Duecredit for the MLE method

.github/workflows/ci.yml

@@ -68,9 +68,11 @@ jobs:
           python -Ic "import cinnabar; print(cinnabar.__version__)"
 
       - name: Run tests
+        env:
+          DUECREDIT_ENABLE: "yes"
         shell: bash -l {0}
         run: |
-          pytest -v --cov=cinnabar --cov-report=xml --cov-report=term --color=yes cinnabar/tests/
+          pytest -v --cov=cinnabar/ --cov-report=xml --cov-report=term --color=yes cinnabar/tests/
 
       - name: codecov
         if: ${{ github.repository == 'OpenFreeEnergy/cinnabar' && github.event_name != 'schedule'}}

cinnabar/_due.py

@@ -0,0 +1,81 @@
+# emacs: at the end of the file
+# ex: set sts=4 ts=4 sw=4 et:
+# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### #
+from __future__ import annotations
+
+from typing import Any
+
+"""
+
+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:  2015-2021  DueCredit developers
+License:    BSD-2
+"""
+
+__version__ = "0.0.9"
+
+
+class InactiveDueCreditCollector:
+    """Just a stub at the Collector which would not do anything"""
+
+    def _donothing(self, *_args: Any, **_kwargs: Any) -> None:
+        """Perform no good and no bad"""
+        pass
+
+    def dcite(self, *_args: Any, **_kwargs: Any):
+        """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) -> str:
+        return self.__class__.__name__ + "()"
+
+
+def _donothing_func(*args: Any, **kwargs: Any) -> None:
+    """Perform no good and no bad"""
+    pass
+
+
+try:
+    from duecredit import BibTeX, Doi, Text, Url, due  # 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(f"Failed to import duecredit due to {e}")
+    # Initiate due stub
+    due = InactiveDueCreditCollector()  # type: ignore[assignment]
+    BibTeX = Doi = Url = Text = _donothing_func  # type: ignore[assignment, misc]
+
+# Emacs mode definitions
+# Local Variables:
+# mode: python
+# py-indent-offset: 4
+# tab-width: 4
+# indent-tabs-mode: nil
+# End:

cinnabar/stats.py

@@ -4,6 +4,14 @@
 import sklearn.metrics
 from typing import Union
 
+from ._due import due, Doi
+
+due.cite(
+    Doi("10.1021/acs.jcim.9b00528"),
+    description="Compute maximum likelihood estimate of free energies and covariance in their estimates",
+    path="cinnabar.stats.mle",
+    cite_module=True
+)
 
 def bootstrap_statistic(
     y_true: np.ndarray,
@@ -139,7 +147,6 @@ def unique_differences(x):
 
     return rmse_stats
 
-
 def mle(
     graph: nx.DiGraph, factor: str = "f_ij", node_factor: Union[str, None] = None
 ) -> np.ndarray:
@@ -151,7 +158,7 @@ def mle(
     We assume the free energy of node 0 is zero.
 
     Reference : https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b00528
-    Xu, Huafengraph. "Optimal measurement network of pairwise differences."
+    Xu, Huafeng. "Optimal measurement network of pairwise differences."
     Journal of Chemical Information and Modeling 59.11 (2019): 4720-4728.
 
     NOTE: Self-edges (edges that connect a node to itself) will be ignored.

cinnabar/tests/test_due.py

@@ -0,0 +1,12 @@
+import pytest
+
+
+from cinnabar._due import due
+
+
+pytest.importorskip("duecredit")
+
+def test_duecredit_mle():
+    """Make sure duecredit is captured when the stats module is used"""
+    mle_key = ("cinnabar.stats.mle", "10.1021/acs.jcim.9b00528")
+    assert due.citations[mle_key].cites_module

devtools/conda-envs/env.yaml

@@ -14,6 +14,7 @@ dependencies:
   - scikit-learn
   - adjustText
   - openff-units
+  - duecredit<0.10
 
   # format
   - black

pyproject.toml

@@ -51,4 +51,9 @@ exclude_lines = [
   "pragma: no-cover",
   "-no-cov",
   "raise NotImplementedError",
-]
+]
+
+[tool.coverage.run]
+omit = [
+    "cinnabar/_due.py",
+]