Add DOI information to the json syntax file

[gtribello]

Description

I have added a command so you can put the DOIs of papers that describe the functionality in an action in the syntax.json file. To add a doi to your paperyou simply use the command:

keys.addDOI("<DOI>");

in the registerKeywords method of your action. Hopefully this will help users quickly build documentation for their methods when we get the new manual working

Target release

I would like my code to appear in release 2.11

Type of contribution

• changes to code or doc authored by PLUMED developers, or additions of code in the core or within the default modules
• changes to a module not authored by you
• new module contribution or edit of a module authored by you

Copyright

• I agree to transfer the copyright of the code I have written to the PLUMED developers or to the author of the code I am modifying.

• the module I added or modified contains a COPYRIGHT file with the correct license information. Code should be released under an open source license. I also used the command cd src && ./header.sh mymodulename in order to make sure the headers of the module are correct.

Tests

• I added a new regtest or modified an existing regtest to validate my changes.
• I verified that all regtests are passed successfully on GitHub Actions.

[GiovanniBussi]

Hi Gareth this is a bit redundant with the cite() method. I am afraid that having two parallel implementation will create confusion and also make both lists possibly incomplete. Is there a way to merge the two? In particular, what we need is: - multiple references for an action (maybe also possible with your new implementation) - possibility (in the output) to switch them on or off based on the actual flags - I guess you want this in the manual, so you probably need a complete list there. But still I would like the log to continue to report correctly the bibliography, with selected references. Shall we discuss about this? Thanks! Sent from Gmail mobile Il giorno ven 27 set 2024 alle 15:58 Gareth Tribello < ***@***.***> ha scritto:

…

Description I have added a command so you can put the DOIs of papers that describe the functionality in an action in the syntax.json file. To add a doi to your paperyou simply use the command: keys.addDOI("<DOI>"); in the registerKeywords method of your action. Hopefully this will help users quickly build documentation for their methods when we get the new manual working Target release I would like my code to appear in release 2.11 Type of contribution - changes to code or doc authored by PLUMED developers, or additions of code in the core or within the default modules - changes to a module not authored by you - new module contribution or edit of a module authored by you Copyright - I agree to transfer the copyright of the code I have written to the PLUMED developers or to the author of the code I am modifying. - the module I added or modified contains a COPYRIGHT file with the correct license information. Code should be released under an open source license. I also used the command cd src && ./header.sh mymodulename in order to make sure the headers of the module are correct. Tests - I added a new regtest or modified an existing regtest to validate my changes. - I verified that all regtests are passed successfully on GitHub Actions <https://github.com/plumed/plumed2/actions>. ------------------------------ You can view, comment on, or merge this pull request online at: #1115 Commit Summary - 2b9e6ed <2b9e6ed> Added an option to include DOIs in the syntax file so that references can be put on action pages in the new manual - c3c14e8 <c3c14e8> Ran astyle File Changes (4 files <https://github.com/plumed/plumed2/pull/1115/files>) - *M* src/cltools/GenJson.cpp <https://github.com/plumed/plumed2/pull/1115/files#diff-ff75368fcdec59384b56079c50febe2b8823cfa2b5c7cc32df72d7194e92729a> (8) - *M* src/clusters/ClusteringBase.cpp <https://github.com/plumed/plumed2/pull/1115/files#diff-a2968c5b1855d55a81e9958833d69b2433bc95a49416bbb1676ed6ea67150fdf> (1) - *M* src/tools/Keywords.cpp <https://github.com/plumed/plumed2/pull/1115/files#diff-3652bdaa03b0c2f3caf549ff022e03b49e43f7ac8270ea448a60f6cc5d03799b> (8) - *M* src/tools/Keywords.h <https://github.com/plumed/plumed2/pull/1115/files#diff-4857fc24bf53177af747095078eceb5e5a8aa31ebb1a4f8bbc63c091d0ef27fc> (6) Patch Links: - https://github.com/plumed/plumed2/pull/1115.patch - https://github.com/plumed/plumed2/pull/1115.diff — Reply to this email directly, view it on GitHub <#1115>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABBNCXVOTYC67ZTLJFQTTTTZYVP7TAVCNFSM6AAAAABO7HJIJCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGU2TGMBRHAYTEOA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>