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Fatiando Development Calls 2023

📱 Join the video call: https://meet.jit.si/fatiando-a-terra

📅 Shared calendar: https://www.fatiando.org/calendar

IMPORTANT: Everyone is required to follow our Code of Conduct when participating in the Fatiando community. Please review it carefully.

Development calls are open to everyone! Here we discuss project development, socialize, and do some live coding from time to time.

Everyone is encouraged to participate and edit the notes below.

Parking lot for next meeting

  • Leo: Trying to find a good magnetic microscopy dataset to add to Ensaio. Will clean up the one we used in this paper because it's relatively good with a bunch of well behaved dipoles. Great for running grid-related examples in Harmonica since the data is on a regular grid at constant height from the very start. Would also be good for an Euler Deconvolution example since they're all very close to dipoles.
  • Improving tests for Pooch downloaders:
    • Right now Pooch's tests rely on third-party servers being available when testing
    • If those servers go down, Pooch tests start failing
    • Idea: mock httpservers with pytest-httpserver for testing purposes.
    • Keep the current tests, but maybe make them optional
  • Lu: In Antarctica! See you all next year!
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  • Leo: Started playing with spherical harmonics. SHTools is a bit large and overkill when we just want simple synthesis of a low degree model (like a lot of magnetic models). Plus, there is no package I found that can do the inversion part for scattered data (SHTools only does it for grids). I'll need this for class and for some projects so will start coding something and maybe get a student involved. Should this be part of Harmonica or its own package? The surface harmonics can be used for other things and the associated Legendre function calculation as well (scipy has it but it wraps an ugly fortran code and the normalization isn't very clear). But otherwise, this fits with the equivalent source stuff in Harmonica.

2023-12-07

Time: 17:00 UTC

Participants:

  • Santi
  • India

Quick updates:

  • India's first PR in Harmonica
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  • Discussing the need to add more examples to our functions:
    • Good opportunity for getting new contributions with ppl that are getting familiar with the code
    • Feel free to open an issue with an idea for improvement or just open a PR with a new example!
  • Discussions about how science could improve embracing some ideas from open-source software communities:
    • Foster collaboration
    • Constructive reviews towards improving the science
    • Science in the open: more reproducible and encourage collaboration
  • Thoughts about BIRS workshop and future events
  • Advent of Code 2023 started: https://adventofcode.com/
    • Set of programming puzzles. Good to practice and learn new stuff.
    • No preassure, just do it for the fun!

2023-11-30

Time: 00:00 UTC

Participants:

  • Santi
  • Mariana

Quick updates:

2023-11-23

Time: 17:00 UTC

Participants:

  • Santi
  • India
  • Leo
  • Mariana

Quick updates:

  • Leo: Been thinking a bit about Verde and how some of the things it does are more widely useful. In particular, the generation of grid/profile/scatter points and the point partitioning (windows, blocking, etc) could be used elsewhere but right now Verde pulls in a lot of dependencies. Would it make sense to have a separate package that would include the following?
    • All of these https://www.fatiando.org/verde/dev/api/index.html#coordinate-manipulation
    • And this https://www.fatiando.org/verde/dev/api/generated/verde.median_distance.html#verde.median_distance
    • These are all fairly consistent: point generation and manipulation
    • Could be expanded to generate other types of coordinates and take spherical geometries into account in a more consistent manner.
    • Fairly simple with minimal dependencies (numpy, scipy, opt pykdtree)
    • Thought of a name
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      : Bordado (images)
    • Most of this is already done and could be a drop-in replacement in packages that use them. Or maybe we use this to simplify those functions (since taking spacing or shape creates some usability problems).
    • Thoughts?
    • Define a scope for it. What things should be there, what things won't.
      • Improve profile generation: geographic coordinates and equispacing, profiles perpendicular to a path (for ridges for example)
    • Write down what can be moved and what can't. Then figure out if it makes sense to split.

2023-11-09

Time: 17:00 UTC

Participants:

  • Mariana
  • Leo

Quick updates:

2023-11-02

Time: 00:00 UTC

Participants:

  • Mariana

Quick updates:

  • Post about Matt thesis on LinkedIn/Twitter/Mastodon
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  • Post about move to Mattermost scheduled on LinkedIn /Mastodon/Twitter and Github Forum
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  • Fix Issue with instructions to join the meetings
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  • Update Github post with Weekly meetings
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2023-10-26

Time: 17:00 UTC

Participants:

  • Santi
  • Mariana
  • India

Quick updates:

  • Pooch v1.8.0 has been released
    • It includes the bugfix for the Zenodo issue: now it supports the old and the new API
  • We have moved to Mattermost!
  • Harmonica has now only a pyrpoject.toml for packaging

Discussion points:

  • Issues with instructions to join the meetings:
    • Opened issue on fatiando/community
    • Add the link to the Jitsi meeting to the "location" field in the calendar event
  • Working towards having processing workflow from raw data:
    • India will see if she can get some raw data and release them under open license
  • Internship program opportunities in opensciencelabs: https://opensciencelabs.org
    • They need projects with open issues that interns can start working on
    • Specific project these people can start working on
    • The internship lasts 3 months
    • Questions:
      • Deadline?
      • How many slots for interns do they have?
      • Expected level/knowledge of the interns

2023-10-19

Time: 00:00 UTC

Participants:

  • Lu
  • Mariana
  • Santi

Discussion points:

  • Santi is working on the magnetic simulation for SimPEG using Choclo
  • Santi: Important issue in Pooch (https://github.com/fatiando/pooch/issues/371)
    • Zenodo migrated to InvenioRDM
    • their new API is not backward compatible (although they said it should be in their blogpost)
    • so our Zenodo downloader is not working anymore
    • Santi craeted a bugfix: https://github.com/fatiando/pooch/pull/373
      • Should we merge and release it ASAP?
      • Should we wait for Zenodo to fix their API and make it backward compatible or properly document the specifications of the new API?
      • Santi sent a message to Zenodo explaining the backward incompatibilities.
      • Shall we wait or act quickly? Some users are asking for a quickfix and a new release.
      • Another option: should we keep both codes and allow users to change between them with a flag?
      • Another option: make the methods of ZenodoDownloader figure out which version of the API are we interacting with and act accordingly:
        • This way we keep backward compatibility and support the new API
      • Roadmap
        1. Write Zenodo to info@zenodo.org, they replied Leo within the same day in the past
        2. Let people know that we are waiting for Monday to get a reply. If not, by Tuesday we make a release
        3. Get a PR ready with the new idea: automate everything!
  • Lu:
    • gravity kernel for point sources in choclo
    • interests in multiphysics inversions

2023-10-12

Time: 17:00 UTC

Participants:

  • Mariana
  • India
  • Santi

Discussion points:

2023-10-05

Time: 00:00 UTC

Participants:

  • Mariana
  • Lu
  • Santi

Discussion points:

  • Santi met his first wild bear
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  • Questions about inversions and interpolations
  • What are we using the FFT in Harmonica?
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  • Disussion about how to handle inclination and declinations in south pole with tesseroids
  • Make Fatiando stickers for AGU!
  • New time meetings? India wants to join
    • Mondays 10:00 UTC - 13:00 UTC, 16:00 -20:00 UTC
    • Tuesdays 10:00 - 14:00, 17:00 - 20:00 UTC
    • Thursday 18:00 - 20:00 UTC
    • Make a when2meet for the afternoons and send it to the channel
  • Todo: merge some PRs and make a release

2023-09-27

Time: 20:00 UTC

Participants:

  • Santi
  • Mariana

Discussion points:

  • SWUNG's Mattermost instance is up. Process has been documented in https://github.com/softwareunderground/mattermost/ Yet in testing stages to make the move.
    • I will bring the question to the board to create our own Fatiando Team in the instance, but by now the config is set to allow anyone to create Teams.
    • Discussion if its possible to communicate channels in the same instance but different teams.
      • apparently is not possible yet (at least we couldn't find how to do it)
    • People need to explicitly ask to join to the other Teams, that could create some friction for interactions between swung and fatiando
  • Santi started refactoring the parsers in dependente: https://github.com/fatiando/dependente/pull/8
    • Make dependente work with projects that use pyproject.toml only. It currently fails because it cannot find a setup.cfg file.
    • Simplify the logic of the parsers by defining two classes: one for pyproject.toml and one for setup.cfg.
  • Started to move Harmonica to pyproject.toml only: https://github.com/fatiando/harmonica/pull/438
  • Mariana edited BIRS report with a summary of the "Diversity"
  • Mariana post on LinkedIn about Lindsey's participation in a virtual symposium

2023-09-21

Time: 00:00 UTC

Participants:

  • Lu
  • Mariana
  • Santi

Quick updates:

  • Gelson Ferreira de Souza Junior gave a talk about his research on micropaleomagnetism
  • Santi opened a PR in SIMPEG to include gravity inversion using Choclo. Performance is great in every tested scenario which is great
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Discussion points:

  • Design of the magnetic forward for prisms:
    • The current function returns the three components of B.
    • TMI (or total field anomaly) should be calculated separately.
    • We could probably add a function for doing that.
  • Harmonica has 6! PRs ready to go, we should merge them and aim for a release soon.
  • Mastodon updates in Software Underground
    • The move will start soon
    • Decide what to do with Matrix
      • how many people use Matrix only?
      • is it possible to bridge matrix and mattermost?
      • we should talk with people who knows how to do this
    • Tasks for the future:
      • Update website with new links to Mattermost
      • Ask swung to add a new "community" in the same server for Fatiando (instead of having a #fatiando channel)?
  • Plans for Choclo:
    • add magnetic tensor kernels and forward functions
    • design decisions for point sources in spherical coordinates:
      • ask for long, and cosines and sines
      • explain in documentation pages how to use these functions and why we ask those arguments
  • Mariana and Santi kept working on BIRS report
  • Mariana found a platform for taking decisions in a more horizontal way: https://www.loomio.com/membership-organizations

2023-09-13

Time: 20:00 UTC

Participants:

  • Mariana
  • Santi

Discussion points:

2023-09-07

Time: 00:00 UTC

Participants:

  • Agus
  • Lu
  • Mariana
  • Santi

Discussion points:

  • Mariana. Emails for new participants in BIRS
  • Mariana. Posts about Agustina talk (X, Fosstodon, LinkedIn)
  • Lu found an issue related with a PyVista deprecation
    • The fix has been already merged!
  • Select PRs for the Harmonica v0.7.0 milestone
    • Push the one for the proejctions of GRD files to 0.8.0
    • We can also push some stuff around replacing forward with Choclo to 0.8.0 as well
  • We can make a Choclo release after Lu finishes the point sources in spherical coordinates
    • Then we'll be able to use them in Harmonica
  • Are we moving to mattermost with SWUNG?
    • We can create our own #fatiando channel in Mattermost at the beginning
    • We can ask swung to create a separate "community" for Fatiando in the same server
    • Does it worth having the Matrix community once we move to Mattermost? Is it possible to bridge them?
  • AGU Fatiando Talk
    • We got invited, we already submitted the abstract
    • If Santi cannot attend, Lu is willing to give the talk
    • Otherwise, it will be virtual, but in January, which is weird considering that AGU is mid December
  • Bonus:

2023-08-30

Time: 20:00 UTC

Participants:

  • Mariana
  • Santi
  • Leo
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Discussion points:

  • BIRS debrief

    • Mariana started gathering links and files
    • Santi started writing the LaTeX report for BIRS. They provided a template. (deadline: mid October)
    • Leo has to accept the invite…
    • Leo will link the latex report with Overleaf to optimize collaborative writing.
    • Should we create a "master" document that groups all stuff done in BIRS, and would allow to continue working on them
    • We should gather all the archive (etherpads, docs, videos etc) under https://birs-2023.softwareunderground.org
    • We could use the birs website Projects for adding issues related to the workshop
    • Funding for 2024/25? https://fapesp.br/auxilios/organizacao
    • Ask for Lindsey's talk in case it was recorded: ask Lindsey and BIRS

  • Choclo achievements

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  • Suggestion of the week

Action items:

2023-08-24

Time: 00:00 UTC

Participants:

  • Mariana

Discussion points:

2023-08-16

Time: 20:00 UTC

Participants:

  • Santi

Discussion points:

2023-08-10

Time: 00:00 UTC

Participants:

  • Santi
  • Mariana

Discussion points:

  • BIRS debrief
    • What did you liked?
    • What didn't you liked?
  • Open avenues after BIRS
    • Santi will go through the documents and compile some roadmaps for SimPEG and Fatiando based on the discussion topics
    • Clarify project overview, mainly by Lu and Matt: https://github.com/fatiando/harmonica/issues/427
    • Leo opened a few issues in Harmonica, mostly tighted to the ideas he shared during his BIRS talk
  • Reinbursement procedure
  • Mariana wants to help with some of the afterwork of BIRS
    • LaTeX report for BIRS
      • Santi will create a repo for it
    • Clean and backup shared documents
      • We should publish them in a repo
      • Tink how can we give authorship to participants
    • Publish photos and videos on website
    • Create certificates for attendance?
      • Only if someone asked…
    • BIRS requires to give them some feedback
      • Santi can start a repo for that
      • Ping Mariana when it's created
  • Mariana posted about the EGU blogpost on Twitter and Linkedin

2023-07-13

Time: 00:00 UTC

Participants:

  • Mariana
  • Matt
  • Santi

Discussion points:

2023-06-30

Time: 00:00 UTC

Participants:

  • Mariana
  • Lu
  • Santi
  • junietoc

Discussion points:

  • Santi got invited to write a blogpost at EGU Geodynamics blog
  • Things to do before the workshop
    • pseudo-gravity filter
    • launch Projects for Fatiando
    • make harmonica's gravity point source use Choclo kernels (at least the Cartesian ones for now)
    • Add forward gravity fucntions for point sources in spherical coordinates in Choclo
    • Long term:
      • planting inversions: harvest module in the old fatiando
      • bathymetry, surface, basin inversions
  • Paper on large inversions with gridded observation points
    • Santi will share the link to the paper
  • Transform 2023 Tutorial
    • Read this: https://softwareunderground.org/t23-instructor-info
    • Soft deadline: end of July
    • Hard deadline: 4 September
    • 90 minutes
    • Idea:
      • Pick a use case
      • Some place in North Australia or West Australia
      • Have both gravity and magnetics
    • Make a Harmonica release before the tutorial
    • Include datasets in Ensaio
  • Discuss weather we want to become a NumFOCUS affiliate project

  • Please provide a summary description of your project in a few sentences:

  • Task Why do you want your project to join NumFOCUS?This question is required.

  • How does your project relate to or integrate with the existing ecosystem of NumFOCUS tools?This question is required.

  • Describe how your project furthers the NumFOCUS mission:This question is required. https://numfocus.org/community/mission

  • How many active contributors does your project currently have?This question is required.

  • Any comments you’d like to make on the number of your active contributors:

  • What is your project doing to attract and/or mentor new contributors and maintainers?This question is required.

  • Where do you host conversations about project development and governance (e.g. mailing lists, forums, etc.), and how many participants do you have?

  • What license(s) does your project currently use?This question is required.

  • Projects must adopt the NumFOCUS Code of Conduct or one similar in spirit. Please tell us how you plan to meet this requirement: https://numfocus.org/code-of-conduct

  • Your Name (First & Last):This question is required. *

  • Questions or Comments:

  • BIRS updates
    • Getting closer
    • Santi joined swung board meeting to talk about the proposal
  • Some activity around Pooch in last week
  • Santi found a bug in Harmonica's tesseroid forward model
    • One of the checks eats too much memory, making it impossible to run the forward
    • The good thing is the fix is not that hard to make: replace Numpy code for Numba

2023-06-21

Time: 20:00 UTC

Participants:

  • Mariana
  • Santi

Discussion points:

  • Pair programming with Mariana and Santi
  • Reconsidering using GitHub Projects in Fatiando
    • Leo has been experimenting with it for CompGeoLab
    • Might be a nice tool, specially for maintainers
    • Umbrella Issues involves a lot of manual work, only limited issues can be pinned, etc…
    • With projects we can filter issues by project, asignee, status, etc

2023-06-07

Time: 20:00 UTC

Participants:

  • Santiago
  • Mariana
  • Agus

Discussion points:

2023-06-01

Time: 00:00 UTC

Participants:

  • Lu
  • Vinicius
  • Mariana
  • Santi

Discussion points:

  • Onboarding Vinicius. PhD student in Australia working with magnetic and gravity data
  • BIRS organization
    • Create time zone pods for virtual discussions
    • Check out the answers from the Community Survey from last year to see what the replies were
  • Transform 2023 tutorial
    • Lu is willing to do it!
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    • Mariana commit to help with the logistics of the Transform tutorial but no with core content since she is learning about Harmonica yet.
  • Change all the 14:00 UTC meetings to 00:00 UTC
    • Update calendar
    • Publish announcement in forum, and social media
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2023-05-24

Time: 20:00 UTC

Participants:

  • Lu
  • Vinicius
  • Mariana

Discussion points:

  • Mariana's question about deprecation cycles
  • Move meeting time to 00:00 GMT
  • Verde v1.8.0 was released
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  • Choclo v0.1.0 was released
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  • Santi was playing with GH Projects
  • Implementing forward models in Harmonica using Choclo
  • BIRS event has a website: https://birs-2023.softwareunderground.org
    • Ideas for the workshop from within Fatiando?
    • What our community want to discuss, solve?
    • What are our needs?
    • Mariana's fantasy for a documentary/podcast about why open science

2023-05-03

Time:

  • 00:00 GMT

Participants:

  • Lu
  • Federico Esteban
  • Mariana
  • Santiago

Discussion points:

  • BIRS event in July
    • https://www.birs.ca/events/2023/2-day-workshops/23w2014
    • Own website comming soon
    • We have limited slots for in-person, but we have plenty of room for virtual participants
    • If you want to participate (virtually or in-person), let Santi know!
    • Questions about organizing "something" pre and post workshop to make the most of that loong trip!
    • Mariana asked a little bit about how BIRS will go and its organization
      • topics to discuss during those days
  • Choclo with a lot of PRs
    • singular points for gravity tensor components and magnetic fields
      • what should we do with magnetic fields in the interior of the prism
    • Release coming soon?
  • Harmonica
    • Santi stated working on incorporating Choclo into Harmonica:
      • Use choclo for gravity fields of prisms, and extend to all acceleration and tensor components
      • Add magnetic field forward for prisms
    • Agustina started coding functions for converting magnetic vector to intensity, inclination and declination (and viceversa)
      • Inclination is defined positive downwards, while the magnetic field components are defined in easting, northing, upward system
  • Lu wants to implement the geometry inversion
  • Lu is working on 2d modelling

2023-04-12

Time:

  • 20:00 GMT

Participants:

  • Santiago
  • Agustina

Discussion points:

2023-03-29

Time:

  • 20:00 GMT

Participants:

  • Santi
  • Agustina
  • Mariana
  • Matt

Discussion points:

  • Mariana Question's:

  • Problem in Github reported by Agustina https://github.blog/2023-03-23-we-updated-our-rsa-ssh-host-key

  • BIRS event got accepted!

    • 28-30 July in Banff, Canada
    • More details soon!

  • Thinking about creating projects in Harmonica

    • We talked about this before, but Santi never finds the time to do so
    • Topics
      • FFT-filters
        • Pseudogravity
        • Including padding to the transformation functions
        • Handling grids with nans?
      • Forward modelling
        • Magnetic fields of dipoles and prisms (all already in Choclo)
        • Magnetic fields for tesseroids
        • Missing gravity fields in some geometries (tensor components)
        • Extend magnetic fields to prism and tesseroid layers
      • Planting inversions
        • Include a simple 3d mesh
        • Implement the algoritm (Leo should have some draft)
        • Draft here:

  • Update the website:

    • In "About" the idea is to put the last videos, talks and papers
    • Add Choclo to the website: yes!
      • We need a logo
    • Plan for a future release of Choclo

2023-03-15

Time:

  • 20:00 GMT

Participants:

  • Agustina
  • Matt
  • Mariana
  • Santi

Discussion points:

  • KEGS Talk
    • Santi will share link to vide
      • Suggestion about new features
    • Would be nice to upload it to our YT channel
  • Governance:
    • New role: Package Developer
    • Developers
    • Maintainers
  • Pooch
  • Harmonica
    • Released!
    • Future goals
      • Make the next release on September with:
        • magnetic forward models
        • Finish pseudogravity filters
        • use choclo for all the forward models
    • How to handle grids that have "holes" (nans)
      • Write example
      • Maybe handle that directly within the function with an optional argument?
  • Inversion:
  • Meeting time:
    • Maybe we want to work on a meeting time that suits Lu and people in the Pacific Time
    • We miss Lu in the meetings
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  • Transform
    • Ideas from Matt Hall in SWUNG Slack

2023-02-09

Time:

  • 20:00 GMT
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    we changed this week time

Participants:

  • Rodrigo
  • Agustina
  • Mariana

Discussion points:

  • Maybe we have a new user: Rodrigo
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    • He started a master with gravity and sismica data to analyze seamonts in the coco plate (North America subduction zone)
    • We shared Orlando Alvarez Google scholar profile (papers)
    • We presented Fatiando and explained how Fatiando can help him and invited to participate in the meetings
  • Mariana and Agustina talked about general things

2023-02-01

Time:

  • 20:00 GMT

Participants:

  • Santi
  • Agustina
  • Mariana
  • Matt

Discussion points:

  • Matrix bridge with Slack is apparently broken again
    • We had an update on the Matrix room, maybe that triggered the disconection
  • Poll on interface of forward modelling in Harmonica
  • Santi started designing magnetic forward modelling in Harmonica
    • https://github.com/fatiando/harmonica/pull/369
    • I've been trying out a new interface for the forward models. One function for each forward, ditch the field argument.
      • prism_magnetic_field: returns a tuple with the tree components of the magnetic field
      • prism_magnetic_easting: returns easting component
      • prism_magnetic_northing: returns northing component
      • prism_magnetic_upward: returns upward component
    • Pros:
      • We get autocompletion.
      • We can avoid implementing a dispatcher
    • Cons:
      • We have a little bit of repeated code. It could be solved, but I would rather repeat oursevles than make the code more complex.
      • I wrote a private function for computing any component. The public functions for each component just call this private function. Is it too complex?
    • Opinions?
      • better solution:
        • Have only two functions: one that returns the three components and another one that returns just one, selected through a component or field argument
  • FFT filters by Lu
    • Santi think they are ready, except for the pseudogravity one that might need some discussion
    • Possible plan: move that filter to a new PR and merge the ones that are ready
  • Fatiando presentation at KEGS (Canadian Exploration Geophysical Society)
    • Event happening in Toronto on March 4
  • Discussion in using type annotations in Pooch https://github.com/fatiando/pooch/issues/330
    • Maybe we could ask Ryan to draft some annotations in a few functions of Pooch and see if we like it
    • Would love to hear Leo's input on this subject
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Fatiando a Terra
Open-source tools for geophysics
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