Packaging (#140)

* packaging

* run ci on branch

* don't set shell

* coverage on linux only

* fixing future warning

* submodule

* coveragerc

* trying to get coverage to work

* coverage

* trying again

* install editable for coverage

* another

* how about now

* one more try

* specific path

* adding separate coverage workflow and wheels

* getting rid of yaml warning

* removing hanging coverage call

* words in docs

* update pip add changes

.coveragerc

@@ -1,8 +1,10 @@
-[report]
+[run]
 omit =
     docs/*
     *__init__*
+relative_files = True
 
+[report]
 exclude_lines =
     pragma: no cover
     raise NotImplementedError

.github/workflows/tests.yml

@@ -0,0 +1,121 @@
+name: Tests
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  release:
+    types:
+      - published
+jobs:
+  tests:
+    name: "py${{ matrix.python-version }} / ${{ matrix.os }}"
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9"]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+    steps:
+      - name: Clone the repo
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+          submodules: recursive
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Set up windows compilers
+        uses: ilammy/msvc-dev-cmd@v1
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip pytest
+          python -m pip install .
+        env:
+          DISTUTILS_USE_SDK: 1
+          MSSdk: 1
+      - name: Run tests
+        run: python -m pytest -v tests
+
+  coverage:
+    name: "Run tests with coverage"
+    runs-on: ubuntu-latest
+    steps:
+      - name: Clone the repo
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+          submodules: recursive
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip pytest-cov
+          python -m pip install -e .
+      - name: Run tests
+        run: python -m pytest --cov george -v tests
+      - name: Coveralls
+        uses: AndreMiras/coveralls-python-action@v20201129
+
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, windows-2019, macos-10.15]
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: true
+          fetch-depth: 0
+      - uses: ilammy/msvc-dev-cmd@v1
+      - uses: joerick/[email protected]
+        env:
+          CIBW_BUILD: "cp3?-*"
+          CIBW_SKIP: "cp35-* *-win32 *-manylinux_i686"
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
+          DISTUTILS_USE_SDK: 1
+          MSSdk: 1
+      - uses: actions/upload-artifact@v2
+        with:
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: true
+          fetch-depth: 0
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: "3.9"
+      - name: Build sdist
+        run: |
+          python -m pip install -U pip
+          python -m pip install -U build
+          python -m build --sdist .
+      - uses: actions/upload-artifact@v2
+        with:
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [tests, build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - uses: actions/download-artifact@v2
+        with:
+          name: artifact
+          path: dist
+
+      - uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_password }}
+          # To test: repository_url: https://test.pypi.org/legacy/

.gitignore

@@ -11,8 +11,9 @@ dist
 build
 *.cpp
 .coverage
-george/kernels.py
-george/kerneldefs.pxd
-george/solvers/kerneldefs.pxd
-george/include/george/kernels.h
+src/george/george_version.py
+src/george/kernels.py
+src/george/kerneldefs.pxd
+src/george/solvers/kerneldefs.pxd
+src/george/include/george/kernels.h
 kernels/MyLocalGaussian.yml

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "vendor/eigen"]
+	path = vendor/eigen
+	url = https://gitlab.com/libeigen/eigen.git

.rtd-environment.yml

@@ -10,3 +10,6 @@ dependencies:
   - scipy
   - pyyaml
   - jinja2
+  - pip
+  - pip:
+      - .

HISTORY.rst

@@ -1,5 +1,11 @@
 .. :changelog:
 
+0.4.0 (2021-02-15)
+++++++++++++++++++
+
+- Updated packaging and installation issues
+- Updated CI and Python version testing
+
 0.3.1 (2018-01-08)
 ++++++++++++++++++
 

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2012-2017 Daniel Foreman-Mackey and contributors
+Copyright (c) 2012-2021 Daniel Foreman-Mackey and contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in

MANIFEST.in

@@ -1,3 +1,5 @@
-include README.rst LICENSE HISTORY.rst AUTHORS.rst
-graft george/include
-graft vendor
+
+exclude .*
+prune .github
+prune docs
+prune paper

README.rst

@@ -6,13 +6,11 @@ George
 .. image:: https://img.shields.io/badge/GitHub-dfm%2Fgeorge-blue.svg?style=flat
     :target: https://github.com/dfm/george
 .. image:: http://img.shields.io/badge/license-MIT-blue.svg?style=flat
-    :target: https://github.com/dfm/george/blob/master/LICENSE
-.. image:: http://img.shields.io/travis/dfm/george/master.svg?style=flat
-    :target: https://travis-ci.org/dfm/george
-.. image:: https://ci.appveyor.com/api/projects/status/xy4ts3v3sk5lo5ll?svg=true&style=flat
-    :target: https://ci.appveyor.com/project/dfm/george
-.. image:: https://coveralls.io/repos/github/dfm/george/badge.svg?branch=master&style=flat
-    :target: https://coveralls.io/github/dfm/george?branch=master
+    :target: https://github.com/dfm/george/blob/main/LICENSE
+.. image:: https://github.com/dfm/george/workflows/Tests/badge.svg?style=flat
+    :target: https://github.com/dfm/george/actions?query=workflow%3ATests
+.. image:: https://coveralls.io/repos/github/dfm/george/badge.svg?branch=main&style=flat
+    :target: https://coveralls.io/github/dfm/george?branch=main
 .. image:: https://readthedocs.org/projects/george/badge/?version=latest
     :target: http://george.readthedocs.io/en/latest/?badge=latest