_ v2.6.2 or higher 3. `cyclus`_ @@ -13,7 +13,7 @@ Building the Cyclus website requires: 5. `cycamore `_ -6. `Cloud Sphinx Theme `_ +6. `Cloud Sphinx Theme `_ v1.10.1 or higher **NOTE:** The cloud package for Debian and Ubuntu is broken, so do not apt-get this. Please ``pip install cloud_sptheme``, ``easy_install cloud_sptheme``, or install from source instead. @@ -24,16 +24,9 @@ to fix a bug in the package. Modifying the Cyclus Website ============================ -A 2 branch system has been implemented to maintain a clean process of -rebuilding this site. - -1. The `source` branch contains the restructured text documents and -Sphinx configuration used to build the site. All direct editing of -files should be made in the `source` branch. - -2. The `main` branch contains the processed and published web -content that is derived by Sphinx from the `source` branch. These -files should not be editted directly. +The site is built and published via GitHub Actions. The default branch of this repository is `source` +which contains the restructured text documents and Sphinx configuration used to build the site. +All direct editing of files should be made in the `source` branch. The rest of this readme assumes that you have two remotes associated with cyclus.github.com. @@ -57,7 +50,7 @@ run:: There are docker targets in the makefile for doing everything related to the -site - building, previewing, and publishing. See the ``Docker`` section below +site - building, previewing, and testing. See the ``Docker`` section below for more details. Best practice workflow for contributing to site changes @@ -86,7 +79,7 @@ Best practice workflow for contributing to site changes browser. Or if you have docker installed, you can optionally use the docker preview target: - ``make gh-preview-docker`` + ``make docker-gh-preview`` to build the website inside a docker container with all the correct dependencies and configuration taken care of automagically. @@ -107,66 +100,22 @@ Best practice workflow for contributing to site changes 8. Issue a pull request by going to your branch on your fork of the repo and clicking the "Pull Request" button. -Best practice for managing a pull request ------------------------------------------- - -1. Synchronize your repository with the upstream repo:: - - git fetch upstream - git checkout main - git merge upstream/main - git checkout source - git merge upstream/source - -2. Checkout the `pull_request_branch` in the pull request submitter's repo:: - - git fetch https://github.com/[username]/cyclus.github.com pull_request_branch - git checkout -b pull_request_branch - -3. Test the changes by using the `gh-preview` target - - ``make gh-preview`` - - This will build a version of the site in the `gh-build` directory in - your branch, `pull_request_branch`. You can load it directly in a - local browser. +9. Every time you modify your pull request a workflow will be triggered that builds + the site with your changes and uploads the built site as an artifact. The specific workflow run + can be found by viewing the "Details" of the ``build-and-upload`` check within a PR, + and the ``github-pages`` artifact is listed in the "Summary". -4. If satisfied, merge the `pull_request_branch` into the `source` - branch:: +10. If the PR is merged into the ``source`` branch the website will be published to https://fuelcycle.org + automatically via GitHub Actions. - git checkout source - git merge pull_request_branch - -6. If there are no conflicts, push this to the repo - - ``git push upstream source`` - -7. Republish the pages with the `gh-publish` target. (**NOTE: for this step, - the upstream Cyclus repository *must* be called `upstream`**) - - ``make gh-publish`` Docker ------- -The ``make docker-...`` targets require the cyclus/fuelcycle.org-deps docker image +The ``make docker-...`` targets require the `ghcr.io/cyclus/cymetric_22.04_apt/cymetric` docker image which can be retrieved/updated by running:: - docker pull cyclus/fuelcycle.org-deps - -Occasionally (i.e. for a Cyclus release) the image will need to be updated. -This can be done by:: - - cd docker/fuelcycle.org-deps - - # update the image the fuelcycle.org image depends on - docker pull cyclus/cymetric - - # rebuild the image - docker build -t cyclus/fuelcycle.org-deps . - - # push the new image to docker-hub - docker push cyclus/fuelcycle.org-deps + docker pull ghcr.io/cyclus/cymetric_22.04_apt/cymetric:latest .. _Sphinx: http://sphinx-doc.org/ .. _sphinxcontrib-bibtex: http://sphinxcontrib-bibtex.readthedocs.org/en/latest/index.html diff --git a/docker/README.rst b/docker/README.rst index 2df7da4c..25e288f4 100644 --- a/docker/README.rst +++ b/docker/README.rst @@ -1,9 +1,6 @@ ``fuelcycle.org-deps`` contains a dockerfile with all dependencies for building the website. This is used by the docker based build targets added to -the makefile. This image will need to be updated and repushed to docker hub -periodically when dependencies for the website need updating. Particularly, -this image will need to be rebuilt whenever there is a new release of -cyclus+cycamore+cymetric - otherwise new changes in those projects/repos won't -show up/work on the website. +the makefile. This image will automatically use the latest cymetric image from GHCR, +which is updated automatically via GitHub Actions on any changes to Cyclus, Cycamore, or Cymetric. From d69ca9a6ac40c880a40f1f5a8f7a2bbd983cb1a2 Mon Sep 17 00:00:00 2001 From: bennibbelink <79653949+bennibbelink@users.noreply.github.com> Date: Tue, 2 Apr 2024 22:09:26 -0500 Subject: [PATCH 05/22] restructure Dockerfile --- Makefile | 4 ++-- docker/{fuelcycle.org-deps => }/Dockerfile | 1 - docker/README.rst | 2 +- 3 files changed, 3 insertions(+), 4 deletions(-) rename docker/{fuelcycle.org-deps => }/Dockerfile (99%) diff --git a/Makefile b/Makefile index 62dfea57..2cad04fb 100644 --- a/Makefile +++ b/Makefile @@ -75,8 +75,8 @@ gh-preview html: @echo "Build finished. The HTML pages are in $(BUILDDIR)." docker-gh-preview docker-html: - docker build -f docker/fuelcycle.org-deps/Dockerfile -t fuelcycle.org-deps . - docker run -w /cyclus.github.com -v $(PWD):/cyclus.github.com fuelcycle.org-deps bash -c "make gh-preview && chmod -R 777 $(BUILDDIR)" + docker build -f docker/Dockerfile -t site-deps . + docker run -w /cyclus.github.com -v $(PWD):/cyclus.github.com site-deps bash -c "make gh-preview && chmod -R 777 $(BUILDDIR)" serve: html cd $(BUILDDIR) && python -m http.server diff --git a/docker/fuelcycle.org-deps/Dockerfile b/docker/Dockerfile similarity index 99% rename from docker/fuelcycle.org-deps/Dockerfile rename to docker/Dockerfile index ffacd3a4..9a16891a 100644 --- a/docker/fuelcycle.org-deps/Dockerfile +++ b/docker/Dockerfile @@ -1,4 +1,3 @@ - FROM ghcr.io/cyclus/cymetric_22.04_apt/cymetric:latest RUN apt-get update diff --git a/docker/README.rst b/docker/README.rst index 25e288f4..ed322ae0 100644 --- a/docker/README.rst +++ b/docker/README.rst @@ -1,5 +1,5 @@ -``fuelcycle.org-deps`` contains a dockerfile with all dependencies for +This directory contains a dockerfile with all dependencies for building the website. This is used by the docker based build targets added to the makefile. This image will automatically use the latest cymetric image from GHCR, which is updated automatically via GitHub Actions on any changes to Cyclus, Cycamore, or Cymetric. From aff00d1275ff90e1e39f990b1364985d850a703a Mon Sep 17 00:00:00 2001 From: bennibbelink <79653949+bennibbelink@users.noreply.github.com> Date: Tue, 2 Apr 2024 22:09:48 -0500 Subject: [PATCH 06/22] remove references to main branch --- Makefile | 2 -- gh-project.mk | 8 +------- 2 files changed, 1 insertion(+), 9 deletions(-) diff --git a/Makefile b/Makefile index 2cad04fb..7edebc1d 100644 --- a/Makefile +++ b/Makefile @@ -3,8 +3,6 @@ # The included file 'gh-project.mk' should define the following: # GH_SOURCE_DIR = top-level directory of all the ReST source files # GH_SOURCE_BRANCH = repository branch that contains the source -# GH_PUBLISH_BRANCH = repository branch that contains the rendered HTML -# GH_UPSTREAM_REPO = repository that contains the rendered HTML include gh-project.mk # You can set these variables from the command line. diff --git a/gh-project.mk b/gh-project.mk index 8525ad49..92c6880a 100644 --- a/gh-project.mk +++ b/gh-project.mk @@ -4,15 +4,9 @@ GH_SOURCE_DIR = source # GH_SOURCE_BRANCH = repository branch that contains the source GH_SOURCE_BRANCH = source -# GH_PUBLISH_BRANCH = repository branch that contains the rendered HTML -GH_PUBLISH_BRANCH = main -# GH_UPSTREAM_REPO = repository that contains the rendered HTML -GH_UPSTREAM_REPO = upstream # Example for a gh-pages project # # GH_SOURCE_DIR = doc-src -# GH_SOURCE_BRANCH = main -# GH_PUBLISH_BRANCH = gh-pages -# GH_UPSTREAM_REPO = upstream +# GH_SOURCE_BRANCH = main \ No newline at end of file From d2c94c0475a558390f11b25820827956a0bb9fc8 Mon Sep 17 00:00:00 2001 From: bennibbelink <79653949+bennibbelink@users.noreply.github.com> Date: Thu, 4 Apr 2024 16:59:54 -0500 Subject: [PATCH 07/22] split GIT_FORK and GIT_BRANCH into two sets for cyclus and cycamore --- Makefile | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/Makefile b/Makefile index 7edebc1d..e013dd17 100644 --- a/Makefile +++ b/Makefile @@ -10,8 +10,10 @@ SPHINXOPTS = SPHINXBUILD = sphinx-build PAPER = BUILDDIR = ./gh-build -GIT_BRANCH = main -GIT_FORK = cyclus +CYCLUS_GIT_BRANCH = main +CYCLUS_GIT_FORK = cyclus +CYCAMORE_GIT_BRANCH = main +CYCAMORE_GIT_FORK = cyclus # Internal variables. @@ -54,14 +56,14 @@ gh-clean gh-revert clean: -rm -rf $(BUILDDIR) gh-preview html: - wget -nv https://raw.githubusercontent.com/${GIT_FORK}/cyclus/${GIT_BRANCH}/INSTALL.rst -O source/user/CYCLUS_INSTALL.rst || \ - curl https://raw.githubusercontent.com/${GIT_FORK}/cyclus/${GIT_BRANCH}/INSTALL.rst -L -o source/user/CYCLUS_INSTALL.rst - wget -nv https://raw.githubusercontent.com/${GIT_FORK}/cyclus/${GIT_BRANCH}/DEPENDENCIES.rst -O source/user/DEPENDENCIES.rst || \ - curl https://raw.githubusercontent.com/${GIT_FORK}/cyclus/${GIT_BRANCH}/DEPENDENCIES.rst -L -o source/user/DEPENDENCIES.rst - wget -nv https://raw.githubusercontent.com/${GIT_FORK}/cycamore/${GIT_BRANCH}/INSTALL.rst -O source/user/CYCAMORE_INSTALL.rst || \ - curl https://raw.githubusercontent.com/${GIT_FORK}/cycamore/${GIT_BRANCH}/INSTALL.rst -L -o source/user/CYCAMORE_INSTALL.rst - wget -nv https://raw.githubusercontent.com/${GIT_FORK}/cycamore/${GIT_BRANCH}/DEPENDENCIES.rst -O source/user/CYCAMORE_DEPS.rst || \ - curl https://raw.githubusercontent.com/${GIT_FORK}/cycamore/${GIT_BRANCH}/DEPENDENCIES.rst -L -o source/user/CYCAMORE_DEPS.rst + wget -nv https://raw.githubusercontent.com/${CYCLUS_GIT_FORK}/cyclus/${CYCLUS_GIT_BRANCH}/INSTALL.rst -O source/user/CYCLUS_INSTALL.rst || \ + curl https://raw.githubusercontent.com/${CYCLUS_GIT_FORK}/cyclus/${CYCLUS_GIT_BRANCH}/INSTALL.rst -L -o source/user/CYCLUS_INSTALL.rst + wget -nv https://raw.githubusercontent.com/${CYCLUS_GIT_FORK}/cyclus/${CYCLUS_GIT_BRANCH}/DEPENDENCIES.rst -O source/user/DEPENDENCIES.rst || \ + curl https://raw.githubusercontent.com/${CYCLUS_GIT_FORK}/cyclus/${CYCLUS_GIT_BRANCH}/DEPENDENCIES.rst -L -o source/user/DEPENDENCIES.rst + wget -nv https://raw.githubusercontent.com/${CYCAMORE_GIT_FORK}/cycamore/${CYCAMORE_GIT_BRANCH}/INSTALL.rst -O source/user/CYCAMORE_INSTALL.rst || \ + curl https://raw.githubusercontent.com/${CYCAMORE_GIT_FORK}/cycamore/${CYCAMORE_GIT_BRANCH}/INSTALL.rst -L -o source/user/CYCAMORE_INSTALL.rst + wget -nv https://raw.githubusercontent.com/${CYCAMORE_GIT_FORK}/cycamore/${CYCAMORE_GIT_BRANCH}/DEPENDENCIES.rst -O source/user/CYCAMORE_DEPS.rst || \ + curl https://raw.githubusercontent.com/${CYCAMORE_GIT_FORK}/cycamore/${CYCAMORE_GIT_BRANCH}/DEPENDENCIES.rst -L -o source/user/CYCAMORE_DEPS.rst PYTHONDONTWRITEBYTECODE="TRUE" $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR) sed -i.bak 's/function top_offset([$$]node){ return [$$]node\[0\].getBoundingClientRect().top; }/function top_offset($$node){ return (typeof $$node[0] === "undefined") ? 0 : $$node[0].getBoundingClientRect().top; }/' ./gh-build/_static/cloud.js From 06f47bd19d931c23de4ecc70b4b86283673d7148 Mon Sep 17 00:00:00 2001 From: bennibbelink <79653949+bennibbelink@users.noreply.github.com> Date: Thu, 4 Apr 2024 17:00:14 -0500 Subject: [PATCH 08/22] remove unneccesary GH_SOURCE_BRANCH references --- Makefile | 1 - gh-project.mk | 4 ---- 2 files changed, 5 deletions(-) diff --git a/Makefile b/Makefile index e013dd17..2406488b 100644 --- a/Makefile +++ b/Makefile @@ -2,7 +2,6 @@ # # The included file 'gh-project.mk' should define the following: # GH_SOURCE_DIR = top-level directory of all the ReST source files -# GH_SOURCE_BRANCH = repository branch that contains the source include gh-project.mk # You can set these variables from the command line. diff --git a/gh-project.mk b/gh-project.mk index 92c6880a..01631c8d 100644 --- a/gh-project.mk +++ b/gh-project.mk @@ -2,11 +2,7 @@ # # GH_SOURCE_DIR = top-level directory of all the ReST source files GH_SOURCE_DIR = source -# GH_SOURCE_BRANCH = repository branch that contains the source -GH_SOURCE_BRANCH = source - # Example for a gh-pages project # # GH_SOURCE_DIR = doc-src -# GH_SOURCE_BRANCH = main \ No newline at end of file From 02f7ed992420e24a6072072383ac1575ef6ef850 Mon Sep 17 00:00:00 2001 From: abachmann Date: Mon, 1 Apr 2024 14:20:56 -0500 Subject: [PATCH 09/22] add line to create bullet list for contributors --- source/index.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/source/index.rst b/source/index.rst index d4ac14d0..36b742b1 100644 --- a/source/index.rst +++ b/source/index.rst @@ -96,6 +96,7 @@ Contributors ------------ You can find our amazing contributors through their GitHub contributions for each of the projects: + * `Cyclus Contributors `_ * `Cycamore Contributors `_ From 592f5fd025e2522d783484c385b011d9406f1d4c Mon Sep 17 00:00:00 2001 From: abachmann Date: Wed, 3 Apr 2024 17:27:35 -0500 Subject: [PATCH 10/22] add SAI, per @nuclearkatie rec in #337 --- source/basics/projects.rst | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/source/basics/projects.rst b/source/basics/projects.rst index 9741fd9a..c4964156 100644 --- a/source/basics/projects.rst +++ b/source/basics/projects.rst @@ -13,7 +13,17 @@ Consortium for Verification Technology :width: 100 As part of the `Consortium for Verification Technology (CVT) -`_, |Cyclus| is being used to study issues in -nuclear security and non-proliferation. Research areas include the +`_, |Cyclus| was used to study issues in +nuclear security and non-proliferation. Research areas included the incorporation of social-behavioral models to agent interactions, nuclear material tracking and forensics, and detector sensitivity estimation. + +Systems Analysis & Integration Campaign +--------------------------------------- + +As part of the `Systems Analysis & Integration Campaign (SA&I) +`_, |Cyclus| is +used for modeling fuel cycles to understand potential future fuel +cycle needs and the economics of those fuel cycles. + + From d5a34e0d4863d658978a7a258719604280bbc88d Mon Sep 17 00:00:00 2001 From: abachmann Date: Wed, 3 Apr 2024 17:27:58 -0500 Subject: [PATCH 11/22] add NNSA funder, per @nuclearkatie rec in #337 --- source/basics/acknowledgements.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/source/basics/acknowledgements.rst b/source/basics/acknowledgements.rst index 9ce13338..448eec6a 100644 --- a/source/basics/acknowledgements.rst +++ b/source/basics/acknowledgements.rst @@ -21,6 +21,10 @@ by a number of programs and agencies. * Lab-grad program +* National Nuclear Security Administration + + * NNIS Fellowship + The |Cyclus| project benefits greatly from the computational resources of the University of Wisconsin-Madison's `Center for High Throughput Computing `_ and it's `BaTLab `_ build From c73aec8cc2a7165f45ea941bf2be288c01e54359 Mon Sep 17 00:00:00 2001 From: abachmann Date: Wed, 3 Apr 2024 17:28:18 -0500 Subject: [PATCH 12/22] remove news in toc, per @nuclearkatie rec in #337 --- source/index.rst | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/source/index.rst b/source/index.rst index 36b742b1..6d9f8dfc 100644 --- a/source/index.rst +++ b/source/index.rst @@ -30,6 +30,7 @@ The |Cyclus| project repository is located at http://github.com/cyclus/cyclus Quick Start ----------- + :doc:`Get started with Cyclus ` News @@ -51,13 +52,6 @@ News **June 7, 2015:** :doc:`Cyclus v1.3.1 is released ` -.. toctree:: - :maxdepth: 1 - - news/fy16neup - newsletters/oct2017 - - Learn More ---------- From b37f1286e567898884fd493d43b51f9acfa015db Mon Sep 17 00:00:00 2001 From: abachmann Date: Thu, 11 Apr 2024 15:13:51 -0500 Subject: [PATCH 13/22] update numpy documentation link --- source/numpydoc/numpydoc.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/source/numpydoc/numpydoc.py b/source/numpydoc/numpydoc.py index 4c835548..2f9d5055 100644 --- a/source/numpydoc/numpydoc.py +++ b/source/numpydoc/numpydoc.py @@ -12,7 +12,7 @@ - Renumber references. - Extract the signature from the docstring, if it can't be determined otherwise. -.. [1] https://github.com/numpy/numpy/blob/main/doc/HOWTO_DOCUMENT.rst.txt +.. [1] https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard """ from __future__ import division, absolute_import, print_function From 6d504dce6db2c66e48f7dff236ac14ea640387cf Mon Sep 17 00:00:00 2001 From: abachmann Date: Thu, 11 Apr 2024 15:15:05 -0500 Subject: [PATCH 14/22] update link to github3 documentation --- source/cep/cep6.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/source/cep/cep6.rst b/source/cep/cep6.rst index 5a17cdfe..ee7db660 100644 --- a/source/cep/cep6.rst +++ b/source/cep/cep6.rst @@ -3,7 +3,7 @@ CEP 6 - |Cyclus| Pull Request Style Guide :CEP: 6 :Title: |Cyclus| Pull Request Style Guide -:Last-Modified: 2015-05-08 +:Last-Modified: 2024-04-11 :Author: Matthew Gidden :Status: Draft :Type: Process @@ -84,7 +84,7 @@ Automation Using the Github `API `_ either directly or through a module like `github3.py -`_ in conjunction with a standard +`_ in conjunction with a standard style can allow for the automation of otherwise repetitive and time consuming tasks. A chief use case is the generation of release notes. Specifically, if every PR that enables a major and minor feature can be identified and From 12eb8270679c25278136dc3c3d9e063cdf3a37f7 Mon Sep 17 00:00:00 2001 From: abachmann Date: Thu, 11 Apr 2024 15:29:13 -0500 Subject: [PATCH 15/22] remove toctree, add doc for Docker install --- source/user/install.rst | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/source/user/install.rst b/source/user/install.rst index e76db4b8..fe17253f 100644 --- a/source/user/install.rst +++ b/source/user/install.rst @@ -40,21 +40,16 @@ will identify the best approach for you. - **Recommended** for developers or users who **require the bleeding edge version** of |Cyclus| - **Required** for developers who wish to **contribute to kernel development** of |Cyclus| +* :doc:`Install from Docker `: -.. toctree:: - :maxdepth: 1 + - *Requires Docker install on machine and familiarity with Docker* - install_binary - install_docker - install_custom - install_from_git - install_from_tarball - -2. Run Cyclus with a Sample XML File +1. Run Cyclus with a Sample XML File ------------------------------------- -Try running |Cyclus| for yourself. The result will be a :doc:`database ` named cyclus.sqlite. Use the drop down menu to load the sqlite file into Cyclist for data visualization, or use your favorite sqlite browser to peruse. +Try running |Cyclus| for yourself. The result will be a :doc:`database ` named cyclus.sqlite. Use the drop down menu to +load the sqlite file into Cyclist for data visualization, or use your favorite sqlite browser to peruse. .. code-block:: bash From 435d63175e4a7289ca75cdcd326311e33d4bef27 Mon Sep 17 00:00:00 2001 From: abachmann Date: Thu, 11 Apr 2024 15:34:43 -0500 Subject: [PATCH 16/22] add missing >, fix typo --- source/user/tutorial/add_sep.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/source/user/tutorial/add_sep.rst b/source/user/tutorial/add_sep.rst index 927c6a3c..f21c494d 100644 --- a/source/user/tutorial/add_sep.rst +++ b/source/user/tutorial/add_sep.rst @@ -32,7 +32,7 @@ The following is the input template for ``Cycamore::Separations`` archetype: _______ _______ - @@ -47,7 +47,7 @@ The following is the input template for ``Cycamore::Separations`` archetype: * Used-MOX-Fuel * The maximum feed inventory is the most feed material that we'll have on hand: 1000 tonnes. -* The maxium separations throughout is the size of our plant: 80 tonnes/timestep +* The maximum separations throughout is the size of our plant: 80 tonnes/timestep * This simple scenario will have a single output stream: Separated-Fissile * we will hold no more than 5 tonnes of separated material on hand at any time * 99% of all Pu (94000) will go into that stream @@ -82,7 +82,7 @@ Filling in the template, the input block looks like: 94000 0.99 - From 906250d33cdb8fcb8f7472f2265563ff94d4ea48 Mon Sep 17 00:00:00 2001 From: abachmann Date: Thu, 11 Apr 2024 15:35:50 -0500 Subject: [PATCH 17/22] change archetype install to pip --- source/arche/tutorial_py/setup.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/source/arche/tutorial_py/setup.rst b/source/arche/tutorial_py/setup.rst index c175145a..16eca5d8 100644 --- a/source/arche/tutorial_py/setup.rst +++ b/source/arche/tutorial_py/setup.rst @@ -70,7 +70,7 @@ Now we can install the tutorial project via, .. code-block:: console ~ $ cd tutorial - ~/tutorial $ python setup.py install --user + ~/tutorial $ pip install . Let's now make an example input file in a special ``input`` directory: From ad7a49c9045f12458aef0df50383c8bb41ec1e08 Mon Sep 17 00:00:00 2001 From: abachmann Date: Thu, 11 Apr 2024 16:02:54 -0500 Subject: [PATCH 18/22] move news to after Learn More, put quick start in toc tree --- source/index.rst | 40 ++++++++++++++++++++++------------------ 1 file changed, 22 insertions(+), 18 deletions(-) diff --git a/source/index.rst b/source/index.rst index 6d9f8dfc..1c31a1cd 100644 --- a/source/index.rst +++ b/source/index.rst @@ -31,12 +31,31 @@ The |Cyclus| project repository is located at http://github.com/cyclus/cyclus Quick Start ----------- -:doc:`Get started with Cyclus ` +.. toctree:: + :maxdepth: 1 + user/install + + +Learn More +---------- + +.. toctree:: + :maxdepth: 1 + + basics/index + user/index + arche/index + kernel/index + python/index + cep/cep0 + previous/index + cite/index + News ---- -**June 1st, 2018:** :doc:`Cyclus Newsletter Spring 2018! ` +**June 1st, 2018:** :doc:` ` **October 6th, 2017:** :doc:`Cyclus Newsletter Fall 2017! ` @@ -48,25 +67,10 @@ News **July 21-24, 2015:** Joint workshop with CLASS_ project held in Madison, WI -**June 10, 2015:** First Cyclus :doc:`user tutorial ` and :doc:`developer tutorial ` are held at the 2015 ANS Annual Meeting in San Antonio, TX +**June 10, 2015:** First Cyclus :doc:`user tutorial ` and :doc:`developer tutorial ` are held at the 2015 ANS Annual Meeting in San Antonio, TX **June 7, 2015:** :doc:`Cyclus v1.3.1 is released ` -Learn More ----------- - -.. toctree:: - :maxdepth: 1 - - basics/index - user/index - arche/index - kernel/index - python/index - cep/cep0 - previous/index - cite/index - .. _try-it: Try It -- Out-of-Service From a5430aaee33ed3055d387ecfa8c9b9ec390179c9 Mon Sep 17 00:00:00 2001 From: abachmann Date: Mon, 15 Apr 2024 09:03:15 -0500 Subject: [PATCH 19/22] make edits requested by @bennibbelink --- source/arche/tutorial_py/setup.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/source/arche/tutorial_py/setup.rst b/source/arche/tutorial_py/setup.rst index 16eca5d8..f79cb55b 100644 --- a/source/arche/tutorial_py/setup.rst +++ b/source/arche/tutorial_py/setup.rst @@ -70,7 +70,7 @@ Now we can install the tutorial project via, .. code-block:: console ~ $ cd tutorial - ~/tutorial $ pip install . + ~/tutorial $ python -m pip install . Let's now make an example input file in a special ``input`` directory: @@ -81,7 +81,7 @@ Let's now make an example input file in a special ``input`` directory: ~/tutorial $ mkdir -p input ~/tutorial $ touch input/storage.py -Now open up the ``input/storage.`` input file and edit it to look like: +Now open up the ``input/storage.py`` input file and edit it to look like: .. code-block:: python From ae8832a6d05f9accc0369f4384d69e6a7db91f35 Mon Sep 17 00:00:00 2001 From: abachmann Date: Mon, 15 Apr 2024 09:03:41 -0500 Subject: [PATCH 20/22] remove mention of Cyclist, per @gonuke --- source/user/install.rst | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/source/user/install.rst b/source/user/install.rst index fe17253f..9f6ee5cb 100644 --- a/source/user/install.rst +++ b/source/user/install.rst @@ -48,8 +48,9 @@ will identify the best approach for you. 1. Run Cyclus with a Sample XML File ------------------------------------- -Try running |Cyclus| for yourself. The result will be a :doc:`database ` named cyclus.sqlite. Use the drop down menu to -load the sqlite file into Cyclist for data visualization, or use your favorite sqlite browser to peruse. +Try running |Cyclus| for yourself. The result will be a :doc:`database ` named cyclus.sqlite. +Use your favorite sqlite browser to peruse, or explore the data using +`Cymetric `_. .. code-block:: bash From 6cf9a6c6f270966ff78b0fcbe1503d4e369f00b6 Mon Sep 17 00:00:00 2001 From: abachmann Date: Mon, 15 Apr 2024 10:00:21 -0500 Subject: [PATCH 21/22] formatting fixes from @bennibbelink review --- source/index.rst | 3 ++- source/user/install.rst | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/source/index.rst b/source/index.rst index 1c31a1cd..4fdc4942 100644 --- a/source/index.rst +++ b/source/index.rst @@ -33,6 +33,7 @@ Quick Start .. toctree:: :maxdepth: 1 + user/install @@ -55,7 +56,7 @@ Learn More News ---- -**June 1st, 2018:** :doc:` ` +**June 1st, 2018:** :doc:`Cyclus Newsletter Spring 2018 ` **October 6th, 2017:** :doc:`Cyclus Newsletter Fall 2017! ` diff --git a/source/user/install.rst b/source/user/install.rst index 9f6ee5cb..36dcd673 100644 --- a/source/user/install.rst +++ b/source/user/install.rst @@ -45,7 +45,7 @@ will identify the best approach for you. - *Requires Docker install on machine and familiarity with Docker* -1. Run Cyclus with a Sample XML File +2. Run Cyclus with a Sample XML File ------------------------------------- Try running |Cyclus| for yourself. The result will be a :doc:`database ` named cyclus.sqlite. From 3360941046d2bac6bc5b25853d93129c5a1df023 Mon Sep 17 00:00:00 2001 From: Bachmann Date: Thu, 18 Apr 2024 09:16:16 -0500 Subject: [PATCH 22/22] remove xo dependency --- source/arche/tutorial_py/setup.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/source/arche/tutorial_py/setup.rst b/source/arche/tutorial_py/setup.rst index f79cb55b..c8c3234a 100644 --- a/source/arche/tutorial_py/setup.rst +++ b/source/arche/tutorial_py/setup.rst @@ -60,7 +60,6 @@ root tutorial directory. Create one that looks like: setup( name='tut', packages=['tut'], - scripts=['xo'], **setup_kwargs )