Make tests with MPI only

Author: matteobachetti

.github/workflows/ci_test.yml

@@ -95,42 +95,45 @@ jobs:
       matrix:
         include:
           - os: ubuntu-latest
-            python: '3.10'
+            python: '3.13'
             tox_env: 'codestyle'
           - os: ubuntu-latest
-            python: '3.12'
-            tox_env: 'py312-test-cov'
+            python: '3.13'
+            tox_env: 'py313-test-cov'
+          - os: ubuntu-latest
+            python: '3.13'
+            tox_env: 'py313-test-mpi-cov'
           - os: ubuntu-latest
             python: '3.9'
             tox_env: 'py39-test-cov'
           - os: ubuntu-latest
-            python: '3.11'
-            tox_env: 'py311-test-alldeps-cov'
+            python: '3.13'
+            tox_env: 'py313-test-alldeps-cov'
             use_remote_data: true
           - os: macos-14
-            python: '3.11'
-            tox_env: 'py311-test-alldeps-cov'
+            python: '3.13'
+            tox_env: 'py313-test-alldeps-cov'
             use_remote_data: true
           - os: ubuntu-latest
-            python: '3.12'
-            tox_env: 'py312-test-devdeps'
+            python: '3.14'
+            tox_env: 'py314-test-devdeps'
             use_remote_data: true
             continue-on-error: true
           - os: ubuntu-latest
-            python: '3.12'
-            tox_env: 'py312-test-devpint'
+            python: '3.13'
+            tox_env: 'py313-test-devpint'
             use_remote_data: true
             continue-on-error: true
           - os: ubuntu-latest
             python: '3.9'
             tox_env: 'py39-test-oldestdeps-cov'
             use_remote_data: true
           - os: macos-latest
-            python: '3.11'
-            tox_env: 'py311-test'
+            python: '3.13'
+            tox_env: 'py313-test'
           - os: windows-latest
-            python: '3.11'
-            tox_env: 'py311-test'
+            python: '3.13'
+            tox_env: 'py313-test'
 
     steps:
     - name: Check out repository

hendrics/tests/test_parallel.py

@@ -49,11 +49,7 @@ def test_parallel_versions(self, method, norm):
             "--norm",
             norm,
         ]
-        if method == "mpi":
-            command = ["mpirun", "-n", "4", "HENparfspec"] + command
-            sp.check_call(command)
-        else:
-            main_parallel(command)
+        main_parallel(command)
 
         pds = AveragedPowerspectrum.read(out_file.name)
         compare_pds = self.pds.to_norm(norm) if norm != "leahy" else self.pds

pyproject.toml

@@ -58,7 +58,6 @@ test_all = [
     "numba",
     "netcdf4==1.7.0",
     "scikit-image",
-    "mpi4py",
 ]
 recommended = [
     "numba",
@@ -73,7 +72,6 @@ all = [
     "imageio",
     "netcdf4==1.7.0",
     "scikit-image",
-    "mpi4py",
 ]
 docs = [
     "tomli>=1.1.0; python_version < '3.11'",

tox.ini

@@ -36,6 +36,7 @@ description =
     cov: and test coverage
     astropy4: with astropy 4
     astropy5: with astropy 5
+    mpi: with MPI support
 
 setenv =
     devdeps: PIP_EXTRA_INDEX_URL = https://pypi.anaconda.org/scientific-python-nightly-wheels/simple https://pypi.anaconda.org/astropy/simple https://pypi.anaconda.org/liberfa/simple
@@ -58,6 +59,11 @@ deps =
     devpint: git+https://github.com/nanograv/pint.git#egg=pint-pulsar
     devdeps: git+https://github.com/stingraysoftware/stingray.git#egg=stingray
     alldeps: netcdf4==1.7.0
+    mpi: mpi4py
+
+
+allowlist_externals =
+    mpi: mpirun
 
 # The following indicates which extras_require will be installed
 extras =
@@ -67,10 +73,13 @@ extras =
 commands =
     # Force numpy reinstall to work around upper version limits dependencies put on numpy
     devdeps: pip install -U --pre --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy
+    mpi: pip install mpi4py h5py
 
     pip freeze
-    !cov: pytest --pyargs hendrics {toxinidir}/docs {posargs}
-    cov: pytest --pyargs hendrics {toxinidir}/docs --cov hendrics --cov-config={toxinidir}/pyproject.toml {posargs}
+    mpi: mpirun -n 1 pytest --pyargs hendrics -k mpi {posargs} --cov hendrics --cov-config={toxinidir}/pyproject.toml {posargs}
+
+    !mpi-!cov: pytest --pyargs hendrics {toxinidir}/docs {posargs}
+    !mpi-cov: pytest --pyargs hendrics {toxinidir}/docs --cov hendrics --cov-config={toxinidir}/pyproject.toml {posargs}
     cov: coverage xml -o {toxinidir}/coverage.xml
 
 [testenv:build_docs]