Merge branch 'fix-jupyter-stdout'

Author: coldfix

.github/build/manylinux1_x86_64/Dockerfile

@@ -10,7 +10,7 @@ RUN groupadd -o -g $GID runner && \
     if [[ $AUDITWHEEL_PLAT == manylinux2014_* ]]; then \
         yum install -y glibc-static; \
     fi && \
-    pip install --upgrade cmake cython && \
+    pip install --upgrade cmake cython --only-binary=cmake && \
     for PYBIN in /opt/python/cp3*/bin; do \
         "${PYBIN}/pip" install -U setuptools; \
     done

doc/installation/unix.rst

@@ -59,7 +59,8 @@ install location if you prefer (e.g. ``~/.local`` or ``/opt/madx``), but keep
 in mind that there is no ``uninstall`` command other than removing the files
 manually.
 
-The cmake command has many more options, the most important ones being:
+The cmake command has many more options, the most important ones being
+(only use if you now what you're doing!):
 
 - ``-DMADX_STATIC=ON``: Pass this flag to link statically against the
   dependencies of MAD-X (libc, libgfortran, libstdc++, blas, lapack, etc).
@@ -87,7 +88,7 @@ MAD-X headers and library, for example::
     export MADXDIR="$(pwd)"/../dist
 
 Also, set the following variables according to the flags passed to the cmake
-command above::
+command above (ONLY PASS IF NEEDED!)::
 
     set STATIC=1    # if -DMADX_STATIC=ON
     set SHARED=1    # if -DBUILD_SHARED_LIBS=ON
@@ -102,12 +103,14 @@ Install setup requirements::
 
 Enter the cpymad folder, and build as follows::
 
-    python setup.py build_ext
+    python setup.py build_ext -lm
+
+The ``-lm`` might not be necessary on all systems.
 
 If you have installed blas/lapack and MAD-X found it during the cmake step,
 you have to pass them as additional link libraries::
 
-    python setup.py build_ext -lblas -llapack
+    python setup.py build_ext -lm -lblas -llapack
 
 You can now create and install a wheel as follows (however, note that this
 wheel probably won't be fit to be distributed to other systems)::

doc/installation/windows.rst

@@ -97,7 +97,7 @@ In the build environment, type::
         -DMADX_STATIC=ON ^
         -DCMAKE_INSTALL_PREFIX="../dist"
 
-    cmake --build . --target install:
+    cmake --build . --target install
 
 .. note::
 

src/cpymad/madx.py

@@ -19,7 +19,7 @@
 
 from . import _rpc
 from . import util
-from .stream import AsyncReader
+from .stream import AsyncReader, TextCallback
 
 
 __all__ = [
@@ -172,10 +172,32 @@ def __init__(self, libmadx=None, command_log=None, stdout=None,
             if stdout is None:
                 stdout = sys.stdout
             if hasattr(stdout, 'write'):
-                try:
-                    stdout = stdout.fileno()
-                except (AttributeError, OSError, IOError):
+                # Detect if stdout is attached to a jupyter notebook:
+                cls = getattr(stdout, '__class__', type(None))
+                qualname = cls.__module__ + '.' + cls.__name__
+                if qualname == 'ipykernel.iostream.OutStream':
+                    # In that case we want to behave the same way as `print`
+                    # (i.e. log to the notebook not to the terminal). On
+                    # linux, python>=3.7 within notebooks 6.4 `sys.stdout` has
+                    # a valid sys.stdout.fileno(), but writing to it outputs
+                    # to the terminal, so we have to use `sys.stdout.write()`:
                     stdout = stdout.write
+                else:
+                    # Otherwise, let the OS handle MAD-X output, by passing
+                    # the file descriptor if available. This is preferred
+                    # because it is faster, and also because it means that the
+                    # MAD-X output is directly connected to the output as
+                    # binary stream, without potential recoding errors.
+                    try:
+                        stdout = stdout.fileno()
+                    except (AttributeError, OSError, IOError):
+                        stdout = stdout.write
+                # Check for text stream to prevent TypeError (see #110).
+                if callable(stdout):
+                    try:
+                        stdout(b'')
+                    except TypeError:
+                        stdout = TextCallback(stdout)
             Popen_args['stdout'] = \
                 subprocess.PIPE if callable(stdout) else stdout
             # stdin=None leads to an error on windows when STDIN is broken.

src/cpymad/stream.py

@@ -73,3 +73,17 @@ def _read_thread(self):
             if not line:
                 return lines
             lines.append(line)
+
+
+class TextCallback:
+
+    """Decode bytes and pass to callback."""
+
+    def __init__(self, callback, encoding='utf-8', errors='replace'):
+        self.callback = callback
+        self.encoding = encoding
+        self.errors = errors
+
+    def __call__(self, data):
+        text = data.decode(self.encoding, errors=self.errors)
+        return self.callback(text)