From 436982399c40101d9b02e7efc53933ba074e0d7e Mon Sep 17 00:00:00 2001 From: Dominic Power Date: Fri, 6 Feb 2026 12:53:20 -0500 Subject: [PATCH 01/10] Added build command --- .readthedocs.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 74e0648..f742686 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -11,6 +11,8 @@ build: os: ubuntu-24.04 tools: python: "3.13" + commands: + - pip install .[docs] # Build documentation in the "docs/" directory with Sphinx sphinx: From 996f2e8eeeb806daa016742892b6131ba4290a26 Mon Sep 17 00:00:00 2001 From: Dominic Power Date: Fri, 6 Feb 2026 13:00:26 -0500 Subject: [PATCH 02/10] Changed docs build dir --- docs/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Makefile b/docs/Makefile index 401d9a3..8604a73 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -6,7 +6,7 @@ SPHINXOPTS ?= SPHINXBUILD ?= sphinx-build SOURCEDIR = source -BUILDDIR = _build +BUILDDIR = . # Put it first so that "make" without argument is like "make help". help: From 12b7e1458b73c2b628ddf4230d0148c03bd2649c Mon Sep 17 00:00:00 2001 From: Dominic Power Date: Fri, 6 Feb 2026 13:03:31 -0500 Subject: [PATCH 03/10] Changed builddir again --- docs/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Makefile b/docs/Makefile index 8604a73..8ac2c93 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -6,7 +6,7 @@ SPHINXOPTS ?= SPHINXBUILD ?= sphinx-build SOURCEDIR = source -BUILDDIR = . +BUILDDIR = _readthedocs # Put it first so that "make" without argument is like "make help". help: From c98e3b618faf460ec74c139a6630b2318248791e Mon Sep 17 00:00:00 2001 From: Dominic Power Date: Fri, 6 Feb 2026 13:07:49 -0500 Subject: [PATCH 04/10] Trying some different paths --- .readthedocs.yaml | 2 +- docs/Makefile | 2 +- docs/source/conf.py | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index f742686..344767a 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -12,7 +12,7 @@ build: tools: python: "3.13" commands: - - pip install .[docs] + - pip install . # Build documentation in the "docs/" directory with Sphinx sphinx: diff --git a/docs/Makefile b/docs/Makefile index 8ac2c93..269cadc 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -6,7 +6,7 @@ SPHINXOPTS ?= SPHINXBUILD ?= sphinx-build SOURCEDIR = source -BUILDDIR = _readthedocs +BUILDDIR = build # Put it first so that "make" without argument is like "make help". help: diff --git a/docs/source/conf.py b/docs/source/conf.py index 350ea14..e28f502 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -34,7 +34,7 @@ autosummary_generate = True templates_path = ["_templates"] -exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] +exclude_patterns = ["build", "Thumbs.db", ".DS_Store"] autodoc_default_options = {"ignore-module-all": True} autodoc_typehints = "description" @@ -93,4 +93,4 @@ "python": ("https://docs.python.org/3", None), "numpy": ("https://numpy.org/doc/stable", None), "scipy": ("https://docs.scipy.org/doc/scipy", None), -} \ No newline at end of file +} From 87c7ae964331b3c84d40c3f2b17ddea9f4052608 Mon Sep 17 00:00:00 2001 From: Dominic Power Date: Fri, 6 Feb 2026 13:12:07 -0500 Subject: [PATCH 05/10] Trying another method to install --- .readthedocs.yaml | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 344767a..5a9c615 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -11,8 +11,6 @@ build: os: ubuntu-24.04 tools: python: "3.13" - commands: - - pip install . # Build documentation in the "docs/" directory with Sphinx sphinx: @@ -21,8 +19,8 @@ sphinx: # Optionally, but recommended, # declare the Python requirements required to build your documentation # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html -# python: -# install: -# - requirements: docs/requirements.txt +python: + install: + path: . From 15373280ce621595ffbc8ca3322f567454053ba1 Mon Sep 17 00:00:00 2001 From: Dominic Power Date: Fri, 6 Feb 2026 13:13:03 -0500 Subject: [PATCH 06/10] install . --- .readthedocs.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 5a9c615..771967d 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -20,7 +20,9 @@ sphinx: # declare the Python requirements required to build your documentation # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html python: - install: - path: . + version: 3.7 + install: + - method: pip + path: . From b410600834003a953b9d05d7d0042d875de8e8b7 Mon Sep 17 00:00:00 2001 From: Dominic Power Date: Fri, 6 Feb 2026 13:13:34 -0500 Subject: [PATCH 07/10] change python version --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 771967d..1b324dd 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -20,7 +20,7 @@ sphinx: # declare the Python requirements required to build your documentation # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html python: - version: 3.7 + version: 3.13 install: - method: pip path: . From c60d06c6660b80192dea791a974f1da4068292f6 Mon Sep 17 00:00:00 2001 From: Dominic Power Date: Fri, 6 Feb 2026 13:14:03 -0500 Subject: [PATCH 08/10] removed version --- .readthedocs.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 1b324dd..3d3bcff 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -20,7 +20,6 @@ sphinx: # declare the Python requirements required to build your documentation # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html python: - version: 3.13 install: - method: pip path: . From d12c834839e58b661a2ea30d30ec54c19214a46e Mon Sep 17 00:00:00 2001 From: Dominic Power Date: Fri, 6 Feb 2026 13:15:21 -0500 Subject: [PATCH 09/10] added docs deps --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 3d3bcff..63de6cd 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -22,6 +22,6 @@ sphinx: python: install: - method: pip - path: . + path: .[docs] From 1029d9cdc90970f05c7e80038ecc112a323feebe Mon Sep 17 00:00:00 2001 From: Dominic Power Date: Fri, 6 Feb 2026 13:19:11 -0500 Subject: [PATCH 10/10] Added link to docs --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 0b69746..89cddd4 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,5 @@ # SIKE -```{note} -SIKE is a work in progress and documentation will be coming soon. Please contact power8@llnl.gov for any questions running the code in the meantime. -``` - SIKE (**S**crape-off layer **I**mpurities with **K**inetic **E**lectrons) is a simple atomic kinetics solver for impurity species relevant to magnetic fusion plasmas. It is intended to study the effect of non-Maxwellian electron distributions on mean ionisation, radiative loss rates, etc. For a set of atomic state densities $\vec{n}$, it solves the equation $\frac{d\vec{n}}{dt} = \mathbf{M}\vec{n}$, @@ -14,6 +10,10 @@ The SIKE model and atomic data is described in more detail in Power et al. 2025 SIKE was developed to study the sensitivity of atomic rates to non-Maxwellian electron distributions in magnetic fusion plasmas. It is not currently as accurate as commonly used modelling databases such as ADAS, please see the notebook and comparison plots in the benchmarking directory to get an idea of the differences. +## Documentation + +https://sike.readthedocs.io/en/latest/ + ## Quickstart ```{note}