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[WIP] New site: calypr.org (Reopen PR #41)#67

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lbeckman314 wants to merge 124 commits intomainfrom
refactor/new-site
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[WIP] New site: calypr.org (Reopen PR #41)#67
lbeckman314 wants to merge 124 commits intomainfrom
refactor/new-site

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@lbeckman314
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@lbeckman314 lbeckman314 commented Feb 9, 2026

Overview

Revert merging of refactor/new-site into main

Important

Original PR → #41

Deploy Preview → https://deploy-preview-67--calypr.netlify.app

bwalsh and others added 30 commits September 23, 2025 12:16
Copilot AI and others added 12 commits February 10, 2026 23:08
Co-authored-by: bwalsh <47808+bwalsh@users.noreply.github.com>
* docs: Minor formatting + link fixes (Lychee)
* fix: Link checks
* fix: Lychee config rules
* Apply suggestions from code review
Co-authored-by: bwalsh <47808+bwalsh@users.noreply.github.com>
…consolidate-docs-for-git-drs

# Conflicts:
#	docs/calypr/.nav.yml
#	docs/calypr/calypr-admin/creating-project.md
#	docs/calypr/data-management/common-errors.md
#	docs/calypr/data-management/git-drs.md
#	docs/calypr/data-management/metadata.md
#	docs/calypr/index.md
#	docs/calypr/quick-start.md
#	docs/tools/git-drs/.nav.yml
Rebase tool documentation improvements from fixes/doc-fixes
Co-authored-by: bwalsh <47808+bwalsh@users.noreply.github.com>
lbeckman314 and others added 5 commits February 13, 2026 10:32
fix: Remove extra new line when manually copying code blocks
Consolidate data-model and data-management directories into unified data/ directory
@jordan2lee
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on the main page - remove "like you version code"

current:

Git-DRS lets you: - Version large data files (BAM, FASTQ, VCF, etc.) like you version code - Track file lineage and share data with collaborators - Automatically register files with DRS for global discovery``

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I feel that this screenshot isn't needed. it breaks up the flow (the description and the numbered steps) and doesn't add extra info
image

@jordan2lee
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under the quick start, adding text along the lines of "if you have an existing repo start here" would be helpful after "If you're creating a new project or setting up a repository for the first time:"

image

@jordan2lee
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add a subheader so reads (add the 3 things in bold):

  1. Clone or Create a Repository

Clone an exsiting repoository

commands

Or create a new repository

commands

Also to use MyNewCalyprProject or your-data-repo throughout (currently uses both to refer to the same example repo)

@jordan2lee
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add support@calypr.org on the home page where mentioned about reaching out for support

@jordan2lee
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do we want to keep it generic (path/to/creds) or specific (include ~/.gen3/credentials.json)? on the quick start it mentions "Save it in a secure location (e.g., ~/.gen3/credentials.json)" so if we wanted to be specific this would be a good example

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jordan2lee commented Feb 26, 2026

on quick start - this code chunk has some generic values, and to keep this pattern it could be updated to be (for both "Clone and Existing Repo" and "New Repo set Up":

git drs remote add gen3 my-project-shortname \
    --cred /path/to/credentials.json \
    --url https://calypr-public.ohsu.edu \
    --project my-project \
    --bucket my-bucket

@jordan2lee
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this section currently is under "New Repository Setup" but would be a better fit elsewhere

@jordan2lee
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add text (can be brief) on what the output of git lfs ls-files should be. along the lines that should see the file included + it includes all files tracked (not just the file added this time)

image

@jordan2lee
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jordan2lee commented Feb 26, 2026

include an example of what the contents of a pointer file should look like directly on the "Quick Start" page. currently the example is a bit buried at the link

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the docs could be explicit that they can check this way OR when opening the file they see the actual contents (might be more intuitive for users to recognize the actual file contents)
image

@jordan2lee
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the "Quick Reference" at the end of clone an existing repo is great. can we add one for "new repo setup"?

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