Python 3.8 compatibility (#329)

* add py38 to CI * recythonize * add release notes [ci skip] * sort out requirements * fix tox
cggh · Jul 8, 2020 · 10be09a · 10be09a
1 parent 86152f8
commit 10be09a
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diff --git a/.travis.yml b/.travis.yml
@@ -11,6 +11,7 @@ dist: xenial
 python:
   - "3.6"
   - "3.7"
+  - "3.8"
 
 install:
   - pip install -U pip setuptools wheel tox-travis coveralls

diff --git a/allel/opt/io_vcf_read.c b/allel/opt/io_vcf_read.c
diff --git a/allel/opt/model.c b/allel/opt/model.c
diff --git a/allel/opt/stats.c b/allel/opt/stats.c
diff --git a/appveyor.yml b/appveyor.yml
@@ -19,14 +19,15 @@ environment:
     - PYTHON: "C:\\Python37-x64"
       PYTHON_VERSION: "3.7"
 
+    - PYTHON: "C:\\Python38-x64"
+      PYTHON_VERSION: "3.8"
+
 install:
   - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
   - "%CMD_IN_ENV% python -m pip install -U pip setuptools wheel"
-  - "%CMD_IN_ENV% python -m pip install cython==0.29.10"
-  - "%CMD_IN_ENV% python -m pip install numpy==1.16.4"
-  - "%CMD_IN_ENV% python -m pip install -rrequirements_dev.txt"
+  - "%CMD_IN_ENV% python -m pip install -rrequirements_dev_base.txt"
+  - "%CMD_IN_ENV% python -m pip install -rrequirements_dev_optional.txt"
   - "%CMD_IN_ENV% python -m pip install -rrequirements_test.txt"
-  - "%CMD_IN_ENV% python -m pip install pyfasta==0.5.2"
   - "%CMD_IN_ENV% python setup.py build_ext --inplace"
 
 build: off

diff --git a/docs/release.rst b/docs/release.rst
@@ -1,6 +1,16 @@
 Release notes
 =============
 
+
+.. _release_1.3.1:
+
+v1.3.1
+------
+
+* Add compatibility with Python 3.8. By :user:`Alistair Miles
+  <alimanfoo>`, :issue:`329`.
+
+
 .. _release_1.3.0:
 
 v1.3.0

diff --git a/requirements_dev_base.txt b/requirements_dev_base.txt
@@ -0,0 +1,4 @@
+# required
+cython==0.29.20
+numpy==1.19.0
+dask[array]==2.19.0
diff --git a/requirements_dev.txt → requirements_dev_optional.txt b/requirements_dev.txt → requirements_dev_optional.txt
@@ -1,7 +1,3 @@
-# required
-cython==0.29.20
-numpy==1.19.0
-dask[array]==2.19.0
 # optional
 scipy==1.5.0
 matplotlib==3.2.2
@@ -16,3 +12,4 @@ hmmlearn==0.2.3
 # install problems on windows, skip for now
 # https://github.com/jmschrei/pomegranate/issues/333#issuecomment-449151227
 #pomegranate==0.10.0
+pyfasta==0.5.2
diff --git a/tox.ini b/tox.ini
@@ -4,7 +4,7 @@
 # and then run "tox" from this directory.
 
 [tox]
-envlist = py35, py36, py37, docs
+envlist = py36, py37, py38, docs
 # trick to enable pre-installation of numpy and cython
 indexserver =
     preinstall = https://pypi.python.org/simple
@@ -15,17 +15,16 @@ setenv =
     PYTHONHASHSEED = 42
 commands =
     python setup.py build_ext --inplace
-    py35,py36: pytest -v --cov=allel allel
-    py37: pytest -v --cov=allel --doctest-modules allel
+    py36,py37: pytest -v --cov=allel allel
+    py38: pytest -v --cov=allel --doctest-modules allel
     coverage report -m
-    py37: flake8 allel --max-line-length=100
+    py38: flake8 allel --max-line-length=100
     pip freeze
 deps =
     :preinstall: setuptools
-    :preinstall: cython==0.29.10
-    :preinstall: numpy==1.16.4
+    :preinstall: -rrequirements_dev_base.txt
     -rrequirements_test.txt
-    -rrequirements_dev.txt
+    -rrequirements_dev_optional.txt
 
 [testenv:docs]
 install_command = pip install -U --no-cache-dir {opts} {packages}