From 65f7a8ba435e2e628a8a44e7c2882b245104b45c Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Wed, 1 May 2024 16:44:09 -0700
Subject: [PATCH] Update coverage call, don't install in editable mode in
 testing (#188)

---
 .github/workflows/HDMF_dev.yaml    |  4 ++--
 .github/workflows/run_coverage.yml | 16 +++++++++++-----
 CHANGELOG.md                       |  1 +
 pyproject.toml                     | 10 ++++------
 tox.ini                            |  1 -
 5 files changed, 18 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/HDMF_dev.yaml b/.github/workflows/HDMF_dev.yaml
index 47f03bff..eb6a4900 100644
--- a/.github/workflows/HDMF_dev.yaml
+++ b/.github/workflows/HDMF_dev.yaml
@@ -24,14 +24,14 @@ jobs:
       - name: Install HDMF_Zarr Requirements
         run: |
           python -m pip install -r requirements-dev.txt -r requirements.txt
-          pip install -e .
+          pip install .
           
       - name: Clone HDMF Dev Branch
         run: |
           git clone https://github.com/hdmf-dev/hdmf.git --recurse-submodules
           cd hdmf
           python -m pip install -r requirements-dev.txt -r requirements.txt
-          python -m pip install -e .
+          python -m pip install .
           cd ..
 
       - name: Run HDMF_Zarr Tests
diff --git a/.github/workflows/run_coverage.yml b/.github/workflows/run_coverage.yml
index a32ef05d..4e96604d 100644
--- a/.github/workflows/run_coverage.yml
+++ b/.github/workflows/run_coverage.yml
@@ -48,20 +48,26 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -r requirements-dev.txt -r requirements.txt -r requirements-opt.txt
+          python -m pip install -r requirements-dev.txt -r requirements.txt
+
+      - name: Install optional dependencies
+        if: ${{ matrix.opt_req }}
+        run: python -m pip install -r requirements-opt.txt
 
       - name: Install package
         run: |
-          python -m pip install -e .  # must install in editable mode for coverage to find sources
+          python -m pip install .
           python -m pip list
+
       - name: Run tests and generate coverage report
         run: |
-          pytest --cov
-          python -m coverage xml  # codecov uploader requires xml format
-          python -m coverage report -m
+          # coverage is configured in pyproject.toml
+          pytest --cov --cov-report=xml --cov-report=term  # codecov uploader requires xml format
+
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4
         with:
           fail_ci_if_error: true
+          file: ./coverage.xml
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7b9f3673..5c14973d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,7 @@
 ### Enhancements
 * Added support for python 3.12. @mavaylon1 [#172](https://github.com/hdmf-dev/hdmf-zarr/pull/172)
 * Added support for forcing read of files without consolidated metadata using  `mode=r-` in `ZarrIO`. @oruebel [#183](https://github.com/hdmf-dev/hdmf-zarr/pull/183)
+- Updated testing to not install in editable mode and not run `coverage` by default. @rly [#188](https://github.com/hdmf-dev/hdmf-zarr/pull/188)
 
 ### Docs
 * Removed `linkable` from the documentation to keep in line with `hdmf-schema-language`. @mavaylon1 [#180](https://github.com/hdmf-dev/hdmf-zarr/pull/180)
diff --git a/pyproject.toml b/pyproject.toml
index ee1eaa40..56c63b7e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -62,8 +62,6 @@ exclude = [".git_archival.txt"]
 [tool.hatch.build.targets.wheel]
 packages = ["src/hdmf_zarr"]
 
-[tool.pytest.ini_options]
-addopts = "--cov --cov-report html"
 
 [tool.codespell]
 skip = "htmlcov,.git,.mypy_cache,.pytest_cache,.coverage,*.pdf,*.svg,venvs,.tox,./docs/_build/*,*.ipynb"
@@ -71,16 +69,16 @@ ignore-words-list = "datas"
 
 [tool.coverage.run]
 branch = true
-source = ["src/"]
-omit = [
-    "src/hdmf_zarr/_due.py",
-]
+source = ["hdmf_zarr"]
 
 [tool.coverage.report]
 exclude_lines = [
     "pragma: no cover",
     "@abstract"
 ]
+omit = [
+    "*/hdmf_zarr/_due.py",
+]
 
 [tool.black]
 line-length = 120
diff --git a/tox.ini b/tox.ini
index 4ca607de..4722b7c6 100644
--- a/tox.ini
+++ b/tox.ini
@@ -9,7 +9,6 @@ requires = pip >= 22.0
 
 [testenv]
 download = True
-usedevelop = True
 setenv =
   PYTHONDONTWRITEBYTECODE = 1
   VIRTUALENV_python -m pip = 22.3.1