Change: Use pygraphviz to draw the pipeline workflow

env.yml

@@ -4,7 +4,8 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - _libgcc_mutex=0.1=main
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=1_gnu
   - ca-certificates=2020.12.5=ha878542_0
   - cairo=1.14.12=h7636065_2
   - certifi=2020.12.5=py38h578d9bd_1
@@ -26,7 +27,8 @@ dependencies:
   - libedit=3.1.20191231=h14c3975_1
   - libffi=3.3=he6710b0_2
   - libgcc=7.2.0=h69d50b8_2
-  - libgcc-ng=9.1.0=hdf63c60_0
+  - libgcc-ng=9.3.0=h2828fa1_18
+  - libgomp=9.3.0=h2828fa1_18
   - libpng=1.6.37=hbc83047_0
   - libssh2=1.9.0=h1ba5d50_1
   - libstdcxx-ng=9.1.0=hdf63c60_0
@@ -38,11 +40,12 @@ dependencies:
   - ncurses=6.2=he6710b0_1
   - nextflow=20.10.0=hecda079_0
   - openjdk=8.0.152=h7b6447c_3
-  - openssl=1.1.1i=h27cfd23_0
+  - openssl=1.1.1i=h7f98852_0
   - pango=1.42.0=h377f3fa_0
   - pcre=8.44=he6710b0_0
   - pip=20.3.3=py38h06a4308_0
   - pixman=0.40.0=h7b6447c_0
+  - pygraphviz=1.7=py38h0d738da_0
   - python=3.8.5=h7579374_1
   - python_abi=3.8=1_cp38
   - readline=8.0=h7b6447c_0
@@ -82,10 +85,10 @@ dependencies:
     - idna==2.10
     - imagesize==1.2.0
     - iniconfig==1.1.1
-    - ipython==7.19.0
+    - ipython==7.20.0
     - ipython-genutils==0.2.0
     - isort==5.7.0
-    - jedi==0.17.2
+    - jedi==0.18.0
     - jinja2==2.11.3
     - jinja2schema==0.1.4
     - kiwisolver==1.3.1
@@ -104,7 +107,7 @@ dependencies:
     - numpydoc==1.1.0
     - packaging==20.9
     - pandas==1.2.1
-    - parso==0.7.1
+    - parso==0.8.1
     - pathspec==0.8.1
     - patsy==0.5.1
     - pexpect==4.8.0
@@ -141,7 +144,7 @@ dependencies:
     - sphinxcontrib-qthelp==1.0.3
     - sphinxcontrib-serializinghtml==1.1.4
     - spinners==0.0.24
-    - statsmodels==0.12.1
+    - statsmodels==0.12.2
     - termcolor==1.1.0
     - toml==0.10.2
     - traitlets==5.0.5

micone/pipelines/pipeline.py

@@ -3,7 +3,6 @@
 """
 
 import collections
-import math
 import pathlib
 import time
 from itertools import chain
@@ -14,7 +13,6 @@
 import toml
 
 from ..config import Config
-from ..utils.hierarchical_layout import hierarchy_pos
 from .command import Command
 from .process import Process, stringizer
 
@@ -319,9 +317,10 @@ def draw_process_tree(self, fpath: str) -> None:
         gml = pathlib.Path(fpath) / "DAG.gml"
         nodes = list(self.process_tree.nodes)
         labels = {n: n.split(".", 2)[-1] for n in nodes}
-        pos = hierarchy_pos(tree, width=2 * math.pi)
-        # If you want a radial graph
-        # new_pos = {u:(r*math.cos(theta),r*math.sin(theta)) for u, (theta, r) in pos.items()}
+        if len(nodes) > 50:
+            pos = nx.drawing.nx_agraph.graphviz_layout(tree, prog="twopi")
+        else:
+            pos = nx.drawing.nx_agraph.graphviz_layout(tree, prog="dot")
         nx.draw_networkx_nodes(tree, pos, node_size=500, alpha=0.8)
         nx.draw_networkx_edges(tree, pos, width=1.0, arrows=True)
         text = nx.draw_networkx_labels(tree, pos, labels=labels, font_size=8)