requirements for cython version (#322)

in environment yml files, and in installation documentation.

Author: sguillot

basic_environment.yml

@@ -3,7 +3,7 @@ channels:
   - defaults
 dependencies:
   - numpy
-  - cython
+  - cython ~= 0.29
   - matplotlib
   - scipy
   - wrapt

docs/source/HPC_systems.rst

@@ -236,7 +236,7 @@ Let's start by loading the necessary modules and creating a conda environment. A
    conda create -n xpsi_py3 python=3.10.6
    conda activate xpsi_py3
    conda install -c conda-forge mpi4py
-   conda install cython
+   conda install cython ~= 0.29
    conda install scipy
    conda install matplotlib
    conda install wrapt   
@@ -336,7 +336,7 @@ Then, create the conda environnnement and Install python packages with conda (or
     conda create -n xpsi --clone base
     conda activate xpsi
     conda install numpy scipy matplotlib wrapt
-    conda install cython
+    conda install cython ~= 0.29
     conda install h5py
     conda install -c conda-forge fgivenx
     pip install schwimmbad --user

docs/source/install.rst

@@ -44,18 +44,23 @@ contents are:
         - defaults
     dependencies:
         - numpy
-        - cython
+        - cython ~= 0.29
         - matplotlib
         - scipy
         - wrapt
 
 
 The core packages required for likelihood functionality are
 `numpy <https://docs.scipy.org/doc/numpy/index.html>`_,
-`cython <http://cython.readthedocs.io/en/latest>`_,
+`cython <http://cython.readthedocs.io/en/latest>`_ (< 1.0),
 `matplotlib <https://matplotlib.org/stable/index.html>`_,
 `scipy <https://docs.scipy.org/doc//scipy/index.html>`_, and
-`wrapt <https://wrapt.readthedocs.io/en/latest/>`_. 
+`wrapt <https://wrapt.readthedocs.io/en/latest/>`_.  The
+latest versions of ``cython (3.*)`` are not currently
+compatible with X-PSI (versions 1.* and 2.* of ``cython``
+were skipped). Therefore, it is important to install
+``cython ~= 0.29``, which will ensure that a compatible
+version is installed.
 
 
 To create a virtual environment from this file:
@@ -408,8 +413,8 @@ OS. Here we note some of the changes required.
 After creating the environment using the ``environment.yml`` file, 
 install ``xcode`` or ``xcode tools``. Be mindful of the sequence of programs to
 be installed hereafter. Use ``pip install`` to download and install ``h5py``
-and ``emcee`` (and ``maplotlib``, ``numpy``, ``scipy`` and ``cython`` if not
-using the ``environment.yml``. You may use the file as a reference of the
+and ``emcee`` (and ``maplotlib``, ``numpy``, ``scipy`` and ``cython ~= 0.29``
+if not using the ``environment.yml``. You may use the file as a reference of the
 packages required).
 
 On Mac OS, it's preferable to use ``llvm clang`` rather than ``gcc``.  The

environment.yml

@@ -4,7 +4,7 @@ channels:
         - conda-forge
 dependencies:
         - numpy
-        - cython
+        - cython ~= 0.29
         - matplotlib
         - scipy
         - wrapt

setup.py

@@ -306,7 +306,7 @@ def EXTENSION(modname):
                     'xpsi/utilities',
                     'xpsi/pixelmesh'],
         install_requires = ['numpy'],
-        setup_requires = ['cython'],
+        setup_requires = ['cython ~= 0.29'],
         package_data = {'': ['README.rst', 'LICENSE']},
         include_package_data = True,
         ext_modules = extensions,