base distribution on older numpy versions to avoid ABI problems

bwinkel · Feb 24, 2019 · 601f77d · 601f77d
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commit 601f77d
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diff --git a/.travis.yml b/.travis.yml
@@ -40,8 +40,8 @@ env:
         # For this package-template, we include examples of Cython modules,
         # so Cython is required for testing. If your package does not include
         # Cython code, you can set CONDA_DEPENDENCIES=''
-        - CONDA_DEPENDENCIES='Cython pytest'
-        - CONDA_DEPENDENCIES_DOC='Cython sphinx-astropy pytest scipy astroquery reproject'
+        - CONDA_DEPENDENCIES='Cython pytest pytest-doctestplus'
+        - CONDA_DEPENDENCIES_DOC='Cython sphinx-astropy pytest scipy astroquery reproject pytest-doctestplus'
 
         # List other runtime dependencies for the package that are available as
         # pip packages here.
@@ -80,63 +80,61 @@ matrix:
 
     include:
 
+        # We have to make the releases based on rather old numpy version
+        # otherwise users will keep getting "incompatible API" errors
+        # (For more information on ABI problems with numpy see:
+        # https://stackoverflow.com/questions/17709641/valueerror-numpy-dtype-has-the-wrong-size-try-recompiling/18369312)
+        # for Windows we'll use 1.11, for Linux/MacOS 1.9 is used
+
         # Standard linux; also used for sdist'ing
         - os: linux
-          env: DO_DIST=YES
-
-        # MacOS X - clang
-        # not working, even though we added the necessary compiler flags
-        # - os: osx
-        #   osx_image: xcode8.3
-        #   env:
-        #     - LDFLAGS='-L/usr/local/opt/libomp/lib -Wl,-rpath,/usr/local/opt/libomp/lib -lomp'
-        #     - CPPFLAGS='-I/usr/local/opt/libomp/include -Xpreprocessor -stdlib=libc++'
-        #     - COMPILER='clang'
+          env:
+            - DO_DIST=YES
+            - NUMPY_VERSION=1.11
+            # - ASTROPY_VERSION=stable
+            - ASTROPY_VERSION=2.0.11  # need old astropy, for numpy 1.9
 
-        # MacOS X - LLVM
-        # compiles and builds, but tests often not running (seg-fault?)
+        # MacOS X - conda-clang, release
         - os: osx
           osx_image: xcode8.3
           env:
-            - CC='/usr/local/opt/llvm/bin/clang'
-            - CXX='/usr/local/opt/llvm/bin/clang++'
-            - CXX11='/usr/local/opt/llvm/bin/clang++'
-            - LDFLAGS='-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -lgomp'
-            - CPPFLAGS='-I/usr/local/opt/llvm/include -stdlib=libc++'
-            - COMPILER='llvm'
+            - DO_MAC_DIST=YES
+            - COMPILER='conda-clang'
+            - NUMPY_VERSION=1.11
+            - ASTROPY_VERSION=2.0.11
 
-        # MacOS X - gcc
+        # MacOS X - conda-clang, release
         - os: osx
           osx_image: xcode8.3
           env:
-            - COMPILER='gcc'
+            - PYTHON_VERSION=3.6
+            - DO_MAC_DIST=YES
+            - COMPILER='conda-clang'
+            - NUMPY_VERSION=1.11
+            - ASTROPY_VERSION=2.0.11
 
-        # MacOS X - conda-clang
+        # MacOS X - conda-clang, release
         - os: osx
           osx_image: xcode8.3
           env:
+            - PYTHON_VERSION=3.5
             - DO_MAC_DIST=YES
             - COMPILER='conda-clang'
+            - NUMPY_VERSION=1.11
+            - ASTROPY_VERSION=2.0.11
+
+        # MacOS X - gcc
+        - os: osx
+          osx_image: xcode8.3
+          env:
+            - COMPILER='gcc'
 
         # MacOS X - conda-gcc
         - os: osx
           osx_image: xcode8.3
           env:
             - COMPILER='conda-gcc'
 
-        # MacOS X - conda-llvm
-        # not working at all, the packages (see below) seem to not install
-        # a compiler
-        # - os: osx
-        #   osx_image: xcode8.3
-        #   env:
-        #     - CC='/Users/travis/miniconda/bin/clang'
-        #     - CXX='/Users/travis/miniconda/bin/clang++'
-        #     - CXX11='/Users/travis/miniconda/bin/clang++'
-        #     - LDFLAGS='-L/Users/travis/miniconda/lib -Wl,-rpath,/Users/travis/miniconda/lib -lgomp'
-        #     - CPPFLAGS='-I/Users/travis/miniconda/include -stdlib=libc++'
-        #     - COMPILER='conda-llvm'
-
         # Do a coverage test.
         - os: linux
           env: SETUP_CMD='test --coverage'
@@ -148,39 +146,15 @@ matrix:
             - PYTHON_VERSION=3.6
             - SETUP_CMD='build_docs'
             - CONDA_DEPENDENCIES=$CONDA_DEPENDENCIES_DOC
-            - NUMPY_VERSION=1.14.3
-            - ASTROPY_VERSION=3.0.2
+            - NUMPY_VERSION=1.11
+            - ASTROPY_VERSION=2.0.11
             - UPLOAD_DOCS=YES
 
-        # Now try Astropy dev with the latest Python and LTS with Python 2.7 and 3.x.
+        # Now try Astropy dev with the latest Python
         - os: linux
           env: ASTROPY_VERSION=development
                EVENT_TYPE='pull_request push cron'
 
-        # No python 2.7 support anymore!
-        # - os: linux
-        #   env: PYTHON_VERSION=2.7 ASTROPY_VERSION=lts
-
-        # - os: linux
-        #   env: ASTROPY_VERSION=lts
-
-        # Try all python versions and Numpy versions. Since we can assume that
-        # the Numpy developers have taken care of testing Numpy with different
-        # versions of Python, we can vary Python and Numpy versions at the same
-        # time.
-
-        - os: linux
-          env: PYTHON_VERSION=3.5 NUMPY_VERSION=1.12
-        # - os: linux
-        #   env: PYTHON_VERSION=3.6 NUMPY_VERSION=1.13
-        # - os: linux
-        #   env: NUMPY_VERSION=1.14
-
-        # Try numpy pre-release
-        # - os: linux
-        #   env: NUMPY_VERSION=prerelease
-        #        EVENT_TYPE='pull_request push cron'
-
         # Do a PEP8 test with flake8
         - os: linux
           env: MAIN_CMD='flake8 cygrid --count --show-source --statistics $FLAKE8_OPT' SETUP_CMD=''

diff --git a/appveyor.yml b/appveyor.yml
@@ -18,7 +18,7 @@ environment:
       # For this package-template, we include examples of Cython modules,
       # so Cython is required for testing. If your package does not include
       # Cython code, you can set CONDA_DEPENDENCIES: ""
-      CONDA_DEPENDENCIES: "Cython pytest twine"
+      CONDA_DEPENDENCIES: "Cython pytest pytest-doctestplus twine"
 
       # List other runtime dependencies for the package that are available as
       # pip packages here.
@@ -32,28 +32,37 @@ environment:
       CONDA_CHANNELS: "conda-forge"
 
   matrix:
-      # We test Python 2.7 for Python 2 support.
-      # Apparently not working on Windows
-      # - PYTHON_VERSION: "2.7"
-      #   ASTROPY_VERSION: "stable"
-      #   NUMPY_VERSION: "stable"
 
-      # We test Python 3.5 for Python 3 support.
+        # We have to make the releases based on rather old numpy version
+        # otherwise users will keep getting "incompatible API" errors
+        # (For more information on ABI problems with numpy see:
+        # https://stackoverflow.com/questions/17709641/valueerror-numpy-dtype-has-the-wrong-size-try-recompiling/18369312)
+        # for Windows we'll use 1.11, for Linux/MacOS 1.9 is used
+
       - PYTHON_VERSION: "3.5"
-        ASTROPY_VERSION: "stable"
-        NUMPY_VERSION: "stable"
+        ASTROPY_VERSION: "2.0.11"
+        NUMPY_VERSION: "1.11"
+        DO_RELEASE: "yes"
+
+      - PYTHON_VERSION: "3.6"
+        ASTROPY_VERSION: "2.0.11"
+        NUMPY_VERSION: "1.11"
+        DO_RELEASE: "yes"
 
-      # We test Python 3.7 for Python 3 support.
       - PYTHON_VERSION: "3.7"
+        ASTROPY_VERSION: "2.0.11"
+        NUMPY_VERSION: "1.11"
+        DO_RELEASE: "yes"
+
+      # try more recent numpy+astropy
+
+      - PYTHON_VERSION: "3.5"
         ASTROPY_VERSION: "stable"
         NUMPY_VERSION: "stable"
 
-      - PYTHON_VERSION: "3.6"
-        # ASTROPY_VERSION: "2.0"
-        # NUMPY_VERSION: "1.11"
+      - PYTHON_VERSION: "3.7"
         ASTROPY_VERSION: "stable"
         NUMPY_VERSION: "stable"
-        DO_RELEASE: "yes"
 
 platform:
     -x64

diff --git a/docs/user_manual.rst b/docs/user_manual.rst
@@ -412,12 +412,14 @@ we will simply create a mock data set, with the help of a utility function,
     ...         )
 
     >>> np.set_printoptions(precision=4)
-    >>> print(lons)  # doctest: +FLOAT_CMP
-    [59.473  61.3992 56.8253 ... 59.957  57.5156 59.176 ]
-    >>> print(lats)  # doctest: +FLOAT_CMP
-    [28.0106 31.0641 30.3142 ... 28.5785 32.1307 28.8626]
-    >>> print(signal)  # doctest: +FLOAT_CMP
-    [ 0.0856  1.1899 -0.3375 ...  1.7997 -0.5739  0.0358]
+    >>> if np.__version__ >= '1.14':
+    ...     np.set_printoptions(legacy='1.13')
+    >>> print(lons)  # doctest: +FLOAT_CMP +NORMALIZE_WHITESPACE
+    [59.473  61.3992 56.8253 ..., 59.957  57.5156 59.176 ]
+    >>> print(lats)  # doctest: +FLOAT_CMP +NORMALIZE_WHITESPACE
+    [28.0106 31.0641 30.3142 ..., 28.5785 32.1307 28.8626]
+    >>> print(signal)  # doctest: +FLOAT_CMP +NORMALIZE_WHITESPACE
+    [ 0.0856  1.1899 -0.3375 ...,  1.7997 -0.5739  0.0358]
 
 .. note::
 
@@ -481,14 +483,14 @@ the `signal`)::
 The result can be queried using the `~cygrid.WcsGrid.get_data` method::
 
     >>> gridded_data = gridder.get_datacube()
-    >>> print(gridded_data)  # doctest: +FLOAT_CMP
-    [[[ 0.0519 -0.0529  0.0298 ...  0.0086  0.0492  0.1135]
-      [ 0.0456 -0.0954 -0.0979 ... -0.0122 -0.0485 -0.0387]
-      [ 0.0309 -0.0625 -0.0642 ... -0.0075 -0.0275 -0.038 ]
-      ...
-      [-0.0313 -0.0172 -0.0346 ... -0.008   0.117   0.0905]
-      [-0.1239 -0.0636 -0.0854 ... -0.0311  0.0787  0.0655]
-      [-0.0851 -0.0691 -0.0671 ...  0.1039  0.1192  0.0964]]]
+    >>> print(gridded_data)  # doctest: +FLOAT_CMP +NORMALIZE_WHITESPACE
+    [[[ 0.0519 -0.0529  0.0298 ...,  0.0086  0.0492  0.1135]
+      [ 0.0456 -0.0954 -0.0979 ..., -0.0122 -0.0485 -0.0387]
+      [ 0.0309 -0.0625 -0.0642 ..., -0.0075 -0.0275 -0.038 ]
+      ...,
+      [-0.0313 -0.0172 -0.0346 ..., -0.008   0.117   0.0905]
+      [-0.1239 -0.0636 -0.0854 ..., -0.0311  0.0787  0.0655]
+      [-0.0851 -0.0691 -0.0671 ...,  0.1039  0.1192  0.0964]]]
 
 As said above, this has three dimensions, but the third axis (the spectral
 axis) has length-1 and is not necessary in this case. We can get rid of it::
@@ -863,7 +865,7 @@ pairs to the constructor::
     >>> gridder.grid(lons, lats, signal[:, np.newaxis])
 
     >>> gridded_sightlines = gridder.get_datacube().squeeze()
-    >>> print(  # doctest: +FLOAT_CMP
+    >>> print(
     ...     'lon  lat  sightline-value\n',
     ...     '\n'.join(
     ...         '{:4.1f} {:4.1f} {:6.3f}'.format(*t)