Update coverage call, don't install in editable mode in testing

.github/workflows/run_all_tests.yml

@@ -224,7 +224,7 @@ jobs:
       - name: Install run dependencies
         run: |
           pip install -r requirements-dev.txt
-          pip install -e .
+          pip install .
           conda info
           conda list
           pip list
@@ -271,7 +271,7 @@ jobs:
       - name: Install run dependencies
         run: |
           pip install matplotlib
-          pip install -e .
+          pip install .
           pip list
 
       - name: Conda reporting

.github/workflows/run_coverage.yml

@@ -53,20 +53,20 @@ jobs:
 
       - 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 unit tests and generate coverage report
         run: |
           python -m coverage run test.py --pynwb
           python -m coverage xml  # codecov uploader requires xml format
-          python -m coverage report -m
+          python -m coverage report
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4
         with:
           flags: unit
-          files: coverage.xml
+          file: coverage.xml
           fail_ci_if_error: true
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
@@ -77,13 +77,13 @@ jobs:
           # validation CLI tests generate separate .coverage files that need to be merged
           python -m coverage combine
           python -m coverage xml  # codecov uploader requires xml format
-          python -m coverage report -m
+          python -m coverage report
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4
         with:
           flags: integration
-          files: coverage.xml
+          file: coverage.xml
           fail_ci_if_error: true
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/run_dandi_read_tests.yml

@@ -31,7 +31,7 @@ jobs:
         run: |
           python -m pip install dandi fsspec requests aiohttp pytest
           python -m pip uninstall -y pynwb  # uninstall pynwb
-          python -m pip install -e .
+          python -m pip install .
           python -m pip list
 
       - name: Conda reporting

.github/workflows/run_inspector_tests.yml

@@ -34,8 +34,7 @@ jobs:
           git clone https://github.com/NeurodataWithoutBorders/nwbinspector.git
           cd nwbinspector
           python -m pip install -r requirements.txt pytest
-          # must install in editable mode for coverage to find sources
-          python -m pip install -e .  # this might install a pinned version of pynwb instead of the current one
+          python -m pip install .  # this might install a pinned version of pynwb instead of the current one
           cd ..
           python -m pip uninstall -y pynwb  # uninstall the pinned version of pynwb
           python -m pip install .  # reinstall current branch of pynwb

.github/workflows/run_tests.yml

@@ -200,7 +200,7 @@ jobs:
       - name: Install run dependencies
         run: |
           pip install -r requirements-dev.txt
-          pip install -e .
+          pip install .
           conda info
           conda list
           pip list
@@ -245,7 +245,7 @@ jobs:
       - name: Install run dependencies
         run: |
           pip install matplotlib
-          pip install -e .
+          pip install .
           pip list
 
       - name: Conda reporting

pyproject.toml

@@ -58,28 +58,24 @@ version-file = "src/pynwb/_version.py"
 [tool.hatch.build.targets.wheel]
 packages = ["src/pynwb"]
 
-# [tool.pytest.ini_options] # TODO: uncomment when pytest is integrated
-# # Addopts creates a shortcut for pytest. For example below, running `pytest` will actually run `pytest --cov --cov-report html`.
-# addopts = "--cov --cov-report html" # generates coverage report in html format without showing anything on the terminal.
-
 [tool.codespell]
 skip = "htmlcov,.git,.mypy_cache,.pytest_cache,.coverage,*.pdf,*.svg,venvs,.tox,nwb-schema,./docs/_build/*,*.ipynb"
 ignore-words-list = "optin,potatos"
 
 [tool.coverage.run]
 branch = true
-source = ["src/"]
-omit = [
-    "src/pynwb/_due.py",
-    "src/pynwb/testing/*",
-    "src/pynwb/legacy/*"
-]
+source = ["src"]
 
 [tool.coverage.report]
 exclude_lines = [
     "pragma: no cover",
     "@abstract"
 ]
+omit = [
+    "*/pynwb/_due.py",
+    "*/pynwb/testing/*",
+    "*/pynwb/legacy/*"
+]
 
 [tool.ruff]
 select = ["E", "F", "T100", "T201", "T203"]

tox.ini

@@ -9,7 +9,6 @@ requires = pip >= 22.0
 
 [testenv]
 download = True
-usedevelop = True
 setenv =
   PYTHONDONTWRITEBYTECODE = 1
   VIRTUALENV_PIP = 23.3.1
@@ -112,7 +111,7 @@ install_command =
 deps =
     -rrequirements.txt
 commands =
-    python -m pip install -e .
+    python -m pip install .
     python -m pip install -r requirements-doc.txt  # NOTE: allensdk (requirements-doc.txt) requires pynwb
     python -m pip check
     python -m pip list
@@ -144,7 +143,7 @@ basepython = python3.12
 deps =
     -rrequirements-dev.txt
 commands =
-    python -m pip install -U -e .
+    python -m pip install -U .
     python -m pip install -r requirements-doc.txt  # NOTE: allensdk (requirements-doc.txt) requires pynwb
     python -m pip check
     python -m pip list
@@ -156,7 +155,7 @@ basepython = python3.12
 deps =
     -rrequirements-dev.txt
 commands =
-    python -m pip install -U --pre -e .
+    python -m pip install -U --pre .
     python -m pip install -r requirements-doc.txt  # NOTE: allensdk (requirements-doc.txt) requires pynwb
     python -m pip check
     python -m pip list