From 0a24ff2fa9bb7b0930867034d5b4e7fb86afe98f Mon Sep 17 00:00:00 2001 From: "M. Eric Irrgang" Date: Thu, 19 Dec 2019 14:09:18 +0300 Subject: [PATCH] Add issue tracking for deprecations. Provide links in release notes to issue tracking for announced deprecations. Fixes #3251 Change-Id: I246651f8cb868eb1deecac86c2e7d6f0ec81b3f1 --- docs/release-notes/2019/major/deprecated-functionality.rst | 6 +++--- docs/release-notes/2020/major/deprecated-functionality.rst | 10 +++++----- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/release-notes/2019/major/deprecated-functionality.rst b/docs/release-notes/2019/major/deprecated-functionality.rst index 182ed84047..6b9b3ee136 100644 --- a/docs/release-notes/2019/major/deprecated-functionality.rst +++ b/docs/release-notes/2019/major/deprecated-functionality.rst @@ -41,7 +41,7 @@ Functionality deprecated in GROMACS 2019 Generation of virtual sites to replace aromatic rings in standard residues """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" -These are thought to produce artefacts under some circumstances +:issue:`3254` These are thought to produce artefacts under some circumstances (unpublished results), were never well tested, are not widely used, and we need to simplify pdb2gmx. @@ -54,7 +54,7 @@ to do communication between PP ranks less often should choose their Benchmarking options only available with ``gmx benchmark`` """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" -Options such as ``-confout``, ``-resethway``, ``-resetstep`` are not +:issue:`3255` Options such as ``-confout``, ``-resethway``, ``-resetstep`` are not intended for use by regular mdrun users, so making them only available with a dedicated tool is more clear. Also, this permits us to customize defaults for e.g. writing files at the end of a simulation part in ways @@ -63,7 +63,7 @@ will no longer be required. ``gmx mdrun -nsteps`` """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" -The number of simulation steps described by the .tpr file can be +:issue:`3256` The number of simulation steps described by the .tpr file can be changed with ``gmx convert-tpr``, or altered in .mdp file before the call to ``gmx grompp``. The convenience of this mdrun option was outweighted by the doubtful quality of its implementation, no clear diff --git a/docs/release-notes/2020/major/deprecated-functionality.rst b/docs/release-notes/2020/major/deprecated-functionality.rst index 8f1b2494eb..d08f7ade51 100644 --- a/docs/release-notes/2020/major/deprecated-functionality.rst +++ b/docs/release-notes/2020/major/deprecated-functionality.rst @@ -14,25 +14,25 @@ Functionality deprecated in |Gromacs| 2020 Support for 32bit architectures """"""""""""""""""""""""""""""" -There are no current or planned large scale resources using 32bit architectures, +:issue:`3252` There are no current or planned large scale resources using 32bit architectures, and we have no ability to properly test and evaluate them. Free-energy soft-core power 48 """""""""""""""""""""""""""""" -Free-energy soft-core power 48 is almost never used and is therefore deprecated. +:issue:`3253` Free-energy soft-core power 48 is almost never used and is therefore deprecated. Functionality deprecated in |Gromacs| 2019 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Generation of virtual sites to replace aromatic rings in standard residues """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" -These are thought to produce artefacts under some circumstances +:issue:`3254` These are thought to produce artefacts under some circumstances (unpublished results), were never well tested, are not widely used, and we need to simplify pdb2gmx. Benchmarking options only available with ``gmx benchmark`` """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" -Options such as ``-confout``, ``-resethway``, ``-resetstep`` are not +:issue:`3255` Options such as ``-confout``, ``-resethway``, ``-resetstep`` are not intended for use by regular mdrun users, so making them only available with a dedicated tool is more clear. Also, this permits us to customize defaults for e.g. writing files at the end of a simulation part in ways @@ -41,7 +41,7 @@ will no longer be required. ``gmx mdrun -nsteps`` """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" -The number of simulation steps described by the .tpr file can be +:issue:`3256` The number of simulation steps described by the .tpr file can be changed with ``gmx convert-tpr``, or altered in .mdp file before the call to ``gmx grompp``. The convenience of this mdrun option was outweighted by the doubtful quality of its implementation, no clear -- 2.11.4.GIT