#Issue272 Cythonvscython

conda_recipe/meta.yaml

@@ -26,7 +26,7 @@ requirements:
     - numpy
     - scipy
     - matplotlib
-    - cython >=0.26
+    - Cython >=0.26
     - nose
     - pygments
 
@@ -39,7 +39,7 @@ requirements:
     - numpy
     - scipy
     - matplotlib
-    - cython >=0.26
+    - Cython >=0.26
     - nose
     - pygments
 

doc/source/installation.rst

@@ -143,6 +143,6 @@ To install tofu as a developer, we recommend using the conda ecosystem (Minicond
    (long) <https://www.atlassian.com/git/tutorials>`__ or `this short
    one <https://rogerdudler.github.io/git-guide/>`__
 -  Run ``pip install -e .[dev]``. This will install dependencies, compile the
-   tofu Cython extensions and install it into your conda environment while you can still
+   tofu cython extensions and install it into your conda environment while you can still
    modify the source files in the current repository.`
 -  Make sure tofu tests are running by typing ``nosetests``

doc/source/release_notes/release_notes_141.rst

@@ -225,7 +225,7 @@ Code structure and format
 Restructuring of the geometry modules
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Created Cython include files ``*.pxd`` and ``*.pyx`` for the following
+Created cython include files ``*.pxd`` and ``*.pyx`` for the following
 group of functions: - ``_basic_geom_tools.*``: global variables
 definition (``_VSMALL`` and ``_SMALL``), and basic geometric tools
 (vector calculus, path distance point-point, point-vector,...) -
@@ -244,7 +244,7 @@ Installation and portability
    impossible
 -  git dependency is now optional (issue #67 )
 -  changes in ``setup.py`` for **Windows** portability
--  Now only supporting ``Cython`` versions ``>=0.26``
+-  Now only supporting ``cython`` versions ``>=0.26``
 -  Removed all **pandas** dependencies
 -  Using ``-O3`` flag instead of ``-O0`` for faster execution time even
    if compilation is slower

requirements.txt

@@ -4,4 +4,4 @@ scipy
 matplotlib
 
 ######## Requirements with Version Specifier ########
-cython>=0.26
+Cython>=0.26

setup.py

@@ -11,19 +11,31 @@
 import platform
 import subprocess
 from codecs import open
-import Cython as cth
-from Cython.Distutils import build_ext
-from Cython.Build import cythonize
-import numpy as np
+try:
+    import numpy as np
+    import Cython as cth
+    from Cython.Distutils import build_ext
+    from Cython.Build import cythonize
+    from Cython.Build import build_ext as cthBext
+    # Why do we need two different build_ext command ?
+
+    def npgetinclude(): return np.get_include()
+    print("cython version =", cth.__version__)
+    print("numpy  version =", np.__version__)
+    print("cython file =", cth.__file__)
+    print("numpy  file =", np.__file__)
+except ImportError:
+    def npgetinclude():
+        import numpy as np
+        return np.get_include()
+    def cythonize(*args, **kwargs):
+        from Cython.Build import cythonize
+        return cythonize(*args, **kwargs)
+    def cthBext(*args, **kwargs):
+        from Cython.Build import build_ext as cthBext
+        return cthBext(*args, **kwargs)
 import _updateversion as up
 
-from distutils.command.clean import clean as Clean
-
-
-print("cython version =", cth.__version__)
-print("numpy  version =", np.__version__)
-print("cython version =", cth.__file__)
-print("numpy  version =", np.__file__)
 
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger("tofu.setup")
@@ -36,6 +48,9 @@
     from distutils.core import setup
     from distutils.extension import Extension
 
+# Is there a clean command from setuptools instead of distutils ?
+from distutils.command.clean import clean as Clean
+
 is_platform_windows = False
 if platform.system() == "Windows":
     is_platform_windows = True
@@ -282,7 +297,7 @@ def get_version_tofu(path=_HERE):
     # The version is stored only in the setup.py file and read from it (option
     # 1 in https://packaging.python.org/en/latest/single_source_version.html)
     use_scm_version=False,
-    # setup_requires=['setuptools_scm'],
+    setup_requires=['numpy', 'cython>=0.26'],
     description="A python library for Tomography for Fusion",
     long_description=long_description,
     long_description_content_type=long_description_content_type,
@@ -384,7 +399,7 @@ def get_version_tofu(path=_HERE):
     #    ],
     # },
     ext_modules=extensions,
-    cmdclass={"build_ext": cth.Build.build_ext,
+    cmdclass={"build_ext": cthBext,
               "clean": CleanCommand},
-    include_dirs=[np.get_include()],
+    include_dirs=[npgetinclude()],
 )

tofu/geom/_GG.pyx

@@ -10,7 +10,7 @@ import numpy as np
 import scipy.integrate as scpintg
 from matplotlib.path import Path
 
-# -- Cython libraries imports --------------------------------------------------
+# -- cython libraries imports --------------------------------------------------
 from cpython cimport bool
 from cpython.array cimport array, clone
 from cython.parallel import prange
@@ -3679,7 +3679,7 @@ def comp_dist_los_circle(np.ndarray[double,ndim=1,mode='c'] ray_vdir,
        to the circle
     ---
     This is the PYTHON function, use only if you need this computation from
-    Python, if you need it from Cython, use `dist_los_circle_core`
+    Python, if you need it from cython, use `dist_los_circle_core`
     """
     cdef double[2] res
     _dt.dist_los_circle_core(<double*>ray_vdir.data,
@@ -3714,7 +3714,7 @@ def comp_dist_los_circle_vec(int nlos, int ncircles,
         with the distance between each LOS to each circle
     ---
     This is the PYTHON function, use only if you need this computation from
-    Python, if you need it from Cython, use `dist_los_circle_core`
+    Python, if you need it from cython, use `dist_los_circle_core`
     """
     cdef array kmin_tab = clone(array('d'), nlos*ncircles, True)
     cdef array dist_tab = clone(array('d'), nlos*ncircles, True)
@@ -3748,7 +3748,7 @@ def is_close_los_circle(np.ndarray[double,ndim=1,mode='c'] ray_vdir,
     The result is True when distance < epsilon
     ---
     This is the PYTHON function, use only if you need this computation from
-    Python, if you need it from Cython, use `is_los_close_circle_core`
+    Python, if you need it from cython, use `is_los_close_circle_core`
     """
     return _dt.is_close_los_circle_core(<double*>ray_vdir.data,
                                         <double*>ray_orig.data,
@@ -3767,7 +3767,7 @@ def is_close_los_circle_vec(int nlos, int ncircles, double epsilon,
     The result is True when distance < epsilon
     ---
     This is the PYTHON function, use only if you need this computation from
-    Python, if you need it from Cython, use `is_los_close_circle_core`
+    Python, if you need it from cython, use `is_los_close_circle_core`
     """
     cdef array res = clone(array('i'), nlos, True)
 
@@ -3824,7 +3824,7 @@ def comp_dist_los_vpoly(double[:, ::1] ray_orig,
             `distance[i]` is the distance from P_i to the extruded polygon.
     ---
     This is the PYTHON function, use only if you need this computation from
-    Python, if you need it from Cython, use `simple_dist_los_vpoly_core`
+    Python, if you need it from cython, use `simple_dist_los_vpoly_core`
     """
     cdef int npts_poly = ves_poly.shape[1]
     cdef int nlos = ray_orig.shape[1]
@@ -3929,7 +3929,7 @@ def comp_dist_los_vpoly_vec(int nvpoly, int nlos,
             extruded poly.
     ---
     This is the PYTHON function, use only if you need this computation from
-    Python, if you need it from Cython, use `comp_dist_los_vpoly_vec_core`
+    Python, if you need it from cython, use `comp_dist_los_vpoly_vec_core`
     """
     if not algo_type.lower() == "simple" or not ves_type.lower() == "tor":
         assert False, "The function is only implemented with the simple"\
@@ -4003,7 +4003,7 @@ def is_close_los_vpoly_vec(int nvpoly, int nlos,
             and j-th poly are closer than epsilon. (True if distance<epsilon)
     ---
     This is the PYTHON function, use only if you need this computation from
-    Python, if you need it from Cython, use `is_close_los_vpoly_vec_core`
+    Python, if you need it from cython, use `is_close_los_vpoly_vec_core`
     """
     warn("This function supposes that the polys are nested from inner to outer",
          Warning)
@@ -4069,7 +4069,7 @@ def which_los_closer_vpoly_vec(int nvpoly, int nlos,
             among all other LOS without going over it.
     ---
     This is the PYTHON function, use only if you need this computation from
-    Python, if you need it from Cython, use `which_los_closer_vpoly_vec_core`
+    Python, if you need it from cython, use `which_los_closer_vpoly_vec_core`
     """
     warn("This function supposes that the polys are nested from inner to outer",
          Warning)
@@ -4129,7 +4129,7 @@ def which_vpoly_closer_los_vec(int nvpoly, int nlos,
             among all other poly without going over it.
     ---
     This is the PYTHON function, use only if you need this computation from
-    Python, if you need it from Cython, use `which_vpoly_closer_los_vec_core`
+    Python, if you need it from cython, use `which_vpoly_closer_los_vec_core`
     """
     warn("This function supposes that the polys are nested from inner to outer",
          Warning)

tofu/geom/_distance_tools.pyx

@@ -288,7 +288,7 @@ cdef inline void comp_dist_los_circle_vec_core(int num_los, int num_cir,
     # res = [kmin(los1, cir1), kmin(los1, cir2),...]
     # ---
     # This is the PYTHON function, use only if you need this computation from
-    # Python, if you need it from Cython, use `dist_los_circle_core`
+    # Python, if you need it from cython, use `dist_los_circle_core`
     """
     cdef int i, ind_los, ind_cir
     cdef double* loc_res
@@ -550,7 +550,7 @@ cdef inline void is_close_los_circle_vec_core(int num_los, int num_cir,
     res = [kmin(los1, cir1), kmin(los1, cir2),...]
     ---
     This is the PYTHON function, use only if you need this computation from
-    Python, if you need it from Cython, use `dist_los_circle_core`
+    Python, if you need it from cython, use `dist_los_circle_core`
     """
     cdef int i, ind_los, ind_cir
     cdef double* dirv
@@ -632,7 +632,7 @@ cdef inline void comp_dist_los_vpoly_vec_core(int num_poly, int nlos,
             `distance[j, i]` is the distance from P_i to the i-th extruded poly.
     ---
     This is the CYTHON function, use only if you need this computation from
-    Cython, if you need it from Python, use `comp_dist_los_vpoly_vec`
+    cython, if you need it from Python, use `comp_dist_los_vpoly_vec`
     """
     cdef int i, ind_los, ind_pol, ind_pol2
     cdef int npts_poly
@@ -771,7 +771,7 @@ cdef inline void simple_dist_los_vpoly_core(const double[3] ray_orig,
             `distance[i]` is the distance from P_i to the extruded polygon.
              if the i-th LOS intersects the poly, then distance[i] = Cnan
     ---
-    This is the Cython version, only accessible from cython. If you need
+    This is the cython version, only accessible from cython. If you need
     to use it from Python please use: comp_dist_los_vpoly
     """
     cdef int jj
@@ -1096,7 +1096,7 @@ cdef inline void is_close_los_vpoly_vec_core(int num_poly, int nlos,
             and j-th poly are closer than epsilon. (True if distance<epsilon)
     ---
     This is the CYTHON function, use only if you need this computation from
-    Cython, if you need it from Python, use `comp_dist_los_vpoly_vec`
+    cython, if you need it from Python, use `comp_dist_los_vpoly_vec`
     """
     cdef int i, ind_los, ind_pol, ind_pol2
     cdef int npts_poly
@@ -1187,7 +1187,7 @@ cdef inline void which_los_closer_vpoly_vec_core(int num_poly, int nlos,
             among all other LOS without going over it.
     ---
     This is the CYTHON function, use only if you need this computation from
-    Cython, if you need it from Python, use `comp_dist_los_vpoly_vec`
+    cython, if you need it from Python, use `comp_dist_los_vpoly_vec`
     """
     cdef int i, ind_los, ind_pol, ind_pol2, indloc
     cdef int npts_poly
@@ -1264,7 +1264,7 @@ cdef inline void which_vpoly_closer_los_vec_core(int num_poly, int nlos,
             among all other poly without going over it.
     ---
     This is the CYTHON function, use only if you need this computation from
-    Cython, if you need it from Python, use `comp_dist_los_vpoly_vec`
+    cython, if you need it from Python, use `comp_dist_los_vpoly_vec`
     """
     cdef int i, ind_los, ind_pol, ind_pol2, indloc
     cdef int npts_poly

tofu/version.py

@@ -1,2 +1,2 @@
 # Do not edit, pipeline versioning governed by git tags!
-__version__ = '1.4.2-alpha2'
+__version__ = '1.4.2-alpha2-13-g7db6643'