Merge pull request #104 from rseng/update/analysis-2024-01-17

Update from update/analysis-2024-01-17

_repos/github/Zstone19/pypetal/requirements.txt

@@ -1,6 +1,7 @@
 astropy >= 5.1.0
 autograd >= 1.3
 celerite >= 0.4.2
+colorama >= 0.4.6
 corner >= 2.2.1
 emcee >= 3.1.3
 linmix @ git+https://github.com/jmeyers314/linmix.git

_repos/github/cosmicrays/hermes/CMakeLists.txt

@@ -348,10 +348,9 @@ option(ENABLE_PYTHON "Create python library via Pybind11" OFF)
 include(FindPython3)
 find_package(Python3 COMPONENTS Interpreter Development)
 
-if(ENABLE_PYTHON AND PYTHONLIBS_FOUND)
- include_directories(${PYTHON_INCLUDE_DIRS})
- include(cmake/FindPython.cmake)
- set(PYBIND11_PYTHON_VERSION ${PYTHON_DOT_VERSION}) 
+if(ENABLE_PYTHON AND Python3_Development_FOUND)
+ include_directories(${Python3_INCLUDE_DIRS})
+ set(PYBIND11_PYTHON_VERSION ${Python3_VERSION}) 
  add_subdirectory(lib/pybind11)
  # for PYBIND11_EXPAND_SIDE_EFFECTS in pybind11.h - temporary,
  # should be removed after the fix lands to the upstream
@@ -382,8 +381,8 @@ if(ENABLE_PYTHON AND PYTHONLIBS_FOUND)
  LINKER_LANGUAGE CXX)
  target_link_libraries(pyhermes PRIVATE hermes)
 
- install(TARGETS pyhermes LIBRARY DESTINATION "${PYTHON_SITE_PACKAGES}")
-endif(ENABLE_PYTHON AND PYTHONLIBS_FOUND)
+ install(TARGETS pyhermes LIBRARY DESTINATION "${Python3_SITELIB}")
+endif(ENABLE_PYTHON AND Python3_Development_FOUND)
 
 # ------------------------------------------------------------------
 # Documentation

_repos/github/fogellab/multiWGCNA/DESCRIPTION

@@ -1,22 +1,22 @@
 Package: multiWGCNA
 Type: Package
 Title: multiWGCNA
-Version: 0.99.4
+Version: 1.1.1
 Authors@R: c(
- person("Dario", "Tommasini", email="[email protected]", 
- role = c("aut","cre"), 
+ person("Dario", "Tommasini", email="[email protected]",
+ role = c("aut","cre"),
  comment = c(ORCID = "0000-0002-1214-6547")),
  person("Brent", "Fogel", role = c("aut","ctb")))
-Description: An R package for deeping mining gene co-expression networks in 
- multi-trait expression data. Provides functions for analyzing, comparing, 
+Description: An R package for deeping mining gene co-expression networks in
+ multi-trait expression data. Provides functions for analyzing, comparing,
  and visualizing WGCNA networks across conditions. multiWGCNA was designed
- to handle the common case where there are multiple biologically meaningful 
- sample traits, such as disease vs wildtype across development or anatomical 
- region. 
+ to handle the common case where there are multiple biologically meaningful
+ sample traits, such as disease vs wildtype across development or anatomical
+ region.
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
-Suggests: 
+Suggests:
  BiocStyle,
  doParallel,
  ExperimentHub,
@@ -27,9 +27,9 @@ Suggests:
  vegan
 VignetteBuilder: knitr
 RoxygenNote: 7.2.3
-biocViews: Sequencing, RNASeq, GeneExpression, DifferentialExpression, 
+biocViews: Sequencing, RNASeq, GeneExpression, DifferentialExpression,
  Regression, Clustering
-Imports: 
+Imports:
  stringr,
  readr,
  WGCNA,
@@ -46,7 +46,7 @@ Imports:
  ggrepel,
  methods,
  SummarizedExperiment
-Depends: 
- R (>= 4.0.0),
+Depends:
+ R (>= 4.3.0),
  ggalluvial
 Config/testthat/edition: 3

_repos/github/kanaverse/kana/package.json

@@ -1,7 +1,7 @@
 {
  "name": "kana",
  "description": "Single-cell data analysis in the browser",
- "version": "3.0.19",
+ "version": "3.0.20",
  "author": {
  "name": "Jayaram Kancherla",
  "email": "[email protected]",