Add issue tracking for deprecations.

Provide links in release notes to issue tracking for announced
deprecations.

Fixes #3251

Change-Id: I246651f8cb868eb1deecac86c2e7d6f0ec81b3f1

diff --git a/docs/release-notes/2019/major/deprecated-functionality.rst b/docs/release-notes/2019/major/deprecated-functionality.rst
index 182ed840477078998bbc688640fdee7da8a6a466..6b9b3ee13634b998ac122ac33d654fd9837e1283 100644 (file)
--- 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 (unpublished results), were never well tested, are not widely used,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 8f1b2494eb052b21b393bb51dac20ebeeece4476..d08f7ade51bf0a283dfd17a1e3f5bd4daa982b77 100644 (file)
--- 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