Add aarch64 testing via CirrusCI (#4120)

Fixes #4112
Towards #4054
* Use .cirrus.star file for handling CirrusCI jobs
* Add aarch64 entry for CirrusCI
* Don't run certain jobs expecting readonly or permission restricted files when running as root (Issue #4112)

.cirrus.star

@@ -0,0 +1,18 @@
+# See https://cirrus-ci.org/guide/programming-tasks/ for more information on
+# starlark CirrusCI files
+# Inspired by scipy's .cirrus.star script https://github.com/scipy/scipy/blob/main/.cirrus.star
+# In the spirit of ensuring this can also be freely used in derviative works by
+# the community, we release the contents of this file under the MIT license.
+
+
+load("cirrus", "env", "fs")
+
+
+def main(ctx):
+    # Default case: don't do anything if not in the core repo
+    # or if you're not targetting the develop branch
+    if ((env.get("CIRRUS_REPO_FULL_NAME") != "MDAnalysis/mdanalysis")
+        or (env.get("CIRRUS_BASE_BRANCH") != "develop")):
+        return []
+
+    return fs.read("maintainer/ci/cirrus-ci.yml")

maintainer/ci/cirrus-ci.yml

@@ -0,0 +1,31 @@
+linux_aarch64_task:
+  arm_container:
+    image: python:latest
+    cpu: 8
+    memory: 8G
+
+  ci_script: |
+    python3 --version
+    python3 -m venv mda-dev
+    source mda-dev/bin/activate
+    python3 -m pip install ./package
+    python3 -m pip install ./testsuite
+    python3 -m pip install pytest-xdist
+    python3 -m pytest -n 8 ./testsuite/MDAnalysisTests
+
+
+macos_arm64_task:
+  macos_instance:
+    image: ghcr.io/cirruslabs/macos-ventura-base:latest
+
+  ci_script: |
+    brew update
+    brew install [email protected]
+    /opt/homebrew/bin/python3 -m venv ~/py_311
+    source ~/py_311/bin/activate
+    cd package
+    python -m pip install .
+    cd ../testsuite
+    python -m pip install .
+    python -m pip install pytest pytest-xdist
+    python -m pytest -n auto MDAnalysisTests

package/CHANGELOG

@@ -22,6 +22,8 @@ The rules for this file:
  * 2.5.0
 
 Fixes
+  * Skip tests artificially checking for readonly or PermissionError cases
+    when running at root user on linux systems (Issue #4112, PR #4120)
   * Fix chi1_selections() ignored atom names CG1 OG OG1 SG and incorrectly returned
     None for amino acids CYS, ILE, SER, THR, VAL (Issue #4108)
   * Fix parsing of box vector in H5MD reader (Issue #4076)

testsuite/MDAnalysisTests/coordinates/test_xdr.py

@@ -44,6 +44,7 @@
 import MDAnalysis as mda
 from MDAnalysis.coordinates.base import Timestep
 from MDAnalysis.coordinates import XDR
+from MDAnalysisTests.util import get_userid
 
 
 class _XDRReader_Sub(object):
@@ -868,6 +869,7 @@ def test_unsupported_format(self, traj):
         reader = self._reader(traj)
         reader[idx_frame]
 
+    @pytest.mark.skipif(get_userid() == 0, reason="cannot readonly as root")
     def test_persistent_offsets_readonly(self, tmpdir):
         shutil.copy(self.filename, str(tmpdir))
 

testsuite/MDAnalysisTests/core/test_universe.py

@@ -57,6 +57,7 @@
 from MDAnalysisTests import assert_nowarns
 from MDAnalysis.exceptions import NoDataError
 from MDAnalysis.core.topologyattrs import AtomStringAttr
+from MDAnalysisTests.util import get_userid
 
 
 class IOErrorParser(TopologyReaderBase):
@@ -153,6 +154,8 @@ def test_Universe_invalidfile_IE_msg(self, tmpdir):
             else:
                 raise AssertionError
 
+    @pytest.mark.skipif(get_userid() == 0,
+                        reason="cannot permisssionerror as root")
     def test_Universe_invalidpermissionfile_IE_msg(self, tmpdir):
         # check for file with invalid permissions (eg. no read access)
         with tmpdir.as_cwd():

testsuite/MDAnalysisTests/util.py

@@ -251,3 +251,14 @@ def no_deprecated_call(func=None, *args, **kwargs):
         __tracebackhide__ = True
         with _NoDeprecatedCallContext():
             return func(*args, **kwargs)
+
+
+def get_userid():
+    """
+    Calls os.geteuid() where possible, or returns 1000 (usually on windows).
+    """
+    # no such thing as euid on Windows, assuming normal user 1000
+    if (os.name == 'nt' or not hasattr(os, "geteuid")):
+        return 1000
+    else:
+        return os.geteuid()