From 540f85e0f49a7590212e8a7ff38eb8b50f2cbaac Mon Sep 17 00:00:00 2001 From: Vijini Mallawaarachchi Date: Mon, 26 Aug 2024 16:51:31 +0930 Subject: [PATCH] DOC: Setup read the docs to fix #9 --- .readthedocs.yaml | 20 ++++++++++++++++++++ docs/index.md | 3 +++ docs/requirements.txt | 18 ++++++++++++++++++ mkdocs.yml | 16 ++++++++++++++++ 4 files changed, 57 insertions(+) create mode 100644 .readthedocs.yaml create mode 100644 docs/index.md create mode 100644 docs/requirements.txt create mode 100644 mkdocs.yml diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..6dfb51f --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,20 @@ +# .readthedocs.yaml +# Read the Docs configuration file for MkDocs projects +# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + +# Required +version: 2 + +# Set the version of Python and other tools you might need +build: + os: ubuntu-22.04 + tools: + python: "3.12" + +mkdocs: + configuration: mkdocs.yml + +# Optionally declare the Python requirements required to build your docs +python: + install: + - requirements: docs/requirements.txt \ No newline at end of file diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..0b17995 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,3 @@ +# Reneo + +[Reneo](https://en.wiktionary.org/wiki/reneo) means to *unravel* or *untangle* in Latin. Reneo is a software developed to unravel or untangle high-quality genomes from viral communities (including both prokaryotic and eukaryotic viruses) found within metagenomes using assembly graphs. Reneo identifies viral components in the metagenomic assembly using virus orthologous groups from [VOGDB](https://vogdb.org/), models as flow networks and solves a minimum flow decomposition (MFD) problem to resolve genomic paths. Reneo was motivated based on a bacteriophage recovery tool named [Phables](https://github.com/Vini2/phables), specifically to extend the capabilities of Phables to all viruses. \ No newline at end of file diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..29f7de3 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,18 @@ +jinja2==3.1.4 +mkdocs>=1.3.1 +babel>=2.9.0 +click>=7.0 +Jinja2>=2.10.2 +Markdown>=3.2.1,<3.4 +PyYAML>=5.2 +watchdog>=2.0.0 +mdx_gh_links>=0.2 +ghp-import>=1.0 +pyyaml_env_tag>=0.1 +mkdocs-redirects>=1.0.1 +importlib_metadata>=4.3 +packaging>=20.5 +mergedeep>=1.3.4 +pygments>=2.12 +pymdown-extensions +mkdocs-material \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..140214f --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,16 @@ +site_name: Reneo +site_url: "https://github.com/Vini2/reneo" +site_author: "Vijini Mallawaarachchi" +repo_url: "https://github.com/Vini2/reneo" +repo_name: 'GitHub' +theme: + name: readthedocs + highlightjs: true + hljs_languages: + - yaml + - bash + - shell + - text +nav: + - Home: + - Introduction: index.md \ No newline at end of file