Merge pull request #9 from cantinilab/dev_SeuratV5

merging the update on github actions in follow-up to hummuspy update

.github/workflows/pkgdown.yaml

@@ -27,26 +27,17 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::., any::devtools
+          extra-packages: any::pkgdown, any::reticulate, local::., any::devtools
           needs: website
 
       - uses: actions/setup-python@v2
         with:
           python-version: '3.10'
 
       - name: Setup hummuspy env
-        run: reticulate::virtualenv_create("r-reticulate", Sys.which("python"), packages="hummuspy")
-        shell: Rscript {0}
-
-      - name: ubuntu setup for Monocle3
-        run: sudo apt-get install libgdal-dev libgeos-dev libproj-dev
-
-      - name: Install Monocle3
-        run: devtools::install_github('cole-trapnell-lab/monocle3')
-        shell: Rscript {0}
-
-      - name: Install Cicero
-        run: devtools::install_github("cole-trapnell-lab/cicero-release", ref = "monocle3")
+        run: |
+          reticulate::conda_create("r-reticulate", packages="python==3.10")
+          reticulate::py_install("hummuspy", envname = "r-reticulate", pip=TRUE)
         shell: Rscript {0}
 
       - name: Build site

R/explore_network.R

@@ -511,7 +511,7 @@ define_output <- function(
     suffix_bipartites = suffix_bipartites)
 
   # define target_genes with hummuspy function
-  output <- hummuspy$explore_network$get_output_from_dicts(
+  output <- hummuspy$core_grn$get_output_from_dicts(
     output_request = output_type,
     multilayer_f = multilayer_f,
     multiplexes_list = multiplexes_dictionary,

hummuspy/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "hummuspy"
-version = "0.1.4"
+version = "0.1.7"
 description = "HuMMuS is a novel method for the inference of regulatory mechanisms from multi-omics data with any type and number of omics, through a heterogeneous multilayer network framework."
 authors = ["Rémi Trimbour <[email protected]>"]
 license = "GPL-3.0-only"
@@ -9,13 +9,17 @@ readme = "README.md"
 [tool.poetry.dependencies]
 python = ">=3.8"
 multixrank = "^0.1"
-joblib = "^1.2.0"
-tqdm = "^4.65.0"
+joblib = "^1.3.0"
+tqdm = ">=4.65.0"
 numpy = "^1.24.2"
 pandas = "^2.0.0"
 pyyaml = "^6.0"
 matplotlib = "^3.4.3"
 scipy = "^1.8.0"
+distributed = ">=2023.0.0"
+dask = ">=2023.0.0"
+rich = ">=10.12.0"
+bokeh = ">=2.4.2,!=3.0.*"
 
 [build-system]
 requires = ["poetry-core"]

hummuspy/src/hummuspy/__init__.py

@@ -1,2 +1,3 @@
 import hummuspy.config
-import hummuspy.explore_network
+import hummuspy.explore_network
+import hummuspy.core_grn