nomad-remote-tools-hub merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests2021-09-28T12:34:38Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/1Initial checkin of basic project skeleton #82021-09-28T12:34:38ZMarkus ScheidgenInitial checkin of basic project skeleton #8Solves #8.
This is a basic project skeleton with:
- .gitignore
- gitlab ci that runs linting with pycodestyle,pylint, mypy as well as tests with pytest
- basic FastAPI app with example routes and models
- basis FastAPI tests that exampl...Solves #8.
This is a basic project skeleton with:
- .gitignore
- gitlab ci that runs linting with pycodestyle,pylint, mypy as well as tests with pytest
- basic FastAPI app with example routes and models
- basis FastAPI tests that examplefies fixtures and test parameterization
- config.py based on pydantics setting management
- pylint config
- a README, LICENSE, and AUTHORS filehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/2Initial checkin of basic project skeleton. #82021-09-28T12:40:11ZMarkus ScheidgenInitial checkin of basic project skeleton. #8Solves #8.
This is a basic project skeleton with:
* .gitignore
* gitlab ci that runs linting with pycodestyle,pylint, mypy as well as tests with pytest
* basic FastAPI app with example routes and models
* basis FastAPI tests that examp...Solves #8.
This is a basic project skeleton with:
* .gitignore
* gitlab ci that runs linting with pycodestyle,pylint, mypy as well as tests with pytest
* basic FastAPI app with example routes and models
* basis FastAPI tests that examplefies fixtures and test parameterization
* config.py based on pydantics setting management
* pylint config
* a README, LICENSE, and AUTHORS filehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/3Jupyterlab container #152021-09-29T11:05:04ZSherjeel ShabihJupyterlab container #15Solves #15
This is just to store the run command to be used later by the launch endpoint. It also sets up the internal docker uid:gid to be 1000:1000, that's the Nomad default.Solves #15
This is just to store the run command to be used later by the launch endpoint. It also sets up the internal docker uid:gid to be 1000:1000, that's the Nomad default.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/4Corrected line breaks software-list-b5-atom-probe-microscopy.md but I think I...2021-09-30T10:09:18ZMarkus KuehbachCorrected line breaks software-list-b5-atom-probe-microscopy.md but I think I...updated EM and APM lists, prepped for arpes, xps, and optical, plus parsing tools ods2mdupdated EM and APM lists, prepped for arpes, xps, and optical, plus parsing tools ods2mdMarkus KuehbachMarkus Kuehbachhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/5Added a simple hello world docker run test, docker name prefixes, CI runs doc...2021-09-29T15:50:41ZMarkus ScheidgenAdded a simple hello world docker run test, docker name prefixes, CI runs docker. #14This is a step of #14
- Added a simple test that runs a docker container on the target environment
- Added `north.config.docker_url` and `north.config.docker_name_prefix` to configure the target docker environment
- `docker_name_prefix...This is a step of #14
- Added a simple test that runs a docker container on the target environment
- Added `north.config.docker_url` and `north.config.docker_name_prefix` to configure the target docker environment
- `docker_name_prefix` has to be used on all containers. All containers need a name and this as prefix. You have to assume that the target docker environment might run other services.
- The tests will clean up all container with the configured `docker_name_prefix`
- Also added a the architecture image to readme as a bit of documentationhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/6Added missing package __init__.2021-10-01T07:31:22ZMarkus ScheidgenAdded missing package __init__.This is a tiny fix that was necessary to have a proper pip install of the north package.
Please merge after review.This is a tiny fix that was necessary to have a proper pip install of the north package.
Please merge after review.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/7integrated spreadsheet from michael, tommaso, martin, and ralph, added...2021-10-04T10:01:25ZMarkus Kuehbachintegrated spreadsheet from michael, tommaso, martin, and ralph, added...integrated spreadsheet from michael, tommaso, martin, and ralph, added suggestion for importance ranking 1-3 based on comments from all four colleagues, filled in missing visualization and dependencies to the best of my knowledge, might ...integrated spreadsheet from michael, tommaso, martin, and ralph, added suggestion for importance ranking 1-3 based on comments from all four colleagues, filled in missing visualization and dependencies to the best of my knowledge, might need some more clarification for the dependencies columnSandor BrockhauserSandor Brockhauserhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/8Added a simple route response and some testing2021-10-06T09:23:40ZSherjeel ShabihAdded a simple route response and some testingDraft for #14
I want to return a link for us to test through the proxy once the proxy CI building and pushing to registry is done. #13
Other than please bring whatever design choices you have in mind. I am also using a 503 HTTP respon...Draft for #14
I want to return a link for us to test through the proxy once the proxy CI building and pushing to registry is done. #13
Other than please bring whatever design choices you have in mind. I am also using a 503 HTTP response. Will you prefer that or something else if all container 'routes' or lets say instance allocation slots are taken?https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/9Draft: Resolve "ARPES"2021-10-04T10:11:07ZMarkus KuehbachDraft: Resolve "ARPES"Closes #2Closes #2Markus KuehbachMarkus Kuehbachhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/10Added Marks list for XPS tools, filled in missing pieces to the best of my...2021-10-05T09:08:39ZMarkus KuehbachAdded Marks list for XPS tools, filled in missing pieces to the best of my...Added Marks list for XPS tools, filled in missing pieces to the best of my knowledge, Mark mentioned that his importance ranking scale goes from 1 to 10 with 10 representing the most important tool. A key comment is that mainly the parsi...Added Marks list for XPS tools, filled in missing pieces to the best of my knowledge, Mark mentioned that his importance ranking scale goes from 1 to 10 with 10 representing the most important tool. A key comment is that mainly the parsing should be translated. Might need to have here a parser specialist and domain expert working together.
From this list it seems that vendor lock-in in this community is even the most severe of all five techniques.
Isnt the analysis part "just" mainly very sophisticated peak fitting of spectra, i.e. counts over energy, why are there so many tools? Is there a community incentive to develop an open tool, I mean peak-fitting is exactly what the open-source tools have become strong at.Sandor BrockhauserSandor Brockhauserhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/11Added a basic test for the proxy image on CI2021-10-06T07:08:58ZSherjeel ShabihAdded a basic test for the proxy image on CIhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/12software tools for optical spectroscopy2021-10-05T09:14:28ZMarkus Kuehbachsoftware tools for optical spectroscopyfilled in empty cells, to the best of my knowledge, most software tools are vendor-lock-in situations, one for each instrument vendor, I added two open tools I found and two literature situation representing examples of data-processing, ...filled in empty cells, to the best of my knowledge, most software tools are vendor-lock-in situations, one for each instrument vendor, I added two open tools I found and two literature situation representing examples of data-processing, these examples are not necessarily representative of the situation in the field, chris said he will continue to collect and send to meSandor BrockhauserSandor Brockhauserhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/13Added jwt related boilerplate and routes. #22 #232021-10-06T09:42:28ZMarkus ScheidgenAdded jwt related boilerplate and routes. #22 #23- functionality for creating and verifying tokens
- a route for refreshing tokens
- a route for verifying channel access
- Fast API dependencies for tokens- functionality for creating and verifying tokens
- a route for refreshing tokens
- a route for verifying channel access
- Fast API dependencies for tokenshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/14Draft: Resolve "make the result public (FAIRmat-Experiments:github)"2021-10-06T12:00:28ZMarkus KuehbachDraft: Resolve "make the result public (FAIRmat-Experiments:github)"Closes #6Closes #6Sandor BrockhauserSandor Brockhauserhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/15Updating testing and added auth in proxy2021-10-06T12:42:01ZSherjeel ShabihUpdating testing and added auth in proxyCloses #23Closes #23https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/16Removed password req when accessing new jupyter2021-10-07T08:00:36ZSherjeel ShabihRemoved password req when accessing new jupyterThis removes the login page from Jupyterlab and the user can just reach the logged in interface.This removes the login page from Jupyterlab and the user can just reach the logged in interface.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/17Async docker launch2021-10-08T11:32:23ZLauri HimanenAsync docker launchWrapped the docker launch in an async function. This should fix problems with the API hanging on docker startup, but also implies that the API does properly handle and report exceptions happening during the docker launch.Wrapped the docker launch in an async function. This should fix problems with the API hanging on docker startup, but also implies that the API does properly handle and report exceptions happening during the docker launch.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/18Added paths mounting to the launch endpoint2021-10-11T06:50:34ZSherjeel ShabihAdded paths mounting to the launch endpointCloses #18Closes #18https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/20added ipynb notebook and link to real world example (volume heavy) data that ...2021-10-12T06:37:22ZMarkus Kuehbachadded ipynb notebook and link to real world example (volume heavy) data that is located on Zenodo:http://dx.doi.org/10.5281/zenodo.5562389http://dx.doi.org/10.5281/zenodo.5562389Sandor BrockhauserSandor Brockhauserhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/21Draft: Resolve "ipynb: download the data automatically"2021-10-19T08:03:26ZMarkus KuehbachDraft: Resolve "ipynb: download the data automatically"Closes #33Closes #33Markus KuehbachMarkus Kuehbach