Merge pull request #394 from cogent3/release

Release 2019.11.15a

README.md

@@ -22,7 +22,11 @@ Our `cogent3.app` module provides a very different approach to using the library
 
 ## Installation?
 
-We will be up on PyPI as soon as the documentation is written, until then it's install from this repo
+```bash
+$ pip install cogent3
+```
+
+### Installing the development version
 
 ```bash
 $ pip install git+https://github.com/cogent3/cogent3.git@master#egg=cogent3

azure-pipelines.yml

@@ -7,7 +7,7 @@ variables:
   CIBW_BEFORE_BUILD: python -m pip install --upgrade pip
 
 jobs:
-- job: Linux_Test
+- job: Linux_Test_py36
   pool: {vmImage: 'ubuntu-latest'}
   steps:
     - task: UsePythonVersion@0
@@ -16,23 +16,37 @@ jobs:
         python -m pip install .[dev] codecov
     - task: UsePythonVersion@0
       inputs:
-        versionSpec: '3.8'
+        versionSpec: '3.6'
     - bash: |
-        tox -e py38
+        tox -e py36
         codecov
+- job: Linux_Test_py37
+  pool: {vmImage: 'ubuntu-latest'}
+  steps:
+    - task: UsePythonVersion@0
+    - bash: |
+        python -m pip install --upgrade pip
+        python -m pip install .[dev] codecov
     - task: UsePythonVersion@0
       inputs:
         versionSpec: '3.7'
     - bash: |
         tox -e py37
         codecov
+- job: Linux_Test_py38
+  pool: {vmImage: 'ubuntu-latest'}
+  steps:
+    - task: UsePythonVersion@0
+    - bash: |
+        python -m pip install --upgrade pip
+        python -m pip install .[dev] codecov
     - task: UsePythonVersion@0
       inputs:
-        versionSpec: '3.6'
+        versionSpec: '3.8'
     - bash: |
-        tox -e py36
+        tox -e py38
         codecov
-- job: MacOS_Test
+- job: MacOS_Test_py36
   pool: {vmImage: 'macos-latest'}
   steps:
     - task: UsePythonVersion@0
@@ -41,23 +55,37 @@ jobs:
         python -m pip install .[dev] codecov
     - task: UsePythonVersion@0
       inputs:
-        versionSpec: '3.8'
+        versionSpec: '3.6'
     - bash: |
-        tox -e py38
+        tox -e py36
         codecov
+- job: MacOS_Test_py37
+  pool: {vmImage: 'macos-latest'}
+  steps:
+    - task: UsePythonVersion@0
+    - bash: |
+        python -m pip install --upgrade pip
+        python -m pip install .[dev] codecov
     - task: UsePythonVersion@0
       inputs:
         versionSpec: '3.7'
     - bash: |
         tox -e py37
         codecov
+- job: MacOS_Test_py38
+  pool: {vmImage: 'macos-latest'}
+  steps:
+    - task: UsePythonVersion@0
+    - bash: |
+        python -m pip install --upgrade pip
+        python -m pip install .[dev] codecov
     - task: UsePythonVersion@0
       inputs:
-        versionSpec: '3.6'
+        versionSpec: '3.8'
     - bash: |
-        tox -e py36
+        tox -e py38
         codecov
-- job: Windows_Test
+- job: Windows_Test_py37
   pool: {vmImage: 'windows-latest'}
   steps:
     - {task: UsePythonVersion@0, inputs: {versionSpec: '3.7', architecture: x86}}
@@ -76,7 +104,7 @@ jobs:
     - {task: UsePythonVersion@0, inputs: {versionSpec: '3.8'}}
     - bash: |
         python -m pip install --upgrade pip
-        python -m pip install cibuildwheel==1.0.0 numpy
+        python -m pip install cibuildwheel numpy
         cibuildwheel --output-dir wheelhouse .
         python setup.py sdist
         cp dist/*.gz wheelhouse/.
@@ -91,7 +119,7 @@ jobs:
     - {task: UsePythonVersion@0, inputs: {versionSpec: '3.8'}}
     - bash: |
         python -m pip install --upgrade pip
-        python -m pip install cibuildwheel==1.0.0 numpy
+        python -m pip install cibuildwheel numpy
         cibuildwheel --output-dir wheelhouse .
     - task: PublishBuildArtifacts@1
       inputs: {pathtoPublish: 'wheelhouse'}
@@ -107,7 +135,7 @@ jobs:
     - {task: UsePythonVersion@0, inputs: {versionSpec: '3.8', architecture: x64}}
     - bash: |
         python -m pip install --upgrade pip
-        python -m pip install cibuildwheel==1.0.0 numpy
+        python -m pip install cibuildwheel numpy
         cibuildwheel --output-dir wheelhouse .
     - task: PublishBuildArtifacts@1
       inputs: {pathtoPublish: 'wheelhouse'}

doc/conf.py

@@ -34,7 +34,7 @@
 
 version = ""
 
-release = "2019.10.24a"
+release = "2019.11.11a"
 
 # exclude_trees = ["_build"]
 

setup.py

@@ -19,7 +19,7 @@
     "Daniel McDonald",
 ]
 __license__ = "BSD-3"
-__version__ = "2019.10.24a"
+__version__ = "2019.11.11a"
 __maintainer__ = "Peter Maxwell"
 __email__ = "pm67nz@gmail.com"
 __status__ = "Production"
@@ -163,6 +163,9 @@ def CythonExtension(module_name, **kw):
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Topic :: Software Development :: Libraries :: Python Modules",
         "Operating System :: OS Independent",
+        "Programming Language :: Python :: 3.6",
+        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
     ],
     packages=find_packages(where="src"),
     package_dir={"": PACKAGE_DIR},

src/cogent3/__init__.py

@@ -69,7 +69,7 @@
     "Daniel McDonald",
 ]
 __license__ = "BSD-3"
-__version__ = "2019.10.24a"
+__version__ = "2019.11.11a"
 __maintainer__ = "Gavin Huttley"
 __email__ = "gavin.huttley@anu.edu.au"
 __status__ = "Production"

src/cogent3/align/__init__.py

@@ -25,7 +25,7 @@
 __copyright__ = "Copyright 2007-2019, The Cogent Project"
 __credits__ = ["Peter Maxwell", "Jeremy Widmann", "Gavin Huttley", "Rob Knight"]
 __license__ = "BSD-3"
-__version__ = "2019.10.24a"
+__version__ = "2019.11.11a"
 __maintainer__ = "Gavin Huttley"
 __email__ = "gavin.huttley@anu.edu.au"
 __status__ = "Production"

src/cogent3/align/_compare.pyx

@@ -2,7 +2,7 @@
 """
 
 version_info = (1, 3)
-__version__ = "('2019', '10', '24a')"
+__version__ = "('2019', '11', '11a')"
 
 cdef int cmax(int a, int b):
     if a > b:

src/cogent3/align/_pairwise_pogs.pyx

@@ -12,7 +12,7 @@ cdef extern from "math.h":
     double log (double x)
 
 version_info = (3, 2)
-__version__ = "('2019', '10', '24a')"
+__version__ = "('2019', '11', '11a')"
 
 cdef double SCALE_STEP, MIN_FLOAT_VALUE
 SCALE_STEP = 2.0**50