From b1ad9d5516c24f6124d8135809100fc257c2de77 Mon Sep 17 00:00:00 2001
From: Henrik Finsberg <henriknf@simula.no>
Date: Sat, 24 Sep 2022 19:52:05 +0200
Subject: [PATCH 01/12] Remove building docs from testing workflow since this
 is already tested in the build_docs workflow

---
 .github/workflows/test_package.yml | 34 ++++++++++--------------------
 1 file changed, 11 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/test_package.yml b/.github/workflows/test_package.yml
index a1cbc08..793968e 100644
--- a/.github/workflows/test_package.yml
+++ b/.github/workflows/test_package.yml
@@ -25,10 +25,10 @@ jobs:
     steps:
       # This action sets the current path to the root of your github repo
       - uses: actions/checkout@v3
-      
+
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.10' 
+          python-version: "3.10"
 
       - name: "Install code"
         run: pip install .[test,docs]
@@ -38,15 +38,15 @@ jobs:
 
       - name: Mypy check
         run: |
-           pip install mypy
-           python -m mypy . --exclude=build
+          pip install mypy
+          python -m mypy . --exclude=build
 
       - name: Generate coverage report
         run: python -m pytest --cov=mypackage test
 
       - name: Generate html report
         run: python -m coverage html
-           
+
       - name: Upload coverage report as artifact
         uses: actions/upload-artifact@v3
         with:
@@ -54,37 +54,25 @@ jobs:
           path: htmlcov
           if-no-files-found: error
 
-      - name: Build documentation
-        run: |
-           make doc
-
-      - name: Upload documentation
-        uses: actions/upload-artifact@v3
-        with:
-          name: documentation
-          path: docs/_build/html
-          if-no-files-found: error
-
-
   test-code:
     # This code depends on the result of check-code
     needs: check-code
     runs-on: ${{ matrix.os }}
-    
+
     strategy:
       matrix:
-        os: [ubuntu-22.04, windows-latest, macos-12]    
-    
+        os: [ubuntu-22.04, windows-latest, macos-12]
+
     steps:
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.10' 
+          python-version: "3.10"
 
       - uses: actions/checkout@v3
-    
+
       - name: "Install mypackage"
         run: pip install .[test]
 
       - name: Run tests
         run: |
-          python -m pytest test/
\ No newline at end of file
+          python -m pytest test/

From 9326fb49436fe0ae13f9f03d90cd4b1894483f8b Mon Sep 17 00:00:00 2001
From: Henrik Finsberg <henriknf@simula.no>
Date: Sat, 24 Sep 2022 19:57:48 +0200
Subject: [PATCH 02/12] Move coverage report to final step

---
 .github/workflows/test_package.yml | 23 +++++++++--------------
 1 file changed, 9 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/test_package.yml b/.github/workflows/test_package.yml
index 793968e..d76b11f 100644
--- a/.github/workflows/test_package.yml
+++ b/.github/workflows/test_package.yml
@@ -41,19 +41,6 @@ jobs:
           pip install mypy
           python -m mypy . --exclude=build
 
-      - name: Generate coverage report
-        run: python -m pytest --cov=mypackage test
-
-      - name: Generate html report
-        run: python -m coverage html
-
-      - name: Upload coverage report as artifact
-        uses: actions/upload-artifact@v3
-        with:
-          name: code-coverage-report
-          path: htmlcov
-          if-no-files-found: error
-
   test-code:
     # This code depends on the result of check-code
     needs: check-code
@@ -75,4 +62,12 @@ jobs:
 
       - name: Run tests
         run: |
-          python -m pytest test/
+          python -m pytest test --cov=mypackage --cov-report=html
+
+      - name: Upload coverage report as artifact
+        if: matrix.os == 'ubuntu-22.04'
+        uses: actions/upload-artifact@v3
+        with:
+          name: code-coverage-report
+          path: htmlcov
+          if-no-files-found: error

From 9d7d88d15e0255cb15ed307f87abbf34d37dc5bb Mon Sep 17 00:00:00 2001
From: Henrik Finsberg <henriknf@simula.no>
Date: Sat, 24 Sep 2022 20:03:47 +0200
Subject: [PATCH 03/12] Test multiple versions of python

---
 .github/workflows/test_package.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test_package.yml b/.github/workflows/test_package.yml
index d76b11f..911499a 100644
--- a/.github/workflows/test_package.yml
+++ b/.github/workflows/test_package.yml
@@ -49,14 +49,15 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-22.04, windows-latest, macos-12]
+        python-version: [3.8, 3.9, "3.10"]
 
     steps:
       - uses: actions/setup-python@v4
+      - name: Set up Python ${{ matrix.python-version }}
         with:
-          python-version: "3.10"
+          python-version: ${{ matrix.python-version }}
 
       - uses: actions/checkout@v3
-
       - name: "Install mypackage"
         run: pip install .[test]
 

From c3bccb29a3905cb8d68d88336d9bcb2b8f067cbb Mon Sep 17 00:00:00 2001
From: Henrik Finsberg <henriknf@simula.no>
Date: Sat, 24 Sep 2022 20:06:44 +0200
Subject: [PATCH 04/12] Swtich order to uses and name in workflow

---
 .github/workflows/test_package.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test_package.yml b/.github/workflows/test_package.yml
index 911499a..f94657a 100644
--- a/.github/workflows/test_package.yml
+++ b/.github/workflows/test_package.yml
@@ -52,12 +52,13 @@ jobs:
         python-version: [3.8, 3.9, "3.10"]
 
     steps:
-      - uses: actions/setup-python@v4
       - name: Set up Python ${{ matrix.python-version }}
+      - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
       - uses: actions/checkout@v3
+
       - name: "Install mypackage"
         run: pip install .[test]
 

From a611ad63e6a81729b36f6e147e5a1071126e56e9 Mon Sep 17 00:00:00 2001
From: Henrik Finsberg <henriknf@simula.no>
Date: Sat, 24 Sep 2022 20:16:37 +0200
Subject: [PATCH 05/12] Move mypy config to setup.cfg. Add config for pytest.
 Use matrix from python version in check code

---
 .github/workflows/test_package.yml | 17 ++++++++++-------
 pyproject.toml                     |  7 -------
 setup.cfg                          | 10 +++++++++-
 3 files changed, 19 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/test_package.yml b/.github/workflows/test_package.yml
index f94657a..c2bed1a 100644
--- a/.github/workflows/test_package.yml
+++ b/.github/workflows/test_package.yml
@@ -22,24 +22,27 @@ jobs:
     # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
     runs-on: ubuntu-22.04
 
+    strategy:
+      matrix:
+        python-version: [3.8, 3.9, "3.10"]
+
     steps:
       # This action sets the current path to the root of your github repo
       - uses: actions/checkout@v3
 
+      - name: Set up Python ${{ matrix.python-version }}
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: ${{ matrix.python-version }}
 
       - name: "Install code"
-        run: pip install .[test,docs]
+        run: python -m pip install .[test]
 
       - name: Flake8 code
-        run: flake8 .
+        run: python -m flake8
 
       - name: Mypy check
-        run: |
-          pip install mypy
-          python -m mypy . --exclude=build
+        run: python -m mypy
 
   test-code:
     # This code depends on the result of check-code
@@ -64,7 +67,7 @@ jobs:
 
       - name: Run tests
         run: |
-          python -m pytest test --cov=mypackage --cov-report=html
+          python -m pytest
 
       - name: Upload coverage report as artifact
         if: matrix.os == 'ubuntu-22.04'
diff --git a/pyproject.toml b/pyproject.toml
index 1a7ac36..0fec40e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -33,11 +33,4 @@ docs = [
 binder = [ # Required to interface with Binder when having a Dockerfile in root
     "jupyterlab",
     "notebook"
-]
-
-[tool.mypy]
-ignore_missing_imports = true # Does not show errors when importing untyped libraries
-exclude = [ # We only want mypy to consider files that are not generated in installing or building documentation
-    "docs/", 
-    "build/"
 ]
\ No newline at end of file
diff --git a/setup.cfg b/setup.cfg
index e8527bd..9c6d087 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,7 +1,15 @@
 # flake8 does not support pyproject.toml, see:
 # https://github.com/PyCQA/flake8/issues/234
 [flake8]
-exclude = docs
+exclude = docs,venv
 max-line-length = 100
 
+[mypy]
+files = src,test
+ignore_missing_imports = true
+exclude = docs,build
 
+[tool:pytest]
+addopts = --cov=src/mypackage --cov-report html --cov-report term-missing -v
+testpaths =
+    test
\ No newline at end of file

From 3d51dd20b46edc8266d2d9c2264cbbce633a55cb Mon Sep 17 00:00:00 2001
From: Henrik Finsberg <henriknf@simula.no>
Date: Sat, 24 Sep 2022 20:20:43 +0200
Subject: [PATCH 06/12] Remove some dashes

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

diff --git a/.github/workflows/test_package.yml b/.github/workflows/test_package.yml
index c2bed1a..b936e1e 100644
--- a/.github/workflows/test_package.yml
+++ b/.github/workflows/test_package.yml
@@ -31,7 +31,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
-      - uses: actions/setup-python@v4
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -56,7 +56,7 @@ jobs:
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
-      - uses: actions/setup-python@v4
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 

From ffb4390ce7fc6ab49988ff88da4b8c63f2cf4e41 Mon Sep 17 00:00:00 2001
From: Henrik Finsberg <henriknf@simula.no>
Date: Sat, 24 Sep 2022 20:23:25 +0200
Subject: [PATCH 07/12] Only upload artifact from coverage report for
 python3.10 on ubuntu

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

diff --git a/.github/workflows/test_package.yml b/.github/workflows/test_package.yml
index b936e1e..3ce50cf 100644
--- a/.github/workflows/test_package.yml
+++ b/.github/workflows/test_package.yml
@@ -70,7 +70,7 @@ jobs:
           python -m pytest
 
       - name: Upload coverage report as artifact
-        if: matrix.os == 'ubuntu-22.04'
+        if: matrix.os == 'ubuntu-22.04' && matrix.python-version == '3.10'
         uses: actions/upload-artifact@v3
         with:
           name: code-coverage-report

From 660ce5168d4343250337bbf24d42fdfb554e696a Mon Sep 17 00:00:00 2001
From: Henrik Finsberg <henriknf@simula.no>
Date: Sun, 25 Sep 2022 20:40:26 +0200
Subject: [PATCH 08/12] Change python version to strings

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

diff --git a/.github/workflows/test_package.yml b/.github/workflows/test_package.yml
index 3ce50cf..0f9e680 100644
--- a/.github/workflows/test_package.yml
+++ b/.github/workflows/test_package.yml
@@ -24,7 +24,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.8, 3.9, "3.10"]
+        python-version: ["3.8", "3.9", "3.10"]
 
     steps:
       # This action sets the current path to the root of your github repo
@@ -52,7 +52,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-22.04, windows-latest, macos-12]
-        python-version: [3.8, 3.9, "3.10"]
+        python-version: ["3.8", "3.9", "3.10"]
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}

From 0bb6d1ed798dfcaa4781503132f7a341e761c7e3 Mon Sep 17 00:00:00 2001
From: Henrik Finsberg <henriknf@simula.no>
Date: Sun, 25 Sep 2022 20:42:18 +0200
Subject: [PATCH 09/12] Use mypackage as cov target instead of src/mypackage -
 this would only work for editable installs

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 9c6d087..6a7c0ee 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -10,6 +10,6 @@ ignore_missing_imports = true
 exclude = docs,build
 
 [tool:pytest]
-addopts = --cov=src/mypackage --cov-report html --cov-report term-missing -v
+addopts = --cov=mypackage --cov-report html --cov-report term-missing -v
 testpaths =
     test
\ No newline at end of file

From b0a76c425324e4d7630ec7fffb82cd5efaf8d551 Mon Sep 17 00:00:00 2001
From: Henrik Finsberg <henriknf@simula.no>
Date: Sun, 25 Sep 2022 20:43:08 +0200
Subject: [PATCH 10/12] Run test CI only on push to master or PR to master

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

diff --git a/.github/workflows/test_package.yml b/.github/workflows/test_package.yml
index 0f9e680..fca1aa8 100644
--- a/.github/workflows/test_package.yml
+++ b/.github/workflows/test_package.yml
@@ -4,7 +4,7 @@ on:
   push:
     # The CI is executed on every push on every branch
     branches:
-      - "**"
+      - main
   pull_request:
     # The CI is executed on every pull request to the main branch
     branches:

From 8b6a585fa9efee26fc6d6e20c3b0e65b0c9f1f26 Mon Sep 17 00:00:00 2001
From: Henrik Finsberg <henriknf@simula.no>
Date: Sun, 25 Sep 2022 20:59:53 +0200
Subject: [PATCH 11/12] Move mypy and pytest configurations to pyproject.toml
 and flake8 configurations to .flake8

---
 .flake8        |  5 +++++
 pyproject.toml | 13 +++++++++++++
 setup.cfg      | 15 ---------------
 3 files changed, 18 insertions(+), 15 deletions(-)
 create mode 100644 .flake8
 delete mode 100644 setup.cfg

diff --git a/.flake8 b/.flake8
new file mode 100644
index 0000000..2561054
--- /dev/null
+++ b/.flake8
@@ -0,0 +1,5 @@
+# flake8 does not support pyproject.toml, see:
+# https://github.com/PyCQA/flake8/issues/234
+[flake8]
+exclude = docs,venv
+max-line-length = 100
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 0fec40e..732f618 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -33,4 +33,17 @@ docs = [
 binder = [ # Required to interface with Binder when having a Dockerfile in root
     "jupyterlab",
     "notebook"
+]
+
+[tool.mypy]
+ignore_missing_imports = true # Does not show errors when importing untyped libraries
+exclude = [ # We only want mypy to consider files that are not generated in installing or building documentation
+    "docs/", 
+    "build/"
+]
+
+[tool.pytest.ini_options]
+addopts = "--cov=mypackage --cov-report html --cov-report term-missing -v"
+testpaths = [
+    "test"
 ]
\ No newline at end of file
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 6a7c0ee..0000000
--- a/setup.cfg
+++ /dev/null
@@ -1,15 +0,0 @@
-# flake8 does not support pyproject.toml, see:
-# https://github.com/PyCQA/flake8/issues/234
-[flake8]
-exclude = docs,venv
-max-line-length = 100
-
-[mypy]
-files = src,test
-ignore_missing_imports = true
-exclude = docs,build
-
-[tool:pytest]
-addopts = --cov=mypackage --cov-report html --cov-report term-missing -v
-testpaths =
-    test
\ No newline at end of file

From ee2a7e792fa7ddfe554e1b1ff408aea999263eea Mon Sep 17 00:00:00 2001
From: Henrik Finsberg <henriknf@simula.no>
Date: Sun, 25 Sep 2022 21:02:27 +0200
Subject: [PATCH 12/12] Add list of folders to be checked by mypy

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

diff --git a/pyproject.toml b/pyproject.toml
index 732f618..a2c21b8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -41,6 +41,10 @@ exclude = [ # We only want mypy to consider files that are not generated in inst
     "docs/", 
     "build/"
 ]
+files = [  # Folder to which files that should be checked by mypy
+    "src",
+    "test"
+]
 
 [tool.pytest.ini_options]
 addopts = "--cov=mypackage --cov-report html --cov-report term-missing -v"