diff --git a/recipes/bioconda-repodata-patches/gen_patch_json.py b/recipes/bioconda-repodata-patches/gen_patch_json.py
index 34c0225e0f599..94a1c1eefe28e 100755
--- a/recipes/bioconda-repodata-patches/gen_patch_json.py
+++ b/recipes/bioconda-repodata-patches/gen_patch_json.py
@@ -175,7 +175,7 @@ def _gen_new_index(repodata, subdir):
         if record_name in ['htslib', 'staden_io_lib', 'fastp', 'pysam'] and has_dep(record, 'libdeflate'):
             # skip deps that allow anything <1.3, which contained an incompatible library filename
             # TODO adjust the replacement (exclusive) upper bound each time a compatible new libdeflate is released
-            _pin_looser(fn, record, 'libdeflate', min_lower_bound='1.3', upper_bound='1.22')
+            _pin_looser(fn, record, 'libdeflate', min_lower_bound='1.3', upper_bound='1.24')
 
         # nanosim <=3.1.0 requires scikit-learn<=0.22.1
         if record_name.startswith('nanosim') and has_dep(record, "scikit-learn") and version <= "3.1.0":
diff --git a/recipes/bioconda-repodata-patches/meta.yaml b/recipes/bioconda-repodata-patches/meta.yaml
index 0610ed44e66ce..5179e4331acad 100644
--- a/recipes/bioconda-repodata-patches/meta.yaml
+++ b/recipes/bioconda-repodata-patches/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: bioconda-repodata-patches
-  version: 20240913  # ensure that this is the "current" date, and always higher than the latest version in master
+  version: 20241219  # ensure that this is the "current" date, and always higher than the latest version in master
 
 source:
   path: .
diff --git a/recipes/drug2cell/meta.yaml b/recipes/drug2cell/meta.yaml
index 0198746f57917..b9062387784c1 100644
--- a/recipes/drug2cell/meta.yaml
+++ b/recipes/drug2cell/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "drug2cell" %}
-{% set version = "0.1.1" %}
-{% set sha256 = "f9e03762f84320bd2357c92ca576b9a67346dbaf157620a69c617841e089495a" %}
+{% set version = "0.1.2" %}
+{% set sha256 = "bf159adfc569e14ca8bb827e1f9ca4e91fa6a3cfd9239a92544de14aef58fa7b" %}
 package:
   name: {{ name|lower }}
   version: {{ version }}
diff --git a/recipes/polap/meta.yaml b/recipes/polap/meta.yaml
index ddf1a4d5eb7db..18a00e9786dba 100644
--- a/recipes/polap/meta.yaml
+++ b/recipes/polap/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "polap" %}
-{% set version = "0.3.7.3" %}
-{% set sha256 = "755ff93913c687c01a32bdd434bd5fcfeb73ce94c7ddf19bf2304184f294d8bf" %}
+{% set version = "0.4.1.1" %}
+{% set sha256 = "127f493b40994364c58e892c63c18d63d3359a31908ea6a2ffdfc1295e62db9b" %}
 
 package:
   name: "{{ name }}"
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('polap', max_pin="x.x") }}
 
diff --git a/recipes/pypints/meta.yaml b/recipes/pypints/meta.yaml
index 28dc17c5eb35c..28795ee6e7877 100644
--- a/recipes/pypints/meta.yaml
+++ b/recipes/pypints/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "pyPINTS" %}
-{% set version = "1.1.14" %}
+{% set version = "1.1.15" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
-  url: "https://files.pythonhosted.org/packages/24/ec/8606d80f38c842c7d869c65e3bba4bb87f8a0555cfc5b4a7181c8cecdb86/pypints-1.1.14.tar.gz"
-  sha256: 6f5d40ba9a24a3bd610b9a6af746fe357053ad75757d2e0f376662917b98dc7e
+  url: "https://files.pythonhosted.org/packages/ea/29/fa53484cb5b13f992a15dba043222105b5a18340756f8d16b6b4c27b9876/pypints-1.1.15.tar.gz"
+  sha256: 3938adbaa5517d0984eaca2388d9ec121063ad560bcd5a82477c176a5dbebeef
 
 build:
   number: 0
diff --git a/recipes/rdeval/Makefile.patch b/recipes/rdeval/Makefile.patch
index b9243d5f94b5d..fd23495377e3d 100644
--- a/recipes/rdeval/Makefile.patch
+++ b/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
diff --git a/recipes/rdeval/build.sh b/recipes/rdeval/build.sh
index 3f30b2376ac7a..d1e07459b4ea3 100644
--- a/recipes/rdeval/build.sh
+++ b/recipes/rdeval/build.sh
@@ -1,14 +1,14 @@
-#!/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=\"$CPPFLAGS\""
@@ -16,7 +16,7 @@ echo "LDFLAGS=\"$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"
diff --git a/recipes/rdeval/gfalibs-Makefile.patch b/recipes/rdeval/gfalibs-Makefile.patch
index d43d6346dadaa..76cbfbd75f175 100644
--- a/recipes/rdeval/gfalibs-Makefile.patch
+++ b/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:
diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml
index a495d435df647..a3d3cb84f3772 100644
--- a/recipes/rdeval/meta.yaml
+++ b/recipes/rdeval/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "rdeval" %}
-{% set version = "0.0.2" %}
+{% set version = "0.0.3" %}
 
 package:
   name: {{ name|lower }}
@@ -7,13 +7,13 @@ package:
 
 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:
diff --git a/recipes/samshee/meta.yaml b/recipes/samshee/meta.yaml
index 9afe50f4ea404..18692374b691e 100644
--- a/recipes/samshee/meta.yaml
+++ b/recipes/samshee/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "samshee" %}
-{% set version = "0.2.5" %}
+{% set version = "0.2.8" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  url: https://files.pythonhosted.org/packages/27/21/14261b8b928cef7fe65ef58a95591472d302a2e3ad2a41ee856d5e6da153/samshee-0.2.5.tar.gz
-  sha256: 2551b75180b974e22baae120ed3b9176d03ea49aa33240335d6cdc5b91d6a08a
+  url: https://files.pythonhosted.org/packages/73/79/75f69cde91c953bf2dab2c92d324a22a02b5f6e4c742b47ccdaa14ebc377/samshee-0.2.8.tar.gz
+  sha256: 41d133b290cd8d3bf679d7c1b26f77da4e25fa7f73cf7c1e3ab401f250ee4c5b
 
 build:
   noarch: python
diff --git a/recipes/scmidas/meta.yaml b/recipes/scmidas/meta.yaml
index 2ddf1bb026882..3b6ed105b58bb 100644
--- a/recipes/scmidas/meta.yaml
+++ b/recipes/scmidas/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "scmidas" %}
-{% set version = "0.0.18" %}
+{% set version = "0.1.3" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/scmidas-{{ version }}.tar.gz
-  sha256: 62c953d679a7298a25882930098cda8c6f3055ec37b89e5306eb471edec10b3f
+  sha256: d8958200535c2feda3fa795b743c3dd4d4788cfa0544c7de2402a0c32c886102
 
 build:
   number: 0
@@ -20,21 +20,28 @@ requirements:
   host:
     - python >=3.9
     - pip
+    - setuptools
   run:
     - python >=3.9
-    - toml
+    - lightning >=2.4.0
+    - lightning-utilities >=0.11.8
+    - pytorch >=2.5.1
+    - torchaudio >=2.5.1
+    - torchmetrics >=1.5.1
+    - torchvision >=0.20.1
+    - tornado
     - tqdm
-    - numpy
-    - pytorch >1.12
+    - toml
+    - requests
+    - ipykernel
+    - anndata
+    - tensorboard
     - matplotlib-base
+    - numpy
     - pandas
-    - scikit-learn
     - scanpy
-    - louvain
-    - rpy2
-    - anndata2ri
-    - ipykernel
-    - jupyter
+    - scikit-learn
+    - scipy
 
 test:
   imports:
@@ -47,7 +54,7 @@ about:
   license_family: MIT
   license_file: LICENSE
   dev_url: https://github.com/labomics/midas
-  doc_url: https://scmidas.readthedocs.io/en/latest/
+  doc_url: https://scmidas.readthedocs.io/en/latest
 
 extra:
   recipe-maintainers:
diff --git a/recipes/snakemake-interface-executor-plugins/meta.yaml b/recipes/snakemake-interface-executor-plugins/meta.yaml
index 95b8d99e77481..fced483592c5b 100644
--- a/recipes/snakemake-interface-executor-plugins/meta.yaml
+++ b/recipes/snakemake-interface-executor-plugins/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "snakemake-interface-executor-plugins" %}
-{% set version = "9.3.2" %}
+{% set version = "9.3.3" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_executor_plugins-{{ version }}.tar.gz
-  sha256: 19c50dc82989ff25d10386cfb3c99da9d2dc980d95ecd30bbb431374dcd390b3
+  sha256: 11e59af04bf00e9aaee7f0b99f9358910becfccdad7b18a455d37601f6d8d2ea
 
 build:
   noarch: python
diff --git a/recipes/stripepy-hic/meta.yaml b/recipes/stripepy-hic/meta.yaml
new file mode 100644
index 0000000000000..1a6dbcc78a391
--- /dev/null
+++ b/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
diff --git a/recipes/stripepy-hic/run_test.sh b/recipes/stripepy-hic/run_test.sh
new file mode 100644
index 0000000000000..fe4089e1ae3b5
--- /dev/null
+++ b/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
diff --git a/recipes/treesimulator/meta.yaml b/recipes/treesimulator/meta.yaml
index 2e652c8857735..c30ec299a2e15 100644
--- a/recipes/treesimulator/meta.yaml
+++ b/recipes/treesimulator/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "treesimulator" %}
-{% set version = "0.2.0" %}
+{% set version = "0.2.1" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 599507b62cce4d8f77a850fc0f84d003d13530ec39960afdf1efcf356df16176
+  sha256: 10520e629a4ba47e7e5c0012b47f1dc1123389b4b7a96d1ff3f89ba8d60eafb4
 
 build:
   number: 0
@@ -17,14 +17,15 @@ build:
     - generate_bdei = treesimulator.simulate_forest_bdei:main
     - generate_bdss = treesimulator.simulate_forest_bdss:main
     - generate_mtbd = treesimulator.simulate_forest:main
-  script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation"
+  script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir"
   run_exports:
-    - {{ pin_subpackage('treesimulator', max_pin="x") }}
+    - {{ pin_subpackage('treesimulator', max_pin="x.x") }}
 
 requirements:
   host:
     - pip
     - python >=3.9
+    - setuptools
   run:
     - six >=1.16.0
     - ete3 >=3.1.1