From 1aedfbb139d49a44846a5d2ed650f88a86275769 Mon Sep 17 00:00:00 2001
From: andthum <56444687+andthum@users.noreply.github.com>
Date: Wed, 19 Jul 2023 10:27:26 +0200
Subject: [PATCH] [tests.yml]: Install Cython and Numpy Before MDAnalysis

MDAnalysis `<3.0` requires Cython `<3.0` for compilation (see
https://github.com/MDAnalysis/mdanalysis/pull/4129 and
https://github.com/cython/cython/issues/3690).  Otherwise, installing
MDAnalysis via pip throws the following error:

``` shell
Error compiling Cython file:
------------------------------------------------------------
...
    array_wrapper = ArrayWrapper()
    array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type)

    cdef np.ndarray ndarray = np.array(array_wrapper, copy=False)
    # Assign our object to the 'base' of the ndarray object
    ndarray.base = <PyObject*> array_wrapper
           ^
------------------------------------------------------------

MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property

Traceback (most recent call last):
  File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module>
    main()
  File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main
    json_out['return_val'] = hook(**hook_input['kwargs'])
  File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel
    return hook(config_settings)
  File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel
    return self._get_build_requires(config_settings, requirements=['wheel'])
  File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires
    self.run_setup()
  File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup
    self).run_setup(setup_script=setup_script)
  File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup
    exec(code, locals())
  File "<string>", line 590, in <module>
  File "<string>", line 453, in extensions
  File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
    cythonize_one(*args)
  File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
    raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx
```

Furthermore, MDAnalysis requires at leas NumPy `>=1.16.0`, but better
Numpy `>=1.19.2` (see
https://github.com/MDAnalysis/mdanalysis/issues/3374#issuecomment-889189979),
for setup:

``` shell
*** package "numpy" not found ***
MDAnalysis requires a version of NumPy (>=1.16.0), even for setup.
Please get it from http://numpy.scipy.org/ or install it through your package manager.
```
---
 .github/workflows/tests.yml | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index ed21a3ff..d9274e79 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -192,7 +192,12 @@ jobs:
           restore-keys: |
             ${{ runner.os }}-${{ matrix.python-version }}
             ${{ runner.os }}
-      - name: "Install/Upgrade setuptools, wheel and python-dev-tools"
+      - name: "Install/Upgrade setuptools and wheel"
+        # MDAnalysis requires NumPy (>=1.19.2) for setup (see also
+        # https://github.com/MDAnalysis/mdanalysis/issues/3374#issuecomment-889189979).
+        # MDAnalysis <3.0 requires Cython <3.0 (see
+        # https://github.com/MDAnalysis/mdanalysis/pull/4129 and
+        # https://github.com/cython/cython/issues/3690).
         # Without `python-dev-tools` the installation of MDAnalysis
         # fails on MacOS-latest with Python 3.9 while building the wheel
         # for MDAnalysis.  Strangely, the MDAnalysis wheel is only build
@@ -201,9 +206,11 @@ jobs:
         run: |
           python -m pip install --user --upgrade setuptools wheel
           python -m pip install --user --upgrade python-dev-tools
+          python -m pip install --user "Cython <3.0"
+          python -m pip install --user "numpy >=1.19.2"
       - name: "Test installation of MDTools"
         run: |
-          python -m pip install --user --upgrade .
+          python -m pip install --user .
           python -c "import mdtools"
           # Test import of all modules that must be loaded explicitly.
           python -c "import mdtools.plot"