Blog Post for release 0.16.0 #26

kain88-de · 2016-08-17T06:33:05Z

This is a first draft for the next release blog post. It lists major contributions so far or soon merged into develop from non-core devs. There is still some text missing to explain all features especially the auxillary data section.

Commands for some stats that we can include:

List all merge-like commits git log --online --since='2015-05-15' | grep '#'
list all authors git log --pretty=%an --since='2015-05-15' | sort | uniq

TODO paragraphs

MemoryReader including benchmarks (partially PR Contributions on Encore and MemoryReader to Blog on 0.16.0 release #30)
new Topology including final benchmarks and changes (summarize, link to blog post in PR Added new topology system post #41)
~~[x] new Encore module (PR Contributions on Encore and MemoryReader to Blog on 0.16.0 release #30)~~
new way of writing analysis with AnalysisFromFunction
MMTF format (link to http://www.mdanalysis.org/2016/11/30/Support-for-MMTF/)
new citation (SciPy 2016 paper and J Comp Chem 2011)
UpdatingAtomGroups (or maybe spin out into mini blog post?) PR: Added dynamically updating atomgroup selections (#175 and #1074) mdanalysis#1080

kain88-de · 2016-08-17T06:34:31Z

@fiona-naughton and @jbarnoud can you fill in the text for the auxillary data with usage examples. Akso @jbarnoud if panedr already works that would be great and good example to list here (since it's immediately useful for all gromacs simulations)

jbarnoud · 2016-08-17T09:45:56Z

I do not have push right to the directory. Should I do a pull request to you branch? (ping @orbeckst )

kain88-de · 2016-08-17T10:08:25Z

@jbarnoud you should be able to push to this repository now.

jbarnoud · 2016-08-17T11:10:28Z

@kain88-de Thanks

I expended on Fiona's auxiliary reader, I still need to update the link to the doc when I finally merge the feature. I also change the markup of the PCA example so it is syntax highlighted.

kain88-de · 2016-08-17T11:22:22Z

_posts/2016-xx-xx-release-0.16.md

+# Create your universe as usual
+universe = mda.Universe(SIMULATION)
+# Attach an auxiliary time serie with the name `pull_force`
+universe.trajectory.add_auxiliaty('pull_force', 'md_f.xvg')


I think there is a typo here

jbarnoud · 2016-08-22T20:40:00Z

The new shortcut to create analysis classes should appear.

kain88-de · 2016-08-23T07:23:51Z

The new shortcut to create analysis classes should appear.

Done

kain88-de · 2016-10-05T17:22:15Z

@wouterboomsma @mtiberti Do you want to write a paragraph about encore what it is with some small examples, you can add a longer post just about encore after the release. I would also appreciate a small paragraph about the MemoryReader.

wouterboomsma · 2016-10-11T19:08:49Z

@kain88-de Yes, we can certainly do this. And sorry for the late response. We'll try to have something ready in the coming week.

wouterboomsma · 2016-10-21T14:43:08Z

@kain88-de Created a draft in PR #30.

orbeckst · 2016-11-20T17:18:31Z

@richardjgowers can you write a sentence on MMTF (MDAnalysis/mdanalysis#907, possibly MDAnalysis/mdanalysis#810 if we get it in)?

orbeckst

minor things

orbeckst · 2016-11-20T17:21:33Z

_posts/2016-xx-xx-release-0.16.md

+
+## Speed improvements in RMSD
+
+Thanks for work from @rbrtdlgd our RMSD calculations are about 40% faster now.


Thanks to work from NSF REU student @rbrtdlgd our ...

orbeckst · 2016-11-20T17:21:54Z

_posts/2016-xx-xx-release-0.16.md

+## Speed improvements in RMSD
+
+Thanks for work from @rbrtdlgd our RMSD calculations are about 40% faster now.
+If you are using the low-level qcprot algorithm your self intead of our provided


yourself instead

orbeckst · 2016-11-20T17:23:28Z

_posts/2016-xx-xx-release-0.16.md

+So far, only the XVG format used by [gromacs] and [grace] are supported. Open an issue
+if you need support for other time series formats.
+
+## Do a dimension reduction with PCA and Dmaps


Dmaps --> Diffusion Maps

orbeckst · 2016-12-15T19:34:54Z

Remove the details on ENCORE and link to the ENCORE blog post #33.

kain88-de · 2016-12-17T18:00:51Z

I'll should have some time to bring this up to date tomorrow.

kain88-de · 2017-03-01T16:45:15Z

https://github.com/ipython/ipython/blob/master/tools/github_stats.py

might be good to add stats at the beginning of the post

kain88-de · 2017-04-01T08:33:47Z

_posts/2017-11-11-release-0.16.0.md

+This will print a warning for every deprecated function you are using together
+with a short code snippet how your code has to be changed. If you do not want to
+upgrade your existing scripts we [posted a guide]() how to use conda and python
+environments to run different versions of MDAnalysis on the same computer.


Should we make a short list of the most important deprecations? Or is this enough?

When I checked the most important changes are the removal of get_* and set_* functions. As well as the changes to segments.names -> segments.segnames (you always have to use explicit names now).

Maybe we just link to the wiki page for the release and the changes section there and keep it high-level. The most important thing is to be aware that things changed and if there are links to follow then that's good enough.

Also link to the topology post #41 .

(Good to link to your conda/venv guide #47 !)

I thought yesterday that we could move the code examples to a notebook and link to that from the post. That keeps the post shorter and the examples can be tried directly with the notebook.

kain88-de · 2017-04-02T11:47:43Z

_posts/2017-11-11-release-0.16.0.md

+# Create your universe as usual
+universe = mda.Universe(SIMULATION)
+# Attach an auxiliary time serie with the name `pull_force`
+universe.trajectory.add_auxiliaty('pull_force', 'md_f.xvg')


@jbarnoud do we have example aux files in our test data?

I'll have a look this weekend.

kain88-de · 2017-04-02T12:03:52Z

Here is an example how a notebook with code example could look like. https://gist.github.com/kain88-de/32d7b913a63d180b820c7c9af329cc37

If other are OK with this I would shorten the texts in this post and link to the notebook.

orbeckst · 2017-04-03T06:00:43Z

The notebook is nice but I would keep some real code in the blog post. I consider gists/notebooks really secondary data and in most cases do not expect people to bother reading them UNLESS they are already deeply involved. I think the only chance you get to impress new people is in the primary blog post.

…

On 2 Apr, 2017, at 05:03, Max Linke ***@***.***> wrote: Here is an example how a notebook with code example could look like. https://gist.github.com/kain88-de/32d7b913a63d180b820c7c9af329cc37 If other are OK with this I would shorten the texts in this post and link to the notebook. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

-- Oliver Beckstein * [email protected] skype: orbeckst * [email protected]

Also change the markup for the PCA exampled to have it colored.

* Draft of blog post contribution for Encore and MemoryReader * Replaced reference to rms_fit_trj to AlignTraj in blog post for 0.16 release. Fixed link to Encore documentation.

- It now include a section about the topology refactor. - I link to older posts about the new changes - rename the file to showup in a local build - add new verbose keyword - use liquid template syntax highlight

kain88-de · 2017-04-07T21:41:13Z

I just checked the github stats script. So far we had 1884 commits from 29 different people. This will work nice for the release post.

kain88-de · 2017-04-07T21:54:59Z

OK apart from updated stats and links to the correct release news this should be done and ready for a weekend release.

jbarnoud · 2017-04-08T08:13:53Z

I updated @kain88-de notebook to have it run in order (some cells were referencing imports made in latter cells) and to use a running example for the aux reader: https://gist.github.com/jbarnoud/a87b51205dfa89e9a13547bc3aa3c5d7

This depends on MDAnalysis/mdanalysis#1290

This depends on MDAnalysis/mdanalysis#1290 being merged!

sigh

kain88-de · 2017-04-10T12:49:56Z

_posts/2017-11-11-release-0.16.0.md

+[pr868]: https://github.com/MDAnalysis/mdanalysis/pull/868
+[gromacs]: http://www.gromacs.org
+[grace]: http://plasma-gate.weizmann.ac.il/Grace/
+[notes]: https://github.com/MDanalysis/mdanalysis/wiki/...


I think this is that last link that isn't complete yet.

kain88-de · 2017-04-10T13:48:26Z

OK this is good from my side. I checked all links one last time.

@armcdona

* Upload skeleton intro post for gsoc/outreachy * Update 2024-05-03-gsoc-outreachy-students.md * Lawson Post (#22) * Lawson Post * Update _posts/2024-05-03-gsoc-outreachy-students.md * Update _posts/2024-05-03-gsoc-outreachy-students.md --------- Co-authored-by: Jenna M Swarthout Goddard <[email protected]> * GSOC2024 Valerij Post (#23) * Update 2024-05-03-gsoc-outreachy-students.md Added Picture and project description * Update 2024-05-03-gsoc-outreachy-students.md Added Background an social * Update 2024-05-03-gsoc-outreachy-students.md * Change GSOC to GSoC and link to Jupyter Notebook docs * Grammatical edits and fix link to Wolber lab --------- Co-authored-by: Jenna M Swarthout Goddard <[email protected]> * Update 2024-05-03-gsoc-outreachy-students.md (#26) * Add GSoC and Outreachy logos * Luna post (#27) * MDA/MolSSI workshop page with registration (#379) * draft for MDA/MolSSI workshop page * Apply suggestions from code review Co-authored-by: Rocco Meli <[email protected]> * ASU workshop edits - moved public transport before rideshare - add May 29 as deadline for informing bursary applicants * placeholder for registration button * reST fixes * Apply suggestions from code review Co-authored-by: Jenna M Swarthout Goddard <[email protected]> * ASU workshop - single registration deadline May 27 - add paragraph on intended audience and skill level (from reg form) - changed header indentation levels - clarified in-person vs online * add @armcdona to the org team for MolSSI * changed "by May 29" to "on May 29 or earlier" * spell-checked * Remove extra 'will' --------- Co-authored-by: Rocco Meli <[email protected]> Co-authored-by: Jenna M Swarthout Goddard <[email protected]> * update actions * Update UGM event page (#387) * Add registration form link * Add draft agenda link * Upload draft UGM agenda * Add MGMS logo to sponsors * Upload MGMS logo * Fix links for agenda and MGMS logo * Add KCL summer accommodations as hotel option * Update ugm2024.md small edits * Update ugm2024.md highlighted registration vs abstracts * Move registration section further up * Add full venue address * Update Francesca's affiliation Uploading new speaker announcement card (from blog post, https://www.mdanalysis.org/2024/03/14/ugm2024-updates) to reflect the rebranding of Sosei Heptares --> Nxera Pharma (since we will be advertising the keynotes when we send out registration advertisements) --------- Co-authored-by: Micaela Matta <[email protected]> * Update UGM agenda (add Racquel's surname) * Fix typo in Raquel's name * Several updates to UGM page (#389) * Add UGM 2024 logo * Add link to abstracts book * Upload updated agenda and abstracts book * Add food suggestions * Add additional transportation details * Add TYC logo * Change 'verbal' to 'oral' in abstracts book * Change 'Lisbon' to 'London' * Add UGM 2024 logo * Fix link to UGM 2024 logo * Add links to restaurant websites * Line breaks between sponsor images and switch NF logo (previous was poor resolution) * Try putting images on new lines with <p> * Switch <p> to <br> and add hyperlinks to sponsor logos * Remove <br/> tags * Point to MolSSI python lesson (#390) Closes #386 as discussed during the last workshop planning meeting * Upload skeleton intro post for gsoc/outreachy * Update 2024-05-03-gsoc-outreachy-students.md * Lawson Post (#22) * Lawson Post * Update _posts/2024-05-03-gsoc-outreachy-students.md * Update _posts/2024-05-03-gsoc-outreachy-students.md --------- Co-authored-by: Jenna M Swarthout Goddard <[email protected]> * GSOC2024 Valerij Post (#23) * Update 2024-05-03-gsoc-outreachy-students.md Added Picture and project description * Update 2024-05-03-gsoc-outreachy-students.md Added Background an social * Update 2024-05-03-gsoc-outreachy-students.md * Change GSOC to GSoC and link to Jupyter Notebook docs * Grammatical edits and fix link to Wolber lab --------- Co-authored-by: Jenna M Swarthout Goddard <[email protected]> * Update 2024-05-03-gsoc-outreachy-students.md (#26) * Add GSoC and Outreachy logos * Luna post --------- Co-authored-by: Oliver Beckstein <[email protected]> Co-authored-by: Rocco Meli <[email protected]> Co-authored-by: Jenna M Swarthout Goddard <[email protected]> Co-authored-by: Micaela Matta <[email protected]> Co-authored-by: ljwoods2 <[email protected]> Co-authored-by: Valerij Talagayev <[email protected]> Co-authored-by: Adetutu Oluwasanmi <[email protected]> * Update date for blog post * Incorporate Cedric's suggested text for Valerij's project Co-authored-by: Cédric Bouysset <[email protected]> * Streamline code by removing GH profile links * Update to SSL links (where not already) * Edit OpenBabel sentence --------- Co-authored-by: ljwoods2 <[email protected]> Co-authored-by: Valerij Talagayev <[email protected]> Co-authored-by: Adetutu Oluwasanmi <[email protected]> Co-authored-by: Luna Morrow <[email protected]> Co-authored-by: Oliver Beckstein <[email protected]> Co-authored-by: Rocco Meli <[email protected]> Co-authored-by: Micaela Matta <[email protected]> Co-authored-by: Cédric Bouysset <[email protected]>

kain88-de added the Blog blog content and articles label Aug 17, 2016

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blog post for scipy paper #28

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add encore blog post #33

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kain88-de and others added 5 commits April 7, 2017 22:53

add post stub

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Expend on Fiona's aux reader

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Also change the markup for the PCA exampled to have it colored.

Link issue and PR for the aux data

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Add link to the auxiliary doc

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add AnalysisFromFunction section

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kain88-de and others added 6 commits April 7, 2017 22:53

update links

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Update 2016-xx-xx-release-0.16.md

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Update 2016-xx-xx-release-0.16.md

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Contributions on Encore and MemoryReader to Blog on 0.16.0 release (#30)

7f66194

* Draft of blog post contribution for Encore and MemoryReader * Replaced reference to rms_fit_trj to AlignTraj in blog post for 0.16 release. Fixed link to Encore documentation.

remove encore section that got it's own post

36b573f

extensive update of the post

c9929f5

- It now include a section about the topology refactor. - I link to older posts about the new changes - rename the file to showup in a local build - add new verbose keyword - use liquid template syntax highlight

kain88-de added 3 commits April 7, 2017 23:42

update links to other posts

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The XVG auxiliary reader does not use anyopen MDAnalysis/mdanalysis#1289

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Aux cleaning MDAnalysis/mdanalysis#1290

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Use a working example for the aux reader (#52)

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This depends on MDAnalysis/mdanalysis#1290 being merged!

fix more links

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Blog Post for release 0.16.0 #26

Blog Post for release 0.16.0 #26

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		## Speed improvements in RMSD

		Thanks for work from @rbrtdlgd our RMSD calculations are about 40% faster now.

Blog Post for release 0.16.0 #26

Blog Post for release 0.16.0 #26

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TODO paragraphs

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