diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 12b409f012d..ff92d0a53a9 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -56,7 +56,7 @@ jobs: # overwrite installs by picking up nightly wheels - name: nightly_wheels run: | - pip install --pre -U -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple scipy numpy networkx matplotlib + pip install --pre -U -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple scipy numpy networkx matplotlib pandas - name: list_deps run: | diff --git a/package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py b/package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py index 53d6bc73b95..d69040736bb 100644 --- a/package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py +++ b/package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py @@ -250,6 +250,10 @@ from ...due import due, Doi + +logger = logging.getLogger(__name__) + + due.cite(Doi("10.1039/C9CP01532A"), description="Hydrogen bond analysis implementation", path="MDAnalysis.analysis.hydrogenbonds.hbond_analysis", @@ -838,25 +842,25 @@ def lifetime(self, tau_max=20, window_step=1, intermittency=0): """ if self.results.hbonds is None: - logging.error( + logger.error( "Autocorrelation analysis of hydrogen bonds cannot be done" "before the hydrogen bonds are found" ) - logging.error( + logger.error( "Autocorrelation: Please use the .run() before calling this" "function" ) raise NoDataError(".hbonds attribute is None: use .run() first") if self.step != 1: - logging.warning( + logger.warning( "Autocorrelation: Hydrogen bonds were computed with step > 1." ) - logging.warning( + logger.warning( "Autocorrelation: We recommend recomputing hydrogen bonds with" " step = 1." ) - logging.warning( + logger.warning( "Autocorrelation: if you would like to allow bonds to break" " and reform, please use 'intermittency'" )