Update screenshots

README.md

@@ -37,5 +37,5 @@ Bioengineering 2021, 8, 59. [doi.org/10.3390/bioengineering8050059](https://doi.
 
 ## Splash screen
 
-![`seqfu`](docs/img/screenshot-seqfu.svg "SeqFu")
+![`seqfu`](docs/img/screenshot-seqfu.png "SeqFu")
 

screenshots.md

@@ -2,95 +2,95 @@
 
 ## count
 
-![`seqfu count --help`](docs/img/screenshot-count.svg "SeqFu count")
+![`seqfu count --help`](docs/img/screenshot-count.png "SeqFu count")
 
 ## stats
 
-![`seqfu stats --help`](docs/img/screenshot-stats.svg "SeqFu stats")
+![`seqfu stats --help`](docs/img/screenshot-stats.png "SeqFu stats")
 
 ## derep
 
-![`seqfu derep --help`](docs/img/screenshot-derep.svg "SeqFu derep")
+![`seqfu derep --help`](docs/img/screenshot-derep.png "SeqFu derep")
 
 ## interleave
 
-![`seqfu interleave --help`](docs/img/screenshot-interleave.svg "SeqFu interleave")
+![`seqfu interleave --help`](docs/img/screenshot-interleave.png "SeqFu interleave")
 
 ## deinterleave
 
-![`seqfu deinterleave --help`](docs/img/screenshot-deinterleave.svg "SeqFu deinterleave")
+![`seqfu deinterleave --help`](docs/img/screenshot-deinterleave.png "SeqFu deinterleave")
 
 ## metadata
 
-![`seqfu metadata --help`](docs/img/screenshot-metadata.svg "SeqFu metadata")
+![`seqfu metadata --help`](docs/img/screenshot-metadata.png "SeqFu metadata")
 
 ## cat
 
-![`seqfu cat --help`](docs/img/screenshot-cat.svg "SeqFu cat")
+![`seqfu cat --help`](docs/img/screenshot-cat.png "SeqFu cat")
 
 ## grep
 
-![`seqfu grep --help`](docs/img/screenshot-grep.svg "SeqFu grep")
+![`seqfu grep --help`](docs/img/screenshot-grep.png "SeqFu grep")
 
 ## head
 
-![`seqfu head --help`](docs/img/screenshot-head.svg "SeqFu head")
+![`seqfu head --help`](docs/img/screenshot-head.png "SeqFu head")
 
 ## tail
 
-![`seqfu tail --help`](docs/img/screenshot-tail.svg "SeqFu tail")
+![`seqfu tail --help`](docs/img/screenshot-tail.png "SeqFu tail")
 
 ## view
 
-![`seqfu view --help`](docs/img/screenshot-view.svg "SeqFu view")
-![`seqfu view data/primers/small.fq -o CCTACGGGAG -r ATGAGCGTCTCG`](docs/img/screenshot-view-example.svg "SeqFu view example")
+![`seqfu view --help`](docs/img/screenshot-view.png "SeqFu view")
+![`seqfu view data/primers/small.fq -o CCTACGGGAG -r ATGAGCGTCTCG`](docs/img/screenshot-view-example.png "SeqFu view example")
 
 seqfu view data/qualities.fq
 
-![`seqfu view data/qualities.fq`](docs/img/screenshot-view-qual.svg "SeqFu view qualities")
+![`seqfu view data/qualities.fq`](docs/img/screenshot-view-qual.png "SeqFu view qualities")
 
 seqfu view --ascii data/qualities.fq
 
-![`seqfu view --ascii data/qualities.fq`](docs/img/screenshot-view-qual-ascii.svg "SeqFu view qualities")
+![`seqfu view --ascii data/qualities.fq`](docs/img/screenshot-view-qual-ascii.png "SeqFu view qualities")
 
 seqfu view --qual-chars data/qualities.fq
-![`seqfu view --qual-chars data/qualities.fq`](docs/img/screenshot-view-raw.svg "SeqFu view encoded quality")
+![`seqfu view --qual-chars data/qualities.fq`](docs/img/screenshot-view-raw.png "SeqFu view encoded quality")
 
 ## rc
 
-![`seqfu rc --help`](docs/img/screenshot-rc.svg "SeqFu rc")
+![`seqfu rc --help`](docs/img/screenshot-rc.png "SeqFu rc")
 
 ## tab
 
-![`seqfu tab --help`](docs/img/screenshot-tab.svg "SeqFu tab")
+![`seqfu tab --help`](docs/img/screenshot-tab.png "SeqFu tab")
 
 ## lanes
 
-![`seqfu lanes --help`](docs/img/screenshot-lanes.svg "SeqFu lanes")
+![`seqfu lanes --help`](docs/img/screenshot-lanes.png "SeqFu lanes")
 
 ## rotate
 
-![`seqfu rotate --help`](docs/img/screenshot-rotate.svg "SeqFu rotate")
+![`seqfu rotate --help`](docs/img/screenshot-rotate.png "SeqFu rotate")
 
 ## fu-orf
 
-![`fu-orf --help`](docs/img/screenshot-fu-orf.svg "SeqFu fu-orf")
+![`fu-orf --help`](docs/img/screenshot-fu-orf.png "SeqFu fu-orf")
 
 ## fu-nanotags
 
-![`fu-nanotags --help`](docs/img/screenshot-fu-nanotags.svg "SeqFu fu-nanotags")
+![`fu-nanotags --help`](docs/img/screenshot-fu-nanotags.png "SeqFu fu-nanotags")
 
 
 ## fu-split
 
-![`pwd && find .. -name "msa.*"`](docs/img/screenshot-ls.svg "Find MSA")
+![`pwd && find .. -name "msa.*"`](docs/img/screenshot-ls.png "Find MSA")
 
 ## fu-split
 
-![`fu-split --help`](docs/img/screenshot-fu-split.svg "SeqFu split")
+![`fu-split --help`](docs/img/screenshot-fu-split.png "SeqFu split")
 
 ## fu-msa
 
-![`fu-msa ./data/msa.fa --screenshot`](docs/img/screenshot-fu-msa-1.svg "SeqFu MSA viewer")
+![`fu-msa ./data/msa.fa --screenshot`](docs/img/screenshot-fu-msa-1.png "SeqFu MSA viewer")
 
-![`fu-msa ./data/msa.faa --screenshot`](docs/img/screenshot-fu-msa-2.svg "SeqFu MSA viewer")
+![`fu-msa ./data/msa.faa --screenshot`](docs/img/screenshot-fu-msa-2.png "SeqFu MSA viewer")

test/README.md

@@ -1,6 +0,0 @@
-# Testing
-
-![`echo $PATH | sed 's/:/\n/g'`](../docs/img/debug-1.svg)
-![`echo $HOME`](../docs/img/debug-nim.svg)
-![`pwd`](../docs/img/debug-2.svg)
-![`find /home/ -name "seqfu"`](../docs/img/debug-3.svg)

test/screenshot.sh

@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+# Automate screeshots with termshot
+
+# Check if termshot is available
+if ! command -v termshot &> /dev/null
+then
+    echo "termshot could not be found"
+    echo "Install it with:"
+    echo "brew install homeport/tap/termshot"
+    exit
+fi
+echo "termshot found, continuing..."
+make
+echo "Setting up test environment..."
+export PATH=$PWD/bin:$PATH
+
+
+for PROG in cat count deinterleave derep grep head interleave lanes metadata rc rotate stats tab tail;
+do
+
+    termshot --show-cmd --filename docs/img/screenshot-${PROG}.png -- seqfu $PROG --help
+
+done
+termshot --show-cmd --filename docs/img/screenshot-seqfu.png -- seqfu
+