Merge pull request #563 from jeromekelleher/more-packaging

More packaging

Author: jeromekelleher

.github/workflows/ci.yml

@@ -29,7 +29,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install '.[dev,debug]'
+          python -m pip install '.[dev,debug,inference]'
 
       - name: Run tests
         run: |
@@ -54,7 +54,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install '.'
+          python -m pip install '.[inference]'
 
       - name: Create basedir
         run: |

LICENSE

@@ -8,20 +8,16 @@ authors = [
 ]
 requires-python = ">=3.10"
 dependencies = [
-  "tsinfer>=0.5",
   "tskit==1.0.0b3",
-  "pyfaidx",
   "tszip",
   "pandas",
-  "numba",
   "tqdm",
-  "scipy",
+  "zarr<3",
   "click>=8.2",
+  # Not strictly needed for base functionality, but easier to include
+  # as imported by the CLI
   "tomli",
-  "zarr<3",
   "humanize",
-  "resource",
-  "biotite",
 ]
 dynamic = ["version"]
 
@@ -36,6 +32,13 @@ dev = [
   "pytest-coverage",
   "tomli-w",
 ]
+inference = [
+  "scipy",
+  "biotite",
+  "tsinfer>=0.5",
+  "pyfaidx",
+  "numba",
+]
 debug = [
   "matplotlib",
   "IPython",

notebooks/RecombinantAncestry.ipynb

@@ -364,7 +364,7 @@ def label(allele, default=""):
         return html + "</table>"
 
 
-class TreeInfo:
+class ArgInfo:
     def __init__(
         self,
         ts,