Merge branch 'porechop_dep' into 'dev'

drop porechop dependency See merge request research/pomoxis!171
nanoporetech · Dec 19, 2023 · d5b7ca3 · d5b7ca3
2 parents 9fb7c49 + ab60053
commit d5b7ca3
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,9 +4,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [v0.3.15] - 2023-12-2023
+## [v0.3.15] - 2023-12-18
 ### Added
 - `mini_align` can take a bam as input and optionally retain all or subset of bam tags. 
+### Changed
+- Drop porechop dependency from pypi package due to blocking package uploads. Add warning to the user if porechop is called by `mini_assemble` but does not exist.
 
 ## [v0.3.14] - 2023-10-25
 ### Changed

diff --git a/requirements.txt b/requirements.txt
@@ -7,4 +7,3 @@ ncls
 numpy
 pandas
 pysam >= 0.15.4
-porechop @ git+https://github.com/artic-network/porechop
diff --git a/scripts/mini_assemble b/scripts/mini_assemble
@@ -78,6 +78,14 @@ if $eflag && [[ $ERRCORR = *x ]]; then
 fi
 
 
+if $CHOP && [[ ! $(command -v porechop) ]]; then
+  echo "-c requires porechop to be installed.";
+  echo "Run `pip install git+https://github.com/artic-network/porechop` or"
+  echo "`conda install -c bioconda artic-porechop`"
+  exit 1;
+fi
+
+
 if $xflag; then
   set -x;
 fi
-Original file line number
+Diff line change
@@ Expand Up / @@ -7,4 +7,3 @@ ncls @@
     numpy
     pandas
     pysam >= 0.15.4
-    porechop @ git+https://github.com/artic-network/porechop