Merge latest master into aainv

.appveyor.yml

@@ -1,21 +1,24 @@
 build: off
 
 environment:
-  PYTHON_VERSION: 3.6
-  MINICONDA: C:\\Miniconda36-x64
+  PYTHON_VERSION: 3.8
+  MINICONDA: C:\\Miniconda37-x64
 
   matrix:
-    - TEST_FILES: "tests\\ --ignore=tests\\test_actionAngleTorus.py --ignore=tests\\test_snapshotpotential.py --ignore=tests\\test_qdf.py --ignore=tests\\test_pv2qdf.py --ignore=tests\\test_diskdf.py --ignore=tests\\test_orbit.py --ignore=tests\\test_streamdf.py --ignore=tests\\test_streamgapdf.py --ignore=tests\\test_evolveddiskdf.py --ignore=tests\\test_quantity.py --ignore=tests\\test_nemo.py --ignore=tests\\test_coords.py"
-      ADDL_CONDA_PKGS: 
+    - TEST_FILES: tests\test_orbit.py tests\test_orbits.py
+      ADDL_CONDA_PKGS: astropy astroquery
       COMPILE_NOOPENMP: 
+      BUILD_WHEELS: "true"
 
-    - TEST_FILES: tests\test_orbit.py
-      ADDL_CONDA_PKGS: astropy astroquery
-      COMPILE_NOOPENMP: "--no-openmp"
+    - TEST_FILES: "tests\\ --ignore=tests\\test_actionAngleTorus.py --ignore=tests\\test_snapshotpotential.py --ignore=tests\\test_qdf.py --ignore=tests\\test_pv2qdf.py --ignore=tests\\test_diskdf.py --ignore=tests\\test_orbit.py --ignore=tests\\test_orbits.py --ignore=tests\\test_streamdf.py --ignore=tests\\test_streamgapdf.py --ignore=tests\\test_evolveddiskdf.py --ignore=tests\\test_quantity.py --ignore=tests\\test_nemo.py --ignore=tests\\test_amuse.py --ignore=tests\\test_coords.py"
+      ADDL_CONDA_PKGS: 
+      COMPILE_NOOPENMP: 
+      BUILD_WHEELS: "false"
 
     - TEST_FILES: tests\test_quantity.py tests\test_coords.py
       ADDL_CONDA_PKGS: astropy
       COMPILE_NOOPENMP: "--no-openmp"
+      BUILD_WHEELS: "false"
 
 platform:
     - x64
@@ -25,10 +28,9 @@ install:
   - cmd: conda.exe update --yes --quiet conda
   - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%"
   - conda config --set always_yes yes --set changeps1 no
-  - conda update -q conda
   - conda info -a
   - conda config --append channels astropy 
-  - "conda create -n test-environment python=%PYTHON_VERSION% numpy scipy matplotlib setuptools pip cython>=0.20 pytest gsl %ADDL_CONDA_PKGS%"
+  - "conda create -n test-environment python=%PYTHON_VERSION% numpy scipy matplotlib numexpr setuptools pip cython>=0.20 pytest gsl %ADDL_CONDA_PKGS%"
   - activate test-environment
   - pip install coverage
   - pip install pytest-cov
@@ -43,3 +45,46 @@ install:
 
 test_script:
   - pytest -v %TEST_FILES% --cov galpy --cov-config .coveragerc_travis --disable-pytest-warnings
+
+after_test:
+  # Build wheels for different python versions of BUILD_WHEELS, otherwise done
+  - ps: |
+      if ($env:BUILD_WHEELS -eq "false") {
+        Exit-AppVeyorBuild
+      }
+  - conda deactivate
+  - conda remove --name test-environment --all
+  # Python 3.8
+  - conda create -n py38 python=3.8 numpy scipy matplotlib setuptools pip pytest gsl
+  - conda activate py38
+  - pip install wheel
+  - set INCLUDE=%CONDA_PREFIX%\Library\include;%INCLUDE%
+  - set LIB=%CONDA_PREFIX%\Library\lib;%LIB%
+  - set LIBPATH=%CONDA_PREFIX%\Library\lib;%LIBPATH%
+  - python setup.py bdist_wheel
+  - conda deactivate
+  # Python 3.7
+  - conda create -n py37 python=3.7 numpy scipy matplotlib setuptools pip pytest gsl
+  - conda activate py37
+  - conda remove --name py38 --all
+  - pip install wheel
+  - set INCLUDE=%CONDA_PREFIX%\Library\include;%INCLUDE%
+  - set LIB=%CONDA_PREFIX%\Library\lib;%LIB%
+  - set LIBPATH=%CONDA_PREFIX%\Library\lib;%LIBPATH%
+  - python setup.py bdist_wheel
+  - conda deactivate
+  # Python 3.6
+  - conda create -n py36 python=3.6 numpy scipy matplotlib setuptools pip pytest gsl
+  - conda activate py36
+  - conda remove --name py37 --all
+  - pip install wheel
+  - set INCLUDE=%CONDA_PREFIX%\Library\include;%INCLUDE%
+  - set LIB=%CONDA_PREFIX%\Library\lib;%LIB%
+  - set LIBPATH=%CONDA_PREFIX%\Library\lib;%LIBPATH%
+  - python setup.py bdist_wheel
+  - conda deactivate
+  # Upload as artifacts
+  - ps: |
+      if ($env:BUILD_WHEELS -eq "true") {
+        Get-ChildItem dist\*.whl | % { Push-AppveyorArtifact $_.FullName -FileName $_.Name }
+      }

.bumpversion.cfg

@@ -0,0 +1,26 @@
+[bumpversion]
+current_version = 1.7.0.dev0
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<release>[a-z]+)(?P<dev>\d+))?
+serialize = 
+	{major}.{minor}.{patch}.{release}{dev}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = gamma
+values = 
+	dev
+	gamma
+
+[bumpversion:part:dev]
+
+[bumpversion:file:setup.py]
+search = version='{current_version}'
+replace = version='{new_version}'
+
+[bumpversion:file:galpy/__init__.py]
+search = __version__ = "{current_version}"
+replace = __version__ = "{new_version}"
+
+[bumpversion:file:doc/source/conf.py]
+search = version = '{current_version}'
+replace = version = '{new_version}'

.coveragerc

@@ -14,6 +14,7 @@ exclude_lines =
 
 omit = 
     galpy/snapshot/*
+    galpy/potential/amuse.py
     galpy/util/bovy_plot.py
     galpy/util/bovy_ars.py
     galpy/util/multi.py

.coveragerc_travis

@@ -14,6 +14,7 @@ exclude_lines =
 
 omit = 
     galpy/snapshot/*
+    galpy/potential/amuse.py
     galpy/util/bovy_plot.py
     galpy/util/bovy_ars.py
     galpy/util/multi.py

.github/conda-build-environment-macos-latest.yml

@@ -0,0 +1,11 @@
+name: galpywheels
+channels:
+  - conda-forge
+dependencies:
+  - numpy
+  - scipy
+  - matplotlib
+  - setuptools
+  - conda-forge::gsl
+  - conda-forge::compilers
+  - conda-forge::llvm-openmp

.github/conda-build-environment-windows-latest.yml

@@ -0,0 +1,10 @@
+name: galpywheels
+channels:
+  - conda-forge
+dependencies:
+  - numpy
+  - scipy
+  - matplotlib
+  - setuptools
+  - conda-forge::gsl
+  - anaconda::intel-openmp

.github/stale.yml

@@ -0,0 +1,18 @@
+# Number of days of inactivity before an issue becomes stale
+daysUntilStale: 60
+# Number of days of inactivity before a stale issue is closed
+daysUntilClose: 7
+# Issues with these labels will never be considered stale
+exemptLabels:
+  - pinned
+  - security
+# Label to use when marking an issue as stale
+staleLabel: wontfix
+# Comment to post when marking an issue as stale. Set to `false` to disable
+markComment: >
+  This issue has been automatically marked as stale because it has not had
+  recent activity. It will be closed if no further activity occurs. If the 
+  issue has been resolved since the last activity, please close the issue. 
+  Thank you for your contributions.
+# Comment to post when closing a stale issue. Set to `false` to disable
+closeComment: false

.github/workflows/actions/entrypoint.sh

@@ -0,0 +1,16 @@
+#!/bin/sh
+
+yum -y install gsl-devel
+
+PYTHON_VERSIONS=("cp35-cp35m" "cp36-cp36m" "cp37-cp37m" "cp38-cp38")
+
+for PYTHON_VERSION in ${PYTHON_VERSIONS[@]}; do
+    /opt/python/${PYTHON_VERSION}/bin/pip install --upgrade pip
+    /opt/python/${PYTHON_VERSION}/bin/pip install -U wheel auditwheel
+    /opt/python/${PYTHON_VERSION}/bin/python setup.py bdist_wheel -d wheelhouse
+done
+
+for whl in /github/workspace/wheelhouse/*.whl; do
+    auditwheel repair $whl
+    rm $whl
+done

.github/workflows/actions/manylinux2014_x86_64/action.yml

@@ -0,0 +1,7 @@
+name: 'build wheels with manylinux2014_x86_64'
+description: 'build wheels with manylinux2014_x86_64'
+runs:
+    using: 'docker'
+    image: docker://quay.io/pypa/manylinux2014_x86_64
+    args:
+        - .github/workflows/actions/entrypoint.sh

.github/workflows/build_macosx_windows_wheels.yml

@@ -0,0 +1,94 @@
+name: Build Mac OS X & Windows wheels and upload to PyPI upon release
+
+# Update on every push and PR to master, and upon release creation
+on:
+  push:
+    branches:    
+      - master
+    paths-ignore:
+      - 'doc/**'
+  pull_request:
+    branches:
+      - master
+    paths-ignore:
+      - 'doc/**'
+  release:
+    types: [created]
+
+jobs:
+  build:
+    name: Build wheels
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macos-latest,windows-latest]
+        python-version: [3.5,3.6,3.7, 3.8]
+        exclude:
+          - os: windows-latest
+            python-version: 3.5
+    steps:
+      # check-out this repository
+      - uses: actions/checkout@v2
+      # Install Miniconda, as specificed by this repository's environment.yml
+      - uses: goanpeca/setup-miniconda@v1
+        with:
+           activate-environment: galpywheels
+           environment-file: .github/conda-build-environment-${{ matrix.os }}.yml
+           python-version: ${{ matrix.python-version }}
+      - name: Install pip dependencies
+        shell: bash -l {0}
+        run: |
+          python -m pip install --upgrade pip
+          pip install wheel
+      - name: Set environment variables on Mac OS
+        if: matrix.os == 'macos-latest'
+        shell: bash -l {0}
+        run: |
+          echo ::set-env name=CFLAGS::-I$CONDA_PREFIX/include
+          echo ::set-env name=LDFLAGS::-I$CONDA_PREFIX/lib
+          echo ::set-env name=LD_LIBRARY_PATH::-I$CONDA_PREFIX/lib
+      - name: Set environment variables on Windows
+        if: matrix.os == 'windows-latest'
+        shell: bash -l {0}
+        run: |
+          echo ::set-env name=INCLUDE::$CONDA_PREFIX\\Library\\include
+          echo ::set-env name=LIB::$CONDA_PREFIX\\Library\\lib
+          echo ::set-env name=LIBPATH::$CONDA_PREFIX\\Library\\lib
+      - name: Build extension
+        shell: bash -l {0}
+        run: |
+          mkdir wheelhouse
+          python setup.py build_ext
+      - name: Build wheel
+        shell: bash -l {0}
+        run: python setup.py bdist_wheel -d wheelhouse
+      # Upload wheel as artifact
+      - uses: actions/upload-artifact@v2-preview
+        with:
+          name: galpy-wheel-python-${{ matrix.python-version }}-${{ matrix.os }}
+          path: wheelhouse/*.whl
+# We need to run on Ubuntu for pypa/gh-action-pypi-publish action
+# so might as well also combine
+  combine:
+    name: Combine wheels into single artifact and upload to PyPI upon release
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+      - run: |
+          mkdir tmp_wheelhouse
+          mkdir wheelhouse
+      - uses: actions/download-artifact@v2-preview
+        with:
+          path: tmp_wheelhouse/
+      - run: find tmp_wheelhouse/ -mindepth 2 -type f -exec mv -i '{}' wheelhouse/ ';'
+      - uses: actions/upload-artifact@v2-preview
+        with:
+          name: galpy-wheels-macos-windows-latest
+          path: wheelhouse/*.whl
+      # Upload to PyPI if this is a release
+      - name: Publish distribution to PyPI
+        if: github.event_name == 'release' && github.event.action == 'created'
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.pypi_token }}
+          packages_dir: wheelhouse/

.github/workflows/build_manylinux_wheels.yml

@@ -0,0 +1,36 @@
+name: Build manylinux wheels, upload to PyPI upon release
+
+# Update on every push or PR to master (except when only docs) and upon releases
+on:
+  push:
+    branches:    
+      - master
+    paths-ignore:
+      - 'doc/**'
+  pull_request:
+    branches:
+      - master
+    paths-ignore:
+      - 'doc/**'
+  release:
+    types: [created]
+
+jobs:
+  build:
+    name: Build manylinux wheels, upload to PyPI upon release
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Build manylinux2014_x86_64 wheels
+        uses: ./.github/workflows/actions/manylinux2014_x86_64/
+      - uses: actions/upload-artifact@v2-preview
+        with:
+          name: galpy-wheels-manylinux
+          path: wheelhouse/*manylinux*.whl
+      # Upload to PyPI if this is a release
+      - name: Publish distribution to PyPI
+        if: github.event_name == 'release' && github.event.action == 'created'
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.pypi_token }}
+          packages_dir: wheelhouse/

.github/workflows/build_sdist.yml

@@ -0,0 +1,30 @@
+name: Build source directory for release
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build:
+    name: Build source directory for release
+    runs-on: ubuntu-latest
+    steps:
+      # check-out this repository
+      - uses: actions/checkout@v2
+      # Setup python
+      - name: Set up Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.8
+      # Install the GSL (necessary to properly include the C files)
+      - name: Install GSL
+        shell: bash -l {0}
+        run: sudo apt-get install -y libgsl0-dev
+      - name: Build sdist
+        shell: bash -l {0}
+        run: python setup.py sdist
+      # Upload to PyPI if this is a release
+      - name: Publish distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.pypi_token }}

.gitignore

@@ -7,6 +7,7 @@
 *.o
 *.so
 *.pyc
+*.pyd
 
 # Packages #
 ############