From 2046e47fda362dc8d30807cfec7c5cd8755bdb50 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Mon, 14 Aug 2023 21:21:33 +0100 Subject: [PATCH 1/6] Add pandas to nightly wheel installs --- .github/workflows/gh-ci-cron.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 12b409f012..ff92d0a53a 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: | From 1593ac50ec11dd1dd9a7be294051bc89ea6582ac Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Mon, 14 Aug 2023 21:22:26 +0100 Subject: [PATCH 2/6] temporarily enable cron CI --- .github/workflows/gh-ci-cron.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index ff92d0a53a..49a23d4e4e 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -3,6 +3,9 @@ on: schedule: # 3 am Tuesdays and Fridays - cron: "0 3 * * 2,5" + pull_request: + branches: + - develop concurrency: # Probably overly cautious group naming. From cfa5585d682304e2dea95a4f99183186692efe2f Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Mon, 14 Aug 2023 23:13:28 +0100 Subject: [PATCH 3/6] et tu pandas? (investigate logger issue) --- .github/workflows/gh-ci-cron.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 49a23d4e4e..2272c0c13e 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -59,7 +59,7 @@ 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 pandas + pip install --pre -U -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple scipy numpy networkx matplotlib - name: list_deps run: | From 257dd376c1f541ae9471a226a4a28fd0783627ed Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Mon, 14 Aug 2023 23:29:00 +0100 Subject: [PATCH 4/6] add pandas back --- .github/workflows/gh-ci-cron.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 2272c0c13e..49a23d4e4e 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -59,7 +59,7 @@ 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: | From 8b9e88239fbc700911968684d8c83172fb513bf7 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 14 Aug 2023 23:55:02 +0100 Subject: [PATCH 5/6] proctect the logger --- .../analysis/hydrogenbonds/hbond_analysis.py | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py b/package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py index 53d6bc73b9..d69040736b 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'" ) From 8c237b48acc74520e62cbdd1867be3f6a18be691 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Tue, 15 Aug 2023 00:14:09 +0100 Subject: [PATCH 6/6] Update gh-ci-cron.yaml --- .github/workflows/gh-ci-cron.yaml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 49a23d4e4e..ff92d0a53a 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -3,9 +3,6 @@ on: schedule: # 3 am Tuesdays and Fridays - cron: "0 3 * * 2,5" - pull_request: - branches: - - develop concurrency: # Probably overly cautious group naming.