From 1588feb36af4ee44d25ff7781dce590337a53637 Mon Sep 17 00:00:00 2001 From: zethson Date: Fri, 17 Nov 2023 17:10:54 +0100 Subject: [PATCH 1/4] Add notebook to sphinx Signed-off-by: zethson --- docs/requirements.txt | 1 + docs/source/conf.py | 6 ++++-- notebook.ipynb => docs/source/hadge_output.ipynb | 9 ++++++++- 3 files changed, 13 insertions(+), 3 deletions(-) rename notebook.ipynb => docs/source/hadge_output.ipynb (99%) diff --git a/docs/requirements.txt b/docs/requirements.txt index db72b7b..92e893c 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,3 +1,4 @@ sphinx +nb-sphinx myst-parser furo diff --git a/docs/source/conf.py b/docs/source/conf.py index 779af44..e314080 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -3,7 +3,8 @@ author = 'Fabiola Curion, Xichen Wu, Lukas Heumos' release = '1.0.0' -extensions = ['myst_parser'] +extensions = ['myst_parser', + 'nbsphinx'] source_suffix = { '.rst': 'restructuredtext', @@ -16,5 +17,6 @@ exclude_patterns = [] html_theme = "furo" +html_static_path = ['_static'] -html_static_path = ['_static'] \ No newline at end of file +nbsphinx_execute = 'never' diff --git a/notebook.ipynb b/docs/source/hadge_output.ipynb similarity index 99% rename from notebook.ipynb rename to docs/source/hadge_output.ipynb index ecd6e92..ac881e7 100644 --- a/notebook.ipynb +++ b/docs/source/hadge_output.ipynb @@ -1,5 +1,12 @@ { "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Working with hadge output" + ] + }, { "cell_type": "code", "execution_count": 1, @@ -16,7 +23,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "This notebook serves to get familiar with the ouput of hadge and reproduce some figures from the manuscript." + "This notebook serves to get familiar with the output of hadge and reproduce some figures from the manuscript." ] }, { From 0f99fd89d789eafdcc334f856f2e3e6ee7dcbc34 Mon Sep 17 00:00:00 2001 From: zethson Date: Fri, 17 Nov 2023 17:11:52 +0100 Subject: [PATCH 2/4] Fix nbsphinx requirements Signed-off-by: zethson --- docs/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 92e893c..2b919fd 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,4 +1,4 @@ sphinx -nb-sphinx +nbsphinx myst-parser furo From 45c5db7a93148cf4e433657d96a58e1f509b7377 Mon Sep 17 00:00:00 2001 From: zethson Date: Fri, 17 Nov 2023 17:19:41 +0100 Subject: [PATCH 3/4] Pandoc pls Signed-off-by: zethson --- docs/source/conf.py | 2 +- docs/source/index.md | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index e314080..5678883 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -14,7 +14,7 @@ templates_path = ['_templates'] -exclude_patterns = [] +exclude_patterns = ['_build', '**.ipynb_checkpoints'] html_theme = "furo" html_static_path = ['_static'] diff --git a/docs/source/index.md b/docs/source/index.md index fb0656e..6d74528 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -56,7 +56,7 @@ nextflow run main.nf -profile test ## Notebook -Check[](../../notebook.ipynb) to get familiar with the output of hadge. +Check[](hadge_output.ipynb) to get familiar with the output of hadge. ## **Pipeline output** @@ -98,6 +98,7 @@ general genetic hashing rescue +hadge_output ``` # Indices and tables From 9bcebac0931c1a76e529e23a56a19f3e0b49e1c9 Mon Sep 17 00:00:00 2001 From: zethson Date: Fri, 17 Nov 2023 17:21:31 +0100 Subject: [PATCH 4/4] Remove docs wf Signed-off-by: zethson --- .github/workflows/build_docs.yml | 22 ---------------------- 1 file changed, 22 deletions(-) delete mode 100644 .github/workflows/build_docs.yml diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml deleted file mode 100644 index e0c9ef6..0000000 --- a/.github/workflows/build_docs.yml +++ /dev/null @@ -1,22 +0,0 @@ -name: sphinx-docs - -on: - push: - pull_request: - -jobs: - build: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v2 - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: "3.11" - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install -r docs/requirements.txt - - - name: Build documentation - run: cd docs && make html