Force cython<3 for build and docs and revert to mpsort and pfft-pytho…

…n from PyPI

Added missing file and cleanup unused file

Change order in requirements and changes setup

Force cython<3 in ci.yml

Fix cython version in docs as well

Get mpsort from PyPI

Cython<3 in buildDocs and pfft-python from PyPI

.github/workflows/ci.yml

@@ -39,7 +39,7 @@ jobs:
     - name: Install python dependencies
       run: |
         python3 -m pip install --upgrade pip
-        python3 -m pip install --upgrade wheel numpy mpi4py cython
+        python3 -m pip install --upgrade wheel numpy mpi4py "cython<3"
         CC="mpicc" HDF5_MPI="ON" python3 -m pip install --no-binary=h5py h5py
         python3 -m pip install -r requirements.txt
     - name: Install PLUMED

.github/workflows/docs_pages.yml

@@ -31,7 +31,7 @@ jobs:
     - name: Install python dependencies
       run: |
         python3 -m pip install --upgrade pip
-        python3 -m pip install --upgrade wheel numpy mpi4py cython
+        python3 -m pip install --upgrade wheel numpy mpi4py "cython<3"
         python3 -m pip install -r requirements.txt
     - name: Install package
       run: |

docs/buildDocs.sh

@@ -20,7 +20,7 @@ set -e
 sudo apt-get update
 sudo apt-get -y install git make rsync wget pkg-config libhdf5-serial-dev python3-numpy python3-h5py python3-mpi4py python3-pip python3-git
 
-python3 -m pip install -U cython numpy mpi4py
+python3 -m pip install -U "cython<3" numpy mpi4py
 python3 -m pip install -r requirements.txt
 python3 -m pip install -r docs/docs_requirements.txt
 python3 -m pip install .

pyproject.toml

@@ -1,4 +1,4 @@
 [build-system]
-requires = ["setuptools<60", "wheel", "numpy<1.25", "cython", "mpi4py"]
+requires = ["setuptools<60", "wheel", "numpy<1.25", "mpi4py", "cython<3"]
 [tool.black]
 exclude = "\\(./)"

requirements.txt

@@ -1,10 +1,10 @@
-cython
 h5py
 mpi4py
-mpsort @ git+https://github.com/rainwoodman/MP-sort
 networkx
 numpy<1.25
-pfft-python @ git+https://github.com/rainwoodman/pfft-python
-pmesh @ git+https://github.com/rainwoodman/pmesh
 sympy
 tomli
+cython<3
+mpsort
+pfft-python
+pmesh @ git+https://github.com/rainwoodman/pmesh

setup.py

@@ -50,7 +50,7 @@ def find_version(path):
     version=find_version("hymd/version.py"),
     ext_modules=[force_kernels],
     setup_requires=[
-        "cython",
+        "cython<3",
         "numpy",
         "mpi4py",
     ],