Merge pull request #157 from zktuong/swap-nxviz-dependency

remove nxviz from requirements
zktuong · Jun 27, 2022 · 801f5bd · 801f5bd
2 parents 7f38a03 + 57fa582
commit 801f5bd
Show file tree

Hide file tree

Showing 8 changed files with 16 additions and 1 deletion.
diff --git a/README.md b/README.md
@@ -85,6 +85,10 @@ pip install "rpy2>=3.4.2" # or if you don't mind having conda manage R: conda in
 pip install sc-dandelion
 # or pip install git+https://github.com/zktuong/dandelion.git
 # for the development branch, run this: pip install git+https://github.com/zktuong/dandelion.git@devel
+
+# to use ddl.pl.clone_overlap, please install nxviz:
+pip install git+https://github.com/zktuong/nxviz.git@custom_color_mapping_circos_nodes_and_edges
+# separately until the PR is approved and merged.
 ````
 
 #### R

diff --git a/container/environment.yml b/container/environment.yml
@@ -21,3 +21,4 @@ dependencies:
   - scanpy>=1.7.0
   - sc-dandelion>=0.1.0
   - rpy2==3.4.2
+  - git+https://github.com/zktuong/nxviz.git@custom_color_mapping_circos_nodes_and_edges
diff --git a/container/environment_dev.yml b/container/environment_dev.yml
@@ -21,3 +21,4 @@ dependencies:
   - scanpy>=1.7.0
   - git+https://www.github.com/zktuong/dandelion@devel
   - rpy2==3.4.2
+  - git+https://github.com/zktuong/nxviz.git@custom_color_mapping_circos_nodes_and_edges
diff --git a/container/environment_master.yml b/container/environment_master.yml
@@ -21,3 +21,4 @@ dependencies:
   - scanpy>=1.7.0
   - git+https://www.github.com/zktuong/dandelion@master
   - rpy2==3.4.2
+  - git+https://github.com/zktuong/nxviz.git@custom_color_mapping_circos_nodes_and_edges
diff --git a/container/environment_test.yml b/container/environment_test.yml
@@ -20,3 +20,4 @@ dependencies:
 - pip:
   - scanpy>=1.7.0
   - rpy2==3.4.2
+  - git+https://github.com/zktuong/nxviz.git@custom_color_mapping_circos_nodes_and_edges
diff --git a/docs/README.md b/docs/README.md
@@ -80,6 +80,10 @@ pip install "rpy2>=3.4" # or if you don't mind having conda manage R: conda inst
 pip install sc-dandelion
 # or pip install git+https://github.com/zktuong/dandelion.git
 # for the development branch, run this: pip install git+https://github.com/zktuong/dandelion.git@devel
+
+# to use ddl.pl.clone_overlap, please install nxviz:
+pip install git+https://github.com/zktuong/nxviz.git@custom_color_mapping_circos_nodes_and_edges
+# separately until the PR is approved and merged.
 ````
 
 #### R

diff --git a/docs/README.rst b/docs/README.rst
@@ -101,6 +101,10 @@ python/conda packages
     # or pip install git+https://github.com/zktuong/dandelion.git
     # for the development branch, run this: pip install git+https://github.com/zktuong/dandelion.git@devel
 
+    # to use ddl.pl.clone_overlap, please install nxviz:
+    pip install git+https://github.com/zktuong/nxviz.git@custom_color_mapping_circos_nodes_and_edges
+    # separately until the PR is approved and merged.
+
 R packages
 ^^^^^^^^^^
 

diff --git a/requirements.txt b/requirements.txt
@@ -16,4 +16,3 @@ h5py>=3.1.0
 adjustText>=0.7
 distance>=0.1.3
 plotnine>=0.6.0
-nxviz @ git+https://github.com/zktuong/nxviz.git@custom_color_mapping_circos_nodes_and_edges