Update supported Python versions to drop 3.6, include 3.9 and 3.10

.github/workflows/ci.yaml

@@ -5,7 +5,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.6', '3.7', '3.8']
+        python-version: ['3.7', '3.8', '3.9', '3.10']
     defaults:
       run:
         shell: bash -l {0}
@@ -26,7 +26,7 @@ jobs:
     - run: pytest -c pytest.python3.ini  --cov-report=xml --cov=augur
     - run: cram --shell=/bin/bash tests/functional/*.t tests/builds/*.t
     - run: bash tests/builds/runner.sh
-    - if: github.repository == 'nextstrain/augur' && matrix.python-version == 3.8
+    - if: github.repository == 'nextstrain/augur' && matrix.python-version == 3.10
       uses: codecov/codecov-action@v2
       with:
         fail_ci_if_error: true

.readthedocs.yml

@@ -1,7 +1,7 @@
 ---
 version: 2
 python:
-  version: 3.6
+  version: 3.7
   install:
     - method: pip
       path: .

docs/contribute/DEV_DOCS.md

@@ -27,7 +27,7 @@ Please see the [project board](https://github.com/orgs/nextstrain/projects/6) fo
 
 ## Contributing code
 
-We currently target compatibility with Python 3.6 and higher. As Python releases new versions,
+We currently target compatibility with Python 3.7 and higher. As Python releases new versions,
 the minimum target compatibility may be increased in the future.
 
 Versions for this project, Augur, from 3.0.0 onwards aim to follow the

docs/installation/installation.md

@@ -40,7 +40,7 @@ mamba install -c conda-forge -c bioconda augur
 
 ## Using pip from PyPi
 
-Augur is written in Python 3 and requires at least Python 3.6.
+Augur is written in Python 3 and requires at least Python 3.7.
 It's published on [PyPi](https://pypi.org) as [nextstrain-augur](https://pypi.org/project/nextstrain-augur), so you can install it with `pip` like so:
 
 ```bash

setup.py

@@ -2,16 +2,20 @@
 import setuptools
 import sys
 
-min_version = (3, 6)
+py_min_version = (3, 7)  # minimal supported python version
+since_augur_version = (14, 0)  # py_min_version is required since this augur version
 
-if sys.version_info < min_version:
+if sys.version_info < py_min_version:
     error = """
-Beginning with augur 7.0.0, Python {0} or above is required.
+Beginning with augur {0}, Python {1} or above is required.
+You are using Python {2}.
 
 This may be due to an out of date pip.
 
 Make sure you have pip >= 9.0.1.
-""".format('.'.join(str(n) for n in min_version)),
+""".format('.'.join(str(n) for n in since_augur_version),
+           '.'.join(str(n) for n in py_min_version),
+           '.'.join(str(n) for n in sys.version_info[:3]))
     sys.exit(error)
 
 base_dir = Path(__file__).parent.resolve()
@@ -45,7 +49,7 @@
     },
     packages = setuptools.find_packages(),
     package_data = {'augur': ['data/*']},
-    python_requires = '>={}'.format('.'.join(str(n) for n in min_version)),
+    python_requires = '>={}'.format('.'.join(str(n) for n in py_min_version)),
     install_requires = [
         "bcbio-gff >=0.6.0, ==0.6.*",
         "biopython >=1.67, !=1.77, !=1.78",
@@ -87,9 +91,10 @@
 
         # Python 3 only
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
     ],
     # Install an "augur" program which calls augur.__main__.main()
     #   https://setuptools.readthedocs.io/en/latest/setuptools.html#automatic-script-creation