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538c659
docs: remove Go coding conventions documentation
cybersiddhu Apr 21, 2026
e802be0
fix(plasmid): refactor ListPlasmids resolver state pipeline
cybersiddhu Apr 21, 2026
73ccb26
docs: add AGENTS.md with essential development commands
cybersiddhu Apr 21, 2026
eaa1213
refactor(plasmid): extract plasmid filter validation to curried function
cybersiddhu Apr 21, 2026
55a4766
refactor(plasmid): refine types in plasmidResultContext fields
cybersiddhu Apr 21, 2026
cca90af
refactor(plasmid): expand listPlasmidsContext and add filterValidatio…
cybersiddhu Apr 21, 2026
c77d40a
refactor(plasmid): update filter predicates to operate on filterValid…
cybersiddhu Apr 21, 2026
f4b6491
refactor(plasmid): validateAndBuildPlasmidFilter is now univariate vi…
cybersiddhu Apr 21, 2026
8d4234b
refactor(plasmid): buildListPlasmidFilterQuery uses Pa.Pair for point…
cybersiddhu Apr 21, 2026
0737910
refactor(plasmid): all pipeline steps operate on listPlasmidsContext
cybersiddhu Apr 21, 2026
a880a8f
refactor(plasmid): compose list plasmid pipeline as point-free IOEith…
cybersiddhu Apr 21, 2026
333616a
refactor(plasmid): streamline ListPlasmids resolver with functional p…
cybersiddhu Apr 21, 2026
adf9b8d
refactor(plasmid): unify filter validation into Either chain
cybersiddhu Apr 21, 2026
2c9b62f
refactor(plasmid): extract validateAndBuildPlasmidFilter to standalon…
cybersiddhu Apr 21, 2026
ad6bdb8
fix(plasmid): restore ontology in plasmid type filter query
cybersiddhu Apr 21, 2026
7133156
feat(plasmid): use triple equals for exact match in filter queries
cybersiddhu Apr 21, 2026
5de59cb
feat(plasmid): simplify filter query to use only tag with triple equals
cybersiddhu Apr 21, 2026
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22 changes: 22 additions & 0 deletions AGENTS.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
# AGENTS.md


## Essential Commands
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⚠️ Potential issue | 🟡 Minor

Document coding conventions and guidelines, not just commands.

The AI summary indicates that the removed CLAUDE.md file contained Go coding conventions and repository guideline documentation (including style rules). This new file only documents essential commands, resulting in a loss of important developer guidance.

Consider adding sections that cover coding standards, architectural patterns, and contribution guidelines to maintain the documentation that was previously available.

🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@AGENTS.md` around lines 1 - 4, AGENTS.md currently only lists essential
commands and omits the repository's previous developer guidance from CLAUDE.md;
restore and expand documentation by adding sections for Coding Conventions
(naming, formatting, Go-specific style rules), Architectural Patterns (service
boundaries, module responsibilities, common package layout), Contribution
Guidelines (PR process, commit message format, review expectations), and
Repository Policies (testing, linting, CI requirements); ensure these sections
reference existing conventions used in the repo (e.g., Go style rules, test
frameworks, linters) and mirror the key guidance that was in CLAUDE.md so
contributors have the same standards as before.


```bash
# Test
gotestsum --format pkgname-and-test-fails --format-hide-empty-pkg -- ./...

# Test (verbose)
gotestsum --format testdox --format-hide-empty-pkg -- ./...

# Watch mode
gotestsum --watch --format pkgname-and-test-fails --format-hide-empty-pkg -- ./...
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⚠️ Potential issue | 🔴 Critical

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
# Description: Check if gotestsum is used in the project and verify command validity

# Check if gotestsum is in go.mod or referenced elsewhere
rg -n "gotestsum" --type=yaml --type=md --type=go

# Check for any test scripts or Makefile that might define the canonical test command
fd -t f -e mk -e sh -e bash -e zsh --exec rg -l "test"

Repository: dictyBase/graphql-server

Length of output: 323


🏁 Script executed:

# Check if CLAUDE.md exists in the repository
fd -i claude

# Look for CI configuration files
fd -e yml -e yaml | grep -i ci

# Check go.mod for dependencies and tools
head -50 go.mod

Repository: dictyBase/graphql-server

Length of output: 2130


🏁 Script executed:

# Look for Makefile or similar test definitions
fd -e mk

# Search for any references to CI or workflow tests
rg -n "go test" --type=yaml --type=go --type=md -A 2

Repository: dictyBase/graphql-server

Length of output: 50


🌐 Web query:

gotestsum format flags documentation pkgname-and-test-fails testdox

💡 Result:

gotestsum is a Go test runner that wraps go test -json and provides various output formats via the --format flag or GOTESTSUM_FORMAT environment variable. Official documentation is in the GitHub README at https://github.com/gotestyourself/gotestsum. Key formats relevant to the query: - pkgname (default): Prints a line for each package, using icons/color to indicate pass/fail/skip status. Icons customizable via --format-icons or GOTESTSUM_FORMAT_ICONS. For passing packages, shows minimal info; for failing packages, shows number of failures (e.g., "0 failed" implied by pass icon, explicit count for fails). - testdox: Prints a readable sentence for each test using gotestdox (e.g., ✔ TestUserAuth_Login (0.23s), ✖ TestPayment_Stripe (0.92s) --- FAIL: invalid API key). Shows pass/fail with icons and elapsed time. No exact format named "pkgname-and-test-fails" exists in the docs. The pkgname format handles test failures by showing failure counts and details in the post-run summary for failed packages. Use --hide-summary to control summary details (e.g., --hide-summary=skipped). Full list of common formats (run gotestsum --help for all): - dots: character per test - pkgname: line per package (default) - testname: line per test+package - testdox: sentence per test - standard-quiet: go test default - standard-verbose: go test -v Examples: gotestsum --format=pkgname ./... gotestsum --format=testdox ./... After formatted output, a summary shows failures, skips, errors, and DONE line (e.g., DONE 9 tests, 1 failure in 3.2s). Latest version info as of 2026-04-15: v1.13.1-0.20260415004743-3cf14356a16c.

Citations:


Fix invalid gotestsum format flags in test commands.

The test commands in lines 8 and 14 use an invalid format flag: pkgname-and-test-fails does not exist in gotestsum's documented formats. Valid formats are: dots, pkgname, testname, testdox, standard-quiet, and standard-verbose.

Line 11 correctly uses testdox, which is valid. Replace the invalid pkgname-and-test-fails format on lines 8 and 14 with a valid alternative (e.g., pkgname for line 8, or use standard-verbose for verbosity if needed).

Additionally, gotestsum is not listed in go.mod as a dependency, so either add it as a development tool or document that it must be installed separately.

🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@AGENTS.md` around lines 8 - 14, Replace the invalid gotestsum format
"pkgname-and-test-fails" used in the test commands with a valid format (for
example replace it with "pkgname" for package-oriented output or
"standard-verbose" if you need more verbosity) wherever "pkgname-and-test-fails"
appears; also update the AGENTS.md test command examples to use the valid
"testdox" already used for verbose test output if appropriate, and document that
gotestsum must be installed as a dev tool (either add it to go.mod as a
development requirement or add a note that developers must install gotestsum
separately).


# Lint
golangci-lint run ./...

# Format
golangci-lint fmt


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