From 3c1ad9b6b33a851a0129c0895559ff0a073f8171 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Wed, 24 Apr 2024 08:41:43 +0200
Subject: [PATCH 01/35] Added Codecov to CI

---
 .github/workflows/continuous-integration.yml | 22 +++++++-------------
 pyproject.toml                               |  1 +
 2 files changed, 8 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index 730ec6ce7..5a3612802 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -65,20 +65,6 @@ jobs:
         run: |
           python -m pip install --upgrade pip
 
-#      - name: Get pip cache dir
-#        id: pip-cache-dir
-#        run: |
-#          echo "::set-output name=dir::$(python -m pip cache dir)"
-#
-#      - name: pip cache
-#        uses: actions/cache@v2
-#        id: pip-cache
-#        with:
-#          path: ${{ steps.pip-cache-dir.outputs.dir }}
-#          key: ${{ matrix.os }}-${{ matrix.python-version }}-pip-${{ hashFiles('**/requirements.txt') }}
-#          restore-keys: |
-#            ${{ matrix.os }}-${{ matrix.python-version }}-pip-
-
       - name: Determine directory of parallel HDF5 library
         run: |
           if [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then
@@ -135,7 +121,7 @@ jobs:
         run: |
           export PSYDAC_MESH_DIR=$GITHUB_WORKSPACE/mesh
           export OMP_NUM_THREADS=2
-          python -m pytest -n auto --pyargs psydac -m "not parallel and not petsc"
+          python -m pytest -n auto --cov psydac.api --pyargs psydac -m "not parallel and not petsc"
 
       - name: Run MPI tests with Pytest
         working-directory: ./pytest
@@ -158,6 +144,12 @@ jobs:
           export OMP_NUM_THREADS=2
           python mpi_tester.py --mpirun="mpiexec -n 4 ${MPI_OPTS}" --pyargs psydac -m "parallel and petsc"
 
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: kvrigor/psydac
+
       - name: Remove test directory
         if: ${{ always() }}
         run: |
diff --git a/pyproject.toml b/pyproject.toml
index 73d967b17..be53ca003 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,6 +28,7 @@ dependencies = [
     'matplotlib',
     'pytest >= 4.5',
     'pytest-xdist >= 1.16',
+    'pytest-cov',
     'pyyaml >= 5.1',
     'packaging',
     'pyevtk',

From cd78ac3c0f7f724174d5e70e15d95f9c4868e08c Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Wed, 2 Oct 2024 17:06:22 +0200
Subject: [PATCH 02/35] coverage: exlude unit tests and pyccelised kernels in
 the report

---
 pyproject.toml | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index ec2b209f8..05d7a5a23 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -69,3 +69,37 @@ namespaces = false
 
 [tool.setuptools.package-data]
 "*" = ["*.txt"]
+
+[tool.coverage.run]
+branch = true
+omit = [
+    # Exclude pyccelised kernels
+    "*/__psydac__/*",
+    # Unit tests shouldn't be included too
+    "*/tests/*",
+    ]
+
+[tool.coverage.report]
+# Regexes for lines to exclude from consideration
+exclude_also = [
+    # Don't complain about missing debug-only code:
+    "def __repr__",
+    "if self\\.debug",
+
+    # Don't complain if tests don't hit defensive assertion code:
+    "raise AssertionError",
+    "raise NotImplementedError",
+
+    # Don't complain if non-runnable code isn't run:
+    "if 0:",
+    "if __name__ == .__main__.:",
+
+    # Don't complain about abstract methods, they aren't run:
+    "@(abc\\.)?abstractmethod",
+    ]
+
+# Ignore source code that can’t be found, emitting a warning instead of an exception.
+ignore_errors = true
+
+[tool.coverage.html]
+directory = "coverage_html_report"

From 1bafc854f392e1e6d918d82fe83634a767fce66e Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Wed, 2 Oct 2024 17:33:06 +0200
Subject: [PATCH 03/35] CI.yml: added Codacy coverage reporter action

---
 .github/workflows/continuous-integration.yml | 16 ++++++++--------
 pyproject.toml                               |  5 +++++
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index 3f39277ab..bb51c0ae7 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -157,7 +157,7 @@ jobs:
 
       - name: Install project
         run: |
-          python -m pip install .
+          python -m pip install .[test]
           python -m pip freeze
 
       - name: Test Pyccel optimization flags
@@ -174,7 +174,13 @@ jobs:
         run: |
           export PSYDAC_MESH_DIR=$GITHUB_WORKSPACE/mesh
           export OMP_NUM_THREADS=2
-          python -m pytest -n auto --cov psydac.api --pyargs psydac -m "not parallel and not petsc"
+          python -m pytest -n auto --cov psydac --cov-report xml:coverage.xml --pyargs psydac -m "not parallel and not petsc"
+
+      - name: Run Codacy coverage reporter
+        uses: codacy/codacy-coverage-reporter-action@v1.3.0
+        with:
+          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
+          coverage-reports: coverage.xml
 
       - name: Run MPI tests with Pytest
         working-directory: ./pytest
@@ -197,12 +203,6 @@ jobs:
           export OMP_NUM_THREADS=2
           python mpi_tester.py --mpirun="mpiexec -n 4 ${MPI_OPTS}" --pyargs psydac -m "parallel and petsc"
 
-      - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v4.0.1
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          slug: kvrigor/psydac
-
       - name: Remove test directory
         if: ${{ always() }}
         run: |
diff --git a/pyproject.toml b/pyproject.toml
index 05d7a5a23..364d2c0ed 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -54,6 +54,11 @@ dependencies = [
     'igakit @ https://github.com/dalcinl/igakit/archive/refs/heads/master.zip'
 ]
 
+[project.optional-dependencies]
+test = [
+    "pytest-cov >= 5.0.0",
+]
+
 [project.urls]
 Homepage      = "https://github.com/pyccel/psydac"
 Documentation = "https://pyccel.github.io/psydac"

From 1715bfd060bc68db45270d57295686b17f57db57 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Wed, 2 Oct 2024 18:16:50 +0200
Subject: [PATCH 04/35] pyproject.toml: deleted redundant pytest-cov

---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 364d2c0ed..00a08bd50 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,7 +28,6 @@ dependencies = [
     'matplotlib',
     'pytest >= 4.5',
     'pytest-xdist >= 1.16',
-    'pytest-cov',
     'pyyaml >= 5.1',
     'packaging',
     'pyevtk',

From ae33ed03d91992e6c2a888aa73cda705ac575050 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Wed, 2 Oct 2024 18:58:48 +0200
Subject: [PATCH 05/35] CI.yml: Codacy reporter should run under pytest folder

---
 .github/workflows/continuous-integration.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index bb51c0ae7..367f7220e 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -177,6 +177,7 @@ jobs:
           python -m pytest -n auto --cov psydac --cov-report xml:coverage.xml --pyargs psydac -m "not parallel and not petsc"
 
       - name: Run Codacy coverage reporter
+        working-directory: ./pytest
         uses: codacy/codacy-coverage-reporter-action@v1.3.0
         with:
           project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}

From ab102b920638c93c283c7dbcf689d0f77d859b85 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Wed, 2 Oct 2024 19:01:56 +0200
Subject: [PATCH 06/35] CI.yml: Fixed path to coverage.xml

---
 .github/workflows/continuous-integration.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index 367f7220e..c0e95dd6f 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -177,11 +177,10 @@ jobs:
           python -m pytest -n auto --cov psydac --cov-report xml:coverage.xml --pyargs psydac -m "not parallel and not petsc"
 
       - name: Run Codacy coverage reporter
-        working-directory: ./pytest
         uses: codacy/codacy-coverage-reporter-action@v1.3.0
         with:
           project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
-          coverage-reports: coverage.xml
+          coverage-reports: ./pytest/coverage.xml
 
       - name: Run MPI tests with Pytest
         working-directory: ./pytest

From 03f605d846977c752017064910c58a3328e11608 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Fri, 4 Oct 2024 11:54:17 +0200
Subject: [PATCH 07/35] CI.yml: Set coverage config file to pyproject.toml

---
 .github/workflows/continuous-integration.yml | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index c0e95dd6f..308fd766e 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -30,6 +30,10 @@ jobs:
 
     name: ${{ matrix.os }} / Python ${{ matrix.python-version }}
 
+    env:
+      PSYDAC_MESH_DIR: ${{ github.workspace }}/mesh
+      OMP_NUM_THREADS: 2
+
     steps:
       - uses: actions/checkout@v4
 
@@ -171,10 +175,11 @@ jobs:
 
       - name: Run single-process tests with Pytest
         working-directory: ./pytest
-        run: |
-          export PSYDAC_MESH_DIR=$GITHUB_WORKSPACE/mesh
-          export OMP_NUM_THREADS=2
-          python -m pytest -n auto --cov psydac --cov-report xml:coverage.xml --pyargs psydac -m "not parallel and not petsc"
+        run: >- 
+          python -m pytest -n auto --cov psydac
+          --cov-report xml:coverage.xml
+          --cov-config $GITHUB_WORKSPACE/pyproject.toml
+          --pyargs psydac -m "not parallel and not petsc"
 
       - name: Run Codacy coverage reporter
         uses: codacy/codacy-coverage-reporter-action@v1.3.0
@@ -185,22 +190,16 @@ jobs:
       - name: Run MPI tests with Pytest
         working-directory: ./pytest
         run: |
-          export PSYDAC_MESH_DIR=$GITHUB_WORKSPACE/mesh
-          export OMP_NUM_THREADS=2
           python mpi_tester.py --mpirun="mpiexec -n 4 ${MPI_OPTS}" --pyargs psydac -m "parallel and not petsc"
 
       - name: Run single-process PETSc tests with Pytest
         working-directory: ./pytest
         run: |
-          export PSYDAC_MESH_DIR=$GITHUB_WORKSPACE/mesh
-          export OMP_NUM_THREADS=2
           python -m pytest -n auto --pyargs psydac -m "not parallel and petsc"
 
       - name: Run MPI PETSc tests with Pytest
         working-directory: ./pytest
         run: |
-          export PSYDAC_MESH_DIR=$GITHUB_WORKSPACE/mesh
-          export OMP_NUM_THREADS=2
           python mpi_tester.py --mpirun="mpiexec -n 4 ${MPI_OPTS}" --pyargs psydac -m "parallel and petsc"
 
       - name: Remove test directory

From 07aa1e1707ad0e30bb7ee26fcc5bb0be0b370246 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Fri, 4 Oct 2024 15:16:39 +0200
Subject: [PATCH 08/35] CI.yml: Printed detailed coverage results

---
 .github/workflows/continuous-integration.yml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index 308fd766e..d228abdd5 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -177,16 +177,22 @@ jobs:
         working-directory: ./pytest
         run: >- 
           python -m pytest -n auto --cov psydac
+          --cov-report term-missing
           --cov-report xml:coverage.xml
           --cov-config $GITHUB_WORKSPACE/pyproject.toml
           --pyargs psydac -m "not parallel and not petsc"
 
-      - name: Run Codacy coverage reporter
+      - name: Upload coverage report to Codacy
         uses: codacy/codacy-coverage-reporter-action@v1.3.0
         with:
           project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
           coverage-reports: ./pytest/coverage.xml
 
+      - name: Print detailed coverage results
+        working-directory: ./pytest
+        run: |
+          coverage report --ignore-errors --show-missing --sort=cover
+
       - name: Run MPI tests with Pytest
         working-directory: ./pytest
         run: |

From 65c27de7b5c1c8d66fd07d5b1c3f3f22cfa4e649 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Fri, 4 Oct 2024 15:20:02 +0200
Subject: [PATCH 09/35] Excluded examples dir from coverage

---
 pyproject.toml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 00a08bd50..192e13636 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -79,6 +79,8 @@ branch = true
 omit = [
     # Exclude pyccelised kernels
     "*/__psydac__/*",
+    # Examples don't need to be covered
+    "*/examples/*",
     # Unit tests shouldn't be included too
     "*/tests/*",
     ]

From 4949d39477b74700cde0368d7750b19bb6bb900d Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Fri, 4 Oct 2024 16:22:06 +0200
Subject: [PATCH 10/35] '--cov-report term-missing' is redundant

---
 .github/workflows/continuous-integration.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index d228abdd5..97bfc7852 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -177,7 +177,6 @@ jobs:
         working-directory: ./pytest
         run: >- 
           python -m pytest -n auto --cov psydac
-          --cov-report term-missing
           --cov-report xml:coverage.xml
           --cov-config $GITHUB_WORKSPACE/pyproject.toml
           --pyargs psydac -m "not parallel and not petsc"

From 36620af0f45753f215e453bec9b0ec4a4333b072 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Tue, 8 Oct 2024 07:44:46 +0200
Subject: [PATCH 11/35] Dummy change for checking test runtime

---
 pyproject.toml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 192e13636..627a8c452 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -79,9 +79,11 @@ branch = true
 omit = [
     # Exclude pyccelised kernels
     "*/__psydac__/*",
+
     # Examples don't need to be covered
     "*/examples/*",
-    # Unit tests shouldn't be included too
+
+    # Unit tests shouldn't be included
     "*/tests/*",
     ]
 

From 3703d5b28de4b70fa9f0fcdda19f1443b7615896 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Tue, 8 Oct 2024 15:56:17 +0200
Subject: [PATCH 12/35] CI.yml: Generated coverage report on another step

---
 .github/workflows/continuous-integration.yml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index 97bfc7852..65d77eaed 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -177,10 +177,15 @@ jobs:
         working-directory: ./pytest
         run: >- 
           python -m pytest -n auto --cov psydac
-          --cov-report xml:coverage.xml
           --cov-config $GITHUB_WORKSPACE/pyproject.toml
+          --cov-report=""
           --pyargs psydac -m "not parallel and not petsc"
 
+      - name: Generate coverage report for Codacy
+        working-directory: ./pytest
+        run: |
+          coverage xml
+
       - name: Upload coverage report to Codacy
         uses: codacy/codacy-coverage-reporter-action@v1.3.0
         with:

From f175d0bc5c92a38451426742fb577689cedf0f50 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Wed, 9 Oct 2024 08:56:40 +0200
Subject: [PATCH 13/35] CI.yml: Run tests via coverage instead of pytest-cov

---
 .github/workflows/continuous-integration.yml | 6 +++---
 pyproject.toml                               | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index 65d77eaed..ccc4c7c14 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -176,9 +176,9 @@ jobs:
       - name: Run single-process tests with Pytest
         working-directory: ./pytest
         run: >- 
-          python -m pytest -n auto --cov psydac
-          --cov-config $GITHUB_WORKSPACE/pyproject.toml
-          --cov-report=""
+          coverage run
+          --rcfile=pyproject.toml
+          --module pytest -n auto
           --pyargs psydac -m "not parallel and not petsc"
 
       - name: Generate coverage report for Codacy
diff --git a/pyproject.toml b/pyproject.toml
index 627a8c452..bb8104029 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -55,7 +55,7 @@ dependencies = [
 
 [project.optional-dependencies]
 test = [
-    "pytest-cov >= 5.0.0",
+    "coverage",
 ]
 
 [project.urls]

From 10d96d43c3ce68fe3c2690480121fc356e05086c Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Wed, 9 Oct 2024 09:01:48 +0200
Subject: [PATCH 14/35] CI.yml: Specified full path to pyproject.toml

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

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index ccc4c7c14..fe589add0 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -177,7 +177,7 @@ jobs:
         working-directory: ./pytest
         run: >- 
           coverage run
-          --rcfile=pyproject.toml
+          --rcfile=$GITHUB_WORKSPACE/pyproject.toml
           --module pytest -n auto
           --pyargs psydac -m "not parallel and not petsc"
 

From fc6e380b594f5704a622bc53937bc04c0878851d Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Wed, 9 Oct 2024 10:23:52 +0200
Subject: [PATCH 15/35] CI.yml: Be explicit about the location of the .coverage
 file

---
 .github/workflows/continuous-integration.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index fe589add0..68131b423 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -177,14 +177,14 @@ jobs:
         working-directory: ./pytest
         run: >- 
           coverage run
+          --data-file=$GITHUB_WORKSPACE/.coverage
           --rcfile=$GITHUB_WORKSPACE/pyproject.toml
           --module pytest -n auto
           --pyargs psydac -m "not parallel and not petsc"
 
       - name: Generate coverage report for Codacy
-        working-directory: ./pytest
         run: |
-          coverage xml
+          coverage xml --data-file=$GITHUB_WORKSPACE/.coverage
 
       - name: Upload coverage report to Codacy
         uses: codacy/codacy-coverage-reporter-action@v1.3.0

From d2a73f1a480d0a0f63f5c5d81359cfbdab2d9257 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Wed, 9 Oct 2024 12:36:44 +0200
Subject: [PATCH 16/35] CI.yml: Ran 'coverage xml' under ./pytest

---
 .github/workflows/continuous-integration.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index 68131b423..fe589add0 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -177,14 +177,14 @@ jobs:
         working-directory: ./pytest
         run: >- 
           coverage run
-          --data-file=$GITHUB_WORKSPACE/.coverage
           --rcfile=$GITHUB_WORKSPACE/pyproject.toml
           --module pytest -n auto
           --pyargs psydac -m "not parallel and not petsc"
 
       - name: Generate coverage report for Codacy
+        working-directory: ./pytest
         run: |
-          coverage xml --data-file=$GITHUB_WORKSPACE/.coverage
+          coverage xml
 
       - name: Upload coverage report to Codacy
         uses: codacy/codacy-coverage-reporter-action@v1.3.0

From e23716e6c22c38df3a44472b5fe0f0368b26913b Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Wed, 9 Oct 2024 14:05:42 +0200
Subject: [PATCH 17/35] CI.yml: Run coverage at repo root

---
 .github/workflows/continuous-integration.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index fe589add0..5af8a9f91 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -174,7 +174,6 @@ jobs:
           cp mpi_tester.py pytest
 
       - name: Run single-process tests with Pytest
-        working-directory: ./pytest
         run: >- 
           coverage run
           --rcfile=$GITHUB_WORKSPACE/pyproject.toml
@@ -182,7 +181,6 @@ jobs:
           --pyargs psydac -m "not parallel and not petsc"
 
       - name: Generate coverage report for Codacy
-        working-directory: ./pytest
         run: |
           coverage xml
 

From 6d4aedd716f1197b233c445aecbfdf30e1369322 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Mon, 14 Oct 2024 11:53:18 +0200
Subject: [PATCH 18/35] Fixed missing coverage data by setting coverage
 subprocess hooks

See https://coverage.readthedocs.io/en/7.6.3/subprocess.html#measuring-sub-processes
---
 .github/workflows/continuous-integration.yml | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index 5af8a9f91..e70f5f75a 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -173,12 +173,15 @@ jobs:
           mkdir pytest
           cp mpi_tester.py pytest
 
+      # Coverage data is also collected during single process testing.
       - name: Run single-process tests with Pytest
-        run: >- 
-          coverage run
-          --rcfile=$GITHUB_WORKSPACE/pyproject.toml
-          --module pytest -n auto
-          --pyargs psydac -m "not parallel and not petsc"
+        run: | 
+          export COVERAGE_PROCESS_START="pyproject.toml"
+          export PYTHONPATH=$(pwd)
+          echo "import coverage; coverage.process_startup()" > sitecustomize.py
+          coverage run --module pytest -n auto --pyargs psydac -m "not parallel and not petsc"
+          rm sitecustomize.py
+          unset COVERAGE_PROCESS_STARTPYTHONPATH
 
       - name: Generate coverage report for Codacy
         run: |

From d995440905dae7d094925ab319020eb8464cefe7 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Mon, 14 Oct 2024 11:59:40 +0200
Subject: [PATCH 19/35] Fixed typo when unsetting coverage env vars

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

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index e70f5f75a..8ecaa5cfb 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -181,7 +181,7 @@ jobs:
           echo "import coverage; coverage.process_startup()" > sitecustomize.py
           coverage run --module pytest -n auto --pyargs psydac -m "not parallel and not petsc"
           rm sitecustomize.py
-          unset COVERAGE_PROCESS_STARTPYTHONPATH
+          unset COVERAGE_PROCESS_START PYTHONPATH
 
       - name: Generate coverage report for Codacy
         run: |

From 338aa9a491de562f8c40ac81be4eb427bfde043f Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Mon, 14 Oct 2024 15:05:51 +0200
Subject: [PATCH 20/35] Made coverage env settings permanent for now

---
 .github/workflows/continuous-integration.yml | 20 +++++++++-----------
 1 file changed, 9 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index 8ecaa5cfb..0e268d731 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -33,6 +33,8 @@ jobs:
     env:
       PSYDAC_MESH_DIR: ${{ github.workspace }}/mesh
       OMP_NUM_THREADS: 2
+      COVERAGE_PROCESS_START: pyproject.toml
+      PYTHONPATH: ${{ github.workspace }}
 
     steps:
       - uses: actions/checkout@v4
@@ -168,36 +170,32 @@ jobs:
         run: |
           pytest --pyargs psydac -m pyccel --capture=no
 
-      - name: Initialize test directory
-        run: |
-          mkdir pytest
-          cp mpi_tester.py pytest
-
       # Coverage data is also collected during single process testing.
       - name: Run single-process tests with Pytest
         run: | 
-          export COVERAGE_PROCESS_START="pyproject.toml"
-          export PYTHONPATH=$(pwd)
           echo "import coverage; coverage.process_startup()" > sitecustomize.py
           coverage run --module pytest -n auto --pyargs psydac -m "not parallel and not petsc"
-          rm sitecustomize.py
-          unset COVERAGE_PROCESS_START PYTHONPATH
 
       - name: Generate coverage report for Codacy
         run: |
           coverage xml
+          pytest --cache-show | grep cachedir # To be removed in the next commit
 
       - name: Upload coverage report to Codacy
         uses: codacy/codacy-coverage-reporter-action@v1.3.0
         with:
           project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
-          coverage-reports: ./pytest/coverage.xml
+          coverage-reports: coverage.xml
 
       - name: Print detailed coverage results
-        working-directory: ./pytest
         run: |
           coverage report --ignore-errors --show-missing --sort=cover
 
+      - name: Initialize MPI test directory
+        run: |
+          mkdir pytest
+          cp mpi_tester.py pytest
+
       - name: Run MPI tests with Pytest
         working-directory: ./pytest
         run: |

From ee41b764cd4d2685c1bccfdc9cb24120dfb014c0 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Mon, 14 Oct 2024 17:25:53 +0200
Subject: [PATCH 21/35] Try running coverage under ./pytest

---
 .github/workflows/continuous-integration.yml | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index 0e268d731..b7501eea5 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -33,8 +33,8 @@ jobs:
     env:
       PSYDAC_MESH_DIR: ${{ github.workspace }}/mesh
       OMP_NUM_THREADS: 2
-      COVERAGE_PROCESS_START: pyproject.toml
-      PYTHONPATH: ${{ github.workspace }}
+      COVERAGE_PROCESS_START: ${{ github.workspace }}/pyproject.toml
+      PYTHONPATH: ${{ github.workspace }}/pytest
 
     steps:
       - uses: actions/checkout@v4
@@ -170,13 +170,20 @@ jobs:
         run: |
           pytest --pyargs psydac -m pyccel --capture=no
 
+      - name: Initialize test directory
+        run: |
+          mkdir pytest
+          cp mpi_tester.py pytest
+
       # Coverage data is also collected during single process testing.
       - name: Run single-process tests with Pytest
+        working-directory: ./pytest
         run: | 
           echo "import coverage; coverage.process_startup()" > sitecustomize.py
           coverage run --module pytest -n auto --pyargs psydac -m "not parallel and not petsc"
 
       - name: Generate coverage report for Codacy
+        working-directory: ./pytest
         run: |
           coverage xml
           pytest --cache-show | grep cachedir # To be removed in the next commit
@@ -188,14 +195,10 @@ jobs:
           coverage-reports: coverage.xml
 
       - name: Print detailed coverage results
+        working-directory: ./pytest
         run: |
           coverage report --ignore-errors --show-missing --sort=cover
 
-      - name: Initialize MPI test directory
-        run: |
-          mkdir pytest
-          cp mpi_tester.py pytest
-
       - name: Run MPI tests with Pytest
         working-directory: ./pytest
         run: |

From 934a705380538369cc1d090aaff78a1bbe40bb3b Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Wed, 16 Oct 2024 12:52:50 +0200
Subject: [PATCH 22/35] Revert to pytest-cov

Overhead due to coverage data collection is the
same for coverage.py and pytest-cov
---
 .github/workflows/continuous-integration.yml | 10 +++++-----
 pyproject.toml                               |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index b7501eea5..06de22baa 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -33,8 +33,6 @@ jobs:
     env:
       PSYDAC_MESH_DIR: ${{ github.workspace }}/mesh
       OMP_NUM_THREADS: 2
-      COVERAGE_PROCESS_START: ${{ github.workspace }}/pyproject.toml
-      PYTHONPATH: ${{ github.workspace }}/pytest
 
     steps:
       - uses: actions/checkout@v4
@@ -178,9 +176,11 @@ jobs:
       # Coverage data is also collected during single process testing.
       - name: Run single-process tests with Pytest
         working-directory: ./pytest
-        run: | 
-          echo "import coverage; coverage.process_startup()" > sitecustomize.py
-          coverage run --module pytest -n auto --pyargs psydac -m "not parallel and not petsc"
+        run: >- 
+          python -m pytest -n auto --cov psydac
+          --cov-config $GITHUB_WORKSPACE/pyproject.toml
+          --cov-report=""
+          --pyargs psydac -m "not parallel and not petsc"
 
       - name: Generate coverage report for Codacy
         working-directory: ./pytest
diff --git a/pyproject.toml b/pyproject.toml
index bb8104029..627a8c452 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -55,7 +55,7 @@ dependencies = [
 
 [project.optional-dependencies]
 test = [
-    "coverage",
+    "pytest-cov >= 5.0.0",
 ]
 
 [project.urls]

From b7d61a5c23a0be52fba5da34256515d0c400ec59 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Wed, 16 Oct 2024 14:16:39 +0200
Subject: [PATCH 23/35] Fixed path to coverage.xml

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

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index 06de22baa..cbe627ebc 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -192,7 +192,7 @@ jobs:
         uses: codacy/codacy-coverage-reporter-action@v1.3.0
         with:
           project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
-          coverage-reports: coverage.xml
+          coverage-reports: ./pytest/coverage.xml
 
       - name: Print detailed coverage results
         working-directory: ./pytest

From 43b35e3f5d3594e4b0db9f05f7942af6551f1a70 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Wed, 23 Oct 2024 13:01:03 +0200
Subject: [PATCH 24/35] Cached ./pytest_cache

---
 .github/workflows/continuous-integration.yml | 20 ++++++++++++--------
 psydac/api/equation.py                       |  2 +-
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index cbe627ebc..ee64a6a63 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -177,17 +177,12 @@ jobs:
       - name: Run single-process tests with Pytest
         working-directory: ./pytest
         run: >- 
-          python -m pytest -n auto --cov psydac
+          python -m pytest -n auto --failed-first
+          --cov psydac
           --cov-config $GITHUB_WORKSPACE/pyproject.toml
-          --cov-report=""
+          --cov-report xml
           --pyargs psydac -m "not parallel and not petsc"
 
-      - name: Generate coverage report for Codacy
-        working-directory: ./pytest
-        run: |
-          coverage xml
-          pytest --cache-show | grep cachedir # To be removed in the next commit
-
       - name: Upload coverage report to Codacy
         uses: codacy/codacy-coverage-reporter-action@v1.3.0
         with:
@@ -214,6 +209,15 @@ jobs:
         run: |
           python mpi_tester.py --mpirun="mpiexec -n 4 ${MPI_OPTS}" --pyargs psydac -m "parallel and petsc"
 
+      - name: Cache Pytest results
+        uses: actions/cache@v4
+        id: cache-pytest
+        env:
+          cache-name: cache-pytest
+        with:
+          path: ".pytest_cache"
+          key: cache-${{ matrix.os }}-${{ matrix.python-version }}
+
       - name: Remove test directory
         if: ${{ always() }}
         run: |
diff --git a/psydac/api/equation.py b/psydac/api/equation.py
index 69ef5a077..2190f90ba 100644
--- a/psydac/api/equation.py
+++ b/psydac/api/equation.py
@@ -68,7 +68,7 @@ def l2_boundary_projection(equation):
     test_dict = dict(zip(u, v))
 
     # Compute product of (u, v) using dot product for vector quantities
-    product  = lambda f, g: (f * g if g.atoms(ScalarFunction) else dot(f, g))
+    product  = lambda f, g: (f * 0.5 * g if g.atoms(ScalarFunction) else dot(f, g)) # Deliberately fail the test
 
     # Construct variational formulation that performs L2 projection
     # of boundary conditions onto the correct space

From 051f1ec059c2c233d425a5cde526d92a33c3341c Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Wed, 23 Oct 2024 13:14:42 +0200
Subject: [PATCH 25/35] Pytest cache must always be saved regardless of test
 result

---
 .github/workflows/continuous-integration.yml | 22 +++++++++++++-------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index ee64a6a63..171816742 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -108,7 +108,7 @@ jobs:
           cache-name: cache-PETSc
         with:
           path: "./petsc"
-          key: cache-${{ matrix.os }}-${{ matrix.python-version }}
+          key: petsc-${{ matrix.os }}-${{ matrix.python-version }}
 
       - if: steps.cache-petsc.outputs.cache-hit != 'true'
         name: Download a specific release of PETSc
@@ -173,6 +173,13 @@ jobs:
           mkdir pytest
           cp mpi_tester.py pytest
 
+      - name: Restore Pytest cache
+        id: cache-pytest-restore
+        uses: actions/cache/restore@v4
+        with:
+          key: pytest-${{ matrix.os }}-${{ matrix.python-version }}
+          path: "./.pytest_cache"
+
       # Coverage data is also collected during single process testing.
       - name: Run single-process tests with Pytest
         working-directory: ./pytest
@@ -209,14 +216,13 @@ jobs:
         run: |
           python mpi_tester.py --mpirun="mpiexec -n 4 ${MPI_OPTS}" --pyargs psydac -m "parallel and petsc"
 
-      - name: Cache Pytest results
-        uses: actions/cache@v4
-        id: cache-pytest
-        env:
-          cache-name: cache-pytest
+      - name: Always save Pytest cache
+        id: cache-pytest-save
+        if: always() && steps.cache-pytest-restore.outputs.cache-hit != 'true'
+        uses: actions/cache/save@v4
         with:
-          path: ".pytest_cache"
-          key: cache-${{ matrix.os }}-${{ matrix.python-version }}
+          key: ${{ steps.cache-pytest-restore.outputs.cache-primary-key }}
+          path: "./.pytest_cache"
 
       - name: Remove test directory
         if: ${{ always() }}

From 02647bae6d4e0754ae080bd16e041528812cdd0a Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Thu, 24 Oct 2024 11:51:27 +0200
Subject: [PATCH 26/35] Only run coverage tests on macOS

---
 .github/workflows/continuous-integration.yml | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index 171816742..c84e49413 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -180,8 +180,8 @@ jobs:
           key: pytest-${{ matrix.os }}-${{ matrix.python-version }}
           path: "./.pytest_cache"
 
-      # Coverage data is also collected during single process testing.
-      - name: Run single-process tests with Pytest
+      - name: Run coverage tests on macOS
+        if: matrix.os == 'macos-latest'
         working-directory: ./pytest
         run: >- 
           python -m pytest -n auto --failed-first
@@ -190,13 +190,21 @@ jobs:
           --cov-report xml
           --pyargs psydac -m "not parallel and not petsc"
 
+      - name: Run single-process tests with Pytest on Ubuntu
+        if: matrix.os == 'ubuntu-latest'
+        working-directory: ./pytest
+        run: |
+          python -m pytest -n auto --failed-first --pyargs psydac -m "not parallel and not petsc"
+
       - name: Upload coverage report to Codacy
+        if: matrix.os == 'macos-latest'
         uses: codacy/codacy-coverage-reporter-action@v1.3.0
         with:
           project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
           coverage-reports: ./pytest/coverage.xml
 
-      - name: Print detailed coverage results
+      - name: Print detailed coverage results on macOS
+        if: matrix.os == 'macos-latest'
         working-directory: ./pytest
         run: |
           coverage report --ignore-errors --show-missing --sort=cover
@@ -216,7 +224,7 @@ jobs:
         run: |
           python mpi_tester.py --mpirun="mpiexec -n 4 ${MPI_OPTS}" --pyargs psydac -m "parallel and petsc"
 
-      - name: Always save Pytest cache
+      - name: Save Pytest cache
         id: cache-pytest-save
         if: always() && steps.cache-pytest-restore.outputs.cache-hit != 'true'
         uses: actions/cache/save@v4

From cf024e8415a66dc111b1344359166566fc5ca617 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Thu, 24 Oct 2024 11:55:11 +0200
Subject: [PATCH 27/35] Break test_api_3d_scalar

---
 psydac/api/equation.py                 | 2 +-
 psydac/api/tests/test_api_3d_scalar.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/psydac/api/equation.py b/psydac/api/equation.py
index 2190f90ba..69ef5a077 100644
--- a/psydac/api/equation.py
+++ b/psydac/api/equation.py
@@ -68,7 +68,7 @@ def l2_boundary_projection(equation):
     test_dict = dict(zip(u, v))
 
     # Compute product of (u, v) using dot product for vector quantities
-    product  = lambda f, g: (f * 0.5 * g if g.atoms(ScalarFunction) else dot(f, g)) # Deliberately fail the test
+    product  = lambda f, g: (f * g if g.atoms(ScalarFunction) else dot(f, g))
 
     # Construct variational formulation that performs L2 projection
     # of boundary conditions onto the correct space
diff --git a/psydac/api/tests/test_api_3d_scalar.py b/psydac/api/tests/test_api_3d_scalar.py
index 6760b4352..4d24324c9 100644
--- a/psydac/api/tests/test_api_3d_scalar.py
+++ b/psydac/api/tests/test_api_3d_scalar.py
@@ -144,7 +144,7 @@ def run_poisson_3d_dirneu(solution, f, boundary, ncells, degree, comm=None):
     # ...
 
     # ... compute norms
-    l2_error = l2norm_h.assemble(u = uh)
+    l2_error = l2norm_h.assemble(u = uh) + 1
     h1_error = h1norm_h.assemble(u = uh)
     # ...
 

From 70eeff4132b89f5f91e3a85ee78c54a3fb78695d Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Thu, 24 Oct 2024 12:30:03 +0200
Subject: [PATCH 28/35] Pytest cache must be updated every run

---
 .github/workflows/continuous-integration.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index c84e49413..92cece9e3 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -226,13 +226,13 @@ jobs:
 
       - name: Save Pytest cache
         id: cache-pytest-save
-        if: always() && steps.cache-pytest-restore.outputs.cache-hit != 'true'
+        if: always()
         uses: actions/cache/save@v4
         with:
           key: ${{ steps.cache-pytest-restore.outputs.cache-primary-key }}
           path: "./.pytest_cache"
 
       - name: Remove test directory
-        if: ${{ always() }}
+        if: always()
         run: |
           rm -rf pytest

From 45d25b1293af0acf8ad7e67ed21ef49e19936746 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Thu, 24 Oct 2024 13:28:46 +0200
Subject: [PATCH 29/35] Compute cache key based on hash of ./pytest_cache

pytest_cache should be saved whenever its contents changes. Cache saving only
triggers if the associated cache key changes; thus the cache key should
automatically update based on the contents of pytest_cache, which is
uniquely represented by its hash.
---
 .github/workflows/continuous-integration.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index 92cece9e3..be767883e 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -177,7 +177,7 @@ jobs:
         id: cache-pytest-restore
         uses: actions/cache/restore@v4
         with:
-          key: pytest-${{ matrix.os }}-${{ matrix.python-version }}
+          key: pytest-${{ matrix.os }}-${{ matrix.python-version }}-${{ hashFiles('.pytest_cache/**') }}
           path: "./.pytest_cache"
 
       - name: Run coverage tests on macOS
@@ -226,10 +226,10 @@ jobs:
 
       - name: Save Pytest cache
         id: cache-pytest-save
-        if: always()
+        if: always() && steps.cache-primes-restore.outputs.cache-hit != 'true'
         uses: actions/cache/save@v4
         with:
-          key: ${{ steps.cache-pytest-restore.outputs.cache-primary-key }}
+          key: pytest-${{ matrix.os }}-${{ matrix.python-version }}-${{ hashFiles('.pytest_cache/**') }}
           path: "./.pytest_cache"
 
       - name: Remove test directory

From 65742fd68a9e908556a5baceb667b93b24e683b4 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Thu, 24 Oct 2024 14:29:50 +0200
Subject: [PATCH 30/35] Fixed test_api_3d_scalar.py

---
 psydac/api/tests/test_api_3d_scalar.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/psydac/api/tests/test_api_3d_scalar.py b/psydac/api/tests/test_api_3d_scalar.py
index 4d24324c9..6760b4352 100644
--- a/psydac/api/tests/test_api_3d_scalar.py
+++ b/psydac/api/tests/test_api_3d_scalar.py
@@ -144,7 +144,7 @@ def run_poisson_3d_dirneu(solution, f, boundary, ncells, degree, comm=None):
     # ...
 
     # ... compute norms
-    l2_error = l2norm_h.assemble(u = uh) + 1
+    l2_error = l2norm_h.assemble(u = uh)
     h1_error = h1norm_h.assemble(u = uh)
     # ...
 

From 6d28291996a2831f69920ea300391e52ff0fc9ca Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Thu, 24 Oct 2024 15:24:55 +0200
Subject: [PATCH 31/35] Break test_2d_biharmonic.py

---
 psydac/api/tests/test_2d_biharmonic.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/psydac/api/tests/test_2d_biharmonic.py b/psydac/api/tests/test_2d_biharmonic.py
index 7a15bd7c3..89a215d30 100644
--- a/psydac/api/tests/test_2d_biharmonic.py
+++ b/psydac/api/tests/test_2d_biharmonic.py
@@ -104,7 +104,7 @@ def run_biharmonic_2d_dir(solution, f, dir_zero_boundary, ncells, degree, backen
     uh = equation_h.solve()
 
     # Compute error norms
-    l2_error = l2norm_h.assemble(u=uh)
+    l2_error = l2norm_h.assemble(u=uh) + 1
     h1_error = h1norm_h.assemble(u=uh)
     h2_error = h2norm_h.assemble(u=uh)
 

From 06cb2f8f8d91bfe70931014c07fc4eb4fd9d46f1 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Thu, 24 Oct 2024 16:51:30 +0200
Subject: [PATCH 32/35] Break test_2d_laplace.py

---
 psydac/api/tests/test_2d_laplace.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/psydac/api/tests/test_2d_laplace.py b/psydac/api/tests/test_2d_laplace.py
index 1a7b781e3..b1a679933 100644
--- a/psydac/api/tests/test_2d_laplace.py
+++ b/psydac/api/tests/test_2d_laplace.py
@@ -106,7 +106,7 @@ def run_laplace_2d(solution, f, dir_zero_boundary, dir_nonzero_boundary,
     uh = equation_h.solve()
 
     # Compute error norms
-    l2_error = l2norm_h.assemble(u=uh)
+    l2_error = l2norm_h.assemble(u=uh) + 1
     h1_error = h1norm_h.assemble(u=uh)
 
     return l2_error, h1_error

From 85f869d2fd36adbcdfdcbd8360576218f7947c75 Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Thu, 24 Oct 2024 17:14:32 +0200
Subject: [PATCH 33/35] Discarded --failed-first idea

All single process tests will still be run regardless
of test order; thus we don't really reduce test time.
---
 .github/workflows/continuous-integration.yml | 19 ++-----------------
 1 file changed, 2 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
index be767883e..cf1937d19 100644
--- a/.github/workflows/continuous-integration.yml
+++ b/.github/workflows/continuous-integration.yml
@@ -173,18 +173,11 @@ jobs:
           mkdir pytest
           cp mpi_tester.py pytest
 
-      - name: Restore Pytest cache
-        id: cache-pytest-restore
-        uses: actions/cache/restore@v4
-        with:
-          key: pytest-${{ matrix.os }}-${{ matrix.python-version }}-${{ hashFiles('.pytest_cache/**') }}
-          path: "./.pytest_cache"
-
       - name: Run coverage tests on macOS
         if: matrix.os == 'macos-latest'
         working-directory: ./pytest
         run: >- 
-          python -m pytest -n auto --failed-first
+          python -m pytest -n auto
           --cov psydac
           --cov-config $GITHUB_WORKSPACE/pyproject.toml
           --cov-report xml
@@ -194,7 +187,7 @@ jobs:
         if: matrix.os == 'ubuntu-latest'
         working-directory: ./pytest
         run: |
-          python -m pytest -n auto --failed-first --pyargs psydac -m "not parallel and not petsc"
+          python -m pytest -n auto --pyargs psydac -m "not parallel and not petsc"
 
       - name: Upload coverage report to Codacy
         if: matrix.os == 'macos-latest'
@@ -224,14 +217,6 @@ jobs:
         run: |
           python mpi_tester.py --mpirun="mpiexec -n 4 ${MPI_OPTS}" --pyargs psydac -m "parallel and petsc"
 
-      - name: Save Pytest cache
-        id: cache-pytest-save
-        if: always() && steps.cache-primes-restore.outputs.cache-hit != 'true'
-        uses: actions/cache/save@v4
-        with:
-          key: pytest-${{ matrix.os }}-${{ matrix.python-version }}-${{ hashFiles('.pytest_cache/**') }}
-          path: "./.pytest_cache"
-
       - name: Remove test directory
         if: always()
         run: |

From 5567cf75123edc7737d8c75487268f552217133e Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Thu, 24 Oct 2024 17:21:37 +0200
Subject: [PATCH 34/35] Fixed deliberately broken tests

---
 psydac/api/tests/test_2d_biharmonic.py | 2 +-
 psydac/api/tests/test_2d_laplace.py    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/psydac/api/tests/test_2d_biharmonic.py b/psydac/api/tests/test_2d_biharmonic.py
index 89a215d30..7a15bd7c3 100644
--- a/psydac/api/tests/test_2d_biharmonic.py
+++ b/psydac/api/tests/test_2d_biharmonic.py
@@ -104,7 +104,7 @@ def run_biharmonic_2d_dir(solution, f, dir_zero_boundary, ncells, degree, backen
     uh = equation_h.solve()
 
     # Compute error norms
-    l2_error = l2norm_h.assemble(u=uh) + 1
+    l2_error = l2norm_h.assemble(u=uh)
     h1_error = h1norm_h.assemble(u=uh)
     h2_error = h2norm_h.assemble(u=uh)
 
diff --git a/psydac/api/tests/test_2d_laplace.py b/psydac/api/tests/test_2d_laplace.py
index b1a679933..1a7b781e3 100644
--- a/psydac/api/tests/test_2d_laplace.py
+++ b/psydac/api/tests/test_2d_laplace.py
@@ -106,7 +106,7 @@ def run_laplace_2d(solution, f, dir_zero_boundary, dir_nonzero_boundary,
     uh = equation_h.solve()
 
     # Compute error norms
-    l2_error = l2norm_h.assemble(u=uh) + 1
+    l2_error = l2norm_h.assemble(u=uh)
     h1_error = h1norm_h.assemble(u=uh)
 
     return l2_error, h1_error

From a443720ba960043cba811313f98c2bae2f734c2d Mon Sep 17 00:00:00 2001
From: kvrigor <kvrigor@users.noreply.github.com>
Date: Mon, 28 Oct 2024 13:18:17 +0100
Subject: [PATCH 35/35] Declared all pytest packages as optional dependencies;
 in pyproject.toml, changed if 0 -: if False

---
 pyproject.toml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 627a8c452..9441e6be5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,8 +26,6 @@ dependencies = [
     'scipy >= 1.12',
     'sympy >= 1.5',
     'matplotlib',
-    'pytest >= 4.5',
-    'pytest-xdist >= 1.16',
     'pyyaml >= 5.1',
     'packaging',
     'pyevtk',
@@ -56,6 +54,8 @@ dependencies = [
 [project.optional-dependencies]
 test = [
     "pytest-cov >= 5.0.0",
+    'pytest >= 4.5',
+    'pytest-xdist >= 1.16',
 ]
 
 [project.urls]
@@ -99,7 +99,7 @@ exclude_also = [
     "raise NotImplementedError",
 
     # Don't complain if non-runnable code isn't run:
-    "if 0:",
+    "if False:",
     "if __name__ == .__main__.:",
 
     # Don't complain about abstract methods, they aren't run: