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GCEL / CARDAMOM

The CARbon DAta MOdel FraMework. Computer software that retrieves terrestrial carbon (C) cycle variables by combining C cycle observations with a mass balance model.
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Integrate C code and Python framework, Python interface to Fortran, additional DALEC model #7

Closed jfexbrayat closed 6 years ago

jfexbrayat commented 6 years ago

hey @dvalters, here is the pull request to merge my branch with the master branch which should make @vmyrgiotis's life easier

There are lots of commits on my branch but these are mostly for files that were added after branching the master. Additional features in the jeff branch include:

The tricky bit will be to resolve differences in the file CARDAMOM/LIBRARY/CARDAMOM_F/general/cardamom_io.f90 in places where observations and uncertainties are read.

dvalters commented 6 years ago

Thanks @jfexbrayat. I will take a look and work out the best strategy for merging

lsmallma commented 6 years ago

HI guys,

First, can I just check which way round the pull has been requested. When we were using svn to procedure to fold in a branch was to update the branch first with the current trunk (master), debug and then update the master. Is that the direction of travel here also?

Second, I’ve looked through the changes in the files common between both “jeff” and “master” and have some points to highlight

  1. The remaining of “cardamom_functions” -> “R_functions” needs to ensure that the actual files in the master need to take precedence as they have been updated since Jeff’s branch out (related to my first question the order of operations).
  2. The changes in MHMCMC.f90 are ones which Jeff and I discussed as possible solutions to the issues around low acceptance rates. However, testing with more complex datasets indicate that the approaches Jeff has implemented lead to the analysis getting stuck in local minima. I implemented an alternative approach in my source code where I adjust the (P-P0) / a > u(0,1) by a scaler (‘a’, set in the adapt_step_size() ) to make it easier to accept parameter sets which are not better than the currently accepted. I realise that this has a follow on impact on Jeff’s modification to his MODEL_LIKELIHOOD.f90 functions with the division by sample size

The changes listed in 1. and 2. have not been committed to the master yet. Is it more straight forward for me to do so before the merging of Jeff’s branch is completed?

Thanks, Luke

Dr T. Luke Smallman PDRA (GREENHOUSE / Forests2020)

School of GeoSciences, Crew Building, King’s Buildings, University of Edinburgh, EH9 3JN, UK Edinburgh

On 17 Oct 2018, at 16:41, Jean-François Exbrayat notifications@github.com<mailto:notifications@github.com> wrote:

hey @dvaltershttps://github.com/dvalters, here is the pull request to merge my branch with the master branch which should make @vmyrgiotishttps://github.com/vmyrgiotis's life easier

There are lots of commits on my branch but these are mostly for files that were added after branching the master. Additional features in the jeff branch include:

The tricky bit will be to resolve differences in the file CARDAMOM/LIBRARY/CARDAMOM_F/general/cardamom_io.f90 in places where observations and uncertainties are read.

You can view, comment on, or merge this pull request online at:

https://github.com/GCEL/CARDAMOM/pull/7

Commit Summary

File Changes

Patch Links:

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYc3DQwHupcUgZt0R-ZM2LysCQtEw7gnks5ul0-7gaJpZM4XkOJa.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

dvalters commented 6 years ago

Hi all,

You can do it either way. To update the branch first with the latest commits from master jeff would need to run:

git rebase master

Or interactively with

git rebase –i master

from his ‘jeff’ branch

and then force-push the new commit to github on his branch.

git push –f origin jeff

(Note you can still push to your branch when the pull request is active – github brings in the new commits automatically)

Rebasing it in git terminology applies the latest changes from master onto the branch, and re-writes the commits in ‘jeff’ to match. Then you can apply the pull request. (Like the workflow Luke is describing.)

The other way is to just attempt to merge the changes now, which avoids re-writing the commit history with rebase. We have to resolve any conflicting files (i.e. where jeff differs from master) by picking which conflicting sections of the code to keep. It is probably easier to show how to do this rather than over email….but the command is:

git merge master jeff

but this will result in git giving warnings about conflicts as described above

Here is a brief overview:

https://www.atlassian.com/git/tutorials/merging-vs-rebasing

I just have to pop out this afternoon but could go through it tomorrow?

From: Luke Smallman notifications@github.com Sent: 18 October 2018 12:04 To: GCEL/CARDAMOM CARDAMOM@noreply.github.com Cc: VALTERS Declan Declan.Valters@ed.ac.uk; Mention mention@noreply.github.com Subject: Re: [GCEL/CARDAMOM] Integrate C code and Python framework, Python interface to Fortran, additional DALEC model (#7)

HI guys,

First, can I just check which way round the pull has been requested. When we were using svn to procedure to fold in a branch was to update the branch first with the current trunk (master), debug and then update the master. Is that the direction of travel here also?

Second, I’ve looked through the changes in the files common between both “jeff” and “master” and have some points to highlight

  1. The remaining of “cardamom_functions” -> “R_functions” needs to ensure that the actual files in the master need to take precedence as they have been updated since Jeff’s branch out (related to my first question the order of operations).
  2. The changes in MHMCMC.f90 are ones which Jeff and I discussed as possible solutions to the issues around low acceptance rates. However, testing with more complex datasets indicate that the approaches Jeff has implemented lead to the analysis getting stuck in local minima. I implemented an alternative approach in my source code where I adjust the (P-P0) / a > u(0,1) by a scaler (‘a’, set in the adapt_step_size() ) to make it easier to accept parameter sets which are not better than the currently accepted. I realise that this has a follow on impact on Jeff’s modification to his MODEL_LIKELIHOOD.f90 functions with the division by sample size

The changes listed in 1. and 2. have not been committed to the master yet. Is it more straight forward for me to do so before the merging of Jeff’s branch is completed?

Thanks, Luke

Dr T. Luke Smallman PDRA (GREENHOUSE / Forests2020)

School of GeoSciences, Crew Building, King’s Buildings, University of Edinburgh, EH9 3JN, UK Edinburgh

On 17 Oct 2018, at 16:41, Jean-François Exbrayat notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>> wrote:

hey @dvaltershttps://github.com/dvalters, here is the pull request to merge my branch with the master branch which should make @vmyrgiotishttps://github.com/vmyrgiotis's life easier

There are lots of commits on my branch but these are mostly for files that were added after branching the master. Additional features in the jeff branch include:

The tricky bit will be to resolve differences in the file CARDAMOM/LIBRARY/CARDAMOM_F/general/cardamom_io.f90 in places where observations and uncertainties are read.

You can view, comment on, or merge this pull request online at:

https://github.com/GCEL/CARDAMOM/pull/7

Commit Summary

File Changes

Patch Links:

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYc3DQwHupcUgZt0R-ZM2LysCQtEw7gnks5ul0-7gaJpZM4XkOJa.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7#issuecomment-430967288, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKfLW81YmGsywodMTfRKyuYJ7AM8xr4Yks5umGAjgaJpZM4XkOJa.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

lsmallma commented 6 years ago

Hi,

I’m working away from the office today anyway.

Tomorrow morning is fine by me. I’m comfortable doing this on svn but always best on a first go on new sub versioning system to have a second pair of eyes physically there.

Cheers, Luke

P.S. Thanks for the commands in the email before, they will provide a useful cheat sheet in future

Dr T. Luke Smallman PDRA (GREENHOUSE / Forests2020)

School of GeoSciences, Crew Building, King’s Buildings, University of Edinburgh, EH9 3JN, UK Edinburgh

On 18 Oct 2018, at 12:36, Declan Valters notifications@github.com<mailto:notifications@github.com> wrote:

Hi all,

You can do it either way. To update the branch first with the latest commits from master jeff would need to run:

git rebase master

Or interactively with

git rebase –i master

from his ‘jeff’ branch

and then force-push the new commit to github on his branch.

git push –f origin jeff

(Note you can still push to your branch when the pull request is active – github brings in the new commits automatically)

Rebasing it in git terminology applies the latest changes from master onto the branch, and re-writes the commits in ‘jeff’ to match. Then you can apply the pull request. (Like the workflow Luke is describing.)

The other way is to just attempt to merge the changes now, which avoids re-writing the commit history with rebase. We have to resolve any conflicting files (i.e. where jeff differs from master) by picking which conflicting sections of the code to keep. It is probably easier to show how to do this rather than over email….but the command is:

git merge master jeff

but this will result in git giving warnings about conflicts as described above

Here is a brief overview:

https://www.atlassian.com/git/tutorials/merging-vs-rebasing

I just have to pop out this afternoon but could go through it tomorrow?

From: Luke Smallman notifications@github.com<mailto:notifications@github.com> Sent: 18 October 2018 12:04 To: GCEL/CARDAMOM CARDAMOM@noreply.github.com<mailto:CARDAMOM@noreply.github.com> Cc: VALTERS Declan Declan.Valters@ed.ac.uk<mailto:Declan.Valters@ed.ac.uk>; Mention mention@noreply.github.com<mailto:mention@noreply.github.com> Subject: Re: [GCEL/CARDAMOM] Integrate C code and Python framework, Python interface to Fortran, additional DALEC model (#7)

HI guys,

First, can I just check which way round the pull has been requested. When we were using svn to procedure to fold in a branch was to update the branch first with the current trunk (master), debug and then update the master. Is that the direction of travel here also?

Second, I’ve looked through the changes in the files common between both “jeff” and “master” and have some points to highlight

  1. The remaining of “cardamom_functions” -> “R_functions” needs to ensure that the actual files in the master need to take precedence as they have been updated since Jeff’s branch out (related to my first question the order of operations).
  2. The changes in MHMCMC.f90 are ones which Jeff and I discussed as possible solutions to the issues around low acceptance rates. However, testing with more complex datasets indicate that the approaches Jeff has implemented lead to the analysis getting stuck in local minima. I implemented an alternative approach in my source code where I adjust the (P-P0) / a > u(0,1) by a scaler (‘a’, set in the adapt_step_size() ) to make it easier to accept parameter sets which are not better than the currently accepted. I realise that this has a follow on impact on Jeff’s modification to his MODEL_LIKELIHOOD.f90 functions with the division by sample size

The changes listed in 1. and 2. have not been committed to the master yet. Is it more straight forward for me to do so before the merging of Jeff’s branch is completed?

Thanks, Luke

Dr T. Luke Smallman PDRA (GREENHOUSE / Forests2020)

School of GeoSciences, Crew Building, King’s Buildings, University of Edinburgh, EH9 3JN, UK Edinburgh

On 17 Oct 2018, at 16:41, Jean-François Exbrayat notifications@github.com<mailto:notifications@github.commailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com<mailto:notifications@github.com>>> wrote:

hey @dvaltershttps://github.com/dvalters, here is the pull request to merge my branch with the master branch which should make @vmyrgiotishttps://github.com/vmyrgiotis's life easier

There are lots of commits on my branch but these are mostly for files that were added after branching the master. Additional features in the jeff branch include:

The tricky bit will be to resolve differences in the file CARDAMOM/LIBRARY/CARDAMOM_F/general/cardamom_io.f90 in places where observations and uncertainties are read.

You can view, comment on, or merge this pull request online at:

https://github.com/GCEL/CARDAMOM/pull/7

Commit Summary

File Changes

Patch Links:

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYc3DQwHupcUgZt0R-ZM2LysCQtEw7gnks5ul0-7gaJpZM4XkOJa.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7#issuecomment-430967288, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKfLW81YmGsywodMTfRKyuYJ7AM8xr4Yks5umGAjgaJpZM4XkOJa.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7#issuecomment-430975251, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYc3DRin_EcB5iCu8azikXk81GpqzUH-ks5umGergaJpZM4XkOJa.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

dvalters commented 6 years ago

Just remembered this morning I have to be in Bayes centre for a meeting at 10, but I'll be back up at KB after that if you're still around

From: Luke Smallman notifications@github.com Sent: 18 October 2018 12:40:19 To: GCEL/CARDAMOM Cc: VALTERS Declan; Mention Subject: Re: [GCEL/CARDAMOM] Integrate C code and Python framework, Python interface to Fortran, additional DALEC model (#7)

Hi,

I’m working away from the office today anyway.

Tomorrow morning is fine by me. I’m comfortable doing this on svn but always best on a first go on new sub versioning system to have a second pair of eyes physically there.

Cheers, Luke

P.S. Thanks for the commands in the email before, they will provide a useful cheat sheet in future

Dr T. Luke Smallman PDRA (GREENHOUSE / Forests2020)

School of GeoSciences, Crew Building, King’s Buildings, University of Edinburgh, EH9 3JN, UK Edinburgh

On 18 Oct 2018, at 12:36, Declan Valters notifications@github.com<mailto:notifications@github.com> wrote:

Hi all,

You can do it either way. To update the branch first with the latest commits from master jeff would need to run:

git rebase master

Or interactively with

git rebase –i master

from his ‘jeff’ branch

and then force-push the new commit to github on his branch.

git push –f origin jeff

(Note you can still push to your branch when the pull request is active – github brings in the new commits automatically)

Rebasing it in git terminology applies the latest changes from master onto the branch, and re-writes the commits in ‘jeff’ to match. Then you can apply the pull request. (Like the workflow Luke is describing.)

The other way is to just attempt to merge the changes now, which avoids re-writing the commit history with rebase. We have to resolve any conflicting files (i.e. where jeff differs from master) by picking which conflicting sections of the code to keep. It is probably easier to show how to do this rather than over email….but the command is:

git merge master jeff

but this will result in git giving warnings about conflicts as described above

Here is a brief overview:

https://www.atlassian.com/git/tutorials/merging-vs-rebasing

I just have to pop out this afternoon but could go through it tomorrow?

From: Luke Smallman notifications@github.com<mailto:notifications@github.com> Sent: 18 October 2018 12:04 To: GCEL/CARDAMOM CARDAMOM@noreply.github.com<mailto:CARDAMOM@noreply.github.com> Cc: VALTERS Declan Declan.Valters@ed.ac.uk<mailto:Declan.Valters@ed.ac.uk>; Mention mention@noreply.github.com<mailto:mention@noreply.github.com> Subject: Re: [GCEL/CARDAMOM] Integrate C code and Python framework, Python interface to Fortran, additional DALEC model (#7)

HI guys,

First, can I just check which way round the pull has been requested. When we were using svn to procedure to fold in a branch was to update the branch first with the current trunk (master), debug and then update the master. Is that the direction of travel here also?

Second, I’ve looked through the changes in the files common between both “jeff” and “master” and have some points to highlight

  1. The remaining of “cardamom_functions” -> “R_functions” needs to ensure that the actual files in the master need to take precedence as they have been updated since Jeff’s branch out (related to my first question the order of operations).
  2. The changes in MHMCMC.f90 are ones which Jeff and I discussed as possible solutions to the issues around low acceptance rates. However, testing with more complex datasets indicate that the approaches Jeff has implemented lead to the analysis getting stuck in local minima. I implemented an alternative approach in my source code where I adjust the (P-P0) / a > u(0,1) by a scaler (‘a’, set in the adapt_step_size() ) to make it easier to accept parameter sets which are not better than the currently accepted. I realise that this has a follow on impact on Jeff’s modification to his MODEL_LIKELIHOOD.f90 functions with the division by sample size

The changes listed in 1. and 2. have not been committed to the master yet. Is it more straight forward for me to do so before the merging of Jeff’s branch is completed?

Thanks, Luke

Dr T. Luke Smallman PDRA (GREENHOUSE / Forests2020)

School of GeoSciences, Crew Building, King’s Buildings, University of Edinburgh, EH9 3JN, UK Edinburgh

On 17 Oct 2018, at 16:41, Jean-François Exbrayat notifications@github.com<mailto:notifications@github.commailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com<mailto:notifications@github.com>>> wrote:

hey @dvaltershttps://github.com/dvalters, here is the pull request to merge my branch with the master branch which should make @vmyrgiotishttps://github.com/vmyrgiotis's life easier

There are lots of commits on my branch but these are mostly for files that were added after branching the master. Additional features in the jeff branch include:

The tricky bit will be to resolve differences in the file CARDAMOM/LIBRARY/CARDAMOM_F/general/cardamom_io.f90 in places where observations and uncertainties are read.

You can view, comment on, or merge this pull request online at:

https://github.com/GCEL/CARDAMOM/pull/7

Commit Summary

File Changes

Patch Links:

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYc3DQwHupcUgZt0R-ZM2LysCQtEw7gnks5ul0-7gaJpZM4XkOJa.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7#issuecomment-430967288, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKfLW81YmGsywodMTfRKyuYJ7AM8xr4Yks5umGAjgaJpZM4XkOJa.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7#issuecomment-430975251, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYc3DRin_EcB5iCu8azikXk81GpqzUH-ks5umGergaJpZM4XkOJa.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7#issuecomment-430976244, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKfLW3U04jgEVn97Zu-L0oRKKhTfV6HXks5umGijgaJpZM4XkOJa.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

jfexbrayat commented 6 years ago

I have to be away from 1330... perhaps we can just set a meeting for next week? How does Tuesday morning look like for you guys?

Dr Jean-François (Jeff) Exbrayat

National Centre for Earth Observation School of GeoSciences University of Edinburgh Crew Building Alexander Crum Brown Road Edinburgh EH9 3FF United Kingdom

e: j.exbrayat@ed.ac.uk t: +44 (0) 131 650 7721 w: http://www.geos.ed.ac.uk/homes/jexbraya/

From: Declan Valters notifications@github.com Sent: 19 October 2018 08:35:35 To: GCEL/CARDAMOM Cc: EXBRAYAT Jean-Francois; Assign Subject: Re: [GCEL/CARDAMOM] Integrate C code and Python framework, Python interface to Fortran, additional DALEC model (#7)

Just remembered this morning I have to be in Bayes centre for a meeting at 10, but I'll be back up at KB after that if you're still around

From: Luke Smallman notifications@github.com Sent: 18 October 2018 12:40:19 To: GCEL/CARDAMOM Cc: VALTERS Declan; Mention Subject: Re: [GCEL/CARDAMOM] Integrate C code and Python framework, Python interface to Fortran, additional DALEC model (#7)

Hi,

I’m working away from the office today anyway.

Tomorrow morning is fine by me. I’m comfortable doing this on svn but always best on a first go on new sub versioning system to have a second pair of eyes physically there.

Cheers, Luke

P.S. Thanks for the commands in the email before, they will provide a useful cheat sheet in future

Dr T. Luke Smallman PDRA (GREENHOUSE / Forests2020)

School of GeoSciences, Crew Building, King’s Buildings, University of Edinburgh, EH9 3JN, UK Edinburgh

On 18 Oct 2018, at 12:36, Declan Valters notifications@github.com<mailto:notifications@github.com> wrote:

Hi all,

You can do it either way. To update the branch first with the latest commits from master jeff would need to run:

git rebase master

Or interactively with

git rebase –i master

from his ‘jeff’ branch

and then force-push the new commit to github on his branch.

git push –f origin jeff

(Note you can still push to your branch when the pull request is active – github brings in the new commits automatically)

Rebasing it in git terminology applies the latest changes from master onto the branch, and re-writes the commits in ‘jeff’ to match. Then you can apply the pull request. (Like the workflow Luke is describing.)

The other way is to just attempt to merge the changes now, which avoids re-writing the commit history with rebase. We have to resolve any conflicting files (i.e. where jeff differs from master) by picking which conflicting sections of the code to keep. It is probably easier to show how to do this rather than over email….but the command is:

git merge master jeff

but this will result in git giving warnings about conflicts as described above

Here is a brief overview:

https://www.atlassian.com/git/tutorials/merging-vs-rebasing

I just have to pop out this afternoon but could go through it tomorrow?

From: Luke Smallman notifications@github.com<mailto:notifications@github.com> Sent: 18 October 2018 12:04 To: GCEL/CARDAMOM CARDAMOM@noreply.github.com<mailto:CARDAMOM@noreply.github.com> Cc: VALTERS Declan Declan.Valters@ed.ac.uk<mailto:Declan.Valters@ed.ac.uk>; Mention mention@noreply.github.com<mailto:mention@noreply.github.com> Subject: Re: [GCEL/CARDAMOM] Integrate C code and Python framework, Python interface to Fortran, additional DALEC model (#7)

HI guys,

First, can I just check which way round the pull has been requested. When we were using svn to procedure to fold in a branch was to update the branch first with the current trunk (master), debug and then update the master. Is that the direction of travel here also?

Second, I’ve looked through the changes in the files common between both “jeff” and “master” and have some points to highlight

  1. The remaining of “cardamom_functions” -> “R_functions” needs to ensure that the actual files in the master need to take precedence as they have been updated since Jeff’s branch out (related to my first question the order of operations).
  2. The changes in MHMCMC.f90 are ones which Jeff and I discussed as possible solutions to the issues around low acceptance rates. However, testing with more complex datasets indicate that the approaches Jeff has implemented lead to the analysis getting stuck in local minima. I implemented an alternative approach in my source code where I adjust the (P-P0) / a > u(0,1) by a scaler (‘a’, set in the adapt_step_size() ) to make it easier to accept parameter sets which are not better than the currently accepted. I realise that this has a follow on impact on Jeff’s modification to his MODEL_LIKELIHOOD.f90 functions with the division by sample size

The changes listed in 1. and 2. have not been committed to the master yet. Is it more straight forward for me to do so before the merging of Jeff’s branch is completed?

Thanks, Luke

Dr T. Luke Smallman PDRA (GREENHOUSE / Forests2020)

School of GeoSciences, Crew Building, King’s Buildings, University of Edinburgh, EH9 3JN, UK Edinburgh

On 17 Oct 2018, at 16:41, Jean-François Exbrayat notifications@github.com<mailto:notifications@github.commailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com<mailto:notifications@github.com>>> wrote:

hey @dvaltershttps://github.com/dvalters, here is the pull request to merge my branch with the master branch which should make @vmyrgiotishttps://github.com/vmyrgiotis's life easier

There are lots of commits on my branch but these are mostly for files that were added after branching the master. Additional features in the jeff branch include:

The tricky bit will be to resolve differences in the file CARDAMOM/LIBRARY/CARDAMOM_F/general/cardamom_io.f90 in places where observations and uncertainties are read.

You can view, comment on, or merge this pull request online at:

https://github.com/GCEL/CARDAMOM/pull/7

Commit Summary

File Changes

Patch Links:

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYc3DQwHupcUgZt0R-ZM2LysCQtEw7gnks5ul0-7gaJpZM4XkOJa.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7#issuecomment-430967288, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKfLW81YmGsywodMTfRKyuYJ7AM8xr4Yks5umGAjgaJpZM4XkOJa.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7#issuecomment-430975251, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYc3DRin_EcB5iCu8azikXk81GpqzUH-ks5umGergaJpZM4XkOJa.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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dvalters commented 6 years ago

Yes next week would be better actually - Tuesday is good for me

From: Jean-François Exbrayat notifications@github.com Sent: 19 October 2018 09:23:06 To: GCEL/CARDAMOM Cc: VALTERS Declan; Mention Subject: Re: [GCEL/CARDAMOM] Integrate C code and Python framework, Python interface to Fortran, additional DALEC model (#7)

I have to be away from 1330... perhaps we can just set a meeting for next week? How does Tuesday morning look like for you guys?

Dr Jean-François (Jeff) Exbrayat

National Centre for Earth Observation School of GeoSciences University of Edinburgh Crew Building Alexander Crum Brown Road Edinburgh EH9 3FF United Kingdom

e: j.exbrayat@ed.ac.uk t: +44 (0) 131 650 7721 w: http://www.geos.ed.ac.uk/homes/jexbraya/

From: Declan Valters notifications@github.com Sent: 19 October 2018 08:35:35 To: GCEL/CARDAMOM Cc: EXBRAYAT Jean-Francois; Assign Subject: Re: [GCEL/CARDAMOM] Integrate C code and Python framework, Python interface to Fortran, additional DALEC model (#7)

Just remembered this morning I have to be in Bayes centre for a meeting at 10, but I'll be back up at KB after that if you're still around

From: Luke Smallman notifications@github.com Sent: 18 October 2018 12:40:19 To: GCEL/CARDAMOM Cc: VALTERS Declan; Mention Subject: Re: [GCEL/CARDAMOM] Integrate C code and Python framework, Python interface to Fortran, additional DALEC model (#7)

Hi,

I’m working away from the office today anyway.

Tomorrow morning is fine by me. I’m comfortable doing this on svn but always best on a first go on new sub versioning system to have a second pair of eyes physically there.

Cheers, Luke

P.S. Thanks for the commands in the email before, they will provide a useful cheat sheet in future

Dr T. Luke Smallman PDRA (GREENHOUSE / Forests2020)

School of GeoSciences, Crew Building, King’s Buildings, University of Edinburgh, EH9 3JN, UK Edinburgh

On 18 Oct 2018, at 12:36, Declan Valters notifications@github.com<mailto:notifications@github.com> wrote:

Hi all,

You can do it either way. To update the branch first with the latest commits from master jeff would need to run:

git rebase master

Or interactively with

git rebase –i master

from his ‘jeff’ branch

and then force-push the new commit to github on his branch.

git push –f origin jeff

(Note you can still push to your branch when the pull request is active – github brings in the new commits automatically)

Rebasing it in git terminology applies the latest changes from master onto the branch, and re-writes the commits in ‘jeff’ to match. Then you can apply the pull request. (Like the workflow Luke is describing.)

The other way is to just attempt to merge the changes now, which avoids re-writing the commit history with rebase. We have to resolve any conflicting files (i.e. where jeff differs from master) by picking which conflicting sections of the code to keep. It is probably easier to show how to do this rather than over email….but the command is:

git merge master jeff

but this will result in git giving warnings about conflicts as described above

Here is a brief overview:

https://www.atlassian.com/git/tutorials/merging-vs-rebasing

I just have to pop out this afternoon but could go through it tomorrow?

From: Luke Smallman notifications@github.com<mailto:notifications@github.com> Sent: 18 October 2018 12:04 To: GCEL/CARDAMOM CARDAMOM@noreply.github.com<mailto:CARDAMOM@noreply.github.com> Cc: VALTERS Declan Declan.Valters@ed.ac.uk<mailto:Declan.Valters@ed.ac.uk>; Mention mention@noreply.github.com<mailto:mention@noreply.github.com> Subject: Re: [GCEL/CARDAMOM] Integrate C code and Python framework, Python interface to Fortran, additional DALEC model (#7)

HI guys,

First, can I just check which way round the pull has been requested. When we were using svn to procedure to fold in a branch was to update the branch first with the current trunk (master), debug and then update the master. Is that the direction of travel here also?

Second, I’ve looked through the changes in the files common between both “jeff” and “master” and have some points to highlight

  1. The remaining of “cardamom_functions” -> “R_functions” needs to ensure that the actual files in the master need to take precedence as they have been updated since Jeff’s branch out (related to my first question the order of operations).
  2. The changes in MHMCMC.f90 are ones which Jeff and I discussed as possible solutions to the issues around low acceptance rates. However, testing with more complex datasets indicate that the approaches Jeff has implemented lead to the analysis getting stuck in local minima. I implemented an alternative approach in my source code where I adjust the (P-P0) / a > u(0,1) by a scaler (‘a’, set in the adapt_step_size() ) to make it easier to accept parameter sets which are not better than the currently accepted. I realise that this has a follow on impact on Jeff’s modification to his MODEL_LIKELIHOOD.f90 functions with the division by sample size

The changes listed in 1. and 2. have not been committed to the master yet. Is it more straight forward for me to do so before the merging of Jeff’s branch is completed?

Thanks, Luke

Dr T. Luke Smallman PDRA (GREENHOUSE / Forests2020)

School of GeoSciences, Crew Building, King’s Buildings, University of Edinburgh, EH9 3JN, UK Edinburgh

On 17 Oct 2018, at 16:41, Jean-François Exbrayat notifications@github.com<mailto:notifications@github.commailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com<mailto:notifications@github.com>>> wrote:

hey @dvaltershttps://github.com/dvalters, here is the pull request to merge my branch with the master branch which should make @vmyrgiotishttps://github.com/vmyrgiotis's life easier

There are lots of commits on my branch but these are mostly for files that were added after branching the master. Additional features in the jeff branch include:

The tricky bit will be to resolve differences in the file CARDAMOM/LIBRARY/CARDAMOM_F/general/cardamom_io.f90 in places where observations and uncertainties are read.

You can view, comment on, or merge this pull request online at:

https://github.com/GCEL/CARDAMOM/pull/7

Commit Summary

File Changes

Patch Links:

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYc3DQwHupcUgZt0R-ZM2LysCQtEw7gnks5ul0-7gaJpZM4XkOJa.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7#issuecomment-430967288, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKfLW81YmGsywodMTfRKyuYJ7AM8xr4Yks5umGAjgaJpZM4XkOJa.

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— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7#issuecomment-430975251, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYc3DRin_EcB5iCu8azikXk81GpqzUH-ks5umGergaJpZM4XkOJa.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7#issuecomment-430976244, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKfLW3U04jgEVn97Zu-L0oRKKhTfV6HXks5umGijgaJpZM4XkOJa.

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— You are receiving this because you were assigned. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7#issuecomment-431272578, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Ajt2KFXF78YE4K1mqlMKWkw8kISWoopqks5umYDHgaJpZM4XkOJa.

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— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7#issuecomment-431284930, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKfLW-rr5AhZLqwWYkNsn6mA2F2EFn1vks5umYvqgaJpZM4XkOJa.

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lsmallma commented 6 years ago

Tuesday is good for me too

On 19/10/18 09:30, Declan Valters wrote: Yes next week would be better actually - Tuesday is good for me

From: Jean-François Exbrayat notifications@github.commailto:notifications@github.com Sent: 19 October 2018 09:23:06 To: GCEL/CARDAMOM Cc: VALTERS Declan; Mention Subject: Re: [GCEL/CARDAMOM] Integrate C code and Python framework, Python interface to Fortran, additional DALEC model (#7)

I have to be away from 1330... perhaps we can just set a meeting for next week? How does Tuesday morning look like for you guys?

Dr Jean-François (Jeff) Exbrayat

National Centre for Earth Observation School of GeoSciences University of Edinburgh Crew Building Alexander Crum Brown Road Edinburgh EH9 3FF United Kingdom

e: j.exbrayat@ed.ac.ukmailto:j.exbrayat@ed.ac.uk t: +44 (0) 131 650 7721 w: http://www.geos.ed.ac.uk/homes/jexbraya/

From: Declan Valters notifications@github.commailto:notifications@github.com Sent: 19 October 2018 08:35:35 To: GCEL/CARDAMOM Cc: EXBRAYAT Jean-Francois; Assign Subject: Re: [GCEL/CARDAMOM] Integrate C code and Python framework, Python interface to Fortran, additional DALEC model (#7)

Just remembered this morning I have to be in Bayes centre for a meeting at 10, but I'll be back up at KB after that if you're still around

From: Luke Smallman notifications@github.commailto:notifications@github.com Sent: 18 October 2018 12:40:19 To: GCEL/CARDAMOM Cc: VALTERS Declan; Mention Subject: Re: [GCEL/CARDAMOM] Integrate C code and Python framework, Python interface to Fortran, additional DALEC model (#7)

Hi,

I’m working away from the office today anyway.

Tomorrow morning is fine by me. I’m comfortable doing this on svn but always best on a first go on new sub versioning system to have a second pair of eyes physically there.

Cheers, Luke

P.S. Thanks for the commands in the email before, they will provide a useful cheat sheet in future

Dr T. Luke Smallman PDRA (GREENHOUSE / Forests2020)

School of GeoSciences, Crew Building, King’s Buildings, University of Edinburgh, EH9 3JN, UK Edinburgh

On 18 Oct 2018, at 12:36, Declan Valters notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> wrote:

Hi all,

You can do it either way. To update the branch first with the latest commits from master jeff would need to run:

git rebase master

Or interactively with

git rebase –i master

from his ‘jeff’ branch

and then force-push the new commit to github on his branch.

git push –f origin jeff

(Note you can still push to your branch when the pull request is active – github brings in the new commits automatically)

Rebasing it in git terminology applies the latest changes from master onto the branch, and re-writes the commits in ‘jeff’ to match. Then you can apply the pull request. (Like the workflow Luke is describing.)

The other way is to just attempt to merge the changes now, which avoids re-writing the commit history with rebase. We have to resolve any conflicting files (i.e. where jeff differs from master) by picking which conflicting sections of the code to keep. It is probably easier to show how to do this rather than over email….but the command is:

git merge master jeff

but this will result in git giving warnings about conflicts as described above

Here is a brief overview:

https://www.atlassian.com/git/tutorials/merging-vs-rebasing

I just have to pop out this afternoon but could go through it tomorrow?

From: Luke Smallman notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> Sent: 18 October 2018 12:04 To: GCEL/CARDAMOM CARDAMOM@noreply.github.com<mailto:CARDAMOM@noreply.github.commailto:CARDAMOM@noreply.github.commailto:CARDAMOM@noreply.github.com> Cc: VALTERS Declan Declan.Valters@ed.ac.uk<mailto:Declan.Valters@ed.ac.ukmailto:Declan.Valters@ed.ac.ukmailto:Declan.Valters@ed.ac.uk>; Mention mention@noreply.github.com<mailto:mention@noreply.github.commailto:mention@noreply.github.commailto:mention@noreply.github.com> Subject: Re: [GCEL/CARDAMOM] Integrate C code and Python framework, Python interface to Fortran, additional DALEC model (#7)

HI guys,

First, can I just check which way round the pull has been requested. When we were using svn to procedure to fold in a branch was to update the branch first with the current trunk (master), debug and then update the master. Is that the direction of travel here also?

Second, I’ve looked through the changes in the files common between both “jeff” and “master” and have some points to highlight

  1. The remaining of “cardamom_functions” -> “R_functions” needs to ensure that the actual files in the master need to take precedence as they have been updated since Jeff’s branch out (related to my first question the order of operations).
  2. The changes in MHMCMC.f90 are ones which Jeff and I discussed as possible solutions to the issues around low acceptance rates. However, testing with more complex datasets indicate that the approaches Jeff has implemented lead to the analysis getting stuck in local minima. I implemented an alternative approach in my source code where I adjust the (P-P0) / a > u(0,1) by a scaler (‘a’, set in the adapt_step_size() ) to make it easier to accept parameter sets which are not better than the currently accepted. I realise that this has a follow on impact on Jeff’s modification to his MODEL_LIKELIHOOD.f90 functions with the division by sample size

The changes listed in 1. and 2. have not been committed to the master yet. Is it more straight forward for me to do so before the merging of Jeff’s branch is completed?

Thanks, Luke

Dr T. Luke Smallman PDRA (GREENHOUSE / Forests2020)

School of GeoSciences, Crew Building, King’s Buildings, University of Edinburgh, EH9 3JN, UK Edinburgh

On 17 Oct 2018, at 16:41, Jean-François Exbrayat notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com<mailto:notifications@github.commailto:notifications@github.com>>> wrote:

hey @dvaltershttps://github.com/dvaltershttps://github.com/dvalters, here is the pull request to merge my branch with the master branch which should make @vmyrgiotishttps://github.com/vmyrgiotishttps://github.com/vmyrgiotis's life easier

There are lots of commits on my branch but these are mostly for files that were added after branching the master. Additional features in the jeff branch include:

The tricky bit will be to resolve differences in the file CARDAMOM/LIBRARY/CARDAMOM_F/general/cardamom_io.f90 in places where observations and uncertainties are read.

You can view, comment on, or merge this pull request online at:

https://github.com/GCEL/CARDAMOM/pull/7

Commit Summary

File Changes

Patch Links:

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7https://github.com/GCEL/CARDAMOM/pull/7, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYc3DQwHupcUgZt0R-ZM2LysCQtEw7gnks5ul0-7gaJpZM4XkOJahttps://github.com/notifications/unsubscribe-auth/AYc3DQwHupcUgZt0R-ZM2LysCQtEw7gnks5ul0-7gaJpZM4XkOJa.

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7#issuecomment-430967288https://github.com/GCEL/CARDAMOM/pull/7#issuecomment-430967288, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKfLW81YmGsywodMTfRKyuYJ7AM8xr4Yks5umGAjgaJpZM4XkOJahttps://github.com/notifications/unsubscribe-auth/AKfLW81YmGsywodMTfRKyuYJ7AM8xr4Yks5umGAjgaJpZM4XkOJa.

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— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7#issuecomment-430975251https://github.com/GCEL/CARDAMOM/pull/7#issuecomment-430975251, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYc3DRin_EcB5iCu8azikXk81GpqzUH-ks5umGergaJpZM4XkOJahttps://github.com/notifications/unsubscribe-auth/AYc3DRin_EcB5iCu8azikXk81GpqzUH-ks5umGergaJpZM4XkOJa.

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— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7#issuecomment-431284930https://github.com/GCEL/CARDAMOM/pull/7#issuecomment-431284930, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKfLW-rr5AhZLqwWYkNsn6mA2F2EFn1vks5umYvqgaJpZM4XkOJahttps://github.com/notifications/unsubscribe-auth/AKfLW-rr5AhZLqwWYkNsn6mA2F2EFn1vks5umYvqgaJpZM4XkOJa.

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— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/GCEL/CARDAMOM/pull/7#issuecomment-431286902, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AYc3DSdwXIubj75bNwMfeMVf6af7Kt9gks5umY2hgaJpZM4XkOJa.

-- Dr T. Luke Smallman PDRA (GREENHOUSE / Forest2020)

School of GeoSciences Crew Building, King's Buildings, University of Edinburgh EH9 3JN, UK Edinburgh

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

dvalters commented 6 years ago

Closes #6