Merge pull request #33 from RMeli/develop

duecredit

.coveragerc

@@ -1,6 +1,8 @@
 [run]
 source = spyrmsd
-omit = spyrmsd/_version.py
+omit = 
+    spyrmsd/_version.py
+    spyrmsd/due.py
 
 [report]
 exclude_lines =

.github/FUNDING.yml

@@ -0,0 +1,12 @@
+# These are supported funding model platforms
+
+github: #
+patreon: # Replace with a single Patreon username
+open_collective: # Replace with a single Open Collective username
+ko_fi: # Replace with a single Ko-fi username
+tidelift: # Replace with a single Tidelift platform-name/package-name e.g., npm/babel
+community_bridge: # Replace with a single Community Bridge project-name e.g., cloud-foundry
+liberapay: # Replace with a single Liberapay username
+issuehunt: # Replace with a single IssueHunt username
+otechie: # Replace with a single Otechie username
+custom: ["https://www.buymeacoffee.com/rmeli"]

.gitignore

@@ -70,6 +70,9 @@ ENV/
 # mypy
 .mypy_cache/
 
+# duecredit
+.duecredit.p
+
 # macOS
 .DS_Store
 

README.md

@@ -121,6 +121,10 @@ To ensure code quality and consistency the following tools are used during devel
 
 Copyright (c) 2019-2020, Rocco Meli.
 
+## References
+
+References are tracked with [duecredit](https://github.com/duecredit/duecredit/). Run the `credits.sh` script in order to print up-to-date references.
+
 ### Acknowledgements
 
 Project based on the [Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version `1.1`.

credits.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+cd tests
+
+python -m duecredit test_import.py
+
+printf "\n\nBIBTEX\n------\n\n"
+
+duecredit summary --format bibtex

devtools/conda-envs/spyrmsd-all.yaml

@@ -35,7 +35,9 @@ dependencies:
 
   # Doc
   - sphinx
-  - sphinx_rtd_theme 
+  - sphinx_rtd_theme
+  - pip:
+    - duecredit
 
   # Dev
   - mypy

setup.py

@@ -32,6 +32,7 @@
     include_package_data=True,
     url="https://spyrmsd.readthedocs.io",
     install_requires=["numpy", "scipy", "qcelemental", "networkx>=2"],
+    extras_require={"bib": ["duecredit"]},
     platforms=["Linux", "Mac OS-X", "Unix", "Windows"],
     python_requires=">=3.6",
 )

spyrmsd/__init__.py

@@ -2,10 +2,17 @@
 Python RMSD tool with symmetry correction.
 """
 
-# Handle versioneer
+from .due import due, Doi
 from ._version import get_versions
 
 versions = get_versions()
 __version__ = versions["version"]
 __git_revision__ = versions["full-revisionid"]
 del get_versions, versions
+
+# This will print latest Zenodo version
+due.cite(
+    Doi("10.5281/zenodo.3631876"),  # lgtm[py/procedure-return-value-used]
+    path="spyrmsd",
+    description="spyRMSD: Symmetry-Corrected RMSD in Python",
+)

spyrmsd/due.py

@@ -0,0 +1,79 @@
+# emacs: at the end of the file
+# ex: set sts=4 ts=4 sw=4 et:
+# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### #
+"""
+
+Stub file for a guaranteed safe import of duecredit constructs:  if duecredit
+is not available.
+
+To use it, place it into your project codebase to be imported, e.g. copy as
+
+    cp stub.py /path/tomodule/module/due.py
+
+Note that it might be better to avoid naming it duecredit.py to avoid shadowing
+installed duecredit.
+
+Then use in your code as
+
+    from .due import due, Doi, BibTeX, Text
+
+See  https://github.com/duecredit/duecredit/blob/master/README.md for examples.
+
+Origin:     Originally a part of the duecredit
+Copyright:  2015-2019  DueCredit developers
+License:    BSD-2
+"""
+
+__version__ = "0.0.8"
+
+
+class InactiveDueCreditCollector(object):
+    """Just a stub at the Collector which would not do anything"""
+
+    def _donothing(self, *args, **kwargs):
+        """Perform no good and no bad"""
+        pass
+
+    def dcite(self, *args, **kwargs):
+        """If I could cite I would"""
+
+        def nondecorating_decorator(func):
+            return func
+
+        return nondecorating_decorator
+
+    active = False
+    activate = add = cite = dump = load = _donothing
+
+    def __repr__(self):
+        return self.__class__.__name__ + "()"
+
+
+def _donothing_func(*args, **kwargs):
+    """Perform no good and no bad"""
+    pass
+
+
+try:
+    from duecredit import due, BibTeX, Doi, Url, Text  # lgtm[py/unused-import]
+
+    if "due" in locals() and not hasattr(due, "cite"):
+        raise RuntimeError("Imported due lacks .cite. DueCredit is now disabled")
+except Exception as e:
+    if not isinstance(e, ImportError):
+        import logging
+
+        logging.getLogger("duecredit").error(
+            "Failed to import duecredit due to %s" % str(e)
+        )
+    # Initiate due stub
+    due = InactiveDueCreditCollector()
+    BibTeX = Doi = Url = Text = _donothing_func
+
+# Emacs mode definitions
+# Local Variables:
+# mode: python
+# py-indent-offset: 4
+# tab-width: 4
+# indent-tabs-mode: nil
+# End:

spyrmsd/hungarian.py

@@ -1,6 +1,14 @@
 import numpy as np
 import scipy
 
+from .due import due, Doi
+
+due.cite(
+    Doi("10.1021/ci400534h"),  # lgtm[py/procedure-return-value-used]
+    path="spyrmsd.hungarian",
+    description="Hungarian method",
+)
+
 
 def cost_mtx(A: np.ndarray, B: np.ndarray):
     """

spyrmsd/qcp.py

@@ -3,6 +3,14 @@
 import numpy as np
 from scipy import optimize
 
+from .due import due, Doi
+
+due.cite(
+    Doi("10.1107/S0108767305015266"),  # lgtm[py/procedure-return-value-used]
+    path="spyrmsd.qcp",
+    description="QCP method",
+)
+
 
 def M_mtx(A: np.ndarray, B: np.ndarray) -> np.ndarray:
     """

tests/__init__.py

@@ -1,3 +0,0 @@
-"""
-Empty init file in case you choose a package besides PyTest such as Nose which may look for such a file
-"""

tests/test_import.py

@@ -0,0 +1,36 @@
+"""
+Test imported package and modules.
+
+This test is useful to generate a citation report:
+
+.. code
+
+   python -m duecite test_import.py
+
+"""
+
+import sys
+
+import pytest
+
+from spyrmsd import graph, hungarian, io, molecule, qcp, rmsd, spyrmsd, utils
+
+
+@pytest.mark.parametrize(
+    "name",
+    [
+        # Package
+        spyrmsd.__name__,
+        # Modules
+        graph.__name__,
+        hungarian.__name__,
+        io.__name__,
+        molecule.__name__,
+        qcp.__name__,
+        rmsd.__name__,
+        spyrmsd.__name__,
+        utils.__name__,
+    ],
+)
+def test_imported(name):
+    assert name in sys.modules