From caf98d2edc62009105ffcec0d1efd85c392f5c7e Mon Sep 17 00:00:00 2001
From: hyperpolymath <6759885+hyperpolymath@users.noreply.github.com>
Date: Fri, 18 Sep 2026 16:14:57 +0000
Subject: [PATCH] =?UTF-8?q?chore(ci):=20remove=20Codecov=20residue=20?=
 =?UTF-8?q?=E2=80=94=20coverage=20now=20local=20artifact=20only?=
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- Remove codecov.yml (gone)
- Remove badge from README.md
- Replace codecov/codecov-action@v6 upload with actions/upload-artifact@v4 local lcov.info
- Per user request: codecov is gone, residue removed
- No gitar found in repo (grep -i gitar returns 0) — if meant another tool, please clarify
---
 .github/workflows/ci.yml | 12 ++++++------
 README.md                |  1 -
 codecov.yml              | 25 -------------------------
 3 files changed, 6 insertions(+), 32 deletions(-)
 delete mode 100644 codecov.yml

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 715a720..e52a689 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -253,10 +253,10 @@ jobs:
       - name: Process coverage
         uses: julia-actions/julia-processcoverage@v1
 
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v6
+      - name: Upload coverage artifact (local, Codecov removed)
+        if: always()
+        uses: actions/upload-artifact@v4
         with:
-          file: lcov.info
-          token: ${{ secrets.CODECOV_TOKEN }}
-          slug: JoshuaJewell/MetaManifold-WebUI
-          fail_ci_if_error: false
+          name: julia-coverage-lcov
+          path: lcov.info
+          if-no-files-found: warn
diff --git a/README.md b/README.md
index ba2f603..d011e52 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,6 @@ SPDX-License-Identifier: AGPL-3.0-only
 [![Julia ≥ 1.0](https://img.shields.io/badge/Julia-%E2%89%A51.0-9558B2?logo=julia)](https://julialang.org)
 [![R ≥ 4.0](https://img.shields.io/badge/R-%E2%89%A54.0-276DC3?logo=r)](https://www.r-project.org)
 [![CI](https://github.com/JoshuaJewell/MetaManifold-WebUI/actions/workflows/ci.yml/badge.svg)](https://github.com/JoshuaJewell/MetaManifold-WebUI/actions/workflows/ci.yml)
-[![codecov](https://codecov.io/gh/JoshuaJewell/MetaManifold-WebUI/graph/badge.svg?token=20F1VLF590)](https://codecov.io/gh/JoshuaJewell/MetaManifold-WebUI)
 
 MetaManifold wraps standard amplicon sequencing workflows into a single configurable Julia orchestrator: from raw paired-end Next Generation Sequencing reads through denoising, taxonomy assignment, taxonomic filtering, and functional annotation, with interactive configuration and analysis in the browser.
 
diff --git a/codecov.yml b/codecov.yml
deleted file mode 100644
index 52c8efe..0000000
--- a/codecov.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-# SPDX-License-Identifier: AGPL-3.0-only
-## Codecov configuration
-# Only the Julia backend under src/ is instrumented (see the
-# julia-processcoverage step in CI); the TypeScript frontend is not measured
-# through this report.
-
-coverage:
-  status:
-    project:
-      default:
-        ## Compare against the parent commit and tolerate a small dip so that
-        ## routine refactors do not fail the build on coverage alone.
-        target: auto
-        threshold: 1%
-    patch:
-      default:
-        ## Report patch coverage for information without blocking merges.
-        informational: true
-
-## Paths excluded from the coverage denominator
-# MetaManifold.jl is pure module assembly: it contains only include and using
-# statements with no testable branches, so counting it merely depresses the
-# reported percentage without reflecting any real gap in testing.
-ignore:
-  - "src/MetaManifold.jl"