Merge branch 'master' into master

recipes/rdeval/Makefile.patch

@@ -1,24 +1,25 @@
+diff --git a/Makefile b/Makefile
+index 7ec8f12..d81d842 100644
 --- a/Makefile
 +++ b/Makefile
-@@ -12,7 +12,12 @@
+@@ -12,7 +12,11 @@ SOURCE = src
  INCLUDE = include
  BINDIR := $(BUILD)/.o
 
--LDFLAGS := -pthread
+-LDFLAGS += -pthread
 +ifeq ($(origin LDFLAGS), undefined)
-+    LDFLAGS := -pthread
++	LDFLAGS := -pthread
 +else
-+    LDFLAGS := $(LDFLAGS) -pthread
++	LDFLAGS := $(LDFLAGS) -pthread
 +endif
-+
- LIBS = -lz
+ LIBS = -lz -lcrypto -lhts
 
  OBJS := main input reads
-@@ -27,7 +32,7 @@
+@@ -27,7 +31,7 @@ head: $(BINS) gfalibs | $(BUILD)
  all: head validate regenerate
 
  $(BINDIR)%: $(SOURCE)/%.cpp $(INCLUDE)/%.h | $(BINDIR)
--	$(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@
+-	$(CXX) $(CXXFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@
 +	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@
 
  .PHONY: gfalibs

recipes/rdeval/build.sh

@@ -1,22 +1,22 @@
-#!/usr/bin/env bash
+#!/usr/bin/bash
 
 set -o errexit
 set -o nounset
 
 if [ -e "$PREFIX/include" ]; then
-    export CPPFLAGS="${CPPFLAGS:+$CPPFLAGS }-I$PREFIX/include"
+    export CPPFLAGS="${CPPFLAGS:+$CPPFLAGS }-I${PREFIX}/include"
 fi
 
 if [ -e "$PREFIX/lib" ]; then
-    export LDFLAGS="${LDFLAGS:+$LDFLAGS }-L$PREFIX/lib"
+    export LDFLAGS="${LDFLAGS:+$LDFLAGS }-L${PREFIX}/lib"
 fi
 
 echo "CPPFLAGS=\"$CPPFLAGS\""
 echo "LDFLAGS=\"$LDFLAGS\""
 
 cd "$SRC_DIR"
 
-make
+make CXX="${CXX}" CPPFLAGS="${CPPFLAGS}" -j"${CPU_COUNT}"
 
 install -d "$PREFIX/bin"
-install -v -m 0755 build/bin/rdeval "$PREFIX/bin/"
+install -v -m 0755 build/bin/rdeval "$PREFIX/bin"

recipes/rdeval/gfalibs-Makefile.patch

@@ -1,24 +1,25 @@
+diff --git a/gfalibs/Makefile b/gfalibs/Makefile
+index 3c2f269..c71a817 100644
 --- a/gfalibs/Makefile
 +++ b/gfalibs/Makefile
 @@ -1,4 +1,4 @@
--CXX = g++
-+CXX ?= g++
- INCLUDE_DIR = -I./include
+-CXX ?= g++
++CXX ?= $(CXX)
+ INCLUDE_DIR += -I./include
  WARNINGS = -Wall -Wextra
 
-@@ -8,15 +8,13 @@
+@@ -8,14 +8,13 @@ TARGET = gfalibs
  BUILD = build/bin
  SOURCE = src
  INCLUDE = include
--LDFLAGS :=
+-LDFLAGS =
 
  SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory)
 
  all: $(SOURCES)
--	@
 
  %.o: $(SOURCE)/%.cpp $(INCLUDE)/%.h
--	$(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@
+-	$(CXX) $(CXXFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@
 +	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@
 
  clean:

recipes/rdeval/meta.yaml

@@ -1,19 +1,19 @@
 {% set name = "rdeval" %}
-{% set version = "0.0.2" %}
+{% set version = "0.0.3" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://github.com/vgl-hub/{{ name }}/releases/download/v{{ version }}/{{ name }}.v{{ version }}-with_submodules.zip
-  sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d
+  sha256: bd8fd59c98aed5fdbb8930207c3ecd9351f6345c26495e762bcc3c274fdba701
   patches:
     - Makefile.patch
     - gfalibs-Makefile.patch
 
 build: 
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage(name|lower, max_pin="x.x") }}
 
@@ -23,6 +23,11 @@ requirements:
     - make
   host:
     - zlib
+    - htslib
+    - openssl
+  run:
+    - htslib
+    - openssl
 
 test:
   commands:

recipes/stripepy-hic/meta.yaml

@@ -0,0 +1,63 @@
+{% set name = "stripepy-hic" %}
+{% set version = "0.0.2" %}
+{% set sha256 = "4e0e14f365334095b9af04874b01bae25fb385560add5f6f0bc91b35f757e556" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name|replace("-", "_") }}/{{ name|replace("-", "_") }}-{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  noarch: python
+  entry_points:
+    - stripepy = stripepy:main
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -v"
+  run_exports:
+    - {{ pin_subpackage('stripepy-hic', max_pin="x.x") }}
+
+requirements:
+  host:
+    - python >=3.9
+    - pip
+    - hatchling
+    - hatch-vcs
+  run:
+    - h5py >=3
+    - hictkpy >=1
+    - matplotlib-base >=3.8
+    - numpy
+    - pandas >=2
+    - scikit-learn
+    - scipy
+    - seaborn-base >=0.13
+
+about:
+  home: https://github.com/paulsengroup/StripePy
+  license: MIT
+  license_file: LICENCE
+  summary: "StripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoning"
+  dev_url: https://github.com/paulsengroup/StripePy
+  doc_url: https://github.com/paulsengroup/StripePy/blob/main/README.md
+
+test:
+  requires:
+    - curl
+    - perl-digest-md5
+    - pytest>=8
+  source_files:
+    - test/*
+  imports:
+    - stripepy
+
+extra:
+  recipe-maintainers:
+    - robomics
+    - rea1991
+    - jonnings
+  identifiers:
+    - biotools:stripepy-hic
+    - doi:10.5281/zenodo.14394041

recipes/stripepy-hic/run_test.sh

@@ -0,0 +1,21 @@
+#!/usr/bin/env bash
+
+# Download test datasets
+mkdir -p test/data
+
+curl -L 'https://zenodo.org/records/14517632/files/4DNFI9GMP2J8.stripepy.mcool?download=1' -o test/data/4DNFI9GMP2J8.mcool
+curl -L 'https://zenodo.org/records/14517632/files/results_4DNFI9GMP2J8_v1.hdf5?download=1' -o test/data/results_4DNFI9GMP2J8_v1.hdf5
+
+# Checksum datasets
+echo 'a17d08460c03cf6c926e2ca5743e4888  test/data/4DNFI9GMP2J8.mcool' > checksums.md5
+echo '632b2a7a6e5c1a24dc3635710ed68a80  test/data/results_4DNFI9GMP2J8_v1.hdf5' >> checksums.md5
+
+md5sum -c checksums.md5
+
+# Test CLI
+stripepy --help
+stripepy --version
+
+# Run automated test suites
+"$PYTHON" -m pytest test/ -m unit -v --disable-pytest-warnings
+"$PYTHON" -m pytest test/ -m end2end -v -k 'not TestStripePyPlot' --disable-pytest-warnings