From be09a9150c3ad7dc550a284a1464768e482e75de Mon Sep 17 00:00:00 2001 From: Mahfuza Humayra Mohona Date: Mon, 14 Oct 2024 01:16:42 +0600 Subject: [PATCH 1/6] fixed okwarning block warning --- doc/source/conf.py | 9 +++++++++ doc/source/reading_and_writing.rst | 1 + 2 files changed, 10 insertions(+) diff --git a/doc/source/conf.py b/doc/source/conf.py index e5c40d3ab..0dfdd9d2f 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -15,8 +15,17 @@ import datetime import subprocess +import warnings + +warnings.filterwarnings( + 'ignore', + message='DCDReader currently makes independent timesteps', + category=DeprecationWarning, + module='MDAnalysis.coordinates.DCD' +) import MDAnalysis as mda +MDAnalysis_version = mda.__version__ # -- Project information ----------------------------------------------------- diff --git a/doc/source/reading_and_writing.rst b/doc/source/reading_and_writing.rst index a32dd7e52..0b09301b6 100644 --- a/doc/source/reading_and_writing.rst +++ b/doc/source/reading_and_writing.rst @@ -212,6 +212,7 @@ be attached to the new :class:`MDAnalysis.core.groups.AtomGroup`. If the Univers with its :class:`MDAnalysis.core.groups.AtomGroup`, they will still be bound together afterwards: .. ipython:: python + :okwarning: import pickle from MDAnalysis.tests.datafiles import PSF, DCD From 54f0508233cae1008bbe9e8137d56eebad9b7d7e Mon Sep 17 00:00:00 2001 From: Mahfuza Humayra Mohona Date: Mon, 14 Oct 2024 01:30:38 +0600 Subject: [PATCH 2/6] ran pre-commit --- doc/source/conf.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/doc/source/conf.py b/doc/source/conf.py index 0dfdd9d2f..fe62606e6 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -18,13 +18,14 @@ import warnings warnings.filterwarnings( - 'ignore', - message='DCDReader currently makes independent timesteps', + "ignore", + message="DCDReader currently makes independent timesteps", category=DeprecationWarning, - module='MDAnalysis.coordinates.DCD' + module="MDAnalysis.coordinates.DCD", ) import MDAnalysis as mda + MDAnalysis_version = mda.__version__ # -- Project information ----------------------------------------------------- From 9b5b3e8c9a8a2f8823ce2607cd35f5611087df8e Mon Sep 17 00:00:00 2001 From: Mahfuza Humayra Mohona Date: Tue, 15 Oct 2024 01:42:36 +0600 Subject: [PATCH 3/6] remove about google group --- doc/source/contributing.rst | 2 -- 1 file changed, 2 deletions(-) diff --git a/doc/source/contributing.rst b/doc/source/contributing.rst index 638c3c579..1d8b042d6 100644 --- a/doc/source/contributing.rst +++ b/doc/source/contributing.rst @@ -85,8 +85,6 @@ Getting started with Git setting up your SSH key, and configuring git. All these steps need to be completed before you can work seamlessly between your local repository and GitHub. -.. _`mdnalysis-discussion`: - http://groups.google.com/group/mdnalysis-discussion .. _`Code of Conduct`: https://www.mdanalysis.org/pages/conduct/ .. _`Issue Tracker`: https://github.com/MDAnalysis/mdanalysis/issues .. _`MDAKits registry`: https://mdakits.mdanalysis.org/mdakits.html From 837e792e693a50765b8fbe545c9e65a6d5ab757f Mon Sep 17 00:00:00 2001 From: Mahfuza Humayra Mohona Date: Tue, 15 Oct 2024 01:49:16 +0600 Subject: [PATCH 4/6] Revert "remove about google group" This reverts commit 9b5b3e8c9a8a2f8823ce2607cd35f5611087df8e. --- doc/source/contributing.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/source/contributing.rst b/doc/source/contributing.rst index 1d8b042d6..638c3c579 100644 --- a/doc/source/contributing.rst +++ b/doc/source/contributing.rst @@ -85,6 +85,8 @@ Getting started with Git setting up your SSH key, and configuring git. All these steps need to be completed before you can work seamlessly between your local repository and GitHub. +.. _`mdnalysis-discussion`: + http://groups.google.com/group/mdnalysis-discussion .. _`Code of Conduct`: https://www.mdanalysis.org/pages/conduct/ .. _`Issue Tracker`: https://github.com/MDAnalysis/mdanalysis/issues .. _`MDAKits registry`: https://mdakits.mdanalysis.org/mdakits.html From d8713d0933646e3ca8016993dbdf281b502704bb Mon Sep 17 00:00:00 2001 From: Mahfuza Humayra Mohona Date: Thu, 19 Dec 2024 07:02:32 +0600 Subject: [PATCH 5/6] addressed review --- doc/source/conf.py | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/doc/source/conf.py b/doc/source/conf.py index fe62606e6..e5c40d3ab 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -15,19 +15,9 @@ import datetime import subprocess -import warnings - -warnings.filterwarnings( - "ignore", - message="DCDReader currently makes independent timesteps", - category=DeprecationWarning, - module="MDAnalysis.coordinates.DCD", -) import MDAnalysis as mda -MDAnalysis_version = mda.__version__ - # -- Project information ----------------------------------------------------- project = "MDAnalysis User Guide" From 399f94199e34d7780f8c3fccde7d1646be34008d Mon Sep 17 00:00:00 2001 From: Mahfuza Humayra Mohona Date: Thu, 19 Dec 2024 07:02:32 +0600 Subject: [PATCH 6/6] addressed review --- doc/source/conf.py | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/doc/source/conf.py b/doc/source/conf.py index fe62606e6..e5c40d3ab 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -15,19 +15,9 @@ import datetime import subprocess -import warnings - -warnings.filterwarnings( - "ignore", - message="DCDReader currently makes independent timesteps", - category=DeprecationWarning, - module="MDAnalysis.coordinates.DCD", -) import MDAnalysis as mda -MDAnalysis_version = mda.__version__ - # -- Project information ----------------------------------------------------- project = "MDAnalysis User Guide"