From 0feac0c7d4d1a737dea5b578a0c63fff94613089 Mon Sep 17 00:00:00 2001
From: Sangjoon Bob Lee <bobleesj@gmail.com>
Date: Mon, 16 Sep 2024 22:01:11 -0400
Subject: [PATCH 1/7] Create codecov.yml for coverage testing

---
 .github/workflows/codecov.yml | 53 +++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100644 .github/workflows/codecov.yml

diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml
new file mode 100644
index 00000000..7b58122f
--- /dev/null
+++ b/.github/workflows/codecov.yml
@@ -0,0 +1,53 @@
+name: Gather coverage report and upload to codecov
+
+on:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - prereleased
+      - published
+  workflow_dispatch:
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  coverage:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out diffpy.snmf
+        uses: actions/checkout@v4
+
+      - name: Initialize miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: test
+          auto-update-conda: true
+          environment-file: environment.yml
+          auto-activate-base: false
+
+      - name: Conda config
+        run: >-
+          conda config --set always_yes yes
+          --set changeps1 no
+
+      - name: Install diffpy.snmf and requirements
+        run: |
+          conda install --file requirements/run.txt
+          conda install --file requirements/test.txt
+          python -m pip install -r requirements/pip.txt
+          python -m pip install . --no-deps
+
+      - name: Validate diffpy.snmf
+        run: |
+          coverage run -m pytest -vv -s
+          coverage report -m
+          codecov
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

From 1bb657f6407343f9c21768dd9d3a776a9cd3d739 Mon Sep 17 00:00:00 2001
From: Sangjoon Bob Lee <bobleesj@gmail.com>
Date: Mon, 16 Sep 2024 22:07:26 -0400
Subject: [PATCH 2/7] Remove codecov in main.yml

---
 .github/workflows/main.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 581821ea..a90aaeb7 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -50,6 +50,4 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate test
-          coverage run -m pytest -vv -s
-          coverage report -m
-          codecov
+          pytest

From d81f5a1eef78bf70165fc9270299a8e8c0510569 Mon Sep 17 00:00:00 2001
From: Sangjoon Bob Lee <bobleesj@gmail.com>
Date: Mon, 16 Sep 2024 22:10:39 -0400
Subject: [PATCH 3/7] Upload to codecov to PR

---
 .github/workflows/codecov.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml
index 7b58122f..bf19c224 100644
--- a/.github/workflows/codecov.yml
+++ b/.github/workflows/codecov.yml
@@ -4,10 +4,7 @@ on:
   push:
     branches:
       - main
-  release:
-    types:
-      - prereleased
-      - published
+  pull_request:
   workflow_dispatch:
 
 defaults:

From 4b73be92bdf917c99de3766f67835e1f36dc2ad1 Mon Sep 17 00:00:00 2001
From: Sangjoon Bob Lee <bobleesj@gmail.com>
Date: Mon, 16 Sep 2024 22:37:26 -0400
Subject: [PATCH 4/7] Use pytest --cov instead of codecov

---
 .github/workflows/codecov.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml
index bf19c224..0297142c 100644
--- a/.github/workflows/codecov.yml
+++ b/.github/workflows/codecov.yml
@@ -40,7 +40,7 @@ jobs:
 
       - name: Validate diffpy.snmf
         run: |
-          coverage run -m pytest -vv -s
+          pytest --cov
           coverage report -m
           codecov
 

From 7e5e5473bb611e8725a419a69d40811cd374ff6e Mon Sep 17 00:00:00 2001
From: Sangjoon Bob Lee <bobleesj@gmail.com>
Date: Mon, 16 Sep 2024 22:37:58 -0400
Subject: [PATCH 5/7] Update .coveragerc to remove src

---
 .coveragerc | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.coveragerc b/.coveragerc
index fa3fa528..427c7934 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,6 +1,4 @@
 [run]
-source =
-    src
 [report]
 omit =
     */python?.?/*
@@ -11,3 +9,4 @@ omit =
 
 exclude_lines =
     if __name__ == '__main__':
+

From 46e5e263568ab19ff3487f687a0a6ecdb71bf515 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 17 Sep 2024 02:38:33 +0000
Subject: [PATCH 6/7] [pre-commit.ci] auto fixes from pre-commit hooks

---
 .coveragerc | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.coveragerc b/.coveragerc
index 427c7934..bd53f7e6 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -9,4 +9,3 @@ omit =
 
 exclude_lines =
     if __name__ == '__main__':
-

From e41e218dc7771e1678bf1f250ed330d0f3e5013c Mon Sep 17 00:00:00 2001
From: Sangjoon Bob Lee <bobleesj@gmail.com>
Date: Mon, 16 Sep 2024 22:42:43 -0400
Subject: [PATCH 7/7] Add pytest-cov for test.txt

---
 requirements/test.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements/test.txt b/requirements/test.txt
index 6f9ccf84..d808074d 100644
--- a/requirements/test.txt
+++ b/requirements/test.txt
@@ -1,5 +1,5 @@
 flake8
 pytest
 codecov
-coverage
 pytest-env
+pytest-cov