run.do missing adopath isolation

[gitlastoni]

there's some problem in the git diff, at least on gh. if you compare main and setup-modification, the diff shows the code block below is in both, so including on main. but it's not there. there might be other bits that didn't get merged?

/*==============================================================================
                            ISOLATE ADOPATH
==============================================================================*/
==============================================================================*/
// Only use BASE + local ado for reproducibility
// This ensures all users run with identical packages
adopath - PLUS
adopath - PERSONAL
adopath - SITE
adopath - OLDPLACE
adopath + "${project_path}/ado"

[NKeleher]

Investigation Summary

I've investigated this issue and confirmed that the adopath isolation code is indeed missing from do_files/00_run.do on the main branch. This code exists in the stata-setup-modifications branch but was never merged.

What's Missing

The stata-setup-modifications branch (commit 2a5fec1) contains the following adopath isolation section that should be in do_files/00_run.do:

/*==============================================================================
                            ISOLATE ADOPATH
==============================================================================*/

// Only use BASE + local ado for reproducibility
// This ensures all users run with identical packages
adopath - PLUS
adopath - PERSONAL
adopath - SITE
adopath - OLDPLACE
adopath + "${project_path}/ado"

This code should be inserted after the "FIND PROJECT ROOT" section (around line 82) and before the "DEFINE PATHS" section.

Why This Matters for Reproducibility

The adopath isolation:

• Removes user-specific package directories (PLUS, PERSONAL, SITE, OLDPLACE)
• Ensures all users run with identical packages from the local ado/ folder
• Prevents version conflicts from packages installed in user directories
• Is a critical reproducibility feature

Additional Missing Enhancements

The stata-setup-modifications branch also includes two other important improvements:

1. Enhanced .config/stata/install_packages.do: Installs packages to the local ado/ folder instead of the user's PLUS directory, with verification checks

2. Improved setup.do error handling: Better error messages for setroot installation failures and package installation issues

Why Not Just Merge the Branch?

The stata-setup-modifications branch includes a major directory restructuring (do_files/ → scripts/do/) that would be a breaking change. The directory restructuring should be discussed separately and doesn't need to block this bug fix.

Recommended Fix

Cherry-pick the adopath isolation features without the directory restructuring:

1. Add the adopath isolation section to do_files/00_run.do
2. Enhance .config/stata/install_packages.do to install to local ado/ folder
3. Improve error handling in setup.do
4. Update CLAUDE.md to document the adopath isolation feature

This approach maintains backward compatibility while fixing the reproducibility issue.

Files to Modify

1. do_files/00_run.do - Add adopath isolation section after line 82
2. .config/stata/install_packages.do - Add adopath isolation during installation
3. setup.do - Improve error handling
4. CLAUDE.md - Document the feature

[NKeleher]

Comment above generated by Claude. Will pick it up as a PR after we've sorted through some other comments in active issues.

[gitlastoni]

Corrections/comments:

• not important but re "This code exists in the stata-setup-modifications branch but was never merged." it was merged but it was overwritten in later reorg commit (see other comments I left on gh)
• that proposed block will not work well b/c you take out the PLUS path from the adopath and then ssc installs and others fail
• in smiles-main, @dmartinezIPA wrote a fix (works, merged into main) but it was a bit wordy, so we're updating it. we decided to use ieboilstart, adopath() strict there (which is the source code I looked for a leaner fix; but why copy, we can just use their command). are you open to that for the template? would mean that there are two bootstrap dependencies: setroot (already there) and ieboilstart that need to be ssc installed outside the repo.
• I agree w/ your comment on the other issue that setup is getting more involved (I had just added the config_box.do over in smiles-main :) ) but I guess those are the tradeoffs between ad hoc setup and using a reproducible, more universal setup?

@dmartinezIPA could work on a PR for this once we're done setting up over at smiles, based on what he learned / did there

[NKeleher]

Nice. thanks for clarifying. Assigning to @dmartinezIPA to come back to once tested in SMILES

[NKeleher]

And, yes, absolutely open to and prefer to use the ietoolkit if they've implemented a fix that simplifies user experience. Presumably this is the relevant docs: https://worldbank.github.io/ietoolkit/reference/ieboilstart.html