From 3845af3b38725c841f9da24b2d614013bdb9f371 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 4 Jun 2024 18:20:09 +0200 Subject: [PATCH 01/61] add readthedoc yaml file --- .readthedocs.yaml | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 .readthedocs.yaml diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..fff2f4b --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,13 @@ +version: "2" + +build: + os: "ubuntu-22.04" + tools: + python: "3.12" + +python: + install: + - requirements: docs/requirements.txt + +sphinx: + configuration: docs/source/conf.py From 52bbc60638120ba442ed4aa9abd1fadc5ef85eab Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Thu, 6 Jun 2024 15:21:55 +0200 Subject: [PATCH 02/61] add essential set-up files if using rtd --- docs/conf.py | 12 ------------ docs/hello.ipynb | 51 ------------------------------------------------ docs/index.md | 5 ----- 3 files changed, 68 deletions(-) delete mode 100644 docs/conf.py delete mode 100644 docs/hello.ipynb delete mode 100644 docs/index.md diff --git a/docs/conf.py b/docs/conf.py deleted file mode 100644 index 159dd23..0000000 --- a/docs/conf.py +++ /dev/null @@ -1,12 +0,0 @@ -exclude_patterns = [ - "**.ipynb_checkpoints", - ".DS_Store", - ".pixi", - "Thumbs.db", - "_build", -] -extensions = ["myst_nb"] -html_theme = "pydata_sphinx_theme" -master_doc = "index" -nitpicky = True -project = "GlueX N-Star" diff --git a/docs/hello.ipynb b/docs/hello.ipynb deleted file mode 100644 index cb1c2da..0000000 --- a/docs/hello.ipynb +++ /dev/null @@ -1,51 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "id": "0", - "metadata": {}, - "source": [ - "# Starting document" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "1", - "metadata": {}, - "outputs": [], - "source": [ - "print(\"Hello World!\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "2", - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.12.3" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/docs/index.md b/docs/index.md deleted file mode 100644 index ce8b6d0..0000000 --- a/docs/index.md +++ /dev/null @@ -1,5 +0,0 @@ -# MyST-NB Quickstart - -```{toctree} -hello -``` From 5e5a047ee123ac9925f4f19ce5ef8202a8e61bd4 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Thu, 6 Jun 2024 15:23:36 +0200 Subject: [PATCH 03/61] more essential set-up files if using rtd --- docs/Makefile | 20 ++++++++++++++++ docs/make.bat | 35 ++++++++++++++++++++++++++++ docs/requirements.txt | 2 ++ docs/source/conf.py | 28 ++++++++++++++++++++++ docs/source/hello.ipynb | 51 +++++++++++++++++++++++++++++++++++++++++ docs/source/index.rst | 15 ++++++++++++ pyproject.toml | 8 +++++++ 7 files changed, 159 insertions(+) create mode 100644 docs/Makefile create mode 100644 docs/make.bat create mode 100644 docs/requirements.txt create mode 100644 docs/source/conf.py create mode 100644 docs/source/hello.ipynb create mode 100644 docs/source/index.rst create mode 100644 pyproject.toml diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..d0c3cbf --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = source +BUILDDIR = build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..9534b01 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=source +set BUILDDIR=build + +if "%1" == "" goto help + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.http://sphinx-doc.org/ + exit /b 1 +) + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..53fc1f3 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,2 @@ +sphinx==7.1.2 +sphinx-rtd-theme==1.3.0rc1 diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..101a8d7 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,28 @@ +author = "ComPWA" +exclude_patterns = [ + "**.ipynb_checkpoints", + ".DS_Store", + ".pixi", + "Thumbs.db", + "_build", +] +extensions = [ + "myst_nb", + "sphinx.ext.duration", + "sphinx.ext.doctest", + "sphinx.ext.autodoc", + "sphinx.ext.autosummary", + "sphinx.ext.intersphinx", +] +intersphinx_mapping = { + "python": ("https://docs.python.org/3/", None), + "sphinx": ("https://www.sphinx-doc.org/en/master/", None), +} +intersphinx_disabled_domains = ["std"] +templates_path = ["_templates"] +html_theme = "sphinx_rtd_theme" +master_doc = "index" +nitpicky = True +project = "GlueX N-Star" +release = "0.1" +version = "0.1.0" diff --git a/docs/source/hello.ipynb b/docs/source/hello.ipynb new file mode 100644 index 0000000..cb1c2da --- /dev/null +++ b/docs/source/hello.ipynb @@ -0,0 +1,51 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "0", + "metadata": {}, + "source": [ + "# Starting document" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1", + "metadata": {}, + "outputs": [], + "source": [ + "print(\"Hello World!\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.3" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 0000000..7f1cbf9 --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,15 @@ +Welcome to Gluex-Nstar documentation! +=================================== + +Investigation of the N* Resonances in the GlueX Experiment + +.. note:: + + This project is under active development. + +Contents +-------- + +.. toctree:: + + hello diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..8466854 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,8 @@ +[build-system] +build-backend = "flit_core.buildapi" +requires = ["flit_core >=3.2,<4"] + +[project] +authors = [{name = "ComPWA"}] +dynamic = ["description", "version"] +name = "gluex-nstar" From 3d345c2e747fdf039ff8a8f2ad001dee56ce0b26 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Thu, 6 Jun 2024 15:28:08 +0200 Subject: [PATCH 04/61] directory specification --- docs/source/conf.py | 1 - pixi.toml | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 101a8d7..3abd6e4 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -7,7 +7,6 @@ "_build", ] extensions = [ - "myst_nb", "sphinx.ext.duration", "sphinx.ext.doctest", "sphinx.ext.autodoc", diff --git a/pixi.toml b/pixi.toml index 8241a48..8fbcdf4 100644 --- a/pixi.toml +++ b/pixi.toml @@ -9,7 +9,7 @@ docnb = """ sphinx-build \ -nW --keep-going \ -b html \ - docs/ docs/_build/html + docs/source docs/_build/html """ docnblive = """ sphinx-autobuild \ From 1f6e247b562a913b5e876e8a2901850aafc9ae56 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Thu, 6 Jun 2024 15:34:20 +0200 Subject: [PATCH 05/61] location rename --- docs/Makefile | 2 +- docs/{source => }/conf.py | 0 docs/{source => }/hello.ipynb | 0 docs/{source => }/index.rst | 0 pixi.toml | 2 +- 5 files changed, 2 insertions(+), 2 deletions(-) rename docs/{source => }/conf.py (100%) rename docs/{source => }/hello.ipynb (100%) rename docs/{source => }/index.rst (100%) diff --git a/docs/Makefile b/docs/Makefile index d0c3cbf..ed88099 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -5,7 +5,7 @@ # from the environment for the first two. SPHINXOPTS ?= SPHINXBUILD ?= sphinx-build -SOURCEDIR = source +SOURCEDIR = . BUILDDIR = build # Put it first so that "make" without argument is like "make help". diff --git a/docs/source/conf.py b/docs/conf.py similarity index 100% rename from docs/source/conf.py rename to docs/conf.py diff --git a/docs/source/hello.ipynb b/docs/hello.ipynb similarity index 100% rename from docs/source/hello.ipynb rename to docs/hello.ipynb diff --git a/docs/source/index.rst b/docs/index.rst similarity index 100% rename from docs/source/index.rst rename to docs/index.rst diff --git a/pixi.toml b/pixi.toml index 8fbcdf4..8241a48 100644 --- a/pixi.toml +++ b/pixi.toml @@ -9,7 +9,7 @@ docnb = """ sphinx-build \ -nW --keep-going \ -b html \ - docs/source docs/_build/html + docs/ docs/_build/html """ docnblive = """ sphinx-autobuild \ From 95f69ce2093c2382eb369dd11899fe911232462c Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Thu, 6 Jun 2024 15:39:18 +0200 Subject: [PATCH 06/61] install rtd theme --- docs/make.bat | 2 +- pixi.lock | 58 +++++++++++++++++++++++++++++++++++++++++---------- pixi.toml | 1 + 3 files changed, 49 insertions(+), 12 deletions(-) diff --git a/docs/make.bat b/docs/make.bat index 9534b01..3d64bb3 100644 --- a/docs/make.bat +++ b/docs/make.bat @@ -7,7 +7,7 @@ REM Command file for Sphinx documentation if "%SPHINXBUILD%" == "" ( set SPHINXBUILD=sphinx-build ) -set SOURCEDIR=source +set SOURCEDIR=. set BUILDDIR=build if "%1" == "" goto help diff --git a/pixi.lock b/pixi.lock index ba33ed9..7ad2f9a 100644 --- a/pixi.lock +++ b/pixi.lock @@ -39,7 +39,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/decorator-5.1.1-pyhd8ed1ab_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/defusedxml-0.7.1-pyhd8ed1ab_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/distlib-0.3.8-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/docutils-0.21.2-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/docutils-0.20.1-py312h7900ff3_3.conda - conda: https://conda.anaconda.org/conda-forge/noarch/entrypoints-0.4-pyhd8ed1ab_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.2.0-pyhd8ed1ab_2.conda - conda: https://conda.anaconda.org/conda-forge/noarch/executing-2.0.1-pyhd8ed1ab_0.conda @@ -216,9 +216,11 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.5-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/sphinx-7.3.7-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/sphinx-autobuild-2024.4.16-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/sphinx_rtd_theme-2.0.0-pyha770c72_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-applehelp-1.0.8-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-devhelp-1.0.6-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-htmlhelp-2.0.5-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-jquery-4.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-jsmath-1.0.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-qthelp-1.0.7-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.10-pyhd8ed1ab_0.conda @@ -835,18 +837,19 @@ packages: timestamp: 1702383349284 - kind: conda name: docutils - version: 0.21.2 - build: pyhd8ed1ab_0 - subdir: noarch - noarch: python - url: https://conda.anaconda.org/conda-forge/noarch/docutils-0.21.2-pyhd8ed1ab_0.conda - sha256: 362bfe3afaac18298c48c0c6a935641544077ce5105a42a2d8ebe750ad07c574 - md5: e8cd5d629f65bdf0f3bb312cde14659e + version: 0.20.1 + build: py312h7900ff3_3 + build_number: 3 + subdir: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/docutils-0.20.1-py312h7900ff3_3.conda + sha256: b9fb75d806afc53d9d7b98edb0c45ac38a3cc983916b8dac4ad7ddac5c18a024 + md5: 1b90835ae26b9b8250b302649359a989 depends: - - python >=3.9 + - python >=3.12,<3.13.0a0 + - python_abi 3.12.* *_cp312 license: CC-PDDC AND BSD-3-Clause AND BSD-2-Clause AND ZPL-2.1 - size: 403226 - timestamp: 1713930478970 + size: 898253 + timestamp: 1701882735141 - kind: conda name: entrypoints version: '0.4' @@ -3953,6 +3956,24 @@ packages: license_family: MIT size: 16466 timestamp: 1713319509734 +- kind: conda + name: sphinx_rtd_theme + version: 2.0.0 + build: pyha770c72_0 + subdir: noarch + noarch: python + url: https://conda.anaconda.org/conda-forge/noarch/sphinx_rtd_theme-2.0.0-pyha770c72_0.conda + sha256: 8545c806d03092fd0236db6663c88036eab2dc99e34c91cd36c0704db03b148a + md5: baf6d9a33df1a789ca55e3b404c7ea28 + depends: + - docutils <0.21 + - python >=3.6 + - sphinx >=5,<8 + - sphinxcontrib-jquery >=4,<5 + license: MIT + license_family: MIT + size: 2614217 + timestamp: 1701183633165 - kind: conda name: sphinxcontrib-applehelp version: 1.0.8 @@ -4001,6 +4022,21 @@ packages: license_family: BSD size: 33499 timestamp: 1705118297318 +- kind: conda + name: sphinxcontrib-jquery + version: '4.1' + build: pyhd8ed1ab_0 + subdir: noarch + noarch: python + url: https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-jquery-4.1-pyhd8ed1ab_0.conda + sha256: 2e5f16a2d58f9a31443ffbb8ce3852cfccf533a6349045828cd2e994ef0679ca + md5: 914897066d5873acfb13e75705276ad1 + depends: + - python >=2.7 + - sphinx >=1.8 + license: 0BSD AND MIT + size: 112985 + timestamp: 1678809100921 - kind: conda name: sphinxcontrib-jsmath version: 1.0.1 diff --git a/pixi.toml b/pixi.toml index 8241a48..596f510 100644 --- a/pixi.toml +++ b/pixi.toml @@ -36,4 +36,5 @@ python = ">=3.12.3,<3.13" python-graphviz = ">=0.20.3,<0.21" scipy = ">=1.13.0,<1.14" sphinx-autobuild = ">=2024.4.16,<2024.5" +sphinx_rtd_theme = ">=2.0.0,<2.1" sympy = ">=1.12,<2" From 2892baa5539d27d06db24861d5101da9b28288cd Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Thu, 6 Jun 2024 15:56:40 +0200 Subject: [PATCH 07/61] rst file --- docs/{hello.ipynb => hello.rst} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/{hello.ipynb => hello.rst} (100%) diff --git a/docs/hello.ipynb b/docs/hello.rst similarity index 100% rename from docs/hello.ipynb rename to docs/hello.rst From 9d6d073337d97f086438c08fa6cf08238f6c7b20 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Thu, 6 Jun 2024 16:25:39 +0200 Subject: [PATCH 08/61] hello --- docs/hello.ipynb | 43 +++++++++++++++++++++++++++++++++++++++ docs/hello.rst | 52 +----------------------------------------------- 2 files changed, 44 insertions(+), 51 deletions(-) create mode 100644 docs/hello.ipynb diff --git a/docs/hello.ipynb b/docs/hello.ipynb new file mode 100644 index 0000000..38a1baa --- /dev/null +++ b/docs/hello.ipynb @@ -0,0 +1,43 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "0", + "metadata": {}, + "source": [ + "# Hello" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1", + "metadata": {}, + "outputs": [], + "source": [ + "print(\"Hello World!\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.3" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/docs/hello.rst b/docs/hello.rst index cb1c2da..2965834 100644 --- a/docs/hello.rst +++ b/docs/hello.rst @@ -1,51 +1 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "id": "0", - "metadata": {}, - "source": [ - "# Starting document" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "1", - "metadata": {}, - "outputs": [], - "source": [ - "print(\"Hello World!\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "2", - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.12.3" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} +# Hello World From 05ebb9417d7f36b29c4c47d98afd51e59e24b627 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Thu, 6 Jun 2024 16:28:56 +0200 Subject: [PATCH 09/61] hello world --- docs/hello.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/hello.rst b/docs/hello.rst index 2965834..a7af0af 100644 --- a/docs/hello.rst +++ b/docs/hello.rst @@ -1 +1,2 @@ -# Hello World +Hello World +=== From 0ea61f2fd37fbeb697dbd1a936b31002a820e8f6 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Thu, 6 Jun 2024 16:37:44 +0200 Subject: [PATCH 10/61] yaml file confy file location --- .readthedocs.yaml | 2 +- docs/Makefile | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index fff2f4b..2d7e00c 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -10,4 +10,4 @@ python: - requirements: docs/requirements.txt sphinx: - configuration: docs/source/conf.py + configuration: docs/conf.py diff --git a/docs/Makefile b/docs/Makefile index ed88099..9ead246 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -3,8 +3,8 @@ # You can set these variables from the command line, and also # from the environment for the first two. -SPHINXOPTS ?= -SPHINXBUILD ?= sphinx-build +SPHINXOPTS = +SPHINXBUILD = sphinx-build SOURCEDIR = . BUILDDIR = build From a20a5def78162babd18f4a2c752c16b2ebdb53e1 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Fri, 7 Jun 2024 10:48:46 +0200 Subject: [PATCH 11/61] adjust to mystnb --- docs/conf.py | 3 ++ docs/hello.rst | 2 -- docs/index.md | 16 ++++++++++ docs/index.rst | 15 ---------- docs/requirements.txt | 5 ++-- pixi.lock | 69 +++++++++++++++++++++++++++++++++++++++++++ pixi.toml | 2 ++ 7 files changed, 93 insertions(+), 19 deletions(-) delete mode 100644 docs/hello.rst create mode 100644 docs/index.md delete mode 100644 docs/index.rst diff --git a/docs/conf.py b/docs/conf.py index 3abd6e4..82a6b18 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -7,6 +7,8 @@ "_build", ] extensions = [ + "myst_nb", + "nbsphinx", "sphinx.ext.duration", "sphinx.ext.doctest", "sphinx.ext.autodoc", @@ -22,6 +24,7 @@ html_theme = "sphinx_rtd_theme" master_doc = "index" nitpicky = True +nb_execution_mode = "auto" project = "GlueX N-Star" release = "0.1" version = "0.1.0" diff --git a/docs/hello.rst b/docs/hello.rst deleted file mode 100644 index a7af0af..0000000 --- a/docs/hello.rst +++ /dev/null @@ -1,2 +0,0 @@ -Hello World -=== diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..1a22319 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,16 @@ +# Welcome Page + +# Welcome to GlueX-Nstar documentation! + +Investigation of the N\* Resonances in the GlueX Experiment + +> **Note:** This project is under active development. + +## Contents + +```{toctree} +:titlesonly: +:maxdepth: 2 + +hello +``` diff --git a/docs/index.rst b/docs/index.rst deleted file mode 100644 index 7f1cbf9..0000000 --- a/docs/index.rst +++ /dev/null @@ -1,15 +0,0 @@ -Welcome to Gluex-Nstar documentation! -=================================== - -Investigation of the N* Resonances in the GlueX Experiment - -.. note:: - - This project is under active development. - -Contents --------- - -.. toctree:: - - hello diff --git a/docs/requirements.txt b/docs/requirements.txt index 53fc1f3..26cca2e 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,2 +1,3 @@ -sphinx==7.1.2 -sphinx-rtd-theme==1.3.0rc1 +myst-nb +sphinx +sphinx-rtd-theme diff --git a/pixi.lock b/pixi.lock index 7ad2f9a..244232b 100644 --- a/pixi.lock +++ b/pixi.lock @@ -156,9 +156,12 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/myst-nb-1.1.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/myst-parser-3.0.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/nbclient-0.10.0-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.16.4-hd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.16.4-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.16.4-hd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/nbdime-4.0.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/nbformat-5.10.4-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/nbsphinx-0.9.4-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/nest-asyncio-1.6.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/nodeenv-1.8.0-pyhd8ed1ab_0.conda @@ -169,6 +172,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/opt_einsum-3.3.0-pyhc1e730c_2.conda - conda: https://conda.anaconda.org/conda-forge/noarch/overrides-7.7.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/packaging-24.0-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.2-ha770c72_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/pandocfilters-1.5.0-pyhd8ed1ab_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/linux-64/pango-1.52.2-ha41ecd1_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/parso-0.8.4-pyhd8ed1ab_0.conda @@ -2913,6 +2917,22 @@ packages: license_family: BSD size: 27851 timestamp: 1710317767117 +- kind: conda + name: nbconvert + version: 7.16.4 + build: hd8ed1ab_0 + subdir: noarch + noarch: generic + url: https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.16.4-hd8ed1ab_0.conda + sha256: 7a4a759b8930833cbfffbfd92da069f1d3fd43760ea629c8612b9e7ae9fff0e8 + md5: c9d64b8a7ee8e6bdbf0e7d8aa7f39601 + depends: + - nbconvert-core 7.16.4 pyhd8ed1ab_0 + - nbconvert-pandoc 7.16.4 hd8ed1ab_0 + license: BSD-3-Clause + license_family: BSD + size: 8434 + timestamp: 1714477296945 - kind: conda name: nbconvert-core version: 7.16.4 @@ -2947,6 +2967,22 @@ packages: license_family: BSD size: 189004 timestamp: 1714477286178 +- kind: conda + name: nbconvert-pandoc + version: 7.16.4 + build: hd8ed1ab_0 + subdir: noarch + noarch: generic + url: https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.16.4-hd8ed1ab_0.conda + sha256: d3bd8b38a74825e9e502f3251fba167b303d7ad324cd4e41d459bfa3c118c9ee + md5: 391934bd1a79990c23df1d1809ddc821 + depends: + - nbconvert-core 7.16.4 pyhd8ed1ab_0 + - pandoc + license: BSD-3-Clause + license_family: BSD + size: 8479 + timestamp: 1714477291801 - kind: conda name: nbdime version: 4.0.1 @@ -2990,6 +3026,27 @@ packages: license_family: BSD size: 101232 timestamp: 1712239122969 +- kind: conda + name: nbsphinx + version: 0.9.4 + build: pyhd8ed1ab_0 + subdir: noarch + noarch: python + url: https://conda.anaconda.org/conda-forge/noarch/nbsphinx-0.9.4-pyhd8ed1ab_0.conda + sha256: 2d5756e2ab94ba73d630b97bc8ce6b0ea6eb60aadc2ad7e47e6e6d48fe3f87e8 + md5: 9dc80eaeff56fb67dbf4f871b81bc13a + depends: + - docutils + - jinja2 + - nbconvert + - nbformat + - python >=3.6 + - sphinx + - traitlets + license: MIT + license_family: MIT + size: 33630 + timestamp: 1715074950890 - kind: conda name: ncurses version: '6.5' @@ -3153,6 +3210,18 @@ packages: license_family: APACHE size: 49832 timestamp: 1710076089469 +- kind: conda + name: pandoc + version: '3.2' + build: ha770c72_0 + subdir: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.2-ha770c72_0.conda + sha256: 418348076c1a39170efb0bdc8a584ddd11e9ed0ff58ccd905488d3f165ca98ba + md5: 8c924f0b7f3e064b1c954a08e7c32fba + license: GPL-2.0-or-later + license_family: GPL + size: 21088628 + timestamp: 1715499623651 - kind: conda name: pandocfilters version: 1.5.0 diff --git a/pixi.toml b/pixi.toml index 596f510..ea79416 100644 --- a/pixi.toml +++ b/pixi.toml @@ -29,6 +29,8 @@ jupyterlab-git = ">=0.50.0,<0.51" jupyterlab-lsp = ">=5.1.0,<5.2" jupyterlab-myst = ">=2.4.2,<2.5" myst-nb = ">=1.1.0,<1.2" +myst-parser = ">=3.0.1,<3.1" +nbsphinx = ">=0.9.4,<0.10" numpy = ">=1.26.4,<1.27" pre-commit = ">=3.7.1,<3.8" pydata-sphinx-theme = ">=0.15.2,<0.16" From 99fe394c655116bd1fc06cbd4ce58f46a7f24259 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Fri, 7 Jun 2024 11:09:05 +0200 Subject: [PATCH 12/61] Adjust configuration for RTD --- docs/conf.py | 18 +++++++++++++++--- docs/requirements.txt | 1 + pixi.lock | 33 +++++++++++++++++++++++++++++++++ pixi.toml | 1 + 4 files changed, 50 insertions(+), 3 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 82a6b18..bdf5968 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,4 +1,6 @@ +project = "GlueX-Nstar" author = "ComPWA" +release = "0.1" exclude_patterns = [ "**.ipynb_checkpoints", ".DS_Store", @@ -8,12 +10,13 @@ ] extensions = [ "myst_nb", - "nbsphinx", "sphinx.ext.duration", "sphinx.ext.doctest", "sphinx.ext.autodoc", "sphinx.ext.autosummary", "sphinx.ext.intersphinx", + "sphinx.ext.napoleon", + "sphinx.ext.viewcode", ] intersphinx_mapping = { "python": ("https://docs.python.org/3/", None), @@ -22,9 +25,18 @@ intersphinx_disabled_domains = ["std"] templates_path = ["_templates"] html_theme = "sphinx_rtd_theme" +html_static_path = ["_static"] master_doc = "index" nitpicky = True nb_execution_mode = "auto" -project = "GlueX N-Star" -release = "0.1" version = "0.1.0" +myst_enable_extensions = [ + "colon_fence", + "deflist", + "dollarmath", + "html_admonition", + "html_image", + "linkify", + "substitution", + "tasklist", +] diff --git a/docs/requirements.txt b/docs/requirements.txt index 26cca2e..cecc2d8 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,3 +1,4 @@ +linkify-it-py myst-nb sphinx sphinx-rtd-theme diff --git a/pixi.lock b/pixi.lock index 244232b..a1a853c 100644 --- a/pixi.lock +++ b/pixi.lock @@ -143,6 +143,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.7-hc051c1a_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/linkify-it-py-2.0.3-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/livereload-2.6.3-pyh9f0ad1d_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-3.0.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/markupsafe-2.1.5-py312h98912ed_0.conda @@ -244,6 +245,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.11.0-pyha770c72_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/typing_utils-0.1.0-pyhd8ed1ab_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/uc-micro-py-1.0.3-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/ukkonen-1.0.1-py312h8572e83_4.conda - conda: https://conda.anaconda.org/conda-forge/noarch/uri-template-1.3.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.2.1-pyhd8ed1ab_0.conda @@ -2691,6 +2693,22 @@ packages: license_family: Other size: 61588 timestamp: 1686575217516 +- kind: conda + name: linkify-it-py + version: 2.0.3 + build: pyhd8ed1ab_0 + subdir: noarch + noarch: python + url: https://conda.anaconda.org/conda-forge/noarch/linkify-it-py-2.0.3-pyhd8ed1ab_0.conda + sha256: aa99d44e8c83865026575a8af253141c53e0b3ab05f053befaa7757c8525064f + md5: f1b64ca4faf563605cf6f6ca93f9ff3f + depends: + - python >=3.7 + - uc-micro-py + license: MIT + license_family: MIT + size: 24035 + timestamp: 1707129321841 - kind: conda name: livereload version: 2.6.3 @@ -4406,6 +4424,21 @@ packages: license: LicenseRef-Public-Domain size: 119815 timestamp: 1706886945727 +- kind: conda + name: uc-micro-py + version: 1.0.3 + build: pyhd8ed1ab_0 + subdir: noarch + noarch: python + url: https://conda.anaconda.org/conda-forge/noarch/uc-micro-py-1.0.3-pyhd8ed1ab_0.conda + sha256: 54293cd94da3a6b978b353eb7897555055d925ad0008bc73e85cca19e2587ed0 + md5: 3b7fc78d7be7b450952aaa916fb78877 + depends: + - python >=3.6 + license: MIT + license_family: MIT + size: 11162 + timestamp: 1707507514699 - kind: conda name: ukkonen version: 1.0.1 diff --git a/pixi.toml b/pixi.toml index ea79416..2de6106 100644 --- a/pixi.toml +++ b/pixi.toml @@ -28,6 +28,7 @@ jupyterlab = ">=4.2.0,<4.3" jupyterlab-git = ">=0.50.0,<0.51" jupyterlab-lsp = ">=5.1.0,<5.2" jupyterlab-myst = ">=2.4.2,<2.5" +linkify-it-py = ">=2.0.3,<2.1" myst-nb = ">=1.1.0,<1.2" myst-parser = ">=3.0.1,<3.1" nbsphinx = ">=0.9.4,<0.10" From a5ed9746105d9e841500bb0ba46f73930af43c6b Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Fri, 7 Jun 2024 11:17:32 +0200 Subject: [PATCH 13/61] Ensure _static directory exists --- docs/conf.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/conf.py b/docs/conf.py index bdf5968..e0175ad 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,6 +1,7 @@ project = "GlueX-Nstar" author = "ComPWA" release = "0.1" + exclude_patterns = [ "**.ipynb_checkpoints", ".DS_Store", @@ -24,12 +25,15 @@ } intersphinx_disabled_domains = ["std"] templates_path = ["_templates"] + html_theme = "sphinx_rtd_theme" html_static_path = ["_static"] + master_doc = "index" nitpicky = True nb_execution_mode = "auto" version = "0.1.0" + myst_enable_extensions = [ "colon_fence", "deflist", From 85f269e6d73ac52d3cb8cab0e8b8c138c17c5870 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Fri, 7 Jun 2024 11:26:39 +0200 Subject: [PATCH 14/61] add python version in git workflow ci file --- .github/workflows/ci-docs.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/ci-docs.yml b/.github/workflows/ci-docs.yml index eeef184..c6255a4 100644 --- a/.github/workflows/ci-docs.yml +++ b/.github/workflows/ci-docs.yml @@ -9,6 +9,9 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 + - uses: actions/setup-python@v4 + with: + python-version: "3.12" - uses: prefix-dev/setup-pixi@v0.7.0 - run: pixi run docnb - uses: actions/upload-pages-artifact@v3 From b2277625dc063fbdae04deb0acacc6ec5fc0b0ac Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Fri, 7 Jun 2024 11:30:46 +0200 Subject: [PATCH 15/61] Ensure _static directory exists with a .keep file --- docs/_static/.keep | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 docs/_static/.keep diff --git a/docs/_static/.keep b/docs/_static/.keep new file mode 100644 index 0000000..e69de29 From 1635fc9fd8d527fd761563d87d1aa3aa6c961ab4 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Fri, 7 Jun 2024 11:36:06 +0200 Subject: [PATCH 16/61] make _templates directory exists with a .keep file --- docs/_templates/.keep | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 docs/_templates/.keep diff --git a/docs/_templates/.keep b/docs/_templates/.keep new file mode 100644 index 0000000..e69de29 From 6670cf0e2d9d0fc67906f900495cd10f17d8a7c6 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 14:33:15 +0200 Subject: [PATCH 17/61] update most of the request changes --- .github/workflows/ci-docs.yml | 3 --- docs/Makefile | 20 -------------------- docs/_static/.keep | 0 docs/_templates/.keep | 0 docs/conf.py | 17 +++-------------- docs/index.md | 3 --- docs/make.bat | 35 ----------------------------------- 7 files changed, 3 insertions(+), 75 deletions(-) delete mode 100644 docs/Makefile delete mode 100644 docs/_static/.keep delete mode 100644 docs/_templates/.keep delete mode 100644 docs/make.bat diff --git a/.github/workflows/ci-docs.yml b/.github/workflows/ci-docs.yml index c6255a4..eeef184 100644 --- a/.github/workflows/ci-docs.yml +++ b/.github/workflows/ci-docs.yml @@ -9,9 +9,6 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - uses: actions/setup-python@v4 - with: - python-version: "3.12" - uses: prefix-dev/setup-pixi@v0.7.0 - run: pixi run docnb - uses: actions/upload-pages-artifact@v3 diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index 9ead246..0000000 --- a/docs/Makefile +++ /dev/null @@ -1,20 +0,0 @@ -# Minimal makefile for Sphinx documentation -# - -# You can set these variables from the command line, and also -# from the environment for the first two. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -SOURCEDIR = . -BUILDDIR = build - -# Put it first so that "make" without argument is like "make help". -help: - @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) - -.PHONY: help Makefile - -# Catch-all target: route all unknown targets to Sphinx using the new -# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). -%: Makefile - @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/_static/.keep b/docs/_static/.keep deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_templates/.keep b/docs/_templates/.keep deleted file mode 100644 index e69de29..0000000 diff --git a/docs/conf.py b/docs/conf.py index e0175ad..d3d4d01 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,6 +1,5 @@ project = "GlueX-Nstar" author = "ComPWA" -release = "0.1" exclude_patterns = [ "**.ipynb_checkpoints", @@ -19,21 +18,8 @@ "sphinx.ext.napoleon", "sphinx.ext.viewcode", ] -intersphinx_mapping = { - "python": ("https://docs.python.org/3/", None), - "sphinx": ("https://www.sphinx-doc.org/en/master/", None), -} -intersphinx_disabled_domains = ["std"] -templates_path = ["_templates"] - html_theme = "sphinx_rtd_theme" -html_static_path = ["_static"] - master_doc = "index" -nitpicky = True -nb_execution_mode = "auto" -version = "0.1.0" - myst_enable_extensions = [ "colon_fence", "deflist", @@ -44,3 +30,6 @@ "substitution", "tasklist", ] +nitpicky = True +nb_execution_mode = "auto" +version = "0.1.0" diff --git a/docs/index.md b/docs/index.md index 1a22319..38385b6 100644 --- a/docs/index.md +++ b/docs/index.md @@ -9,8 +9,5 @@ Investigation of the N\* Resonances in the GlueX Experiment ## Contents ```{toctree} -:titlesonly: -:maxdepth: 2 - hello ``` diff --git a/docs/make.bat b/docs/make.bat deleted file mode 100644 index 3d64bb3..0000000 --- a/docs/make.bat +++ /dev/null @@ -1,35 +0,0 @@ -@ECHO OFF - -pushd %~dp0 - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set SOURCEDIR=. -set BUILDDIR=build - -if "%1" == "" goto help - -%SPHINXBUILD% >NUL 2>NUL -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.http://sphinx-doc.org/ - exit /b 1 -) - -%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% -goto end - -:help -%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% - -:end -popd From 3b724239e3ed8a69f74d5a1bb3106743b445792a Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 14:45:53 +0200 Subject: [PATCH 18/61] Remove pyproject.toml and rely on pixi.toml --- pyproject.toml | 8 -------- 1 file changed, 8 deletions(-) delete mode 100644 pyproject.toml diff --git a/pyproject.toml b/pyproject.toml deleted file mode 100644 index 8466854..0000000 --- a/pyproject.toml +++ /dev/null @@ -1,8 +0,0 @@ -[build-system] -build-backend = "flit_core.buildapi" -requires = ["flit_core >=3.2,<4"] - -[project] -authors = [{name = "ComPWA"}] -dynamic = ["description", "version"] -name = "gluex-nstar" From 9be9505432c49068b1bc2b8bcf8316bf2a23fc2c Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 15:13:57 +0200 Subject: [PATCH 19/61] Remove requirements.txt and update .readthedoc.yaml --- .readthedocs.yaml | 8 ++++---- docs/requirements.txt | 4 ---- pixi.toml | 1 + 3 files changed, 5 insertions(+), 8 deletions(-) delete mode 100644 docs/requirements.txt diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 2d7e00c..915f9c1 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -5,9 +5,9 @@ build: tools: python: "3.12" -python: - install: - - requirements: docs/requirements.txt - sphinx: configuration: docs/conf.py + +commands: + - pixi shell + - pixi run docnb diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index cecc2d8..0000000 --- a/docs/requirements.txt +++ /dev/null @@ -1,4 +0,0 @@ -linkify-it-py -myst-nb -sphinx -sphinx-rtd-theme diff --git a/pixi.toml b/pixi.toml index 2de6106..fd94169 100644 --- a/pixi.toml +++ b/pixi.toml @@ -38,6 +38,7 @@ pydata-sphinx-theme = ">=0.15.2,<0.16" python = ">=3.12.3,<3.13" python-graphviz = ">=0.20.3,<0.21" scipy = ">=1.13.0,<1.14" +sphinx = ">=7.3.7,<7.4" sphinx-autobuild = ">=2024.4.16,<2024.5" sphinx_rtd_theme = ">=2.0.0,<2.1" sympy = ">=1.12,<2" From 514ea3c3527a0e65ef84b48b0f7e679800769010 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 15:21:32 +0200 Subject: [PATCH 20/61] Add build-docs.sh and update .readthedoc.yaml --- .readthedocs.yaml | 3 +-- build-docs.sh | 3 +++ 2 files changed, 4 insertions(+), 2 deletions(-) create mode 100755 build-docs.sh diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 915f9c1..03ac35e 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -9,5 +9,4 @@ sphinx: configuration: docs/conf.py commands: - - pixi shell - - pixi run docnb + - ./build-docs.sh diff --git a/build-docs.sh b/build-docs.sh new file mode 100755 index 0000000..e143f93 --- /dev/null +++ b/build-docs.sh @@ -0,0 +1,3 @@ +#!/bin/sh +. $(pixi shell --quiet) +pixi run docnb From cead5587f6b8161a954a94c5011adfbd5b1f2a0c Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 15:29:39 +0200 Subject: [PATCH 21/61] update commands in .readthedoc.yaml --- .readthedocs.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 03ac35e..3aa894a 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -9,4 +9,6 @@ sphinx: configuration: docs/conf.py commands: - - ./build-docs.sh + - curl -sSL https://install.pixi.dev | sh + - pixi install + - pixi run docnb From 9f23541e87c2d7ce0020e190f90d84ac3fc04314 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 15:40:07 +0200 Subject: [PATCH 22/61] add custom build steps in .readthedoc.yaml --- .readthedocs.yaml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 3aa894a..84e1d8a 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -4,11 +4,12 @@ build: os: "ubuntu-22.04" tools: python: "3.12" - + steps: + - run: + cmd: curl -sSL https://install.pixi.dev | sh + - run: + cmd: pixi install + - run: + cmd: pixi run docnb sphinx: configuration: docs/conf.py - -commands: - - curl -sSL https://install.pixi.dev | sh - - pixi install - - pixi run docnb From 470bfc933a371b3b987ad43525f385f47468c88f Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 15:44:52 +0200 Subject: [PATCH 23/61] pixi shell custom build steps in .readthedoc.yaml --- .readthedocs.yaml | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 84e1d8a..7b37b8a 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -4,12 +4,9 @@ build: os: "ubuntu-22.04" tools: python: "3.12" - steps: - - run: - cmd: curl -sSL https://install.pixi.dev | sh - - run: - cmd: pixi install - - run: - cmd: pixi run docnb + jobs: + post_install: + - curl -fsSL https://pixi.sh/install.sh | bash + - pixi shell sphinx: configuration: docs/conf.py From 9296e6708ad845e611a9ee7617d695409071063b Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 15:46:21 +0200 Subject: [PATCH 24/61] pixi install custom build steps in .readthedoc.yaml --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 7b37b8a..8b1ae06 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -7,6 +7,6 @@ build: jobs: post_install: - curl -fsSL https://pixi.sh/install.sh | bash - - pixi shell + - pixi install sphinx: configuration: docs/conf.py From ecd55206395ff22a3a3379e6d658c4c561309302 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 15:55:43 +0200 Subject: [PATCH 25/61] pixi custom build steps in .readthedoc.yaml --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 8b1ae06..39a96d9 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -6,7 +6,7 @@ build: python: "3.12" jobs: post_install: - - curl -fsSL https://pixi.sh/install.sh | bash + - source .pixi/bin/activate - pixi install sphinx: configuration: docs/conf.py From 8c789c15eab7c494c36810a1b26618c4ba6194d5 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 16:00:39 +0200 Subject: [PATCH 26/61] pixi source custom build steps in .readthedoc.yaml --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 39a96d9..f19ad79 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -6,7 +6,7 @@ build: python: "3.12" jobs: post_install: - - source .pixi/bin/activate + - source .pixi/bin/pixi - pixi install sphinx: configuration: docs/conf.py From de092ce1ed8128b3a2612c7606375f53ce4a2300 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 16:04:18 +0200 Subject: [PATCH 27/61] pixi source at home folder custom build steps in .readthedoc.yaml --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index f19ad79..347976c 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -6,7 +6,7 @@ build: python: "3.12" jobs: post_install: - - source .pixi/bin/pixi + - source ~/.pixi/bin/pixi - pixi install sphinx: configuration: docs/conf.py From 11b18ce9f1b365e8345c44afe66737cc43341290 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 16:10:35 +0200 Subject: [PATCH 28/61] custom build steps in RTD yaml --- .readthedocs.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 347976c..9cbd990 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -6,7 +6,9 @@ build: python: "3.12" jobs: post_install: - - source ~/.pixi/bin/pixi + - curl -fsSL https://pixi.sh/install.sh | bash + - export PATH="$HOME/.local/bin:$PATH" - pixi install + - pixi run docnb sphinx: configuration: docs/conf.py From 109788bf25ef019091193c0a8da9cf1768f40d77 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 16:15:08 +0200 Subject: [PATCH 29/61] pixi location --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 9cbd990..4d24c9b 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -7,7 +7,7 @@ build: jobs: post_install: - curl -fsSL https://pixi.sh/install.sh | bash - - export PATH="$HOME/.local/bin:$PATH" + - export PATH="$HOME/.pixi/bin:$PATH" - pixi install - pixi run docnb sphinx: From d50722cd3462439e3bca769aba5b3d5d54f75286 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 16:18:39 +0200 Subject: [PATCH 30/61] in 1 line --- .readthedocs.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 4d24c9b..3fe96c4 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -6,9 +6,7 @@ build: python: "3.12" jobs: post_install: - - curl -fsSL https://pixi.sh/install.sh | bash - - export PATH="$HOME/.pixi/bin:$PATH" - - pixi install - - pixi run docnb + - curl -fsSL https://pixi.sh/install.sh | bash && export PATH="$HOME/.pixi/bin:$PATH" && pixi install && pixi run docnb + sphinx: configuration: docs/conf.py From f4d5473fda9964d9ee166e75cd9b52a991ad0d5a Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 16:50:01 +0200 Subject: [PATCH 31/61] change to command --- .readthedocs.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 3fe96c4..acf4c08 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -4,9 +4,10 @@ build: os: "ubuntu-22.04" tools: python: "3.12" - jobs: - post_install: - - curl -fsSL https://pixi.sh/install.sh | bash && export PATH="$HOME/.pixi/bin:$PATH" && pixi install && pixi run docnb sphinx: configuration: docs/conf.py + +commands: + - curl -fsSL https://pixi.sh/install.sh | bash && export PATH="$HOME/.pixi/bin:$PATH" && pixi install + - pixi run docnb From b7c23f17844d1e5e22630885ddfc490c4933f8a0 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 16:57:04 +0200 Subject: [PATCH 32/61] change back to build --- .readthedocs.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index acf4c08..05acb74 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -4,10 +4,9 @@ build: os: "ubuntu-22.04" tools: python: "3.12" + steps: + - run: curl -fsSL https://pixi.sh/install.sh | bash && export PATH="$HOME/.pixi/bin:$PATH" && pixi install + - run: pixi run docnb sphinx: configuration: docs/conf.py - -commands: - - curl -fsSL https://pixi.sh/install.sh | bash && export PATH="$HOME/.pixi/bin:$PATH" && pixi install - - pixi run docnb From 3872f238df43a1bc084554334eda1feedb999557 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 17:00:32 +0200 Subject: [PATCH 33/61] jobs --- .readthedocs.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 05acb74..f6e36f2 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -4,9 +4,10 @@ build: os: "ubuntu-22.04" tools: python: "3.12" - steps: - - run: curl -fsSL https://pixi.sh/install.sh | bash && export PATH="$HOME/.pixi/bin:$PATH" && pixi install - - run: pixi run docnb + jobs: + post_install: + - run: curl -fsSL https://pixi.sh/install.sh | bash && export PATH="$HOME/.pixi/bin:$PATH" && pixi install + - run: pixi run docnb sphinx: configuration: docs/conf.py From 1066b6879330fd37c12840889420ad4e7fc53740 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 17:04:04 +0200 Subject: [PATCH 34/61] pixi install shell --- .readthedocs.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index f6e36f2..333492d 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -6,8 +6,9 @@ build: python: "3.12" jobs: post_install: - - run: curl -fsSL https://pixi.sh/install.sh | bash && export PATH="$HOME/.pixi/bin:$PATH" && pixi install - - run: pixi run docnb + - curl -fsSL https://pixi.sh/install.sh | bash + - export PATH="$HOME/.pixi/bin:$PATH" && pixi install + - pixi shell sphinx: configuration: docs/conf.py From c764ba74b36b8ca6132d7d48f0b30be757f3c7bb Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 17:07:52 +0200 Subject: [PATCH 35/61] export --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 333492d..94fbda1 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,7 +8,7 @@ build: post_install: - curl -fsSL https://pixi.sh/install.sh | bash - export PATH="$HOME/.pixi/bin:$PATH" && pixi install - - pixi shell + - export PATH="$HOME/.pixi/bin:$PATH" && pixi shell sphinx: configuration: docs/conf.py From ef82961afa14bce0fa7bddd5fa66b0d503d0859d Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 17:10:28 +0200 Subject: [PATCH 36/61] remove pixi shell in rtd yaml --- .readthedocs.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 94fbda1..3cc55f1 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,7 +8,6 @@ build: post_install: - curl -fsSL https://pixi.sh/install.sh | bash - export PATH="$HOME/.pixi/bin:$PATH" && pixi install - - export PATH="$HOME/.pixi/bin:$PATH" && pixi shell sphinx: configuration: docs/conf.py From 13a82a220c5a9440216aa397cde13cb24e49f010 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 17:19:54 +0200 Subject: [PATCH 37/61] modify again in rtd yaml --- .readthedocs.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 3cc55f1..793a028 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,6 +8,9 @@ build: post_install: - curl -fsSL https://pixi.sh/install.sh | bash - export PATH="$HOME/.pixi/bin:$PATH" && pixi install - + environment: + - PATH: "$HOME/.pixi/bin:$PATH" + run: + - pixi run docnb sphinx: configuration: docs/conf.py From 20d625636a82a7fc55d7cc44fd16977536599326 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 17:20:56 +0200 Subject: [PATCH 38/61] correction again in rtd yaml --- .readthedocs.yaml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 793a028..ddd808d 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,9 +8,6 @@ build: post_install: - curl -fsSL https://pixi.sh/install.sh | bash - export PATH="$HOME/.pixi/bin:$PATH" && pixi install - environment: - - PATH: "$HOME/.pixi/bin:$PATH" - run: - pixi run docnb sphinx: configuration: docs/conf.py From 276d10334364e99e8c9126b9d9391ea5fb8d80e7 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 17:25:46 +0200 Subject: [PATCH 39/61] change sphinx in rtd yaml --- .readthedocs.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index ddd808d..76c26e6 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,6 +8,7 @@ build: post_install: - curl -fsSL https://pixi.sh/install.sh | bash - export PATH="$HOME/.pixi/bin:$PATH" && pixi install - - pixi run docnb sphinx: configuration: docs/conf.py + builder: html + build_command: export PATH="$HOME/.pixi/bin:$PATH" && pixi shell -c "sphinx-build -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html" From 94c5c4ba184331297957dfde4c0be84cff56cf46 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 17:28:31 +0200 Subject: [PATCH 40/61] move to above in rtd yaml --- .readthedocs.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 76c26e6..249e8af 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,7 +8,7 @@ build: post_install: - curl -fsSL https://pixi.sh/install.sh | bash - export PATH="$HOME/.pixi/bin:$PATH" && pixi install + commands: + - export PATH="$HOME/.pixi/bin:$PATH" && pixi shell -c "sphinx-build -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html" sphinx: configuration: docs/conf.py - builder: html - build_command: export PATH="$HOME/.pixi/bin:$PATH" && pixi shell -c "sphinx-build -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html" From 7085d98b5cb7728de758c167f6ec506a36b00f04 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 17:30:53 +0200 Subject: [PATCH 41/61] remove commands in rtd yaml --- .readthedocs.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 249e8af..a5a6f3f 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,7 +8,6 @@ build: post_install: - curl -fsSL https://pixi.sh/install.sh | bash - export PATH="$HOME/.pixi/bin:$PATH" && pixi install - commands: - export PATH="$HOME/.pixi/bin:$PATH" && pixi shell -c "sphinx-build -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html" sphinx: configuration: docs/conf.py From 657d99615fb898b14a15e8f7f62efa95f5cf0e0b Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 17:34:07 +0200 Subject: [PATCH 42/61] post_build --- .readthedocs.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index a5a6f3f..9bd3e1d 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,6 +8,8 @@ build: post_install: - curl -fsSL https://pixi.sh/install.sh | bash - export PATH="$HOME/.pixi/bin:$PATH" && pixi install - - export PATH="$HOME/.pixi/bin:$PATH" && pixi shell -c "sphinx-build -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html" -sphinx: + post_build: + - export PATH="$HOME/.pixi/bin:$PATH" && pixi run docnb + + sphinx: configuration: docs/conf.py From 3b4f9adfa6182bc0b4877de4fcc8b39697103c58 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 17:40:57 +0200 Subject: [PATCH 43/61] only essentials in post_install --- .readthedocs.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 9bd3e1d..543b07d 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -7,9 +7,9 @@ build: jobs: post_install: - curl -fsSL https://pixi.sh/install.sh | bash - - export PATH="$HOME/.pixi/bin:$PATH" && pixi install - post_build: - - export PATH="$HOME/.pixi/bin:$PATH" && pixi run docnb + - |- + /home/.pixi/bin/pixi pixi shell - sphinx: +sphinx: + builder: html configuration: docs/conf.py From 5b812ce6410dc74287ee4b9c6ff79d18bd735e80 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 17:43:48 +0200 Subject: [PATCH 44/61] location update --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 543b07d..c6c3dff 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,7 +8,7 @@ build: post_install: - curl -fsSL https://pixi.sh/install.sh | bash - |- - /home/.pixi/bin/pixi pixi shell + /home/docs/.pixi/bin pixi shell sphinx: builder: html From 5d2025de1ca77b869b0f9730496fb1d07535b991 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 17:49:36 +0200 Subject: [PATCH 45/61] stucks here --- .readthedocs.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index c6c3dff..c837566 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -7,9 +7,7 @@ build: jobs: post_install: - curl -fsSL https://pixi.sh/install.sh | bash - - |- - /home/docs/.pixi/bin pixi shell - + - export PATH="$HOME/.pixi/bin:$PATH" && pixi install sphinx: builder: html configuration: docs/conf.py From bd5d1e2aa915fa80c139769f9c346e0d7c28aa6f Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 17:52:20 +0200 Subject: [PATCH 46/61] add build_commends maybe --- .readthedocs.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index c837566..dddaa0c 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -11,3 +11,4 @@ build: sphinx: builder: html configuration: docs/conf.py + build_command: export PATH="$HOME/.pixi/bin:$PATH" && pixi shell -c "sphinx-build -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html" From dd52c077d71691a4d47d0ae649b22416807d92fc Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 17:56:57 +0200 Subject: [PATCH 47/61] again post build maybe --- .readthedocs.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index dddaa0c..fc63062 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,7 +8,9 @@ build: post_install: - curl -fsSL https://pixi.sh/install.sh | bash - export PATH="$HOME/.pixi/bin:$PATH" && pixi install + post_build: + - export PATH="$HOME/.pixi/bin:$PATH" + - pixi shell -c "sphinx-build -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html" sphinx: builder: html configuration: docs/conf.py - build_command: export PATH="$HOME/.pixi/bin:$PATH" && pixi shell -c "sphinx-build -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html" From 8a9dbde752e1c0b4a915234e055beae9bf12219e Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 18:03:02 +0200 Subject: [PATCH 48/61] add back python maybe --- .readthedocs.yaml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index fc63062..db1abb3 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -14,3 +14,8 @@ build: sphinx: builder: html configuration: docs/conf.py + fail_on_warning: true + +python: + install: + - requirements: pixi.toml From e63b3820bb83f760f51d8251b06a475246367200 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Tue, 11 Jun 2024 18:07:12 +0200 Subject: [PATCH 49/61] wrap into post_install --- .readthedocs.yaml | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index db1abb3..4353a4c 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,14 +8,8 @@ build: post_install: - curl -fsSL https://pixi.sh/install.sh | bash - export PATH="$HOME/.pixi/bin:$PATH" && pixi install - post_build: - - export PATH="$HOME/.pixi/bin:$PATH" - - pixi shell -c "sphinx-build -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html" + - pixi shell -c "pixi install && sphinx-build -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html" sphinx: builder: html configuration: docs/conf.py fail_on_warning: true - -python: - install: - - requirements: pixi.toml From 980f2549e822b53b7f832e59c2c4afbdf72c8191 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Wed, 12 Jun 2024 11:06:44 +0200 Subject: [PATCH 50/61] add pre_biild --- .readthedocs.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 4353a4c..a496847 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -7,8 +7,8 @@ build: jobs: post_install: - curl -fsSL https://pixi.sh/install.sh | bash - - export PATH="$HOME/.pixi/bin:$PATH" && pixi install - - pixi shell -c "pixi install && sphinx-build -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html" + pre_build: + - pixi shell -c "true" sphinx: builder: html configuration: docs/conf.py From 8e35409b0442416741660a23c94bfa43a3b3a4e0 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Wed, 12 Jun 2024 11:08:53 +0200 Subject: [PATCH 51/61] add install before pre_biild --- .readthedocs.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index a496847..ff7af21 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -7,7 +7,9 @@ build: jobs: post_install: - curl -fsSL https://pixi.sh/install.sh | bash + - export PATH="$HOME/.pixi/bin:$PATH" && pixi install pre_build: + - export PATH="$HOME/.pixi/bin:$PATH" && pixi install - pixi shell -c "true" sphinx: builder: html From 5523780ebe2d55a971fb333fb39c917e7f93cb90 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Wed, 12 Jun 2024 11:14:26 +0200 Subject: [PATCH 52/61] try only pixi shell in pre_biild --- .readthedocs.yaml | 4 +--- docs/conf.py | 3 ++- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index ff7af21..b1e231b 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -7,10 +7,8 @@ build: jobs: post_install: - curl -fsSL https://pixi.sh/install.sh | bash - - export PATH="$HOME/.pixi/bin:$PATH" && pixi install pre_build: - - export PATH="$HOME/.pixi/bin:$PATH" && pixi install - - pixi shell -c "true" + - export PATH="$HOME/.pixi/bin:$PATH" && pixi shell sphinx: builder: html configuration: docs/conf.py diff --git a/docs/conf.py b/docs/conf.py index d3d4d01..68bfb08 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -30,6 +30,7 @@ "substitution", "tasklist", ] -nitpicky = True + nb_execution_mode = "auto" +nitpicky = True version = "0.1.0" From 6a051d782c70e979d67663b8609399280dfc4a03 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Wed, 12 Jun 2024 11:20:48 +0200 Subject: [PATCH 53/61] attempt to run command bypassing the need of an interactive shell in pre_biild --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index b1e231b..9dfcb81 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,7 +8,7 @@ build: post_install: - curl -fsSL https://pixi.sh/install.sh | bash pre_build: - - export PATH="$HOME/.pixi/bin:$PATH" && pixi shell + - export PATH="$HOME/.pixi/bin:$PATH" && pixi shell -c "echo Pixi shell activated" sphinx: builder: html configuration: docs/conf.py From e5992b4a98cc30aedcb48c9919997ebae54018ed Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Wed, 12 Jun 2024 11:41:37 +0200 Subject: [PATCH 54/61] only pixi shell and then python --- .readthedocs.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 9dfcb81..0a45662 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,7 +8,13 @@ build: post_install: - curl -fsSL https://pixi.sh/install.sh | bash pre_build: - - export PATH="$HOME/.pixi/bin:$PATH" && pixi shell -c "echo Pixi shell activated" + - export PATH="$HOME/.pixi/bin:$PATH" && pixi shell + +python: + install: + - method: pip + path: . + sphinx: builder: html configuration: docs/conf.py From 0ca76fac76c581243c763f10f17b5b855be6bec1 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Wed, 12 Jun 2024 11:56:41 +0200 Subject: [PATCH 55/61] Add back pyproject again --- .gitattributes | 2 ++ pyproject.toml | 20 ++++++++++++++++++++ 2 files changed, 22 insertions(+) create mode 100644 .gitattributes create mode 100644 pyproject.toml diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..d5799bd --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# GitHub syntax highlighting +pixi.lock linguist-language=YAML diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..2566216 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,20 @@ +[project] +authors = [{name = "Vitor Shen", email = "17490173+shenvitor@users.noreply.github.com"}] +dependencies = [] +description = "Add a short description here" +name = "gluex-nstar" +requires-python = ">= 3.11" +version = "0.1.0" + +[build-system] +build-backend = "setuptools.build_meta" +requires = ["setuptools"] + +[tool.pixi.project] +channels = ["conda-forge"] +platforms = ["linux-64"] + +[tool.pixi.pypi-dependencies] +gluex-nstar = {path = ".", editable = true} + +[tool.pixi.tasks] From c2c8b1522e85b916fd23d240af7aed79409c1447 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Wed, 12 Jun 2024 11:59:30 +0200 Subject: [PATCH 56/61] remove build-docs.sh --- build-docs.sh | 3 --- 1 file changed, 3 deletions(-) delete mode 100755 build-docs.sh diff --git a/build-docs.sh b/build-docs.sh deleted file mode 100755 index e143f93..0000000 --- a/build-docs.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/sh -. $(pixi shell --quiet) -pixi run docnb From d760eeba3112f08ddc1df444354be95ea56b0cf5 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Wed, 12 Jun 2024 12:26:13 +0200 Subject: [PATCH 57/61] remove pyproject again --- .readthedocs.yaml | 5 ----- pyproject.toml | 20 -------------------- 2 files changed, 25 deletions(-) delete mode 100644 pyproject.toml diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 0a45662..cb3f5a9 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -10,11 +10,6 @@ build: pre_build: - export PATH="$HOME/.pixi/bin:$PATH" && pixi shell -python: - install: - - method: pip - path: . - sphinx: builder: html configuration: docs/conf.py diff --git a/pyproject.toml b/pyproject.toml deleted file mode 100644 index 2566216..0000000 --- a/pyproject.toml +++ /dev/null @@ -1,20 +0,0 @@ -[project] -authors = [{name = "Vitor Shen", email = "17490173+shenvitor@users.noreply.github.com"}] -dependencies = [] -description = "Add a short description here" -name = "gluex-nstar" -requires-python = ">= 3.11" -version = "0.1.0" - -[build-system] -build-backend = "setuptools.build_meta" -requires = ["setuptools"] - -[tool.pixi.project] -channels = ["conda-forge"] -platforms = ["linux-64"] - -[tool.pixi.pypi-dependencies] -gluex-nstar = {path = ".", editable = true} - -[tool.pixi.tasks] From f7231ef6c873f0959cc3cac9b75a78db92e7c03b Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:56:38 +0200 Subject: [PATCH 58/61] update .readthedoc.yaml by an example --- .readthedocs.yaml | 17 +++++------------ docs/conf.py | 2 +- 2 files changed, 6 insertions(+), 13 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index cb3f5a9..7b03d88 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -1,16 +1,9 @@ version: "2" - build: os: "ubuntu-22.04" tools: - python: "3.12" - jobs: - post_install: - - curl -fsSL https://pixi.sh/install.sh | bash - pre_build: - - export PATH="$HOME/.pixi/bin:$PATH" && pixi shell - -sphinx: - builder: html - configuration: docs/conf.py - fail_on_warning: true + python: mambaforge-latest + commands: + - mamba install -c conda-forge -c nodefaults pixi + - pixi install + - pixi run docnb diff --git a/docs/conf.py b/docs/conf.py index 68bfb08..bed179b 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -18,7 +18,7 @@ "sphinx.ext.napoleon", "sphinx.ext.viewcode", ] -html_theme = "sphinx_rtd_theme" +html_theme = "sphinx_book_theme" master_doc = "index" myst_enable_extensions = [ "colon_fence", From 5c3746c498b1b0946a9e72747824c07f5bc12d84 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:12:04 +0200 Subject: [PATCH 59/61] reduce diff with main branch --- README.md | 11 + docs/conf.py | 25 +- docs/hello.ipynb | 43 -- docs/index.md | 19 +- docs/pgamma-state.ipynb | 780 +++++++++++++++++++++++++++ docs/reaction.md | 73 +++ pixi.lock | 1124 +++++++++++++++++++++++++++++++++------ pixi.toml | 13 +- 8 files changed, 1848 insertions(+), 240 deletions(-) create mode 100644 README.md delete mode 100644 docs/hello.ipynb create mode 100644 docs/pgamma-state.ipynb create mode 100644 docs/reaction.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..dd975b7 --- /dev/null +++ b/README.md @@ -0,0 +1,11 @@ +# Research Project on Amplitude Models Involving N-Star and K-Star Resonances in the GlueX Experiment + +This repository is under active development. + +We are doing amplitude analysis / Partial Wave Analysis (PWA) with the use of symbolic expressions, which is included in the ComPWA packages, or CAS(Computer Algebra System)-assisted model building in general (the python package SymPy in this case). + +The first demonstration example is: $p \gamma \to$ Resonances (e.g. N\*) $\to \eta \pi^0 p$ + +The main focus of this research would be: $p \gamma \to$ Resonances (e.g. N\*, K\*) $\to K^+ \pi^0 \Lambda$ + +Current long term plan: This research project focuses on developing and applying amplitude models to analyze data from the GlueX experiment, specifically targeting N-star (N*) and K-star (K*) resonances. diff --git a/docs/conf.py b/docs/conf.py index bed179b..70fccf8 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,6 +1,3 @@ -project = "GlueX-Nstar" -author = "ComPWA" - exclude_patterns = [ "**.ipynb_checkpoints", ".DS_Store", @@ -8,29 +5,15 @@ "Thumbs.db", "_build", ] -extensions = [ - "myst_nb", - "sphinx.ext.duration", - "sphinx.ext.doctest", - "sphinx.ext.autodoc", - "sphinx.ext.autosummary", - "sphinx.ext.intersphinx", - "sphinx.ext.napoleon", - "sphinx.ext.viewcode", -] +extensions = ["myst_nb"] html_theme = "sphinx_book_theme" master_doc = "index" myst_enable_extensions = [ + "amsmath", "colon_fence", - "deflist", "dollarmath", - "html_admonition", "html_image", - "linkify", - "substitution", - "tasklist", + "smartquotes", ] - -nb_execution_mode = "auto" nitpicky = True -version = "0.1.0" +project = "GlueX N-Star" diff --git a/docs/hello.ipynb b/docs/hello.ipynb deleted file mode 100644 index 38a1baa..0000000 --- a/docs/hello.ipynb +++ /dev/null @@ -1,43 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "id": "0", - "metadata": {}, - "source": [ - "# Hello" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "1", - "metadata": {}, - "outputs": [], - "source": [ - "print(\"Hello World!\")" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.12.3" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/docs/index.md b/docs/index.md index 38385b6..b08e62e 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,13 +1,20 @@ -# Welcome Page +# Amplitude Analysis 101 / PWA101 (v2.0) -# Welcome to GlueX-Nstar documentation! +## CAS-assisted Amplitude Models building for photoproduction reaction -Investigation of the N\* Resonances in the GlueX Experiment +This document is a follow-up of PWA101 (v1.0) (temporarily see [here](https://compwa--217.org.readthedocs.build/report/999.html)), +as an introduction to Amplitude Analysis / Partial Wave Analysis (PWA) by demonstrating its application to a specific reaction channel and amplitude model. -> **Note:** This project is under active development. +Now the focus is the use of symbolic expressions (computations), with the use of [ComPWA packages](https://compwa.github.io/), or CAS(Computer Algebra System)-assisted model building in general (the python package `SymPy` in this case) to illustrate the general process in PWA. -## Contents +This tutorial aims to equip readers with deeper understanding of PWA methodologies and full workflow in the context of hadron physics through a practical, hands-on example with symbolic expressions via [ComPWA](https://compwa.github.io/). + +Furthermore, +address to the issue ✅ [ComPWA/gluex-nstar#1](https://github.com/ComPWA/gluex-nstar/issues/1), this document is PWA101(v2.0), which shows PWA methodologies and full workflow in the context of hadron physics with symbolic expressions via [ComPWA](https://compwa.github.io/). + +# Table of contents: ```{toctree} -hello +reaction +pgamma-state ``` diff --git a/docs/pgamma-state.ipynb b/docs/pgamma-state.ipynb new file mode 100644 index 0000000..24fa056 --- /dev/null +++ b/docs/pgamma-state.ipynb @@ -0,0 +1,780 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "0", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "source": [ + "# Virtual particle that represents the state pγ " + ] + }, + { + "cell_type": "markdown", + "id": "1", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "source": [ + "Address to issue ✅ [ComPWA/gluex-nstar#5](https://github.com/ComPWA/gluex-nstar/issues/5), this section is an investigation of creating a virtual particle that represents the state $p \\gamma$ in `QRules`" + ] + }, + { + "cell_type": "markdown", + "id": "2", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "source": [ + "As an example of side note, create a virtual particle that represents state $e^+ e^-$ can be seen [here](https://qrules.readthedocs.io/0.10.x/usage/particle/#adding-custom-particle-definitions-through-python)." + ] + }, + { + "cell_type": "markdown", + "id": "3", + "metadata": {}, + "source": [ + "## Finding particles" + ] + }, + { + "cell_type": "markdown", + "id": "4", + "metadata": {}, + "source": [ + "Our reaction is $p + \\gamma \\to \\eta + \\pi^0 + p$, so we can look for each of the reaction and decay particles" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "from __future__ import annotations\n", + "from IPython.display import Math\n", + "from qrules.particle import load_pdg\n", + "from ampform.io import aslatex, improve_latex_rendering\n", + "\n", + "improve_latex_rendering()\n", + "particle_db = load_pdg()\n", + "print(\"Number of loaded particles:\", len(particle_db))" + ] + }, + { + "cell_type": "markdown", + "id": "6", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "source": [ + "The [`ParticleCollection`](https://qrules.readthedocs.io/0.10.x/api/qrules.particle/#qrules.particle.ParticleCollection) class offers some methods to search for particles by name or by PID, name, or other properties." + ] + }, + { + "cell_type": "markdown", + "id": "7", + "metadata": {}, + "source": [ + "### Proton" + ] + }, + { + "cell_type": "markdown", + "id": "8", + "metadata": {}, + "source": [ + "Search by Particle ID (PID) for proton:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "9", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "particle_db.find(2212)" + ] + }, + { + "cell_type": "markdown", + "id": "10", + "metadata": {}, + "source": [ + "Search by Particle name for proton:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "11", + "metadata": {}, + "outputs": [], + "source": [ + "particle_db.find(\"p\")\n", + "proton = particle_db[\"p\"]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "12", + "metadata": {}, + "outputs": [], + "source": [ + "from IPython.display import Math\n", + "\n", + "Math(proton.latex)" + ] + }, + { + "cell_type": "markdown", + "id": "13", + "metadata": {}, + "source": [ + "### $\\gamma$" + ] + }, + { + "cell_type": "markdown", + "id": "14", + "metadata": {}, + "source": [ + "similarly for $\\gamma$:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "15", + "metadata": {}, + "outputs": [], + "source": [ + "particle_db.find(\"gamma\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "16", + "metadata": {}, + "outputs": [], + "source": [ + "gamma = particle_db[\"gamma\"]\n", + "Math(gamma.latex)" + ] + }, + { + "cell_type": "markdown", + "id": "17", + "metadata": {}, + "source": [ + "### $\\eta$" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "18", + "metadata": {}, + "outputs": [], + "source": [ + "particle_db.find(\"eta\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "19", + "metadata": {}, + "outputs": [], + "source": [ + "eta = particle_db[\"eta\"]\n", + "Math(gamma.latex)" + ] + }, + { + "cell_type": "markdown", + "id": "20", + "metadata": {}, + "source": [ + "### $\\pi^0$" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "21", + "metadata": {}, + "outputs": [], + "source": [ + "particle_db.find(\"pi0\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "22", + "metadata": {}, + "outputs": [], + "source": [ + "pi0 = particle_db[\"pi0\"]\n", + "Math(pi0.latex)" + ] + }, + { + "cell_type": "markdown", + "id": "23", + "metadata": {}, + "source": [ + "# Adding custom particle" + ] + }, + { + "cell_type": "markdown", + "id": "24", + "metadata": {}, + "source": [ + "We add the virtual particle $p\\gamma$ to represent the state of $p-\\gamma$ system in the photoproduction reaction.\n", + "See PWA101 (temporary [here](https://compwa--217.org.readthedocs.build/report/999.html)), the value of the mass of the system $m_{p\\gamma}$ in CM frame is about 4.102 GeV in this analysis.\n", + "\n", + "\n", + "We use `Particle` from `QRules` for adding custom particle, so that some quantum numbers we need to determine for the $p\\gamma$ virtual state particle:\n", + "\n", + "* (Total) Spin\n", + " * $J_{p\\gamma} = \\frac{1}{2}$ or $\\frac{3}{2}$\n", + " \n", + " because $J_{p\\gamma}$ = from $|s_p-s_{\\gamma}|$ to $s_p + s_{\\gamma}$ = from $|\\frac{1}{2}-1|$ to $\\frac{1}{2} + 1$\n", + " \n", + "* Mass\n", + " * $m_{p\\gamma} = E_{p\\gamma} \\approx 4.102$\n", + " \n", + "* Charge\n", + " * $Q_{p\\gamma} = Q_p + Q_{\\gamma} = 1 $\n", + " \n", + "* Isospin and $3^{rd}$ component of isospin\n", + " * $I_{p\\gamma} = I_p = \\frac{1}{2}$\n", + " * $I_{3_{p\\gamma}} = I_{3_p} = +\\frac{1}{2}$\n", + " \n", + "* Baryon Number\n", + " * $B_{p\\gamma} = B_p = 1$\n", + "\n", + "* Parity\n", + " * $P_{p\\gamma} = P_p \\times P_{\\gamma} = +1 \\times (-1) = -1$" + ] + }, + { + "cell_type": "markdown", + "id": "25", + "metadata": {}, + "source": [ + "These quantum numbers provide a complete and accurate description of the virtual particle representing the p−γ system with a mass of 4.102 GeV.\n", + "The pγ virtual particle has two possibilities for the total spin, while the other quantum numbers are fixed." + ] + }, + { + "cell_type": "markdown", + "id": "26", + "metadata": {}, + "source": [ + "We add the spin-$\\frac{1}{2}$ $p\\gamma$ virtual particle via `QRules` and named it $p\\gamma$ with a make-up pid number 99990" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "27", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "from qrules.particle import Particle, Spin\n", + "\n", + "pgamma = Particle(\n", + " name=\"pgamma\",\n", + " latex=r\"p\\gamma (s1/2)\",\n", + " spin=0.5,\n", + " mass=4.101931071854584,\n", + " charge=1,\n", + " isospin=Spin(1 / 2, +1 / 2),\n", + " baryon_number=1,\n", + " parity=-1,\n", + " pid=99990,\n", + ")\n", + "pgamma" + ] + }, + { + "cell_type": "markdown", + "id": "28", + "metadata": {}, + "source": [ + "We add the spin-$\\frac{3}{2}$ $p\\gamma$ virtual particle via `QRules` and named it $p\\gamma (s3/2)$ with a make-up pid number 99991" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "29", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "pgamma2 = Particle(\n", + " name=\"pgamma2\",\n", + " latex=R\"p\\gamma (s3/2)\",\n", + " spin=1.5,\n", + " mass=4.101931071854584,\n", + " charge=1,\n", + " isospin=Spin(1 / 2, +1 / 2),\n", + " baryon_number=1,\n", + " parity=-1,\n", + " pid=99991,\n", + ")\n", + "pgamma2" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "30", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "Math(pgamma.latex)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "31", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "Math(pgamma2.latex)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "32", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "particle_db.add(pgamma)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "33", + "metadata": {}, + "outputs": [], + "source": [ + "particle_db.add(pgamma2)" + ] + }, + { + "cell_type": "markdown", + "id": "34", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "source": [ + "The $`p\\gamma`$ virtual states generated via `QRules` will be used in later stages, both possible spin states $(J= \\frac{1}{2}$ and $\\frac{3}{2})$ should be taken into account if possible, otherwise simplified if necessary." + ] + }, + { + "cell_type": "markdown", + "id": "35", + "metadata": {}, + "source": [ + ":::{important}\n", + "It is possible to add any kind of custom Particle, as long as its quantum numbers comply with the [gellmann_nishijima()](https://qrules.readthedocs.io/0.10.x/api/qrules.conservation_rules/#qrules.conservation_rules.gellmann_nishijima) rule:\n", + ":::\n" + ] + }, + { + "cell_type": "markdown", + "id": "36", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "source": [ + ":::{note}\n", + "[Gell-Mann-Nishijima formula](https://en.wikipedia.org/wiki/Gell-Mann–Nishijima_formula):\n", + "$Q = I_3 + \\frac{1}{2}(B+S+C+B'+T)$\n", + "\n", + "where \n", + "Q is charge, \n", + "$I_3$ is Spin projection of isospin, \n", + " B is baryon number, \n", + " S is strangeness, \n", + " C is charmness, \n", + " B' is bottomness, and \n", + " T is topness.\n", + ":::\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "37", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "import qrules\n", + "import graphviz\n", + "\n", + "reaction1_all = qrules.generate_transitions(\n", + " initial_state=(\"pgamma\"),\n", + " final_state=[\"eta\", \"pi0\", \"p\"],\n", + " # allowed_intermediate_particles=[\"a(2)\", \"Delta\", \"N\"],\n", + " allowed_interaction_types=[\"strong\", \"EM\", \"weak\"],\n", + " formalism=\"canonical-helicity\",\n", + " particle_db=particle_db,\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "38", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "dot_all = qrules.io.asdot(reaction1_all, collapse_graphs=True)\n", + "graphviz.Source(dot_all)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "39", + "metadata": {}, + "outputs": [], + "source": [ + "reaction1_strong_EM = qrules.generate_transitions(\n", + " initial_state=(\"pgamma\"),\n", + " final_state=[\"eta\", \"pi0\", \"p\"],\n", + " # allowed_intermediate_particles=[\"a(2)\", \"Delta\", \"N\"],\n", + " allowed_interaction_types=[\"strong\", \"EM\"],\n", + " formalism=\"canonical-helicity\",\n", + " particle_db=particle_db,\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "40", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "dot_se = qrules.io.asdot(reaction1_strong_EM, collapse_graphs=True)\n", + "graphviz.Source(dot_se)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "41", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "reaction1_strong = qrules.generate_transitions(\n", + " initial_state=(\"pgamma\"),\n", + " final_state=[\"eta\", \"pi0\", \"p\"],\n", + " # allowed_intermediate_particles=[\"a(2)\", \"Delta\", \"N\"],\n", + " allowed_interaction_types=[\"strong\"],\n", + " formalism=\"canonical-helicity\",\n", + " particle_db=particle_db,\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "42", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "dot_s = qrules.io.asdot(reaction1_strong, collapse_graphs=True)\n", + "graphviz.Source(dot_s)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "43", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "from qrules import InteractionType, StateTransitionManager\n", + "\n", + "stm = StateTransitionManager(\n", + " initial_state=[\"pgamma\"],\n", + " final_state=[\"eta\", \"pi0\", \"p\"],\n", + " formalism=\"canonical-helicity\",\n", + " particle_db=particle_db,\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "44", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "problem_sets = stm.create_problem_sets()\n", + "sorted(problem_sets, reverse=True)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "45", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "from qrules import io\n", + "\n", + "some_problem_set = problem_sets[60.0][0]\n", + "dot = io.asdot(some_problem_set, render_node=True)\n", + "graphviz.Source(dot)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "46", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "some_problem_set = problem_sets[1][0]\n", + "dot = io.asdot(some_problem_set, render_node=True)\n", + "graphviz.Source(dot)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "47", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "some_problem_set = problem_sets[0.0001][1]\n", + "dot = io.asdot(some_problem_set, render_node=True)\n", + "graphviz.Source(dot)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "48", + "metadata": {}, + "outputs": [], + "source": [ + "reaction = stm.find_solutions(problem_sets)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "49", + "metadata": {}, + "outputs": [], + "source": [ + "print(\"found\", len(reaction.transitions), \"solutions!\")\n", + "reaction.get_intermediate_particles().names" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "50", + "metadata": {}, + "outputs": [], + "source": [ + "stm.set_allowed_interaction_types([InteractionType.STRONG])\n", + "problem_sets = stm.create_problem_sets()\n", + "reaction = stm.find_solutions(problem_sets)\n", + "\n", + "print(\"found\", len(reaction.transitions), \"solutions!\")\n", + "reaction.get_intermediate_particles().names" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "51", + "metadata": {}, + "outputs": [], + "source": [ + "stm.set_allowed_interaction_types([InteractionType.STRONG, InteractionType.EM])\n", + "problem_sets = stm.create_problem_sets()\n", + "reaction = stm.find_solutions(problem_sets)\n", + "\n", + "print(\"found\", len(reaction.transitions), \"solutions!\")\n", + "reaction.get_intermediate_particles().names" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "52", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.3" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/docs/reaction.md b/docs/reaction.md new file mode 100644 index 0000000..17f3519 --- /dev/null +++ b/docs/reaction.md @@ -0,0 +1,73 @@ +# Reaction and Models + + + + +## Reaction with Resonances and Decay + +The (photo-production) reaction is $ \gamma p \to \eta \pi^0 p$, its decay is described by an amplitude model with three possible resonances: $a_2$, $\Delta^+$, and $N^*$. + +```{image} https://github.com/ComPWA/compwa-org/assets/17490173/ec6bf191-bd5f-43b0-a6cb-da470b071630 +:width: 100% +``` + +## Amplitude Models + +The amplitude model is adapted from the [Lecture 11 in STRONG2020 HaSP School](https://indico.ific.uv.es/event/6803/contributions/21223/), only the Breit-Wigner and Spherical harmonics terms are kept for doing PWA eventually, as shown in equation {eq}`BW_SH_label`. + +$$ +\begin{eqnarray} +A^{12} &=& \frac{\sum a_m Y_2^m (\Omega_1)}{s-m^2_{a_2}+im_{a_2} \Gamma_{a_2}} \\ +A^{23} &=& \frac{\sum b_m Y_1^m (\Omega_2)}{s-m^2_{\Delta}+im_{\Delta} \Gamma_{\Delta}} \\ +\ +A^{31} &=& \frac{c_0}{s-m^2_{N^*}+im_{N^*} \Gamma_{N^*}} +\end{eqnarray} +$$ (BW_SH_label) + +where s is the Mandelstam variable, m is the mass, $\Gamma$ is the width, $Y^m_l$ is the spherical harmonics, $\Omega_i$ is the decay angles (a pair of Euler angles), and $a_i$, $b_i$, and $c_i$ are coefficients + +:::{note} +Mandelstam variables $s_{ij}=(p_i+p_j)^2$, $t_i=(p_a-p_i)^2$, and $u_i=(p_b-p_i)^2$. +::: + +with intensity $I$ and amplitude $A$: + + +$$ + +\begin{eqnarray} +I &=& |A|^2 \nonumber \\ +A &=& A^{12} + A^{23} + A^{31} \\ +\end{eqnarray} + +$$ +(123_label) + +where $\quad 1 \equiv \eta ; \quad 2 \equiv \pi^0 ; \quad 3 \equiv p$ + +:::{note} +The choice of the amplitude model (equations (1) and (2)) for PWA in this tutorial consists of three resonances, and each of them are formed by two terms: Breit-Wigner with Spherical harmonics ($l = 2, 1, 0$). +::: + +:::{important} +The spin of $\eta$ meson and $\pi^0$ meson are all 0. But the spin of proton is not 0, it is spin-$\frac{1}{2}$. + +In this amplitude model **spin** of baryon is simplified (not realistic): +$\eta$, $\pi^0$ and $p$ are all treated as spin-0 particles. + +This means that total intrinsic spin $s$ is ignored in this model, +the total angular momentum +$J$ of the system or any subsystems within this model will solely depend on the orbital angular momentum +$L$, characterized by quantum number $l$. +And this simplifies the use of spherical harmonics $Y_l^m(\theta,\phi)$, +since only the orbital angular momentum component is involved, and thus the combination of contribution is not considered (e.g. Clebsch-Gordan Coefficients). + +In our case: +- $A^{12}$ amplitude represents a d-wave interaction, as indicated by $l=2$. + - The possible $m$ values are $−2,−1,0,1,2$. Each of these values corresponds to different orientations of the d-wave. The wave type is solely determined by $l$ and all these $m$ values still describe d-wave characteristics. +- $A^{23}$ amplitude represents a p-wave interaction, as indicated by $l=1$. + - The possible $m$ values are $−1,0,1$. Each of these values corresponds to different orientations of the p-wave. Similarly, these values are all p-wave orientations. +- $A^{31}$ amplitude represents a s-wave interaction, as indicated by $l=0$. + - The only possible $m$ value is 0, which is consistent with the spherical symmetry of s-waves. +::: +$$ diff --git a/pixi.lock b/pixi.lock index a1a853c..6e93627 100644 --- a/pixi.lock +++ b/pixi.lock @@ -9,6 +9,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/accessible-pygments-0.0.4-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/alabaster-0.7.16-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/ampform-0.15.4-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.3.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/argon2-cffi-23.1.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-21.2.0-py312h98912ed_4.conda @@ -38,8 +39,9 @@ environments: - 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pkg:pypi/uri-template size: 23999 timestamp: 1688655976471 - kind: conda @@ -4488,6 +5226,8 @@ packages: - python >=3.7 license: MIT license_family: MIT + purls: + - pkg:pypi/urllib3 size: 94669 timestamp: 1708239595549 - kind: conda @@ -4505,6 +5245,8 @@ packages: - python_abi 3.12.* *_cp312 license: BSD-3-Clause license_family: BSD + purls: + - pkg:pypi/uvicorn size: 126964 timestamp: 1710932152563 - kind: conda @@ -4522,6 +5264,9 @@ packages: - platformdirs <5,>=3.9.1 - python >=3.8 license: MIT + license_family: MIT + purls: + - pkg:pypi/virtualenv size: 3458445 timestamp: 1715681264937 - kind: conda @@ -4539,6 +5284,8 @@ packages: - python_abi 3.12.* *_cp312 license: MIT license_family: MIT + purls: + - pkg:pypi/watchfiles size: 1094669 timestamp: 1701078026995 - kind: conda @@ -4554,6 +5301,8 @@ packages: - python >=3.8 license: MIT license_family: MIT + purls: + - pkg:pypi/wcwidth size: 32709 timestamp: 1704731373922 - kind: conda @@ -4569,6 +5318,8 @@ packages: - python >=3.5 license: BSD-3-Clause license_family: BSD + purls: + - pkg:pypi/webcolors size: 18186 timestamp: 1679900907305 - kind: conda @@ -4585,6 +5336,8 @@ packages: - python >=2.6 license: BSD-3-Clause license_family: BSD + purls: + - pkg:pypi/webencodings size: 15600 timestamp: 1694681458271 - kind: conda @@ -4600,6 +5353,8 @@ packages: - python >=3.8 license: Apache-2.0 license_family: APACHE + purls: + - pkg:pypi/websocket-client size: 47066 timestamp: 1713923494501 - kind: conda @@ -4616,8 +5371,45 @@ packages: - python_abi 3.12.* *_cp312 license: BSD-3-Clause license_family: BSD + purls: + - pkg:pypi/websockets size: 201426 timestamp: 1697914826988 +- kind: conda + name: widgetsnbextension + version: 4.0.10 + build: pyhd8ed1ab_0 + subdir: noarch + noarch: python + url: https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-4.0.10-pyhd8ed1ab_0.conda + sha256: 981b06c76a1a86bb84be09522768be0458274926b22f4b0225dfcdd30a6593e0 + md5: 521f489e3babeddeec638c2add7e9e64 + depends: + - python >=3.7 + license: BSD-3-Clause + license_family: BSD + purls: + - pkg:pypi/widgetsnbextension + size: 886369 + timestamp: 1707420479741 +- kind: conda + name: wrapt + version: 1.16.0 + build: py312h98912ed_0 + subdir: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/wrapt-1.16.0-py312h98912ed_0.conda + sha256: dc8431b343961347ad93b33d2d8270e8c15d8825382f4f2540835c94aba2de05 + md5: fa957a1c7bee7e47ad44633caf7be8bc + depends: + - libgcc-ng >=12 + - python >=3.12,<3.13.0a0 + - python_abi 3.12.* *_cp312 + license: BSD-2-Clause + license_family: BSD + purls: + - pkg:pypi/wrapt + size: 62482 + timestamp: 1699532968076 - kind: conda name: xorg-kbproto version: 1.0.7 @@ -4818,12 +5610,12 @@ packages: - kind: conda name: zeromq version: 4.3.5 - build: h75354e8_3 - build_number: 3 + build: h75354e8_4 + build_number: 4 subdir: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.5-h75354e8_3.conda - sha256: c2f2db5d19b603546db025b47fb71765f8dda0a0fe8feb42bd4e6a46194a5590 - md5: 1b0ea5d6674e4e7dde0537c890813edb + url: https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.5-h75354e8_4.conda + sha256: bc9aaee39e7be107d7daff237435dfd8f791aca460a98583a36a263615205262 + md5: 03cc8d9838ad9dd0060ab532e81ccb21 depends: - krb5 >=1.21.2,<1.22.0a0 - libgcc-ng >=12 @@ -4831,8 +5623,8 @@ packages: - libstdcxx-ng >=12 license: MPL-2.0 license_family: MOZILLA - size: 351803 - timestamp: 1714545110790 + size: 353229 + timestamp: 1715607188837 - kind: conda name: zipp version: 3.17.0 @@ -4846,6 +5638,8 @@ packages: - python >=3.8 license: MIT license_family: MIT + purls: + - pkg:pypi/zipp size: 18954 timestamp: 1695255262261 - kind: conda diff --git a/pixi.toml b/pixi.toml index fd94169..a6442bd 100644 --- a/pixi.toml +++ b/pixi.toml @@ -20,25 +20,28 @@ sphinx-autobuild \ """ [dependencies] +ampform = ">=0.15.4,<0.16" black = ">=24.4.2,<24.5" +graphviz = ">=9.0.0,<9.1" +ipython = ">=8.24.0,<8.25" +ipywidgets = ">=8.1.2,<8.2" isort = ">=5.13.2,<5.14" jax = ">=0.4.26,<0.5" jaxlib = ">=0.4.23,<0.5" +jupyter = ">=1.0.0,<1.1" jupyterlab = ">=4.2.0,<4.3" jupyterlab-git = ">=0.50.0,<0.51" jupyterlab-lsp = ">=5.1.0,<5.2" jupyterlab-myst = ">=2.4.2,<2.5" -linkify-it-py = ">=2.0.3,<2.1" +jupyterlab_code_formatter = ">=2.2.1,<2.3" myst-nb = ">=1.1.0,<1.2" -myst-parser = ">=3.0.1,<3.1" -nbsphinx = ">=0.9.4,<0.10" numpy = ">=1.26.4,<1.27" pre-commit = ">=3.7.1,<3.8" pydata-sphinx-theme = ">=0.15.2,<0.16" python = ">=3.12.3,<3.13" python-graphviz = ">=0.20.3,<0.21" +qrules = ">=0.10.1,<0.11" scipy = ">=1.13.0,<1.14" -sphinx = ">=7.3.7,<7.4" sphinx-autobuild = ">=2024.4.16,<2024.5" -sphinx_rtd_theme = ">=2.0.0,<2.1" +sphinx-book-theme = ">=1.1.2,<1.2" sympy = ">=1.12,<2" From 418daad85cf667ea89efca56e4851105031f3435 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:38:07 +0200 Subject: [PATCH 60/61] remove cell timeout and print traceback --- docs/conf.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/conf.py b/docs/conf.py index 70fccf8..c04ca7d 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -15,5 +15,7 @@ "html_image", "smartquotes", ] +nb_execution_show_tb = True +nb_execution_timeout = -1 nitpicky = True project = "GlueX N-Star" From 7fee9c9a97b6dd64ea06c6a855314caee0218ae2 Mon Sep 17 00:00:00 2001 From: Vitor Shen <17490173+shenvitor@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:45:23 +0200 Subject: [PATCH 61/61] move html output to RTD location --- .readthedocs.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 7b03d88..c8e09ae 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -7,3 +7,4 @@ build: - mamba install -c conda-forge -c nodefaults pixi - pixi install - pixi run docnb + - pixi run "rm -rf $READTHEDOCS_OUTPUT/html && cp -r docs/_build/html $READTHEDOCS_OUTPUT/html"