Changes between Initial Version and Version 1 of 2019-08-29


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Timestamp:
Sep 4, 2019, 10:45:53 AM (6 years ago)
Author:
Conrad Huang
Comment:

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  • 2019-08-29

    v1 v1  
     1== This is a summary of discussions relevant to ChimeraX that took place at some group meetings.==
     2
     3= Attendees =
     4
     5* Eric, Conrad, TomG, Elaine, Greg, TomF, Scooter
     6
     7= Agenda =
     8* Action items
     9* ChimeraX
     10  * Should 2D models be selectable as shown w/ green outline for later actions?
     11  * More general REST interface
     12  * Permissions on ChimeraX wiki
     13  * Mechanism for updating from 1.0 to 1.1
     14  * RBVI bundles on toolshed
     15    - Change build process to trim down list of bundles in standard release while still testing toolshed-only bundles
     16  * Stable APIs, #922
     17  * Documentation strategy
     18  * 1.0 features (roadmap)
     19
     20= Discussion =
     21* ChimeraX
     22  * Should 2D models be selectable as shown w/ green outline for later actions?
     23    - Summary from group meeting.
     24    - See #2365 for more details.
     25    - 2D models should be selectable and shown with green outlines.
     26    - Commands that do not depend on coordinate systems, e.g., "color" and "display", should apply to 2D models when they are included in the atomspec
     27    - Commands that do depend on coordinate systems, e.g., "move" and "turn", should **not** apply to 2D models even when they are included in the atomspec
     28    -
     29  * More general REST interface
     30    - Summary from earlier group meeting.
     31    - Tristan's implementation is "over the top", including:
     32      * registration that automatically pulls argument types from function
     33      * GET queries return the list of registered functions
     34      * Python client that will mimic the registered functions so client-side code looks very similar to server-side code
     35    - Scooter ~~suggested~~ insisted that the implementation must support Swagger (now known as [https://github.com/OAI/OpenAPI-Specification OpenAPI]).  Python's [https://pypi.org/project/fastapi/ FastAPI] may be the perfect fit, but it is very heavyweight in terms of dependent packages.
     36    - Need to investigate whether FastAPI is compatible with Tristan's approach (a real-life client).
     37  * Permissions on ChimeraX wiki
     38    - Should move ancient crud to archeological part of site
     39    - Option 1:
     40      - Adopt Chimera wiki permission plugin
     41      - Move selected private links to protected area (are there any?)
     42      - Open most of site
     43    - Option 2:
     44      - Move private stuff to another site (wiki, GoogleDocs)
     45      - Open all of site
     46    - Option 3:
     47      - Move to github?
     48  * Mechanism for updating from 1.0 to 1.1
     49    - Option 1: 1 site-packages for all versions, need to delete/update old bundles
     50    - Option 2: 1 site-packages per version, need to install/copy old bundles
     51    - Option 3: 1 site-packages per version, sys.path = new_personal:installed:old_personal:...
     52    - Option 4: do not use Python import statement; use toolshed.load_module (or something) to get modules
     53    - Need decision before 1.0 release
     54  * Putting RBVI bundles on toolshed
     55    - Want separate run-time vs build-time dependencies in bundle_info.xml
     56    - Visit the bundle-release page (from intranet) and release your bundles
     57    - Need to segregate "standard" bundles from "extra" bundles
     58  * Stable APIs
     59    - See action items
     60  * Move to github
     61    - Move to private RBVI github project
     62      - Easier to share with collaborators with github admin tools
     63      - "pull requests" should simplify enhancement/fix submission
     64      - will not happen that soon
     65
     66= Action Items =
     67  * Scooter and Conrad will investigate moving wiki pages to private subtree
     68  * ~~Greg will update rotamer library license in ChimeraX embedded license page
     69  * ~~Scooter will look into private wiki pages in Trac
     70  * ~~Greg will update Linux notes on download page
     71  * ~~Greg will add "VR Notes" link below "Platform Notes" link (https://www.rbvi.ucsf.edu/chimerax/docs/user/vr.html)
     72  * ~~Conrad will investigate how Tristan's mechanism works and start discussion on what style of REST is best (how to specify arguments, etc.)