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;}