v0.2.0.12

cellsnake/command_line.py

@@ -36,7 +36,7 @@
 
 
 __author__ = 'Sinan U. Umu'
-__version__= '0.2.0.12rc2'
+__version__= '0.2.0.12'
 __logo__="""
              _  _                     _           
             | || |                   | |          

docs/conf.py

@@ -22,7 +22,7 @@
 author = 'Sinan U. Umu'
 
 # The full version, including alpha/beta/rc tags
-release = '0.2.0.12rc1'
+release = '0.2.0.12'
 
 
 # -- General configuration ---------------------------------------------------

environment.yml

@@ -13,17 +13,16 @@ dependencies:
  - pysam >=0.16.0.1
  - python
  - regex >=2021.4.4
- - scipy 
+ - scipy
  - snakemake >=7.22.0
  - umap-learn
  - plotly
  - python-kaleido
- - r-base==4.2.2
- - r-igraph==1.3.4
+ - r-base==4.3
+   # - r-base
  - r-ggraph==2.1.0
  - r-seurat==4.3.0
  - r-clustree==0.5.0
- - r-ggthemes
  - r-viridis
  - r-librarian
  - r-patchwork
@@ -48,18 +47,20 @@ dependencies:
  - r-monocle3 #version 1.0.0 is the current
  - r-randomcolor
  - bioconductor-rhdf5lib
- - bioconductor-clusterprofiler==4.6.0
- - bioconductor-scater==1.26.0
+ #- bioconductor-clusterprofiler==4.6.0
+ - bioconductor-clusterprofiler
+ #- bioconductor-scater==1.26.0
+ - bioconductor-scater
  - bioconductor-limma
  - bioconductor-complexheatmap
  - bioconductor-topgo
  - bioconductor-org.hs.eg.db
- - bioconductor-miqc 
+ - bioconductor-miqc
  - bioconductor-rhdf5lib
  - bioconductor-singler
  - bioconductor-celldex
  - bioconductor-enhancedvolcano
- - geos==3.11.1
+ - geos
  - cmake
  - hdf5
  - numba>=0.56.4
@@ -72,6 +73,13 @@ dependencies:
  - pip
  - scanpy>=1.9.1
  - cython
+ - r-matrixstats==1.0.0
+ - r-matrix==1.6_1.1
+ #- r-ggthemes==4.2.4
+ - r-ggthemes
+ #- r-gplots==3.1.3
+ - r-gplots
+ - r-igraph
 # - pip:
 #   - scipy>=1.6.2
 #   - regex>=2021.4.4
@@ -85,4 +93,4 @@ dependencies:
 #   - snakemake>=7.22.0
 #   - umap-learn
 #   - plotly
-#   - kaleido
+#   - kaleido

setup.py

@@ -20,7 +20,7 @@ def run(self):
 
 setup(
     name="cellsnake",
-    version="0.2.0.12.rc2",
+    version="0.2.0.12",
     packages=find_packages(exclude=('tests*','testing*')),
     long_description=long_description,
     long_description_content_type="text/markdown",