diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..69e650b --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,10 @@ +version: 2 +build: + os: ubuntu-22.04 + tools: + python: "3.12" +mkdocs: + configuration: mkdocs.yml +python: + install: + - requirements: requirements/requirements-docs.txt diff --git a/README.md b/README.md index d348ed9..0b4d38d 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ `geofetch` is a command-line tool that downloads sequencing data and metadata from GEO and SRA and creates [standard PEPs](https://pep.databio.org/). `geofetch` is hosted at [pypi](https://pypi.org/project/geofetch/). You can convert the result of geofetch into unmapped `bam` or `fastq` files with the included `sraconvert` command. -Key geofetch features: +## Key geofetch features: - Works with GEO and SRA metadata - Combines samples from different projects diff --git a/docs/README.md b/docs/README.md index 936da43..1976829 100644 --- a/docs/README.md +++ b/docs/README.md @@ -14,7 +14,7 @@ ![](./img/pipeline.svg) -Key geofetch advantages: +## Key geofetch advantages: - Works with GEO and SRA metadata - Combines samples from different projects diff --git a/docs/img/meta_integration.svg b/docs/img/meta_integration.svg index 63368e9..4bb0024 100644 --- a/docs/img/meta_integration.svg +++ b/docs/img/meta_integration.svg @@ -2,14 +2,14 @@ .fil1 {fill:none} .fil0 {fill:black} .fil0 {fill:#000000;fill-rule:nonzero} .fil1 {fill:none} .fil0 {fill:black} .fil1 {fill:none} .fil0 {fill:black} .fil1 {fill:none} .fil0 {fill:black} .fil1 {fill:none} .fil0 {fill:black} .fil0 {fill:#000000;fill-rule:nonzero} .fil1 {fill:none} .fil0 {fill:black} .fil0 {fill:black} .fil0 {fill:black} .fil1 {fill:none} .fil0 {fill:black} .fil0 {fill:#000000;fill-rule:nonzero} .fil1 {fill:none} .fil0 {fill:black} .fil0 {fill:#000000;fill-rule:nonzero} .fil1 {fill:none} .fil0 {fill:black} .fil1 {fill:none} .fil0 {fill:black} .fil1 {fill:none} .fil0 {fill:black} .fil0 {fill:#000000;fill-rule:nonzero} .fil1 {fill:none} .fil0 {fill:black} .fil0 {fill:black} .fil0 {fill:black} .fil1 {fill:none} .fil0 {fill:black} .fil0 {fill:#000000;fill-rule:nonzero} - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Integration of multiple project GSE1GSE2GSE3geofetch GEO projects PEP Integration of multiple GEO projects GSE1GSE2GSE3GEO projects PortableEncapsulatedProject + type="text/css"> .st0{fill:#000000;} .st1{fill:#000000;} diff --git a/docs/img/pipeline.svg b/docs/img/pipeline.svg index ef4d501..e411359 100644 --- a/docs/img/pipeline.svg +++ b/docs/img/pipeline.svg @@ -9,7 +9,7 @@ id="svg5" xml:space="preserve" sodipodi:docname="pipeline.svg" - inkscape:version="1.2 (1:1.2+202206011327+fc4e4096c5)" + inkscape:version="1.3 (1:1.3+202307231459+0e150ed6c4)" xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape" xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd" xmlns:xlink="http://www.w3.org/1999/xlink" @@ -28,9 +28,9 @@ inkscape:zoom="1.237125" inkscape:cx="301.50551" inkscape:cy="193.59402" - inkscape:window-width="1848" - inkscape:window-height="1016" - inkscape:window-x="72" + inkscape:window-width="2488" + inkscape:window-height="1343" + inkscape:window-x="1272" inkscape:window-y="27" inkscape:window-maximized="1" inkscape:current-layer="layer1" @@ -159,19 +159,9 @@ stop-opacity="1" id="stop14" /> .fil1 {fill:none} .fil0 {fill:black} .fil0 {fill:#000000;fill-rule:nonzero} .fil1 {fill:none} .fil0 {fill:black} .fil1 {fill:none} .fil0 {fill:black} .fil1 {fill:none} .fil0 {fill:black} .fil1 {fill:none} .fil0 {fill:black} .fil0 {fill:#000000;fill-rule:nonzero} .fil1 {fill:none} .fil0 {fill:black} .fil0 {fill:black} .fil0 {fill:black} .fil1 {fill:none} .fil0 {fill:black} .fil0 {fill:#000000;fill-rule:nonzero} .fil0 {fill:#000000;fill-rule:nonzero} geofetchgeofetch + type="text/css"> .st0{fill:#000000;} .st1{fill:#000000;}