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Utkarsh Bansal
May 14, 2017, 1:57:58 AM5/14/17
to MDnalysis-devel
Hi all,
Its been a week since the accepted students were announced. I'd like to update you all what I've been working on this past week.
- I've written a blog post describing my journey in the open source world so far. It live on utkarshbansal.me
- I've been reading documentation on creation of pytest plugins.
- I'm also working on the memory leak plugin alternatives - #1343
Also, I'm having a couple of exams in the coming week (as mentioned in my proposal), so most of my time will be devoted to academics for this week.
Best,
Utkarsh
Max Linke
May 14, 2017, 7:23:56 AM5/14/17
to MDnalysis-devel
This reminds me what is the plan to freeze test in the develop branch to help with the pytest transition?
btw for the travis setup in your proect timeline. You shouldn't need to do anything pytest is installed by default on our travis tests with the ci-helpers--
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Jonathan Barnoud
May 14, 2017, 7:46:51 AM5/14/17
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On 05/14/2017 01:23 PM, Max Linke
wrote:
This reminds me what is the plan to freeze test in the develop branch to help with the pytest transition?
Could we have something more progressive than a full freeze? The
effort to port to python 3 will run in parallel, and there will be
the need to modify the tests.
One thing we could do is to have the parts that are ported to pytest running on pytest, and the rest still running on nose. When Utkarsh starts working on a module, we freeze that module. When the PR is merged, we un-freeze the module in its pytest version. In addition to not freeze the whole test-suite, it would make it easier to merge PR progressively.
On the travis side, this would require to have both nose and pytest running, but each only on the modules that its support.
One thing we could do is to have the parts that are ported to pytest running on pytest, and the rest still running on nose. When Utkarsh starts working on a module, we freeze that module. When the PR is merged, we un-freeze the module in its pytest version. In addition to not freeze the whole test-suite, it would make it easier to merge PR progressively.
On the travis side, this would require to have both nose and pytest running, but each only on the modules that its support.
btw for the travis setup in your proect timeline. You shouldn't need to do anything pytest is installed by default on our travis tests with the ci-helpers
There is still the need to make sure it works. If it is easy to have
it run, great !
--On Sun, May 14, 2017 at 7:57 AM Utkarsh Bansal <bansalu...@gmail.com> wrote:
Hi all,--
Its been a week since the accepted students were announced. I'd like to update you all what I've been working on this past week.
- I've written a blog post describing my journey in the open source world so far. It live on utkarshbansal.me
- I've been reading documentation on creation of pytest plugins.
- I'm also working on the memory leak plugin alternatives - #1343
Also, I'm having a couple of exams in the coming week (as mentioned in my proposal), so most of my time will be devoted to academics for this week.
Best,Utkarsh
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Max Linke
May 14, 2017, 8:53:26 AM5/14/17
to mdnalys...@googlegroups.com
On 05/14/2017 01:46 PM, Jonathan Barnoud wrote:
> On 05/14/2017 01:23 PM, Max Linke wrote:
>> This reminds me what is the plan to freeze test in the develop branch
>> to help with the pytest transition?
> Could we have something more progressive than a full freeze? The effort
> to port to python 3 will run in parallel, and there will be the need to
> modify the tests.
>
> One thing we could do is to have the parts that are ported to pytest
> running on pytest, and the rest still running on nose. When Utkarsh
> starts working on a module, we freeze that module. When the PR is
> merged, we un-freeze the module in its pytest version. In addition to
> not freeze the whole test-suite, it would make it easier to merge PR
> progressively.
a nose and pytest folder and slowly shift modules from one to the other.
> On the travis side, this would require to have both nose and pytest
> running, but each only on the modules that its support.
>>
>> btw for the travis setup in your proect timeline. You shouldn't need
>> to do anything pytest is installed by default on our travis tests with
>> the ci-helpers
> There is still the need to make sure it works. If it is easy to have it
> run, great !
>>
>> On Sun, May 14, 2017 at 7:57 AM Utkarsh Bansal
>> <bansalu...@gmail.com <mailto:bansalu...@gmail.com>> wrote:
>>
>> Hi all,
>>
>> Its been a week since the accepted students were announced. I'd
>> like to update you all what I've been working on this past week.
>>
>> source world so far. It live on utkarshbansal.me
>> <http://utkarshbansal.me>
>> * I've been reading documentation on creation of pytest plugins.
>> * I'm also working on the memory leak plugin alternatives -
>> #1343 <https://github.com/MDAnalysis/mdanalysis/issues/1343>
>>
>>
>> Also, I'm having a couple of exams in the coming week (as
>> mentioned in my proposal), so most of my time will be devoted to
>> academics for this week.
>>
>> Best,
>> Utkarsh
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>>
>> Also, I'm having a couple of exams in the coming week (as
>> mentioned in my proposal), so most of my time will be devoted to
>> academics for this week.
>>
>> Best,
>> Utkarsh
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Utkarsh Bansal
May 14, 2017, 10:37:38 AM5/14/17
to MDnalysis-devel
On Sunday, May 14, 2017 at 5:16:51 PM UTC+5:30, Jonathan Barnoud wrote:
On 05/14/2017 01:23 PM, Max Linke wrote:
Could we have something more progressive than a full freeze? The effort to port to python 3 will run in parallel, and there will be the need to modify the tests.This reminds me what is the plan to freeze test in the develop branch to help with the pytest transition?
One thing we could do is to have the parts that are ported to pytest running on pytest, and the rest still running on nose. When Utkarsh starts working on a module, we freeze that module. When the PR is merged, we un-freeze the module in its pytest version. In addition to not freeze the whole test-suite, it would make it easier to merge PR progressively.
How would the coverage work then? We will lose the certainty that I don't mess up the coverage and endup missing tests.
Jonathan Barnoud
May 14, 2017, 11:35:59 AM5/14/17
to mdnalys...@googlegroups.com
To answer Max question, the dirty way I
was thinking about was to explicitly list the files to run to
mda-nose and the pytest equivalent.
To answer Utkarsh, it seems possible to combine coverage outputs: <http://stackoverflow.com/questions/26214055/combine-python-coverage-files>.
To answer Utkarsh, it seems possible to combine coverage outputs: <http://stackoverflow.com/questions/26214055/combine-python-coverage-files>.
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Utkarsh Bansal
May 14, 2017, 12:22:52 PM5/14/17
to MDnalysis-devel
On Sunday, May 14, 2017 at 9:05:59 PM UTC+5:30, Jonathan Barnoud wrote:
To answer Max question, the dirty way I was thinking about was to explicitly list the files to run to mda-nose and the pytest equivalent.
To answer Utkarsh, it seems possible to combine coverage outputs: <http://stackoverflow.com/questions/26214055/combine-python-coverage-files>.
Looks easy enough to implement on travis.
On a side note, should I start compiling a wiki to show nose vs pytest to ease the transition for other developers?
Jonathan Barnoud
May 14, 2017, 12:27:01 PM5/14/17
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Please, do. It will also help you when
the coding period will actually start.
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Max Linke
May 14, 2017, 3:27:50 PM5/14/17
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A plan how freezes happen would also be nice. We try to get a bug-fix
release out before coding starts so you can have the go ahead to freeze
certain parts of the codebase.
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release out before coding starts so you can have the go ahead to freeze
certain parts of the codebase.
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Richard Gowers
May 25, 2017, 10:27:46 AM5/25/17
to MDnalysis-devel
Hi Guys
I've been thinking about this, it might be a good idea to break up the tests so that tests can get converted to pytest piece by piece. This means that each submodule (of the testsuite) can get moved to using pytest as a runner in individual PRs to develop rather than one huge monstrosity of a PR
For this to work smoothly, coverage will have to be gathered from many coverage files. As a proof of concept and first step, we need to split the current test run into many separate nosetests commands, so:
./mda_nosetests args
to
./mda_nosetests coordinates/ args
./mda_nosetests topology/ args
./mda_nosetests lib/ args
etc
./gather_coverage
Then once/if this works, we can slowly proceed to
./mda_pytest coordinates/ args
./mda_nosetests topology/ args
etc
Until everything is mda_pytest, at which point we merge again.
Thoughts?
Richard
I've been thinking about this, it might be a good idea to break up the tests so that tests can get converted to pytest piece by piece. This means that each submodule (of the testsuite) can get moved to using pytest as a runner in individual PRs to develop rather than one huge monstrosity of a PR
For this to work smoothly, coverage will have to be gathered from many coverage files. As a proof of concept and first step, we need to split the current test run into many separate nosetests commands, so:
./mda_nosetests args
to
./mda_nosetests coordinates/ args
./mda_nosetests topology/ args
./mda_nosetests lib/ args
etc
./gather_coverage
Then once/if this works, we can slowly proceed to
./mda_pytest coordinates/ args
./mda_nosetests topology/ args
etc
Until everything is mda_pytest, at which point we merge again.
Thoughts?
Richard
>> <mailto:mdnalysis-devel+unsub...@googlegroups.com>.
Jonathan Barnoud
May 25, 2017, 10:35:58 AM5/25/17
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Hey,
I am all in favor of that. This is what I had in mind in my previous messages in the thread.
Utkarsh, could you have a look at this if your exams are done? It would be good if you could have that running for you by the beginning of the coding period.
Jonathan
I am all in favor of that. This is what I had in mind in my previous messages in the thread.
Utkarsh, could you have a look at this if your exams are done? It would be good if you could have that running for you by the beginning of the coding period.
Jonathan
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Oliver Beckstein
May 25, 2017, 12:16:46 PM5/25/17
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Apparently, coverage has the combine command that can combine multiple coverage files http://coverage.readthedocs.io/en/latest/cmd.html
Also, I think you can just do
mda_nosetests [args] directory
(Maybe with some adjustment for how coverage is run and stored)
--
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Oliver Beckstein
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Utkarsh Bansal
May 26, 2017, 12:09:18 PM5/26/17
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Hi,
I'll work on this and try to send a PR over the weekend.
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Utkarsh Bansal
Jun 11, 2017, 11:52:03 AM6/11/17
to MDnalysis-devel
Hi devs,
As you might be aware I wasn't actively working on my project for the last week. I'm feeling better now and have started working. I hope to cover up the time lost by the end of this phase.
Best,
Utkarsh
Jonathan Barnoud
Jun 14, 2017, 3:32:55 AM6/14/17
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Hi,
When was the deadline for the blog post? Wasn't it yesterday?
Jonathan
When was the deadline for the blog post? Wasn't it yesterday?
Jonathan
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Max Linke
Jun 14, 2017, 3:47:38 AM6/14/17
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We already send him a reminder for that in private from the NumFOCUS admins.
On 06/14/2017 09:32 AM, Jonathan Barnoud wrote:
> Hi,
>
> When was the deadline for the blog post? Wasn't it yesterday?
>
> Jonathan
>
> On 06/11/2017 05:52 PM, Utkarsh Bansal wrote:
>> Hi devs,
>>
>> As you might be aware I wasn't actively working on my project for the
>> last week. I'm feeling better now and have started working. I hope to
>> cover up the time lost by the end of this phase.
>>
>> Best,
>> Utkarsh
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On 06/14/2017 09:32 AM, Jonathan Barnoud wrote:
> Hi,
>
> When was the deadline for the blog post? Wasn't it yesterday?
>
> Jonathan
>
> On 06/11/2017 05:52 PM, Utkarsh Bansal wrote:
>> Hi devs,
>>
>> As you might be aware I wasn't actively working on my project for the
>> last week. I'm feeling better now and have started working. I hope to
>> cover up the time lost by the end of this phase.
>>
>> Best,
>> Utkarsh
>> --
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Jonathan Barnoud
Jun 14, 2017, 3:49:08 AM6/14/17
to mdnalys...@googlegroups.com
Sorry I did not see. At that point it was more curiosity on my side.
Utkarsh Bansal
Jun 14, 2017, 5:39:24 AM6/14/17
to mdnalys...@googlegroups.com
Hi Jonathan,
I have a draft ready and will make it live by EOD.
Best,
Utkarsh
On Wed, Jun 14, 2017 at 1:18 PM, Jonathan Barnoud <jona...@barnoud.net> wrote:
Sorry I did not see. At that point it was more curiosity on my side.
On 06/14/2017 09:47 AM, Max Linke wrote:
We already send him a reminder for that in private from the NumFOCUS admins.
On 06/14/2017 09:32 AM, Jonathan Barnoud wrote:
Hi,
When was the deadline for the blog post? Wasn't it yesterday?
Jonathan
On 06/11/2017 05:52 PM, Utkarsh Bansal wrote:
Hi devs,
As you might be aware I wasn't actively working on my project for the last week. I'm feeling better now and have started working. I hope to cover up the time lost by the end of this phase.
Best,
Utkarsh
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Utkarsh Bansal
Jun 14, 2017, 7:43:44 AM6/14/17
to mdnalys...@googlegroups.com
Hi all,
I've published my latest blog post. If you'd like, you can read it at http://utkarshbansal.me/blog/GSoC-The-Beginning/
Looking forward to your comments!
Best,
Utkarsh
Utkarsh Bansal
Jun 14, 2017, 5:34:23 PM6/14/17
to MDnalysis-devel
Hi all,
I am mostly done with my work on splitting the TravisCI build(#1370) - only need to follow up on reviews.
So I should now be able to work on porting tests to pytest. The first step is to make them discoverable for pytest which will involve getting rid of all __init__ methods from the test classes. We need to discuss the testing freeze regading this - when and how.
Also, as a reminder - if you haven't yet voted on the time slots for next week's meeting, please do so. I will close the poll on Sunday. I'd like to do a lot of porting and make most of tests discoverable over this weekend so that we can discuss any remaining cases/issue in the meeting, so it will be great if most of the community could join.
Best,
Utkarsh
Richard Gowers
Jun 15, 2017, 2:07:17 AM6/15/17
to MDnalysis-devel
Hey Utkarsh
Nice work on the PR, I'll give it a review today.
Can you look into the caching thing for travis first? Without that, it's hard to make any progress.
Richard
Nice work on the PR, I'll give it a review today.
Can you look into the caching thing for travis first? Without that, it's hard to make any progress.
Richard
Utkarsh Bansal
Jun 15, 2017, 3:28:50 AM6/15/17
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Yes, I agree without the coverage data It would be hard to make any solid progress. I'll work on it and will try to send a PR by EOD.
Best,
Utkarsh
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Jonathan Barnoud
Jun 15, 2017, 4:30:20 AM6/15/17
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Hi Utkarsh,
I dropped a couple of comments on the PR. I am happy to see things going forward. As Richard mentioned, I would like to see the full build fixed before you move to the next step. For the testing freeze, I would suggest you start with the easiest file, one that needs little to no change, so you can have pytest called by travis instead of the second batch of nose. Only then we can freeze a big block, following the order in your proposal.
Best,
Jonathan
I dropped a couple of comments on the PR. I am happy to see things going forward. As Richard mentioned, I would like to see the full build fixed before you move to the next step. For the testing freeze, I would suggest you start with the easiest file, one that needs little to no change, so you can have pytest called by travis instead of the second batch of nose. Only then we can freeze a big block, following the order in your proposal.
Best,
Jonathan
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Utkarsh Bansal
Jun 17, 2017, 6:26:57 AM6/17/17
to MDnalysis-devel
Hi all,
I looked through the testuite, and concluded that "lib/test_util.py" might be the easiest file to port to pytest. The test classes all inherit from object - so no inheritance problems and the __init__ methods are fairly simple to convert to setUp methods.
Best,
Utkarsh
Jonathan Barnoud
Jun 17, 2017, 10:23:01 AM6/17/17
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Hi Utkarsh,
It is OK for me. Notice however that there are quite a few test generators there. We can free `lib/test_util.py` until you are done with it and you have replaced the second call to nose by a call to pytest.
Best,
Jonathan
It is OK for me. Notice however that there are quite a few test generators there. We can free `lib/test_util.py` until you are done with it and you have replaced the second call to nose by a call to pytest.
Best,
Jonathan
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Max Linke
Jun 17, 2017, 11:38:36 AM6/17/17
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Hi Utkarsh
when will the next Video Conference be? I might join but I'm usually
busy at the times you suggested.
best Max
On 06/17/2017 04:22 PM, Jonathan Barnoud wrote:
> Hi Utkarsh,
>
> It is OK for me. Notice however that there are quite a few test
> generators there. We can free `lib/test_util.py` until you are done with
> it and you have replaced the second call to nose by a call to pytest.
>
> Best,
> Jonathan
>
> On 06/17/2017 12:26 PM, Utkarsh Bansal wrote:
>> Hi all,
>>
>> I looked through the testuite, and concluded that "lib/test_util.py"
>> might be the easiest file to port to pytest. The test classes all
>> inherit from object- so no inheritanceproblems and the __init__
>> methodsare fairly simple to convert to setUpmethods.
> <https://groups.google.com/d/msgid/mdnalysis-devel/5282df9e-abd4-145b-7fad-fd7c1ac60331%40barnoud.net?utm_medium=email&utm_source=footer>.
when will the next Video Conference be? I might join but I'm usually
busy at the times you suggested.
best Max
On 06/17/2017 04:22 PM, Jonathan Barnoud wrote:
> Hi Utkarsh,
>
> It is OK for me. Notice however that there are quite a few test
> generators there. We can free `lib/test_util.py` until you are done with
> it and you have replaced the second call to nose by a call to pytest.
>
> Best,
> Jonathan
>
> On 06/17/2017 12:26 PM, Utkarsh Bansal wrote:
>> Hi all,
>>
>> I looked through the testuite, and concluded that "lib/test_util.py"
>> might be the easiest file to port to pytest. The test classes all
>> inherit from object- so no inheritanceproblems and the __init__
>>
>> Best,
>> Utkarsh
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>> Best,
>> Utkarsh
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Utkarsh Bansal
Jun 18, 2017, 8:12:22 AM6/18/17
to MDnalysis-devel
Hi Max,
Sorry for the late reply, looks like we are going to have it tomorrow, 7:00 PM – 8:00 PM IST
Again, if the time slots are a problem, you can suggest me some better ones.
Best,
Utkarsh
Utkarsh Bansal
Jun 19, 2017, 1:36:45 AM6/19/17
to MDnalysis-devel
Hi all,
So I have closed the Doodle poll, and we will be having the meeting on Tuesday. I have sent out calendar invites to all the participants, if you did not receive your's, I must be having an incorrect email id, so please share your email.
Best,
Utkarsh
Manuel Nuno Melo
Jun 19, 2017, 9:36:36 AM6/19/17
to mdnalys...@googlegroups.com
Hi Utkarsh,
I didn't get an invite (please use manuel.n...@gmail.com).
It was also a bit disruptive to find out yesterday the meeting was scheduled for today, and then now that it was postponed for tomorrow. Maybe next time we could decide a bit earlier?
It was also a bit disruptive to find out yesterday the meeting was scheduled for today, and then now that it was postponed for tomorrow. Maybe next time we could decide a bit earlier?
Manel
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Utkarsh Bansal
Jun 19, 2017, 9:42:30 AM6/19/17
to MDnalysis-devel
Hi Manuel,
Sorry for that. I have made another calendar event and invited all. Looks like the previous one didn't send out the invites.
Apologies again.
Best,
Utkarsh
Utkarsh Bansal
Jun 20, 2017, 9:36:17 AM6/20/17
to MDnalysis-devel
Hi all,
The meeting has started, you can join at https://hangouts.google.com/group/LEFLamCzwbr61QQz2
Best,
Utkarsh
Jonathan Barnoud
Jun 20, 2017, 9:36:26 AM6/20/17
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Hi,
I've seen the call but I was not ready to answer. Is there a link to join the conversation?
Jonathan
I've seen the call but I was not ready to answer. Is there a link to join the conversation?
Jonathan
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Max Linke
Jun 20, 2017, 9:45:50 AM6/20/17
to mdnalys...@googlegroups.com
python 3 has a module to trace malloc calls and trace them
https://docs.python.org/3/library/tracemalloc.html
On 06/20/2017 03:36 PM, Jonathan Barnoud wrote:
> Hi,
>
> I've seen the call but I was not ready to answer. Is there a link to
> join the conversation?
>
> Jonathan
>
> On 06/19/2017 03:42 PM, Utkarsh Bansal wrote:
>> Hi Manuel,
>>
>> Sorry for that. I have made another calendar event and invited all.
>> Looks like the previous one didn't send out the invites.
>>
>> Apologies again.
>>
>> Best,
>> Utkarsh
>> --
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https://docs.python.org/3/library/tracemalloc.html
On 06/20/2017 03:36 PM, Jonathan Barnoud wrote:
> Hi,
>
> I've seen the call but I was not ready to answer. Is there a link to
> join the conversation?
>
> Jonathan
>
> On 06/19/2017 03:42 PM, Utkarsh Bansal wrote:
>> Hi Manuel,
>>
>> Sorry for that. I have made another calendar event and invited all.
>> Looks like the previous one didn't send out the invites.
>>
>> Apologies again.
>>
>> Best,
>> Utkarsh
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>> https://groups.google.com/d/msgid/mdnalysis-devel/52b7c88c-b6d8-4cf3-b7ba-e2b1f328e329%40googlegroups.com
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Max Linke
Jun 20, 2017, 2:38:22 PM6/20/17
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Hi Utkarsh
Can you post a small summary of the topics we discussed, our conclusions
and your plan until our next meeting. Plus a doodle for the next
meeting. Thanks
best Max
Can you post a small summary of the topics we discussed, our conclusions
and your plan until our next meeting. Plus a doodle for the next
meeting. Thanks
best Max
Utkarsh Bansal
Jun 21, 2017, 6:12:12 AM6/21/17
to MDnalysis-devel
Hi all,
We had a meeting yesterday and discussed quite a bit about how I'll be moving forward in the next couple of weeks.
- Complete porting the lib module and most importantly - merge coverage reports generated from nose and pytest.
- Next module to be worked on is the coordinates module (because I already have some part of it done).
- For most of the part, I will be working on porting two modules in parallel.
- The memory plugin can be skipped for now because by using fixtures we are deliberately leaking memory(as seen by our existing plugin).
- The open files plugin will be ported once the complete test suite works with pytest (it is currently deactivated).
- Only the knownfailure plugin has to be implemented - all others have alternatives in pytest or are available as a plugin.
The doodle poll for next week's meeting is available here. Feel free to ask me to add more time slots if needed.
Also, can I consider the coordinates module frozen? I'm mostly done with the lib module.
Best,
Utkarsh
Utkarsh Bansal
Jun 21, 2017, 7:44:39 AM6/21/17
to MDnalysis-devel
Hi all,
My PR to port the lib module to pytest (#1413) has been merged. I am currently working on porting the coordinates module and it should be done by tonight. Which module can I work on next?
Best,
Utkarsh
Richard Gowers
Jun 21, 2017, 9:53:06 AM6/21/17
to MDnalysis-devel
Maybe topology & formats next, they should be similar in feel to coordinates, so it might help doing them at roughly the same time
Max Linke
Jun 21, 2017, 9:54:16 AM6/21/17
to mdnalys...@googlegroups.com
formats should be easy. the tests in their already look a lot like
pytest tests and are mostly simple functions.
On 06/21/2017 03:53 PM, Richard Gowers wrote:
> Maybe topology & formats next, they should be similar in feel to
> coordinates, so it might help doing them at roughly the same time
>
> On Wednesday, 21 June 2017 12:44:39 UTC+1, Utkarsh Bansal wrote:
>
> Hi all,
>
> My PR to port the lib module to pytest (#1413
> <https://github.com/MDAnalysis/mdanalysis/pull/1413>) has been
> <https://groups.google.com/d/msgid/mdnalysis-devel/1e9d1ba0-536e-480a-8dcf-10b91675d754%40googlegroups.com?utm_medium=email&utm_source=footer>.
pytest tests and are mostly simple functions.
On 06/21/2017 03:53 PM, Richard Gowers wrote:
> Maybe topology & formats next, they should be similar in feel to
> coordinates, so it might help doing them at roughly the same time
>
> On Wednesday, 21 June 2017 12:44:39 UTC+1, Utkarsh Bansal wrote:
>
> Hi all,
>
> My PR to port the lib module to pytest (#1413
> merged. I am currently working on porting the coordinates module and
> it should be done by tonight. Which module can I work on next?
>
> Best,
> Utkarsh
>
> it should be done by tonight. Which module can I work on next?
>
> Best,
> Utkarsh
>
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Max Linke
Jun 23, 2017, 7:30:24 AM6/23/17
to mdnalys...@googlegroups.com
On 06/21/2017 12:12 PM, Utkarsh Bansal wrote:
> Hi all,
> suite works with pytest (it is currently deactivated).
https://github.com/astropy/astropy/pull/5770
Astropy has a open-file test plugin for pytest. They recommended the PR
linked above to have a look at the code of the plugin.
Utkarsh Bansal
Jun 24, 2017, 6:09:15 AM6/24/17
to MDnalysis-devel
Hi all,
Just a reminder, the poll for next week's meeting closes tonight (in around 12 hours). In case you haven't voted, please do so here.
Best,
Utkarsh
Utkarsh Bansal
Jun 25, 2017, 5:51:38 AM6/25/17
to MDnalysis-devel
Hi all,
I've closed the polling for next week's meeting. The meeting will be on Monday, 8:45 PM – 9:30 PM IST.
I'll be sending out Google calendar invites to the participants.
Best,
Utkarsh
Utkarsh Bansal
Jun 25, 2017, 1:52:20 PM6/25/17
to MDnalysis-devel
Hi all,
Just wanted to tell that I have written a blog post documenting my last week. It available at http://utkarshbansal.me/blog/Why-do-you-even-write-tests-!/
Do tell me what you think!
Best,
Utkarsh
Utkarsh Bansal
Jun 26, 2017, 1:21:38 PM6/26/17
to MDnalysis-devel
Hi all,
I was going through the evaluation form and I'm a bit confused regarding the question "How often do you interact with your mentor(s)?"
What is interaction counted as? I do interact regularly (at least a couple of times) via reviews on Github. Is that counted as interaction? Or are the video call only counted as interactions, which happen less frequently?
Best,
Utkarsh
Max Linke
Jun 27, 2017, 2:26:20 AM6/27/17
to MDnalysis-devel
Usually all interactions are counted. Also GitHub which where most of the project discussions happen.
Could you write up a small summary of your call with Richard yesterday. Would be nice for the rest of us who couldn't make it.
Do you have some code for the reader tests yet? If so please open a PR even if the code doesn't pass the tests yet. A PR and commits to GitHub are the only way we can see your are actively working.
Best Maz
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Richard Gowers
Jun 27, 2017, 5:22:15 AM6/27/17
to MDnalysis-devel
I had to cancel on the call yesterday because of work, so I think it might have been cancelled altogether.
Utkarsh Bansal
Jun 27, 2017, 8:16:45 AM6/27/17
to MDnalysis-devel
Hi all,
As Richard mentioned, we couldn't do the hangout meeting yesterday. I'll setup another doodle poll for next week soon.
Just to update you all on the current progress, I've ported 3 modules - utils, lib and topology completely (no loss in coverage). Some work on coordinates has also been done and I'll open another PR to complete that in a couple of hours from now.
Going forward, this week I'll complete the coordinates module and complete the remaining three modules (analysis, auxiliary and core) as well. Once that is done, we will move to Phase 2 which will involve using pytest specific features to improve our test suite.
Best,
Utkarsh
Utkarsh Bansal
Jun 27, 2017, 8:47:50 AM6/27/17
to MDnalysis-devel
Hi all,
Another question, there are options for the communication question I mentioned before - Daily, Twice a week, Once a week, Twice a month, Once a month. I feel the communication has largely been more than twice a week, but we have also skipped a couple of days here and there. So I can't say that we discuss daily, but I feel that's the more appropriate answer!? Thoughts?
Best,
Utkarsh
Manuel Nuno Melo
Jun 27, 2017, 11:22:13 AM6/27/17
to mdnalys...@googlegroups.com
I'd say the communication lately qualifies more as daily, having progressed there from less than 'twice a week' earlier on in your project.
I'm ok with 'daily', since that's where the exchange is at now, but maybe other mentors think differently?
I'm ok with 'daily', since that's where the exchange is at now, but maybe other mentors think differently?
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Utkarsh Bansal
Jun 27, 2017, 11:25:51 AM6/27/17
to mdnalys...@googlegroups.com
Yes, that's what is confusing me, I had zero communication in the first week after the community bonding, but that has largely improved by now.
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Max Linke
Jun 27, 2017, 4:02:13 PM6/27/17
to mdnalys...@googlegroups.com
Yes communication has improved now. That is nice.
In the evaluation you can write how you think the communication is
going. You are not going to be judged by it.
This is however a good time for you to tell is if you are happy with the
mentoring. Are you OK with the contact you are having. Do you prefer the
video calls or are you good with the github comments.
best Max
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In the evaluation you can write how you think the communication is
going. You are not going to be judged by it.
This is however a good time for you to tell is if you are happy with the
mentoring. Are you OK with the contact you are having. Do you prefer the
video calls or are you good with the github comments.
best Max
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Utkarsh Bansal
Jun 29, 2017, 2:52:38 AM6/29/17
to mdnalys...@googlegroups.com
Hi all,
Just wanted to let you know that I submitted my evaluations yesterday. In case you haven't submitted the evaluations, please do so. The last day to submit evaluations is Friday.
Best,
Utkarsh
On Wed, Jun 28, 2017 at 1:32 AM, Max Linke <max.l...@gmail.com> wrote:
Yes communication has improved now. That is nice.
In the evaluation you can write how you think the communication is going. You are not going to be judged by it.
This is however a good time for you to tell is if you are happy with the mentoring. Are you OK with the contact you are having. Do you prefer the video calls or are you good with the github comments.
best Max
On 06/27/2017 05:25 PM, Utkarsh Bansal wrote:
Yes, that's what is confusing me, I had zero communication in the first week after the community bonding, but that has largely improved by now.
On Tue, Jun 27, 2017 at 8:51 PM, Manuel Nuno Melo <manuel.n...@gmail.com <mailto:manuel.nuno.melo@gmail.com>> wrote:
I'd say the communication lately qualifies more as daily, having
progressed there from less than 'twice a week' earlier on in your
project.
I'm ok with 'daily', since that's where the exchange is at now, but
maybe other mentors think differently?
On Tue, Jun 27, 2017 at 1:47 PM, Utkarsh Bansal
<bansalu...@gmail.com <mailto:bansalutkarsh3@gmail.com>> wrote:
Hi all,
Another question, there are options for the
communication question I mentioned before - Daily, Twice a week,
Once a week, Twice a month, Once a month. I feel the
communication has largely been more than twice a week, but we
have also skipped a couple of days here and there. So I can't
say that we discuss daily, but I feel that's the more
appropriate answer!? Thoughts?
Best,
Utkarsh
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Richard Gowers
Jun 29, 2017, 3:06:30 AM6/29/17
to mdnalys...@googlegroups.com
Hey Utkarsh, we did ours yesterday.
On Thu, 29 Jun 2017, 7:52 a.m. Utkarsh Bansal, <bansalu...@gmail.com> wrote:
Hi all,Just wanted to let you know that I submitted my evaluations yesterday. In case you haven't submitted the evaluations, please do so. The last day to submit evaluations is Friday.Best,Utkarsh
On Wed, Jun 28, 2017 at 1:32 AM, Max Linke <max.l...@gmail.com> wrote:
Yes communication has improved now. That is nice.
In the evaluation you can write how you think the communication is going. You are not going to be judged by it.
This is however a good time for you to tell is if you are happy with the mentoring. Are you OK with the contact you are having. Do you prefer the video calls or are you good with the github comments.
best Max
On 06/27/2017 05:25 PM, Utkarsh Bansal wrote:
Yes, that's what is confusing me, I had zero communication in the first week after the community bonding, but that has largely improved by now.
On Tue, Jun 27, 2017 at 8:51 PM, Manuel Nuno Melo <manuel.n...@gmail.com <mailto:manuel.n...@gmail.com>> wrote:
I'd say the communication lately qualifies more as daily, having
progressed there from less than 'twice a week' earlier on in your
project.
I'm ok with 'daily', since that's where the exchange is at now, but
maybe other mentors think differently?
On Tue, Jun 27, 2017 at 1:47 PM, Utkarsh Bansal
<bansalu...@gmail.com <mailto:bansalu...@gmail.com>> wrote:
Hi all,
Another question, there are options for the
communication question I mentioned before - Daily, Twice a week,
Once a week, Twice a month, Once a month. I feel the
communication has largely been more than twice a week, but we
have also skipped a couple of days here and there. So I can't
say that we discuss daily, but I feel that's the more
appropriate answer!? Thoughts?
Best,
Utkarsh
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Utkarsh Bansal
Jun 29, 2017, 9:10:43 AM6/29/17
to MDnalysis-devel
Hi all,
The Doodle poll for next week's meeting is available at http://doodle.com/poll/p5f5whwkudk2s35r
I'll close the poll on Sunday.
Best,
Utkarsh
Manuel Nuno Melo
Jun 29, 2017, 11:33:08 AM6/29/17
to mdnalys...@googlegroups.com
The afternoons of the next couple of weeks will be tough for me because I'll be lecturing a Python course. I'll try to keep on top of Utkarsh's work, though.
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Utkarsh Bansal
Jun 29, 2017, 11:58:33 AM6/29/17
to mdnalys...@googlegroups.com
Hi Manuel,
I can also schedule the call at late night 12:01 AM - 3:00 AM (UTC+5:30), if that is a more suitable time.
Best,
Utkarsh
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Max Linke
Jun 29, 2017, 12:02:52 PM6/29/17
to mdnalys...@googlegroups.com
You mean after midnight European time? Could you please give times as middle European time and Indian. That would make it easier than judge how good a time works for all of us.
On Thu, Jun 29, 2017, 17:58 Utkarsh Bansal <bansalu...@gmail.com> wrote:
Hi Manuel,I can also schedule the call at late night 12:01 AM - 3:00 AM (UTC+5:30), if that is a more suitable time.Best,UtkarshOn Thu, Jun 29, 2017 at 9:02 PM, Manuel Nuno Melo <manuel.n...@gmail.com> wrote:
The afternoons of the next couple of weeks will be tough for me because I'll be lecturing a Python course. I'll try to keep on top of Utkarsh's work, though.
On Thu, Jun 29, 2017 at 2:10 PM, Utkarsh Bansal <bansalu...@gmail.com> wrote:
Hi all,The Doodle poll for next week's meeting is available at http://doodle.com/poll/p5f5whwkudk2s35rI'll close the poll on Sunday.Best,Utkarsh
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Utkarsh Bansal
Jun 29, 2017, 12:05:38 PM6/29/17
to mdnalys...@googlegroups.com
What is you timezone relative to UTC?
Best,
Utkarsh
On Thu, Jun 29, 2017 at 9:32 PM, Max Linke <max.l...@gmail.com> wrote:
You mean after midnight European time? Could you please give times as middle European time and Indian. That would make it easier than judge how good a time works for all of us.
On Thu, Jun 29, 2017, 17:58 Utkarsh Bansal <bansalu...@gmail.com> wrote:
Hi Manuel,I can also schedule the call at late night 12:01 AM - 3:00 AM (UTC+5:30), if that is a more suitable time.Best,UtkarshOn Thu, Jun 29, 2017 at 9:02 PM, Manuel Nuno Melo <manuel.n...@gmail.com> wrote:
The afternoons of the next couple of weeks will be tough for me because I'll be lecturing a Python course. I'll try to keep on top of Utkarsh's work, though.
On Thu, Jun 29, 2017 at 2:10 PM, Utkarsh Bansal <bansalu...@gmail.com> wrote:
Hi all,The Doodle poll for next week's meeting is available at http://doodle.com/poll/p5f5whwkudk2s35rI'll close the poll on Sunday.Best,Utkarsh
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Max Linke
Jun 29, 2017, 12:06:56 PM6/29/17
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My time zone is middle European. Google should figure what that is in UTC. I always forget.
On Thu, Jun 29, 2017, 18:05 Utkarsh Bansal <bansalu...@gmail.com> wrote:
What is you timezone relative to UTC?Best,UtkarshOn Thu, Jun 29, 2017 at 9:32 PM, Max Linke <max.l...@gmail.com> wrote:
You mean after midnight European time? Could you please give times as middle European time and Indian. That would make it easier than judge how good a time works for all of us.
On Thu, Jun 29, 2017, 17:58 Utkarsh Bansal <bansalu...@gmail.com> wrote:
Hi Manuel,I can also schedule the call at late night 12:01 AM - 3:00 AM (UTC+5:30), if that is a more suitable time.Best,UtkarshOn Thu, Jun 29, 2017 at 9:02 PM, Manuel Nuno Melo <manuel.n...@gmail.com> wrote:
The afternoons of the next couple of weeks will be tough for me because I'll be lecturing a Python course. I'll try to keep on top of Utkarsh's work, though.
On Thu, Jun 29, 2017 at 2:10 PM, Utkarsh Bansal <bansalu...@gmail.com> wrote:
Hi all,The Doodle poll for next week's meeting is available at http://doodle.com/poll/p5f5whwkudk2s35rI'll close the poll on Sunday.Best,Utkarsh
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Oliver Beckstein
Jun 29, 2017, 12:19:28 PM6/29/17
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https://www.timeanddate.com/worldclock/meeting.html is a useful tool to figure out good times when planning meetings in different time zones.
Oliver
Utkarsh Bansal
Jun 29, 2017, 12:28:12 PM6/29/17
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MET is UTC+1:00, so 12:01 AM - 3:00 AM (UTC+5:30) would be 7:30 to 10:30 in your time.
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Utkarsh Bansal
Jul 2, 2017, 5:00:33 AM7/2/17
to MDnalysis-devel
Hi all,
Just a reminder - the doodle poll closes today in about 12 hours. If you haven't voted yet, please do so now.
Best,
Utkarsh
Max Linke
Jul 3, 2017, 11:34:40 AM7/3/17
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Hi Utkarsh
Please have a look at the following PR's and issues before tomorrow.
https://github.com/MDAnalysis/mdanalysis/pull/1442
https://github.com/MDAnalysis/mdanalysis/issues/1444
best Max
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Please have a look at the following PR's and issues before tomorrow.
https://github.com/MDAnalysis/mdanalysis/pull/1442
https://github.com/MDAnalysis/mdanalysis/issues/1444
best Max
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Utkarsh Bansal
Jul 12, 2017, 10:25:50 AM7/12/17
to MDnalysis-devel
Hi all,
My latest blog post is live! You can read it at http://utkarshbansal.me/blog/Hey-there-bots!/
Best,
Utkarsh
Utkarsh Bansal
Jul 18, 2017, 12:42:25 PM7/18/17
to MDnalysis-devel
Hi all,
Thought I'd post an update here too - just to keep everyone in the loop.
Port to pytest (#884) is now officially closed! This completes the basic shift to pytest i.e. nose is no longer a dependency. I'm now working towards refactoring the test suite to follow the pytest style of testing and to leverage the great features in pytest - fixtures. This should help up to bring down the execution time of the tests and make the test suite more maintainable in general.
So far I've worked on utils (only one file left) and have a PR open for the lib module.
Best,
Utkarsh
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