Yeban bowerise #718

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nathandunn commented Mar 28, 2016

I adopted this from #333 . . I added a little readme and updated dojo to use 1.9.2 and bumped to the 1.12.2 version. NPM is required for bower.

@enuggetry Can you take a look?

yeban and others added some commits Aug 29, 2013

Use Bower, instead of git submodules, for dependencies.
Stick to the latest release of the dependencies that do semantic
versioning.

dojo         1.9.1
dojox        1.9.1
util         1.9.1
dijit        1.9.1
put-selector 0.3.4
dgrid        0.3.9
xstyle       0.2.0
json-schema  0.2.1

Except, lazyload.  The latest release of lazyload is 2.0.3, however, JB
uses an additional commit from Robert Buels which seems relevant.

dbind, jDataView, FileSaver.js and jszlib don't do semantic versioning.
So we stick to git 'master'.

jsdoc_toolkit-2.4.0, perl5, and wig2png are a part of source tree.
Nothing to bowerize there.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Exclude some directories from the build manually since git clean with…
… -x flag will remove even things in gitignore
Revert xstyle back to version 0.1.3 which is after the current commit…
… number that the submodule is at (december 2012) but before 0.2.0 removes a dependency

@nathandunn nathandunn added this to the 1.12.0 milestone Mar 28, 2016

@nathandunn nathandunn modified the milestones: 1.12.2, 1.12.0 Mar 28, 2016

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nathandunn Mar 28, 2016

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If you want to use this in favor of #333 that is fine . . . it was just a little out of sync with master.

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nathandunn commented Mar 28, 2016

If you want to use this in favor of #333 that is fine . . . it was just a little out of sync with master.

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Just to lay out the "cards" so to say

  1. this PR does not necessary enable "bower install jbrowse" like I thought (maybe it would be possible through "post install" hooks for bower, but the flat dependency tree ends up not putting things in the right place. you can try "bower install https://github.com/gmod/jbrowse.git#yeban-bowerise" to see what happens).
  2. Despite (1), this still enables some new use cases. For example, you can just get the .tar.gz from https://github.com/GMOD/jbrowse/archive/1.12.1-release.tar.gz and then run "bower install" inside that folder. It would not have been possible to initialize the git submodules from the downloaded https://github.com/GMOD/jbrowse/archive/1.12.1-release.tar.gz, so now that is possible with bower. I think distributing the builds on jbrowse.org is still relevant so that people don't have to do this though
  3. The thing where I removed xstyle/load-css from src/JBrowse/main.js was kind of just a weird workaround to get tests to pass. I don't really know why but the "build" (closure compiler) kept saying xstyle/load-css was missing. I don't know the logic behind that but I don't see any consequences of it. I also removed dojox/gfx/svg which might not have been strictly necessary, but I thought it is unused too, so I removed it
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cmdcolin commented Mar 28, 2016

Just to lay out the "cards" so to say

  1. this PR does not necessary enable "bower install jbrowse" like I thought (maybe it would be possible through "post install" hooks for bower, but the flat dependency tree ends up not putting things in the right place. you can try "bower install https://github.com/gmod/jbrowse.git#yeban-bowerise" to see what happens).
  2. Despite (1), this still enables some new use cases. For example, you can just get the .tar.gz from https://github.com/GMOD/jbrowse/archive/1.12.1-release.tar.gz and then run "bower install" inside that folder. It would not have been possible to initialize the git submodules from the downloaded https://github.com/GMOD/jbrowse/archive/1.12.1-release.tar.gz, so now that is possible with bower. I think distributing the builds on jbrowse.org is still relevant so that people don't have to do this though
  3. The thing where I removed xstyle/load-css from src/JBrowse/main.js was kind of just a weird workaround to get tests to pass. I don't really know why but the "build" (closure compiler) kept saying xstyle/load-css was missing. I don't know the logic behind that but I don't see any consequences of it. I also removed dojox/gfx/svg which might not have been strictly necessary, but I thought it is unused too, so I removed it
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I think that use-case 2) sums up why I think that this is important. Also, every release, this information can be cached and dojo is automatically versioned.

For 1) . . . I didn’t think we could do that, but it would still be great thing to explore.

Nathan

On Mar 28, 2016, at 1:35 PM, Colin Diesh notifications@github.com wrote:

Just to lay out the "cards" so to say

  1. this PR does not necessary enable "bower install jbrowse" like I thought (maybe it would be possible through "post install" hooks for bower, but the flat dependency tree ends up not putting things in the right place. you can try "bower install https://github.com/gmod/jbrowse#yeban-bowerise https://github.com/gmod/jbrowse#yeban-bowerise" to see what happens).
  2. Despite (1), this still enables some new use cases. For example, you can just get the .tar.gz from https://github.com/GMOD/jbrowse/archive/1.12.1-release.tar.gz https://github.com/GMOD/jbrowse/archive/1.12.1-release.tar.gz and then run "bower install" inside that folder. It would not have been possible to initialize the git submodules from the downloaded https://github.com/GMOD/jbrowse/archive/1.12.1-release.tar.gz https://github.com/GMOD/jbrowse/archive/1.12.1-release.tar.gz, so now that is possible with bower. I think distributing the builds on jbrowse.org is still relevant so that people don't have to do this though
  3. The thing where I removed xstyle/load-css from src/JBrowse/main.js was kind of just a weird workaround to get tests to pass. I don't really know why but the "build" (closure compiler) kept saying xstyle/load-css was missing. I don't know the logic behind that but I don't see any consequences of it. I also removed dojox/gfx/svg which might not have been strictly necessary, but I thought it is unused too, so I removed it


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nathandunn commented Mar 28, 2016

I think that use-case 2) sums up why I think that this is important. Also, every release, this information can be cached and dojo is automatically versioned.

For 1) . . . I didn’t think we could do that, but it would still be great thing to explore.

Nathan

On Mar 28, 2016, at 1:35 PM, Colin Diesh notifications@github.com wrote:

Just to lay out the "cards" so to say

  1. this PR does not necessary enable "bower install jbrowse" like I thought (maybe it would be possible through "post install" hooks for bower, but the flat dependency tree ends up not putting things in the right place. you can try "bower install https://github.com/gmod/jbrowse#yeban-bowerise https://github.com/gmod/jbrowse#yeban-bowerise" to see what happens).
  2. Despite (1), this still enables some new use cases. For example, you can just get the .tar.gz from https://github.com/GMOD/jbrowse/archive/1.12.1-release.tar.gz https://github.com/GMOD/jbrowse/archive/1.12.1-release.tar.gz and then run "bower install" inside that folder. It would not have been possible to initialize the git submodules from the downloaded https://github.com/GMOD/jbrowse/archive/1.12.1-release.tar.gz https://github.com/GMOD/jbrowse/archive/1.12.1-release.tar.gz, so now that is possible with bower. I think distributing the builds on jbrowse.org is still relevant so that people don't have to do this though
  3. The thing where I removed xstyle/load-css from src/JBrowse/main.js was kind of just a weird workaround to get tests to pass. I don't really know why but the "build" (closure compiler) kept saying xstyle/load-css was missing. I don't know the logic behind that but I don't see any consequences of it. I also removed dojox/gfx/svg which might not have been strictly necessary, but I thought it is unused too, so I removed it


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Reply to this email directly or view it on GitHub #718 (comment)

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cmdcolin Mar 29, 2016

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I don't agree with this change 0e37d5e

If a user downloads jbrowse from jbrowse.org, it will be prebuilt, and they will not need bower

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cmdcolin commented Mar 29, 2016

I don't agree with this change 0e37d5e

If a user downloads jbrowse from jbrowse.org, it will be prebuilt, and they will not need bower

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nathandunn Mar 29, 2016

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Hmm . . was wondering about that. Would you A) not exit or B) detect if files were present (i.e. its prebuilt)?

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nathandunn commented Mar 29, 2016

Hmm . . was wondering about that. Would you A) not exit or B) detect if files were present (i.e. its prebuilt)?

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cmdcolin Mar 29, 2016

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Probably only run if it is not pre-built, or not try and automate that step from setup.sh. Just tell user to run it. Apollo might be able to automate it separately too. Apollo for example, does not run setup.sh during setup.

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cmdcolin commented Mar 29, 2016

Probably only run if it is not pre-built, or not try and automate that step from setup.sh. Just tell user to run it. Apollo might be able to automate it separately too. Apollo for example, does not run setup.sh during setup.

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nathandunn Mar 29, 2016

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Cool part:

bower install https://github.com/GMOD/jbrowse.git#yeban-bowerise
cd bower_components/jbrowse
./setup.sh 
python -m SimpleHTTPServer

The only downside is that it extracts all of the packages into the bower_components directory. Would probably delete after processing anyways, so not a big deal.

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nathandunn commented Mar 29, 2016

Cool part:

bower install https://github.com/GMOD/jbrowse.git#yeban-bowerise
cd bower_components/jbrowse
./setup.sh 
python -m SimpleHTTPServer

The only downside is that it extracts all of the packages into the bower_components directory. Would probably delete after processing anyways, so not a big deal.

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I would not recommend that workflow. As I said, above "bower install jbrowse", or "bower install https://github.com/GMOD/jbrowse.git#yeban-bowerise" does not have good behavior. The behavior you might see here is that

(a) Running "bower install https://github.com/GMOD/jbrowse.git#yeban-bowerise" will actually download jbrowse and the dojo, dijit, dojox dependencies etc into bower_componenets.
(b) Then you go to bower_componenets/jbrowse and run bower install which re-installs dojo, dijit, dojox again, this time in the proper location

This is because it flattens the dependency tree in (a) which is not wanted

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cmdcolin commented Mar 29, 2016

I would not recommend that workflow. As I said, above "bower install jbrowse", or "bower install https://github.com/GMOD/jbrowse.git#yeban-bowerise" does not have good behavior. The behavior you might see here is that

(a) Running "bower install https://github.com/GMOD/jbrowse.git#yeban-bowerise" will actually download jbrowse and the dojo, dijit, dojox dependencies etc into bower_componenets.
(b) Then you go to bower_componenets/jbrowse and run bower install which re-installs dojo, dijit, dojox again, this time in the proper location

This is because it flattens the dependency tree in (a) which is not wanted

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nathandunn Mar 29, 2016

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Yeah, you end up not using the additional packages. I think that moving them to devDependencies may fix that, but more of a proof of concept. If we're going to do minification, etc. you'll want some sort of staging area anyway. More importantly is they get cached.

@cmdcolin / @enuggetry
Is there a reliable way to detect if it is pre-built?

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nathandunn commented Mar 29, 2016

Yeah, you end up not using the additional packages. I think that moving them to devDependencies may fix that, but more of a proof of concept. If we're going to do minification, etc. you'll want some sort of staging area anyway. More importantly is they get cached.

@cmdcolin / @enuggetry
Is there a reliable way to detect if it is pre-built?

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nathandunn Mar 30, 2016

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  • add --allow-root
  • detect if pre-installed and don't run bower
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nathandunn commented Mar 30, 2016

  • add --allow-root
  • detect if pre-installed and don't run bower
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nathandunn Mar 30, 2016

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FYI @enuggetry I added this per our conversation. Let me know if I missed anything or if there are further things I should test.

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nathandunn commented Mar 30, 2016

FYI @enuggetry I added this per our conversation. Let me know if I missed anything or if there are further things I should test.

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enuggetry Mar 30, 2016

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Oops. I should have commented here.

Reiterating:
As root, this worked:
bower install -f --allow-root
As sudo user, this is what worked for me:

sudo bower install -f --allow-root
sudo ./setup.sh

I also had to setup in /etc/sudoers, the NOPASSWD option for my users.

Generally, It should work:

  1. root user
  2. user with adequate privilege in the given directory
  3. sudo user

As part of the testing, we should probably include a couple of recent versions of:
CentOS
Debian / Ubuntu
OSX.
Windows? (don't know if it's necessary, given VMs)

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enuggetry commented Mar 30, 2016

Oops. I should have commented here.

Reiterating:
As root, this worked:
bower install -f --allow-root
As sudo user, this is what worked for me:

sudo bower install -f --allow-root
sudo ./setup.sh

I also had to setup in /etc/sudoers, the NOPASSWD option for my users.

Generally, It should work:

  1. root user
  2. user with adequate privilege in the given directory
  3. sudo user

As part of the testing, we should probably include a couple of recent versions of:
CentOS
Debian / Ubuntu
OSX.
Windows? (don't know if it's necessary, given VMs)

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As part of the testing, we should probably include a couple of recent versions of:

  • CentOS: root, sudo, user
  • Debian / Ubuntu: root, sudo, user
  • OSX: root, sudo, user
  • test apollo2.0.2 (if it will conflict if going from master into other branch . . -f ? )
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nathandunn commented Mar 30, 2016

As part of the testing, we should probably include a couple of recent versions of:

  • CentOS: root, sudo, user
  • Debian / Ubuntu: root, sudo, user
  • OSX: root, sudo, user
  • test apollo2.0.2 (if it will conflict if going from master into other branch . . -f ? )
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nathandunn Mar 31, 2016

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Going to try to have it follow this script here:

#!/bin/sh
TARGET=jbrowse
if [ ! -n "$1" ];then
  TARGET=$1
fi  

bower --allow-root -f install GMOD/jbrowse#yeban-bowerise
echo "Installing to $TARGET"
mv bower_components/jbrowse $TARGET
cd $TARGET
./setup.sh
# TODO: upstream scripts should use bower_move to avoid creating the components directory
cd ..
rm -rf bower_components
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nathandunn commented Mar 31, 2016

Going to try to have it follow this script here:

#!/bin/sh
TARGET=jbrowse
if [ ! -n "$1" ];then
  TARGET=$1
fi  

bower --allow-root -f install GMOD/jbrowse#yeban-bowerise
echo "Installing to $TARGET"
mv bower_components/jbrowse $TARGET
cd $TARGET
./setup.sh
# TODO: upstream scripts should use bower_move to avoid creating the components directory
cd ..
rm -rf bower_components
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nathandunn Apr 1, 2016

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Just read this:

https://github.com/nodesource/distributions/blob/master/OLDER_DISTROS.md

I don't think we can use bower (easily) on older installations). However, I think since node and npm are going to be requirements sooner than later, its should be fine as most distros have a way to install newer versions of node:

https://www.euperia.com/development/install-nodejs-and-bower-on-ubuntu-12-04-precise/1269

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nathandunn commented Apr 1, 2016

Just read this:

https://github.com/nodesource/distributions/blob/master/OLDER_DISTROS.md

I don't think we can use bower (easily) on older installations). However, I think since node and npm are going to be requirements sooner than later, its should be fine as most distros have a way to install newer versions of node:

https://www.euperia.com/development/install-nodejs-and-bower-on-ubuntu-12-04-precise/1269

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tested with a denovo download of 2.0.2 . . . it just worked! I used a checkout of this branch.

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nathandunn commented Apr 1, 2016

tested with a denovo download of 2.0.2 . . . it just worked! I used a checkout of this branch.

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I used a checkout of this branch.

If it is using 2.0.2 and this branch that means that it is not really 2.0.2, it is a modified 2.0.2, right?

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cmdcolin commented Apr 1, 2016

I used a checkout of this branch.

If it is using 2.0.2 and this branch that means that it is not really 2.0.2, it is a modified 2.0.2, right?

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I changed it to checkout yeban-browerise instead of tags/1.11.6-release

The worry was that it would clone master (which it does) and when it does the checkout there would be a problem with the directories.

I think a more reasonable test would be changing to tags/1.11.6-release

To simulate that I did:

git clone --recursive --depth 1 -b yeban-bowerise  --single-branch https://github.com/GMOD/jbrowse       jbrowse-download 
git fetch --tags
git checkout tags/1.11.6-release  

And of course there are no recursive directories and no command to refresh the dependencies. Will definitely have to wait until 2.0.3 release then. Opportunity for more testing than.

Thanks for catching (again).

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nathandunn commented Apr 1, 2016

I changed it to checkout yeban-browerise instead of tags/1.11.6-release

The worry was that it would clone master (which it does) and when it does the checkout there would be a problem with the directories.

I think a more reasonable test would be changing to tags/1.11.6-release

To simulate that I did:

git clone --recursive --depth 1 -b yeban-bowerise  --single-branch https://github.com/GMOD/jbrowse       jbrowse-download 
git fetch --tags
git checkout tags/1.11.6-release  

And of course there are no recursive directories and no command to refresh the dependencies. Will definitely have to wait until 2.0.3 release then. Opportunity for more testing than.

Thanks for catching (again).

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However, I think we could do a "patch" release of 2.0.2 - retagging it. The problem is that the command should be (have always been):

git clone --recursive -b 1.11.6-release --single-branch https://github.com/GMOD/jbrowse jbrowse-download 

Weirdly, it does clones synchronously, which always seems to be more reliable.

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nathandunn commented Apr 1, 2016

However, I think we could do a "patch" release of 2.0.2 - retagging it. The problem is that the command should be (have always been):

git clone --recursive -b 1.11.6-release --single-branch https://github.com/GMOD/jbrowse jbrowse-download 

Weirdly, it does clones synchronously, which always seems to be more reliable.

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I retagged it with this fix and it seems to work.

https://github.com/GMOD/Apollo/releases/tag/2.0.2

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nathandunn commented Apr 1, 2016

I retagged it with this fix and it seems to work.

https://github.com/GMOD/Apollo/releases/tag/2.0.2

@nathandunn nathandunn added needs review and removed in progress labels Apr 1, 2016

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@enuggetry This is ready for review next week. Any system that you can get a relatively new node (4 or better . . . probably less) should work just fine. Most stable systems allow you to install newer versions of node with minimal effort.

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nathandunn commented Apr 1, 2016

@enuggetry This is ready for review next week. Any system that you can get a relatively new node (4 or better . . . probably less) should work just fine. Most stable systems allow you to install newer versions of node with minimal effort.

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@enuggetry This is probably the recommended method.

git clone -b yeban-bowerise  --single-branch https://github.com/GMOD/jbrowse jbrowse-download 
cd jbrowse-download
bower --allow-root -f install
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nathandunn commented Apr 5, 2016

@enuggetry This is probably the recommended method.

git clone -b yeban-bowerise  --single-branch https://github.com/GMOD/jbrowse jbrowse-download 
cd jbrowse-download
bower --allow-root -f install

@enuggetry enuggetry merged commit 7dd2bdd into master Apr 6, 2016

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Woot!

On Apr 6, 2016, at 1:58 PM, Eric Y notifications@github.com wrote:

Merged #718 #718.


You are receiving this because you authored the thread.
Reply to this email directly or view it on GitHub #718 (comment)

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nathandunn commented Apr 6, 2016

Woot!

On Apr 6, 2016, at 1:58 PM, Eric Y notifications@github.com wrote:

Merged #718 #718.


You are receiving this because you authored the thread.
Reply to this email directly or view it on GitHub #718 (comment)

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and thanks @yeban for suggesting this

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nathandunn commented Apr 6, 2016

and thanks @yeban for suggesting this

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I am glad it was of help :)

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yeban commented Apr 7, 2016

I am glad it was of help :)

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Is there any reason not to just upgrade to the latest dojo 1.9 version? Most recently we were on the latest 1.8.10 version of the 1.8 branch, so this is actually a step backwards probably in terms of the patchsets

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cmdcolin commented Apr 7, 2016

Is there any reason not to just upgrade to the latest dojo 1.9 version? Most recently we were on the latest 1.8.10 version of the 1.8 branch, so this is actually a step backwards probably in terms of the patchsets

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I also debugged the reasons behind the xstyle/load-css failing (it was renamed xstyle/core/load-css)

added it back here e950c03

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cmdcolin commented Apr 7, 2016

I also debugged the reasons behind the xstyle/load-css failing (it was renamed xstyle/core/load-css)

added it back here e950c03

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great . . thanks @cmdcolin

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nathandunn commented Apr 7, 2016

great . . thanks @cmdcolin

@nathandunn nathandunn deleted the yeban-bowerise branch Apr 7, 2016

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WRT to dojo, I was just matching the current version. It looks like on master it is 1.9.2.

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nathandunn commented Apr 7, 2016

WRT to dojo, I was just matching the current version. It looks like on master it is 1.9.2.

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On master branch it was 1.8.10 #666

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cmdcolin commented Apr 7, 2016

On master branch it was 1.8.10 #666

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I am fine using either 1.8.10 or 1.9.2. It looked like 1.9.2 was the most stable, but I wasn't sure if that broke anything. I leave it up to @enuggetry to decide.

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nathandunn commented Apr 7, 2016

I am fine using either 1.8.10 or 1.9.2. It looked like 1.9.2 was the most stable, but I wasn't sure if that broke anything. I leave it up to @enuggetry to decide.

@nathandunn nathandunn removed the needs review label Apr 7, 2016

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nathandunn Apr 7, 2016

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I am fine with either.

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nathandunn commented Apr 7, 2016

I am fine with either.

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enuggetry Apr 7, 2016

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If you have had experience with 1.9.2 or better, then by all means, move
forward.

On Thu, Apr 7, 2016 at 4:11 PM, Nathan Dunn notifications@github.com
wrote:

I am fine with either.


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#718 (comment)

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enuggetry commented Apr 7, 2016

If you have had experience with 1.9.2 or better, then by all means, move
forward.

On Thu, Apr 7, 2016 at 4:11 PM, Nathan Dunn notifications@github.com
wrote:

I am fine with either.


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Went ahead and bumped to 1.9.8 edf5f9d

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cmdcolin commented Apr 8, 2016

Went ahead and bumped to 1.9.8 edf5f9d

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I think we should also remove the automatic bower install from setup.sh

It's usage is fairly confusing and it ends up running bower install even when it is precompiled

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cmdcolin commented Apr 8, 2016

I think we should also remove the automatic bower install from setup.sh

It's usage is fairly confusing and it ends up running bower install even when it is precompiled

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This should be fixed.

907e0ca 907e0ca

Nathan

On Apr 8, 2016, at 9:21 AM, Colin Diesh notifications@github.com wrote:

I think we should also remove the automatic bower install from setup.sh

It's usage is fairly confusing and it ends up running bower install even when it is precompiled


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nathandunn commented Apr 8, 2016

This should be fixed.

907e0ca 907e0ca

Nathan

On Apr 8, 2016, at 9:21 AM, Colin Diesh notifications@github.com wrote:

I think we should also remove the automatic bower install from setup.sh

It's usage is fairly confusing and it ends up running bower install even when it is precompiled


You are receiving this because you authored the thread.
Reply to this email directly or view it on GitHub #718 (comment)

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