Python 3.10, and macOS integration testing

.github/workflows/build-and-test.yml

@@ -8,16 +8,16 @@ on:
 
 jobs:
   build:
-    if: "!contains(github.event.commits[0].message, '[skip ci]')"
-    runs-on: ubuntu-latest
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.7, 3.8, 3.9, "3.10"] # https://github.com/actions/runner/issues/1989
+
+    runs-on: ${{ matrix.os }}
 
     steps:
       - name: Checkout 🛎️
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Pandoc
         uses: r-lib/actions/setup-pandoc@v2
@@ -46,6 +46,8 @@ jobs:
         run: make test
 
       - name: Test docs build
+        # NOTE: only run on ubuntu-latest to save on compute usage
+        if: matrix.os == 'ubuntu-latest'
         shell: bash -l {0}
         run: |
           make docs

.github/workflows/docs-build-and-deploy.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout 🛎️
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Pandoc
         uses: r-lib/actions/setup-pandoc@v2

.github/workflows/python-publish.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
       uses: actions/setup-python@v2
       with:

docs/developer.rst

@@ -10,6 +10,13 @@ Developer install::
 
   make install
 
+.. warning:: 
+
+    If you're working on an ARM Mac, you may run into trouble installing the PyQt5 dependency
+    (which is also a dependency of the ``historydag`` package) via pip. As a workaround,
+    we recommend commenting out the the ``PyQt5``, ``ete3``, and ``historydag`` lines from
+    the ``setup.py`` and installing those via Conda.
+
 Run tests::
 
   make test

docs/install.rst

@@ -7,7 +7,7 @@ The preferred way to install gctree is with Conda:
 
 .. code-block:: bash
 
-  conda create -n gctree python=3.9
+  conda create -n gctree python=3.10
   conda activate gctree
   conda install -c conda-forge gctree
 

gctree/_version.py

@@ -6,7 +6,6 @@
 
 # This file is released into the public domain. Generated by
 # versioneer-0.18 (https://github.com/warner/python-versioneer)
-
 """Git implementation of _version.py."""
 
 import errno

gctree/branching_processes.py

@@ -433,7 +433,7 @@ def simulate(self, p: np.float64, q: np.float64, root: bool = True):
             self._build_cm_counts()
 
     def __repr__(self):
-        r"""return a string representation for printing."""
+        r"""Return a string representation for printing."""
         return str(self.tree)
 
     def render(
@@ -1266,7 +1266,8 @@ def mask(weighttuple, n=10):
         dagweight_kwargs = ll_dagfuncs + iso_funcs + mut_funcs + allele_funcs
         trimdag = dag.copy()
         trimdag.trim_optimal_weight(
-            **dagweight_kwargs, optimal_func=lambda l: min(l, key=minfunckey)
+            **dagweight_kwargs,
+            optimal_func=lambda l: min(l, key=minfunckey),  # noqa: E741
         )
         # make sure trimming worked as expected:
         min_weightcounter = trimdag.weight_count(**dagweight_kwargs)
@@ -1278,7 +1279,8 @@ def mask(weighttuple, n=10):
             )
 
         best_weighttuple = trimdag.optimal_weight_annotate(
-            **dagweight_kwargs, optimal_func=lambda l: min(l, key=minfunckey)
+            **dagweight_kwargs,
+            optimal_func=lambda l: min(l, key=minfunckey),  # noqa: E741
         )
         if summarize_forest:
             with open(outbase + ".forest_summary.log", "w") as fh:
@@ -1347,7 +1349,7 @@ def mask(weighttuple, n=10):
         return (self._trimmed_self(trimdag), best_weighttuple)
 
     def likelihood_rankplot(self, outbase, p, q, img_type="svg"):
-        """save a rank plot of likelihoods to the file
+        """Save a rank plot of likelihoods to the file
         `[outbase].inference.likelihood_rank.[img_type]`."""
         ll_dagfuncs = _ll_genotype_dagfuncs(p, q)
         if self._forest is not None:
@@ -1587,7 +1589,7 @@ def _clade_tree_to_ctree(
         return ctree
 
     def __repr__(self):
-        r"""return a string representation for printing."""
+        r"""Return a string representation for printing."""
         return f"n_trees = {self.n_trees}\n" "\n".join([str(tree) for tree in self])
 
     def __iter__(self):
@@ -1615,7 +1617,7 @@ def _mle_helper(
     bounds = ((1e-6, 1 - 1e-6), (1e-6, 1 - 1e-6))
 
     def f(x):
-        """negative log likelihood."""
+        """Negative log likelihood."""
         return tuple(-y for y in ll(*x, **kwargs))
 
     grad_check = sco.check_grad(lambda x: f(x)[0], lambda x: f(x)[1], x_0)

gctree/cli.py

@@ -155,7 +155,7 @@ def test(args):
 
 
 def infer(args):
-    """inference subprogram."""
+    """Inference subprogram."""
 
     def isotype_add(forest):
         forest.add_isotypes(

gctree/mkconfig.py

@@ -3,15 +3,14 @@
 r"""Read a PHYLIP-format file and produce an appropriate config file for passing
 to `dnapars`.
 
-`dnapars` doesn't play very well in a
-pipeline.  It prompts the user for configuration information and reads
-responses from stdin.  The config file generated by this script is
-meant to mimic the responses to the expected prompts.
+`dnapars` doesn't play very well in a pipeline.  It prompts the user for
+configuration information and reads responses from stdin.  The config
+file generated by this script is meant to mimic the responses to the
+expected prompts.
 
 Typical usage is,
 
-     $ mkconfig sequence.phy > dnapars.cfg
-     $ dnapars < dnapars.cfg
+$ mkconfig sequence.phy > dnapars.cfg $ dnapars < dnapars.cfg
 """
 import os
 import argparse

gctree/mutation_model.py

@@ -105,7 +105,7 @@ def __init__(
 
     @staticmethod
     def _disambiguate(sequence):
-        r"""generator of all possible nt sequences implied by a sequence
+        r"""Generator of all possible nt sequences implied by a sequence
         containing ambiguous bases."""
         return _sequence_disambiguations(sequence)
 

gctree/phylip_parse.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-
 """Given an outputfile from one of the PHYLIP tools - `dnaml` or `dnapars` -
 produce a CollapsedForest containing the trees in that outputfile."""
 
@@ -100,7 +99,7 @@ def parse_seqdict(fh, mode="dnaml"):
 # list biopython.SeqRecords and a dict containing adjacency
 # relationships and distances between nodes.
 def parse_outfile(outfile, abundance_file=None, root="root", disambiguate=False):
-    """parse phylip outfile, and return dnapars trees."""
+    """Parse phylip outfile, and return dnapars trees."""
     if abundance_file is not None:
         counts = {
             line.split(",")[0]: int(line.split(",")[1]) for line in open(abundance_file)

setup.py

@@ -26,7 +26,7 @@
         "License :: OSI Approved :: GNU General Public License (GPL)",
         "Operating System :: OS Independent",
     ],
-    python_requires=">=3.7, <3.10",
+    python_requires=">=3.7",
     install_requires=[
         "PyQt5",
         "ete3",

tests/test_isotype.py

@@ -47,7 +47,7 @@ def test_trim_byisotype():
     # idmap_file=None,
     # isotype_names=None,
     tdag = dag.copy()
-    tdag.optimal_weight_annotate(**kwargs, optimal_func=lambda l: l[0])
+    tdag.optimal_weight_annotate(**kwargs, optimal_func=lambda l: l[0])  # noqa: E741
     for node in tdag.preorder():
         if node.attr is not None:
             node.attr["isotype"] = node._dp_data