runtime tests

.gitattributes

@@ -0,0 +1 @@
+sf_ip_ea/_static_version.py export-subst

.travis.yml

@@ -6,7 +6,7 @@ install:
   - sudo apt-get update
   # We do this conditionally because it saves us some downloading if the
   # version is the same.
-  - wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH="$HOME/miniconda/bin:$PATH"
   - conda config --set always_yes yes --set changeps1 no

LICENSE.txt

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2019-2021, Shannon E. Houck
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

setup.py

@@ -1,14 +1,49 @@
 from distutils.core import setup
+import setuptools
+
+
+def get_version_and_cmdclass(package_path):
+    """Load version.py module without importing the whole package.
+
+    Template code from miniver
+    """
+    import os
+    from importlib.util import module_from_spec, spec_from_file_location
+
+    spec = spec_from_file_location("version", os.path.join(package_path, "_version.py"))
+    module = module_from_spec(spec)
+    spec.loader.exec_module(module)
+    return module.__version__, module.cmdclass
+
+
+version, cmdclass = get_version_and_cmdclass("sf_ip_ea")
+
 
 setup(
     name='sf_ip_ea',
-    version='0.1.0',
+    version=version,
+    cmdclass=cmdclass,
     author='Shannon E. Houck',
     author_email='shouck@vt.edu',
-    packages=['sf_ip_ea', 'sf_ip_ea.test'],
+    packages=setuptools.find_packages(),
+    include_package_data=True,
     scripts=[],
     url='',
     license='LICENSE.txt',
+    install_requires=[
+        "numpy>=1.7",
+        "scipy",
+    ],
+    extras_require={
+        "tests": ["pytest",],
+    },
+    tests_require=["pytest",],
+    classifiers=[
+        "Development Status :: 4 - Beta",
+        "Intended Audience :: Science/Research",
+        "Programming Language :: Python :: 3",
+    ],
+    zip_safe=False,
     description='Stand-alone RAS-SF-IP/EA code.',
     long_description=open('README.md').read(),
 )

sf_ip_ea/__init__.py

@@ -119,3 +119,4 @@ def fock_ci(delta_a, delta_b, mol, conf_space="", ref_opts={}, sf_opts={},
         print("ERROR: Program %s is not yet supported. Exiting..." %(program) )
         exit()
 
+from ._version import __version__

sf_ip_ea/_static_version.py

@@ -0,0 +1,12 @@
+# -*- coding: utf-8 -*-
+# This file is part of 'miniver': https://github.com/jbweston/miniver
+#
+# This file will be overwritten by setup.py when a source or binary
+# distribution is made.  The magic value "__use_git__" is interpreted by
+# version.py.
+
+version = "__use_git__"
+
+# These values are only set if the distribution was created with 'git archive'
+refnames = "$Format:%D$"
+git_hash = "$Format:%h$"

sf_ip_ea/_version.py

@@ -0,0 +1,207 @@
+# -*- coding: utf-8 -*-
+# This file is part of 'miniver': https://github.com/jbweston/miniver
+#
+from collections import namedtuple
+import os
+import subprocess
+
+from setuptools.command.build_py import build_py as build_py_orig
+from setuptools.command.sdist import sdist as sdist_orig
+
+Version = namedtuple("Version", ("release", "dev", "labels"))
+
+# No public API
+__all__ = []
+
+package_root = os.path.dirname(os.path.realpath(__file__))
+package_name = os.path.basename(package_root)
+distr_root = os.path.dirname(package_root)
+# If the package is inside a "src" directory the
+# distribution root is 1 level up.
+if os.path.split(distr_root)[1] == "src":
+    _package_root_inside_src = True
+    distr_root = os.path.dirname(distr_root)
+else:
+    _package_root_inside_src = False
+
+STATIC_VERSION_FILE = "_static_version.py"
+
+
+def get_version(version_file=STATIC_VERSION_FILE):
+    version_info = get_static_version_info(version_file)
+    version = version_info["version"]
+    if version == "__use_git__":
+        version = get_version_from_git()
+        if not version:
+            version = get_version_from_git_archive(version_info)
+        if not version:
+            version = Version("unknown", None, None)
+        return pep440_format(version)
+    else:
+        return version
+
+
+def get_static_version_info(version_file=STATIC_VERSION_FILE):
+    version_info = {}
+    with open(os.path.join(package_root, version_file), "rb") as f:
+        exec(f.read(), {}, version_info)
+    return version_info
+
+
+def version_is_from_git(version_file=STATIC_VERSION_FILE):
+    return get_static_version_info(version_file)["version"] == "__use_git__"
+
+
+def pep440_format(version_info):
+    release, dev, labels = version_info
+
+    version_parts = [release]
+    if dev:
+        if release.endswith("-dev") or release.endswith(".dev"):
+            version_parts.append(dev)
+        else:  # prefer PEP440 over strict adhesion to semver
+            version_parts.append(".dev{}".format(dev))
+
+    if labels:
+        version_parts.append("+")
+        version_parts.append(".".join(labels))
+
+    return "".join(version_parts)
+
+
+def get_version_from_git():
+    try:
+        p = subprocess.Popen(
+            ["git", "rev-parse", "--show-toplevel"],
+            cwd=distr_root,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+        )
+    except OSError:
+        return
+    if p.wait() != 0:
+        return
+    if not os.path.samefile(p.communicate()[0].decode().rstrip("\n"), distr_root):
+        # The top-level directory of the current Git repository is not the same
+        # as the root directory of the distribution: do not extract the
+        # version from Git.
+        return
+
+    # git describe --first-parent does not take into account tags from branches
+    # that were merged-in. The '--long' flag gets us the 'dev' version and
+    # git hash, '--always' returns the git hash even if there are no tags.
+    for opts in [["--first-parent"], []]:
+        try:
+            p = subprocess.Popen(
+                ["git", "describe", "--long", "--always"] + opts,
+                cwd=distr_root,
+                stdout=subprocess.PIPE,
+                stderr=subprocess.PIPE,
+            )
+        except OSError:
+            return
+        if p.wait() == 0:
+            break
+    else:
+        return
+
+    description = (
+        p.communicate()[0]
+        .decode()
+        .strip("v")  # Tags can have a leading 'v', but the version should not
+        .rstrip("\n")
+        .rsplit("-", 2)  # Split the latest tag, commits since tag, and hash
+    )
+
+    try:
+        release, dev, git = description
+    except ValueError:  # No tags, only the git hash
+        # prepend 'g' to match with format returned by 'git describe'
+        git = "g{}".format(*description)
+        release = "unknown"
+        dev = None
+
+    labels = []
+    if dev == "0":
+        dev = None
+    else:
+        labels.append(git)
+
+    try:
+        p = subprocess.Popen(["git", "diff", "--quiet"], cwd=distr_root)
+    except OSError:
+        labels.append("confused")  # This should never happen.
+    else:
+        if p.wait() == 1:
+            labels.append("dirty")
+
+    return Version(release, dev, labels)
+
+
+# TODO: change this logic when there is a git pretty-format
+#       that gives the same output as 'git describe'.
+#       Currently we can only tell the tag the current commit is
+#       pointing to, or its hash (with no version info)
+#       if it is not tagged.
+def get_version_from_git_archive(version_info):
+    try:
+        refnames = version_info["refnames"]
+        git_hash = version_info["git_hash"]
+    except KeyError:
+        # These fields are not present if we are running from an sdist.
+        # Execution should never reach here, though
+        return None
+
+    if git_hash.startswith("$Format") or refnames.startswith("$Format"):
+        # variables not expanded during 'git archive'
+        return None
+
+    VTAG = "tag: v"
+    refs = set(r.strip() for r in refnames.split(","))
+    version_tags = set(r[len(VTAG) :] for r in refs if r.startswith(VTAG))
+    if version_tags:
+        release, *_ = sorted(version_tags)  # prefer e.g. "2.0" over "2.0rc1"
+        return Version(release, dev=None, labels=None)
+    else:
+        return Version("unknown", dev=None, labels=["g{}".format(git_hash)])
+
+
+__version__ = get_version()
+
+
+# The following section defines a module global 'cmdclass',
+# which can be used from setup.py. The 'package_name' and
+# '__version__' module globals are used (but not modified).
+
+
+def _write_version(fname):
+    # This could be a hard link, so try to delete it first.  Is there any way
+    # to do this atomically together with opening?
+    try:
+        os.remove(fname)
+    except OSError:
+        pass
+    with open(fname, "w") as f:
+        f.write(
+            "# This file has been created by setup.py.\n"
+            "version = '{}'\n".format(__version__)
+        )
+
+
+class _build_py(build_py_orig):
+    def run(self):
+        super().run()
+        _write_version(os.path.join(self.build_lib, package_name, STATIC_VERSION_FILE))
+
+
+class _sdist(sdist_orig):
+    def make_release_tree(self, base_dir, files):
+        super().make_release_tree(base_dir, files)
+        if _package_root_inside_src:
+            p = os.path.join("src", package_name)
+        else:
+            p = package_name
+        _write_version(os.path.join(base_dir, p, STATIC_VERSION_FILE))
+
+
+cmdclass = dict(sdist=_sdist, build_py=_build_py)

sf_ip_ea/test/__init__.py

@@ -0,0 +1 @@
+

sf_ip_ea/test/conftest.py

@@ -0,0 +1,21 @@
+import pytest
+
+
+def pytest_configure(config):
+    # Register marks to avoid warnings in installed testing
+    # sync with setup.cfg
+    config.addinivalue_line("markers", "blochtest")
+    config.addinivalue_line("markers", "davidsontest")
+    config.addinivalue_line("markers", "dftest")
+    config.addinivalue_line("markers", "frozentest")
+    config.addinivalue_line("markers", "methodtest")
+
+
+@pytest.fixture(scope="function", autouse=True)
+def set_up():
+    import psi4
+
+    psi4.core.clean()
+    # psi4.core.clean_timers()  # uncomment when v1.4 is lowest supported
+    psi4.core.clean_options()
+    psi4.set_output_file("pytest_output.dat", True)

sf_ip_ea/test/pytest.ini

@@ -3,3 +3,5 @@ markers =
     methodtest: test the SF-IP/EA methods for correct energy values
     blochtest: test the Bloch effective Hamiltonian build
     frozentest: test frozen core/virtual
+    dftest
+    davidsontest