From f375360f64d222b36cf63850b5f05342ccb5fa4a Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 30 Aug 2024 11:19:11 -0400
Subject: [PATCH 01/25] add pyproject.toml

---
 pyproject.toml          | 17 +++++++++++++++++
 python/requirements.txt |  4 +++-
 2 files changed, 20 insertions(+), 1 deletion(-)
 create mode 100644 pyproject.toml

diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 000000000..f1b097368
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,17 @@
+[tool.ruff]
+include = ["python/*.py"]
+exclude = ["python/react-series-data-viewer"]
+line-length = 120
+preview = true
+
+[tool.ruff.lint]
+ignore = ["E202", "E203", "E221", "E241", "E251", "E272"]
+# TODO: Add and apply "F", "I", "N", "UP"
+select = ["E", "W"]
+
+[tool.pyright]
+include = ["python"]
+exclude = ["python/react-series-data-viewer"]
+
+[tool.pytest.ini-options]
+testpaths = ["python/tests"]
diff --git a/python/requirements.txt b/python/requirements.txt
index 0d1abe193..9e5eaa6ed 100644
--- a/python/requirements.txt
+++ b/python/requirements.txt
@@ -1,5 +1,4 @@
 boto3
-flake8
 google
 mat73
 matplotlib
@@ -13,7 +12,10 @@ nose
 numpy
 protobuf>=3.0.0
 pybids==0.17.0
+pyright
+pytest
 python-dateutil
+ruff
 scikit-learn
 scipy
 sqlalchemy>=2.0.0

From b8727caf11c142e168bee7f7a5917724d4bc23cf Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 30 Aug 2024 11:21:27 -0400
Subject: [PATCH 02/25] keep flake8 (for now)

---
 python/requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/python/requirements.txt b/python/requirements.txt
index 9e5eaa6ed..9f258ee1b 100644
--- a/python/requirements.txt
+++ b/python/requirements.txt
@@ -1,4 +1,5 @@
 boto3
+flake8
 google
 mat73
 matplotlib

From 4cc3bae5d69f110661c07049acfd50cb76979a1c Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Tue, 3 Sep 2024 10:52:17 -0400
Subject: [PATCH 03/25] double type checking

---
 pyproject.toml           | 24 +++++++++++++++++++++++-
 python/lib/db/connect.py |  2 +-
 python/requirements.txt  |  1 +
 3 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index f1b097368..235685c6c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,12 +6,34 @@ preview = true
 
 [tool.ruff.lint]
 ignore = ["E202", "E203", "E221", "E241", "E251", "E272"]
-# TODO: Add and apply "F", "I", "N", "UP"
+# TODO: Select "F", "I", "N", "UP" and format the codebase accordingly.
 select = ["E", "W"]
 
+# We use Mypy to type check modern (typed) modules, and run a few Pyright-specific type checks on
+# all code including untyped modules. We could also run a few Mypy type checks on untyped code in
+# addition to the typed modules but configuring this behaviour is a little awkward at the time of
+# this comment (Mypy 1.11.2).
+
+[tool.mypy]
+files = "python"
+exclude = "python/react-series-data-viewer"
+ignore_errors = true
+
+[[tool.mypy.overrides]]
+module = [
+    "lib.db.*",
+    "lib.exception.*",
+    "lib.dataclass.*",
+]
+ignore_errors = false
+strict = true
+
 [tool.pyright]
 include = ["python"]
 exclude = ["python/react-series-data-viewer"]
+typeCheckingMode = "off"
+reportDeprecated = "error"
+reportMissingImports = "error"
 
 [tool.pytest.ini-options]
 testpaths = ["python/tests"]
diff --git a/python/lib/db/connect.py b/python/lib/db/connect.py
index a58912f0f..0e2d406be 100644
--- a/python/lib/db/connect.py
+++ b/python/lib/db/connect.py
@@ -6,7 +6,7 @@
 default_port = 3306
 
 
-def connect_to_db(credentials: dict[str, Any]):
+def connect_to_db(credentials: dict[str, Any]) -> Session:
     host     = credentials['host']
     port     = credentials['port']
     username = credentials['username']
diff --git a/python/requirements.txt b/python/requirements.txt
index 9f258ee1b..80ef36b70 100644
--- a/python/requirements.txt
+++ b/python/requirements.txt
@@ -5,6 +5,7 @@ mat73
 matplotlib
 mne
 mne-bids>=0.6
+mypy
 mysql-connector
 mysqlclient
 nilearn

From 6feea527ae9001f6745986af7a2952eb381b862a Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Wed, 4 Sep 2024 11:27:22 -0400
Subject: [PATCH 04/25] Use Pyright as main type checker

---
 pyproject.toml           | 33 ++++++++++-----------------------
 python/lib/db/connect.py |  2 +-
 python/requirements.txt  |  1 -
 test/pyrightconfig.json  |  9 +++++++++
 4 files changed, 20 insertions(+), 25 deletions(-)
 create mode 100644 test/pyrightconfig.json

diff --git a/pyproject.toml b/pyproject.toml
index 235685c6c..2d09b6937 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,31 +9,18 @@ ignore = ["E202", "E203", "E221", "E241", "E251", "E272"]
 # TODO: Select "F", "I", "N", "UP" and format the codebase accordingly.
 select = ["E", "W"]
 
-# We use Mypy to type check modern (typed) modules, and run a few Pyright-specific type checks on
-# all code including untyped modules. We could also run a few Mypy type checks on untyped code in
-# addition to the typed modules but configuring this behaviour is a little awkward at the time of
-# this comment (Mypy 1.11.2).
-
-[tool.mypy]
-files = "python"
-exclude = "python/react-series-data-viewer"
-ignore_errors = true
-
-[[tool.mypy.overrides]]
-module = [
-    "lib.db.*",
-    "lib.exception.*",
-    "lib.dataclass.*",
-]
-ignore_errors = false
-strict = true
+# The strict type checking configuration is used to type check only the modern (typed) modules. An
+# additional basic type checking configuration to type check legacy modules can be found in the
+# `test` directory.
 
 [tool.pyright]
-include = ["python"]
-exclude = ["python/react-series-data-viewer"]
-typeCheckingMode = "off"
-reportDeprecated = "error"
-reportMissingImports = "error"
+include = [
+    "python/lib/db",
+    "python/lib/exception",
+    "python/lib/validate_subject_ids.py"
+]
+typeCheckingMode = "strict"
+reportMissingTypeStubs = "none"
 
 [tool.pytest.ini-options]
 testpaths = ["python/tests"]
diff --git a/python/lib/db/connect.py b/python/lib/db/connect.py
index 0e2d406be..a58912f0f 100644
--- a/python/lib/db/connect.py
+++ b/python/lib/db/connect.py
@@ -6,7 +6,7 @@
 default_port = 3306
 
 
-def connect_to_db(credentials: dict[str, Any]) -> Session:
+def connect_to_db(credentials: dict[str, Any]):
     host     = credentials['host']
     port     = credentials['port']
     username = credentials['username']
diff --git a/python/requirements.txt b/python/requirements.txt
index 80ef36b70..9f258ee1b 100644
--- a/python/requirements.txt
+++ b/python/requirements.txt
@@ -5,7 +5,6 @@ mat73
 matplotlib
 mne
 mne-bids>=0.6
-mypy
 mysql-connector
 mysqlclient
 nilearn
diff --git a/test/pyrightconfig.json b/test/pyrightconfig.json
new file mode 100644
index 000000000..cabc7dec9
--- /dev/null
+++ b/test/pyrightconfig.json
@@ -0,0 +1,9 @@
+// Global Pyright configuration used to check all Python code.
+// It is a very lax configuration as it must work even on untyped code.
+{
+    "include": ["../python"],
+    "exclude": ["../python/react-series-data-viewer"],
+    "typeCheckingMode": "off",
+    "reportDeprecated": "error",
+    "reportMissingImports": "error"
+}

From 6a79f7ccbc6c1e029de1c71bf5145205c56ec3fb Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Wed, 4 Sep 2024 12:48:43 -0400
Subject: [PATCH 05/25] remove comment

---
 test/pyrightconfig.json | 2 --
 1 file changed, 2 deletions(-)

diff --git a/test/pyrightconfig.json b/test/pyrightconfig.json
index cabc7dec9..69c890f86 100644
--- a/test/pyrightconfig.json
+++ b/test/pyrightconfig.json
@@ -1,5 +1,3 @@
-// Global Pyright configuration used to check all Python code.
-// It is a very lax configuration as it must work even on untyped code.
 {
     "include": ["../python"],
     "exclude": ["../python/react-series-data-viewer"],

From 2d639f8b385f573d51a674c256866a4c6947f82a Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 09:53:10 -0400
Subject: [PATCH 06/25] test

---
 .github/workflows/flake8_python_linter.yml | 42 -----------------
 .github/workflows/python.yml               | 54 ++++++++++++++++++++++
 2 files changed, 54 insertions(+), 42 deletions(-)
 delete mode 100644 .github/workflows/flake8_python_linter.yml
 create mode 100644 .github/workflows/python.yml

diff --git a/.github/workflows/flake8_python_linter.yml b/.github/workflows/flake8_python_linter.yml
deleted file mode 100644
index 3c52466ca..000000000
--- a/.github/workflows/flake8_python_linter.yml
+++ /dev/null
@@ -1,42 +0,0 @@
-# This workflow runs flake8 with reviewdog. The documentation can be found below:
-# https://github.com/marketplace/actions/run-flake8-with-reviewdog
-# Flake8 is a Python linter that analyzes code and checks for programming and stylistic errors
-name: Flake8 Linter
-
-# This workflow acts only on pull requests
-on: pull_request
-
-jobs:
-
-  flake8-lint:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.11", "3.12"]
-    
-    steps:
-      - name: Check out source repository
-        uses: actions/checkout@v2
-
-      - name: Set up Python environment
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-      
-      - name: Flake8 Lint
-        uses: reviewdog/action-flake8@v3
-        with:
-          # For more flake 8 arguments, visit the link below:
-          # https://flake8.pycqa.org/en/latest/user/options.html
-          # Currently, flake8 ignores the following;
-          #     E202: Whitespace before ')'
-          #     E203: Whitespace before ':'
-          #     E221: Multiple spaces before operator
-          #     E241: Multiple spaces after ','
-          #     E251: Unexpected spaces around keyword / parameter equals
-          #     E272: Multiple spaces before keyword
-          flake8_args: "--ignore=W503,E202,E203,E221,E241,E251,E272,E126,E131,E121,E111,E127
-                        --max-line-length 120
-                        --exclude python/react-series-data-viewer/protocol_buffers/
-                        --exclude Loris "
-          github_token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
new file mode 100644
index 000000000..75afad511
--- /dev/null
+++ b/.github/workflows/python.yml
@@ -0,0 +1,54 @@
+# This workflow runs flake8 with reviewdog. The documentation can be found below:
+# https://github.com/marketplace/actions/run-flake8-with-reviewdog
+# Flake8 is a Python linter that analyzes code and checks for programming and stylistic errors
+name: Flake8 Linter
+
+# This workflow acts only on pull requests
+on: pull_request
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12"]
+
+    steps:
+    - name: Check out source repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python environment
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install Python dependencies
+      run: pip install -r python/requirements.txt
+
+  ruff:
+    runs-on: ubuntu-latest
+    needs: setup
+
+    steps:
+      - name: Run Ruff
+        run: ruff check
+
+  pyright-strict:
+    runs-on: ubuntu-latest
+    needs: setup
+
+    steps:
+    - name: Run Pyright
+      run: pyright
+
+  pyright-loose:
+    runs-on: ubuntu-latest
+    needs: setup
+
+    steps:
+    - name: Run Pyright
+      run: |
+        cd test
+        pyright

From 42b0187a6dad830e8987693c2ce2b7ac371edfb0 Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 09:59:50 -0400
Subject: [PATCH 07/25] test

---
 .github/workflows/python.yml | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 75afad511..609920917 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -1,10 +1,8 @@
-# This workflow runs flake8 with reviewdog. The documentation can be found below:
-# https://github.com/marketplace/actions/run-flake8-with-reviewdog
-# Flake8 is a Python linter that analyzes code and checks for programming and stylistic errors
-name: Flake8 Linter
+name: Python checks
 
-# This workflow acts only on pull requests
-on: pull_request
+on:
+  - push
+  - pull_request
 
 jobs:
 

From e7e531e5bb278ead444bfc89f0ed562983dbb5a2 Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 11:31:12 -0400
Subject: [PATCH 08/25] change configuration

---
 .github/workflows/python.yml | 55 +++++++++++++++++++++++++++---------
 python/requirements.txt      |  1 -
 test/pyrightconfig.json      |  2 +-
 3 files changed, 43 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 609920917..6835e4f1a 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -6,7 +6,8 @@ on:
 
 jobs:
 
-  setup:
+  ruff:
+    name: "Ruff"
     runs-on: ubuntu-latest
 
     strategy:
@@ -14,38 +15,66 @@ jobs:
         python-version: ["3.11", "3.12"]
 
     steps:
-    - name: Check out source repository
+    - name: Check out LORIS-MRI
       uses: actions/checkout@v4
 
-    - name: Set up Python environment
+    - name: Set up the Python environment
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+        cache: 'pip'
 
     - name: Install Python dependencies
       run: pip install -r python/requirements.txt
 
-  ruff:
-    runs-on: ubuntu-latest
-    needs: setup
-
-    steps:
-      - name: Run Ruff
-        run: ruff check
+    - name: Run Ruff
+      run: ruff check
 
   pyright-strict:
+    name: "Pyright strict"
     runs-on: ubuntu-latest
-    needs: setup
+
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12"]
 
     steps:
+    - name: Check out LORIS-MRI
+      uses: actions/checkout@v4
+
+    - name: Set up the Python environment
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+
+    - name: Install Python dependencies
+      run: pip install -r python/requirements.txt
+
     - name: Run Pyright
       run: pyright
 
-  pyright-loose:
+  pyrigh-global:
+    name: "Pyright global"
     runs-on: ubuntu-latest
-    needs: setup
+
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12"]
 
     steps:
+    - name: Check out LORIS-MRI
+      uses: actions/checkout@v4
+
+    - name: Set up the Python environment
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+
+    - name: Install Python dependencies
+      run: pip install -r python/requirements.txt
+
     - name: Run Pyright
       run: |
         cd test
diff --git a/python/requirements.txt b/python/requirements.txt
index 9f258ee1b..9e5eaa6ed 100644
--- a/python/requirements.txt
+++ b/python/requirements.txt
@@ -1,5 +1,4 @@
 boto3
-flake8
 google
 mat73
 matplotlib
diff --git a/test/pyrightconfig.json b/test/pyrightconfig.json
index 69c890f86..b9189aa38 100644
--- a/test/pyrightconfig.json
+++ b/test/pyrightconfig.json
@@ -2,6 +2,6 @@
     "include": ["../python"],
     "exclude": ["../python/react-series-data-viewer"],
     "typeCheckingMode": "off",
-    "reportDeprecated": "error",
+    "reportDeprecated": "warning",
     "reportMissingImports": "error"
 }

From 8011638e0589ab9a44667902084051715a10c38b Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 11:38:28 -0400
Subject: [PATCH 09/25] add python environment variables

---
 .github/workflows/python.yml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 6835e4f1a..ffad7b65c 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -27,6 +27,9 @@ jobs:
     - name: Install Python dependencies
       run: pip install -r python/requirements.txt
 
+    - name: Set up environment variables
+      run: export PYTHONPATH=$PYTHONPATH:/`pwd`/python:/`pwd`/python/react-series-data-viewer
+
     - name: Run Ruff
       run: ruff check
 
@@ -51,6 +54,9 @@ jobs:
     - name: Install Python dependencies
       run: pip install -r python/requirements.txt
 
+    - name: Set up Python environment variables
+      run: export PYTHONPATH=$PYTHONPATH:/`pwd`/python:/`pwd`/python/react-series-data-viewer
+
     - name: Run Pyright
       run: pyright
 
@@ -75,6 +81,9 @@ jobs:
     - name: Install Python dependencies
       run: pip install -r python/requirements.txt
 
+    - name: Set up Python environment variables
+      run: export PYTHONPATH=$PYTHONPATH:/`pwd`/python:/`pwd`/python/react-series-data-viewer
+
     - name: Run Pyright
       run: |
         cd test

From d4673ab7f5c223f698ff96b50cee073d9bd7aac2 Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 11:51:21 -0400
Subject: [PATCH 10/25] try factorization

---
 .github/actions/setup-python.yml              | 21 ++++++++++++
 .../{python.yml => python-checks.yml}         | 33 ++++---------------
 2 files changed, 27 insertions(+), 27 deletions(-)
 create mode 100644 .github/actions/setup-python.yml
 rename .github/workflows/{python.yml => python-checks.yml} (51%)

diff --git a/.github/actions/setup-python.yml b/.github/actions/setup-python.yml
new file mode 100644
index 000000000..000ef0a20
--- /dev/null
+++ b/.github/actions/setup-python.yml
@@ -0,0 +1,21 @@
+name: Set up Python
+input:
+inputs:
+  python-version:
+    required: true
+
+runs:
+  using: composite
+
+  steps:
+  - name: Set up the Python environment
+    uses: actions/setup-python@v5
+    with:
+      python-version: ${{ matrix.python-version }}
+      cache: 'pip'
+
+  - name: Install Python dependencies
+    run: pip install -r python/requirements.txt
+
+  - name: Set up environment variables
+    run: export PYTHONPATH=$PYTHONPATH:/`pwd`/python:/`pwd`/python/react-series-data-viewer
diff --git a/.github/workflows/python.yml b/.github/workflows/python-checks.yml
similarity index 51%
rename from .github/workflows/python.yml
rename to .github/workflows/python-checks.yml
index ffad7b65c..cc99004be 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python-checks.yml
@@ -18,17 +18,10 @@ jobs:
     - name: Check out LORIS-MRI
       uses: actions/checkout@v4
 
-    - name: Set up the Python environment
-      uses: actions/setup-python@v5
+    - name: Set up Python
+      uses: setup-python
       with:
         python-version: ${{ matrix.python-version }}
-        cache: 'pip'
-
-    - name: Install Python dependencies
-      run: pip install -r python/requirements.txt
-
-    - name: Set up environment variables
-      run: export PYTHONPATH=$PYTHONPATH:/`pwd`/python:/`pwd`/python/react-series-data-viewer
 
     - name: Run Ruff
       run: ruff check
@@ -45,17 +38,10 @@ jobs:
     - name: Check out LORIS-MRI
       uses: actions/checkout@v4
 
-    - name: Set up the Python environment
-      uses: actions/setup-python@v5
+    - name: Set up Python
+      uses: setup-python
       with:
         python-version: ${{ matrix.python-version }}
-        cache: 'pip'
-
-    - name: Install Python dependencies
-      run: pip install -r python/requirements.txt
-
-    - name: Set up Python environment variables
-      run: export PYTHONPATH=$PYTHONPATH:/`pwd`/python:/`pwd`/python/react-series-data-viewer
 
     - name: Run Pyright
       run: pyright
@@ -72,17 +58,10 @@ jobs:
     - name: Check out LORIS-MRI
       uses: actions/checkout@v4
 
-    - name: Set up the Python environment
-      uses: actions/setup-python@v5
+    - name: Set up Python
+      uses: setup-python
       with:
         python-version: ${{ matrix.python-version }}
-        cache: 'pip'
-
-    - name: Install Python dependencies
-      run: pip install -r python/requirements.txt
-
-    - name: Set up Python environment variables
-      run: export PYTHONPATH=$PYTHONPATH:/`pwd`/python:/`pwd`/python/react-series-data-viewer
 
     - name: Run Pyright
       run: |

From a163069388476cc7bbeeca1bc15ae14132cc1acc Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 11:57:51 -0400
Subject: [PATCH 11/25] test

---
 .github/workflows/loristest.yml     | 4 +---
 .github/workflows/python-checks.yml | 7 +++----
 2 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/loristest.yml b/.github/workflows/loristest.yml
index 1937f107b..e033c7c5b 100644
--- a/.github/workflows/loristest.yml
+++ b/.github/workflows/loristest.yml
@@ -1,8 +1,6 @@
 name: LORIS Test Suite
 
-on:
-  - push
-  - pull_request
+on: workflow_dispatch
 
 jobs:
   docker:
diff --git a/.github/workflows/python-checks.yml b/.github/workflows/python-checks.yml
index cc99004be..59cdddae9 100644
--- a/.github/workflows/python-checks.yml
+++ b/.github/workflows/python-checks.yml
@@ -5,7 +5,6 @@ on:
   - pull_request
 
 jobs:
-
   ruff:
     name: "Ruff"
     runs-on: ubuntu-latest
@@ -19,7 +18,7 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: setup-python
+      uses: ./.github/actions/setup-python.yml
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -39,7 +38,7 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: setup-python
+      uses: ./.github/actions/setup-python.yml
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -59,7 +58,7 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: setup-python
+      uses: ./.github/actions/setup-python.yml
       with:
         python-version: ${{ matrix.python-version }}
 

From 1e4e94a5a2b23ac05ba66e85733801918e73f246 Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 11:59:52 -0400
Subject: [PATCH 12/25] test

---
 .../actions/{setup-python.yml => setup-python/action.yml}   | 0
 .github/workflows/python-checks.yml                         | 6 +++---
 2 files changed, 3 insertions(+), 3 deletions(-)
 rename .github/actions/{setup-python.yml => setup-python/action.yml} (100%)

diff --git a/.github/actions/setup-python.yml b/.github/actions/setup-python/action.yml
similarity index 100%
rename from .github/actions/setup-python.yml
rename to .github/actions/setup-python/action.yml
diff --git a/.github/workflows/python-checks.yml b/.github/workflows/python-checks.yml
index 59cdddae9..43d06068a 100644
--- a/.github/workflows/python-checks.yml
+++ b/.github/workflows/python-checks.yml
@@ -18,7 +18,7 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: ./.github/actions/setup-python.yml
+      uses: ./.github/actions/setup-python
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -38,7 +38,7 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: ./.github/actions/setup-python.yml
+      uses: ./.github/actions/setup-python
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -58,7 +58,7 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: ./.github/actions/setup-python.yml
+      uses: ./.github/actions/setup-python
       with:
         python-version: ${{ matrix.python-version }}
 

From 43cda038d99b09a25c88830d3daa77f4fe98ee0a Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 12:03:22 -0400
Subject: [PATCH 13/25] test

---
 .github/actions/setup-python/action.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/actions/setup-python/action.yml b/.github/actions/setup-python/action.yml
index 000ef0a20..c152a9782 100644
--- a/.github/actions/setup-python/action.yml
+++ b/.github/actions/setup-python/action.yml
@@ -16,6 +16,8 @@ runs:
 
   - name: Install Python dependencies
     run: pip install -r python/requirements.txt
+    shell: bash
 
   - name: Set up environment variables
     run: export PYTHONPATH=$PYTHONPATH:/`pwd`/python:/`pwd`/python/react-series-data-viewer
+    shell: bash

From 88e9c19d756b53bb58e82a854c442060e2bcd960 Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 12:11:20 -0400
Subject: [PATCH 14/25] test

---
 .github/actions/setup-python/action.yml | 2 +-
 .github/workflows/python-checks.yml     | 3 +++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/actions/setup-python/action.yml b/.github/actions/setup-python/action.yml
index c152a9782..921d96b61 100644
--- a/.github/actions/setup-python/action.yml
+++ b/.github/actions/setup-python/action.yml
@@ -19,5 +19,5 @@ runs:
     shell: bash
 
   - name: Set up environment variables
-    run: export PYTHONPATH=$PYTHONPATH:/`pwd`/python:/`pwd`/python/react-series-data-viewer
+    run: echo PYTHONPATH=$PYTHONPATH:/`pwd`/python:/`pwd`/python/react-series-data-viewer >> $GITHUB_ENV
     shell: bash
diff --git a/.github/workflows/python-checks.yml b/.github/workflows/python-checks.yml
index 43d06068a..872928be8 100644
--- a/.github/workflows/python-checks.yml
+++ b/.github/workflows/python-checks.yml
@@ -22,6 +22,9 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Print Python path
+      run: echo $PYTHON_PATH
+
     - name: Run Ruff
       run: ruff check
 

From c5bbd9e9504948f118af34cdcdc9576b5ab56a62 Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 12:18:16 -0400
Subject: [PATCH 15/25] remove temporary things

---
 .github/workflows/loristest.yml     | 4 +++-
 .github/workflows/python-checks.yml | 3 ---
 pyproject.toml                      | 2 +-
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/loristest.yml b/.github/workflows/loristest.yml
index e033c7c5b..1937f107b 100644
--- a/.github/workflows/loristest.yml
+++ b/.github/workflows/loristest.yml
@@ -1,6 +1,8 @@
 name: LORIS Test Suite
 
-on: workflow_dispatch
+on:
+  - push
+  - pull_request
 
 jobs:
   docker:
diff --git a/.github/workflows/python-checks.yml b/.github/workflows/python-checks.yml
index 872928be8..43d06068a 100644
--- a/.github/workflows/python-checks.yml
+++ b/.github/workflows/python-checks.yml
@@ -22,9 +22,6 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Print Python path
-      run: echo $PYTHON_PATH
-
     - name: Run Ruff
       run: ruff check
 
diff --git a/pyproject.toml b/pyproject.toml
index 2d09b6937..bc66769a8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,5 @@
 [tool.ruff]
-include = ["python/*.py"]
+include = ["python/**/*.py"]
 exclude = ["python/react-series-data-viewer"]
 line-length = 120
 preview = true

From e53ea49d29feed5cdb225803f96731ba5a697ba6 Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 12:21:55 -0400
Subject: [PATCH 16/25] test ruff error

---
 python/lib/bidsreader.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/python/lib/bidsreader.py b/python/lib/bidsreader.py
index 8ccedb3ec..81082a98a 100755
--- a/python/lib/bidsreader.py
+++ b/python/lib/bidsreader.py
@@ -21,6 +21,7 @@
 __license__ = "GPLv3"
 
 
+
 class BidsReader:
     """
     This class reads a BIDS structure into a data dictionary using BIDS grabbids.

From 954a584ad0ea240c9ae214bd7266e8e15904473f Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 12:26:14 -0400
Subject: [PATCH 17/25] ruff output github

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

diff --git a/.github/workflows/python-checks.yml b/.github/workflows/python-checks.yml
index 43d06068a..672df5835 100644
--- a/.github/workflows/python-checks.yml
+++ b/.github/workflows/python-checks.yml
@@ -23,7 +23,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     - name: Run Ruff
-      run: ruff check
+      run: ruff check --output-format=github
 
   pyright-strict:
     name: "Pyright strict"

From b309b97e6c632155eac2c0734254c384ca67ddac Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 12:29:03 -0400
Subject: [PATCH 18/25] further test errors

---
 .github/workflows/python-checks.yml | 4 ++--
 python/lib/db/base.py               | 3 +++
 python/lib/imaging_io.py            | 1 +
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-checks.yml b/.github/workflows/python-checks.yml
index 672df5835..6fc0ce21b 100644
--- a/.github/workflows/python-checks.yml
+++ b/.github/workflows/python-checks.yml
@@ -43,7 +43,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     - name: Run Pyright
-      run: pyright
+      run: pyright --outputjson
 
   pyrigh-global:
     name: "Pyright global"
@@ -65,4 +65,4 @@ jobs:
     - name: Run Pyright
       run: |
         cd test
-        pyright
+        pyright --outputjson
diff --git a/python/lib/db/base.py b/python/lib/db/base.py
index 7d23cab17..55e0736a1 100644
--- a/python/lib/db/base.py
+++ b/python/lib/db/base.py
@@ -1,6 +1,9 @@
 from sqlalchemy.orm import DeclarativeBase
 
 
+a: int = "Hello"
+
+
 class Base(DeclarativeBase):
     """
     Base SQLAlchemy class that must be inherited by all the ORM model classes.
diff --git a/python/lib/imaging_io.py b/python/lib/imaging_io.py
index ed048aafb..6aed0d175 100644
--- a/python/lib/imaging_io.py
+++ b/python/lib/imaging_io.py
@@ -5,6 +5,7 @@
 import os
 import sys
 from lib.exitcode import COPY_FAILURE
+import b
 
 """Set of io functions."""
 

From d0b07b13a9cd937b8e046041ceef9a16edece6d8 Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 12:37:39 -0400
Subject: [PATCH 19/25] test pyright output github

---
 .github/workflows/python-checks.yml | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-checks.yml b/.github/workflows/python-checks.yml
index 6fc0ce21b..58136fa49 100644
--- a/.github/workflows/python-checks.yml
+++ b/.github/workflows/python-checks.yml
@@ -43,7 +43,11 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     - name: Run Pyright
-      run: pyright --outputjson
+      run: |
+        pyright --outputjson > pyright-output.json
+        cat pyright-output.json \
+          | jq -r '.generalDiagnostics[] \
+          | "::error file=\(.file),line=\(.range.start.line),col=\(.range.start.character)::\(.message)"'
 
   pyrigh-global:
     name: "Pyright global"
@@ -65,4 +69,7 @@ jobs:
     - name: Run Pyright
       run: |
         cd test
-        pyright --outputjson
+        pyright --outputjson > pyright-output.json
+        cat pyright-output.json \
+          | jq -r '.generalDiagnostics[] \
+          | "::error file=\(.file),line=\(.range.start.line),col=\(.range.start.character)::\(.message)"'

From 833d532faff7f58297e990c902fec5a66d3e47a8 Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 12:43:37 -0400
Subject: [PATCH 20/25] test

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

diff --git a/.github/workflows/python-checks.yml b/.github/workflows/python-checks.yml
index 58136fa49..3963b3628 100644
--- a/.github/workflows/python-checks.yml
+++ b/.github/workflows/python-checks.yml
@@ -44,7 +44,7 @@ jobs:
 
     - name: Run Pyright
       run: |
-        pyright --outputjson > pyright-output.json
+        pyright --outputjson > pyright-output.json || true
         cat pyright-output.json \
           | jq -r '.generalDiagnostics[] \
           | "::error file=\(.file),line=\(.range.start.line),col=\(.range.start.character)::\(.message)"'
@@ -69,7 +69,7 @@ jobs:
     - name: Run Pyright
       run: |
         cd test
-        pyright --outputjson > pyright-output.json
+        pyright --outputjson > pyright-output.json || true
         cat pyright-output.json \
           | jq -r '.generalDiagnostics[] \
           | "::error file=\(.file),line=\(.range.start.line),col=\(.range.start.character)::\(.message)"'

From 69580b5e04f28627de0a5cc5f687052f3af564a5 Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 12:45:55 -0400
Subject: [PATCH 21/25] test

---
 .github/workflows/python-checks.yml | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/python-checks.yml b/.github/workflows/python-checks.yml
index 3963b3628..24c7d8ddb 100644
--- a/.github/workflows/python-checks.yml
+++ b/.github/workflows/python-checks.yml
@@ -45,9 +45,7 @@ jobs:
     - name: Run Pyright
       run: |
         pyright --outputjson > pyright-output.json || true
-        cat pyright-output.json \
-          | jq -r '.generalDiagnostics[] \
-          | "::error file=\(.file),line=\(.range.start.line),col=\(.range.start.character)::\(.message)"'
+        cat pyright-output.json | jq -r '.generalDiagnostics[] | "::error file=\(.file),line=\(.range.start.line),col=\(.range.start.character)::\(.message)"'
 
   pyrigh-global:
     name: "Pyright global"
@@ -70,6 +68,4 @@ jobs:
       run: |
         cd test
         pyright --outputjson > pyright-output.json || true
-        cat pyright-output.json \
-          | jq -r '.generalDiagnostics[] \
-          | "::error file=\(.file),line=\(.range.start.line),col=\(.range.start.character)::\(.message)"'
+        cat pyright-output.json | jq -r '.generalDiagnostics[] | "::error file=\(.file),line=\(.range.start.line),col=\(.range.start.character)::\(.message)"'

From a5558db8a00ce0e9c05f50c73193c4bd90d6a3d5 Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 12:58:12 -0400
Subject: [PATCH 22/25] test

---
 .github/workflows/python-checks.yml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/python-checks.yml b/.github/workflows/python-checks.yml
index 24c7d8ddb..35796c7ae 100644
--- a/.github/workflows/python-checks.yml
+++ b/.github/workflows/python-checks.yml
@@ -42,10 +42,12 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
+      # Like in the other run Pyrihgt step, the `jq` arcane is used to format the errors to the
+      # GitHub actions format
     - name: Run Pyright
       run: |
-        pyright --outputjson > pyright-output.json || true
-        cat pyright-output.json | jq -r '.generalDiagnostics[] | "::error file=\(.file),line=\(.range.start.line),col=\(.range.start.character)::\(.message)"'
+        pyright --outputjson | jq -r '.generalDiagnostics[] | "::error file=\(.file),line=\(.range.start.line),col=\(.range.start.character)::\(.message)"'
+        (exit ${PIPESTATUS[0]})
 
   pyrigh-global:
     name: "Pyright global"
@@ -67,5 +69,5 @@ jobs:
     - name: Run Pyright
       run: |
         cd test
-        pyright --outputjson > pyright-output.json || true
-        cat pyright-output.json | jq -r '.generalDiagnostics[] | "::error file=\(.file),line=\(.range.start.line),col=\(.range.start.character)::\(.message)"'
+        pyright --outputjson | jq -r '.generalDiagnostics[] | "::error file=\(.file),line=\(.range.start.line),col=\(.range.start.character)::\(.message)"'
+        (exit ${PIPESTATUS[0]})

From 78729df7926debef55bd13f3742208f5c4e5268a Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 13:04:55 -0400
Subject: [PATCH 23/25] change comment

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

diff --git a/.github/workflows/python-checks.yml b/.github/workflows/python-checks.yml
index 35796c7ae..a9bcdc4e7 100644
--- a/.github/workflows/python-checks.yml
+++ b/.github/workflows/python-checks.yml
@@ -42,7 +42,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-      # Like in the other run Pyrihgt step, the `jq` arcane is used to format the errors to the
+      # Like in the other Pyrihgt run, the `jq` arcane is used to translate the errors to the
       # GitHub actions format
     - name: Run Pyright
       run: |

From 99d5ce681513530b996298bbddd230f115b2c87d Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 13:05:36 -0400
Subject: [PATCH 24/25] remove test errors

---
 python/lib/bidsreader.py | 1 -
 python/lib/db/base.py    | 3 ---
 python/lib/imaging_io.py | 1 -
 3 files changed, 5 deletions(-)

diff --git a/python/lib/bidsreader.py b/python/lib/bidsreader.py
index 81082a98a..8ccedb3ec 100755
--- a/python/lib/bidsreader.py
+++ b/python/lib/bidsreader.py
@@ -21,7 +21,6 @@
 __license__ = "GPLv3"
 
 
-
 class BidsReader:
     """
     This class reads a BIDS structure into a data dictionary using BIDS grabbids.
diff --git a/python/lib/db/base.py b/python/lib/db/base.py
index 55e0736a1..7d23cab17 100644
--- a/python/lib/db/base.py
+++ b/python/lib/db/base.py
@@ -1,9 +1,6 @@
 from sqlalchemy.orm import DeclarativeBase
 
 
-a: int = "Hello"
-
-
 class Base(DeclarativeBase):
     """
     Base SQLAlchemy class that must be inherited by all the ORM model classes.
diff --git a/python/lib/imaging_io.py b/python/lib/imaging_io.py
index 6aed0d175..ed048aafb 100644
--- a/python/lib/imaging_io.py
+++ b/python/lib/imaging_io.py
@@ -5,7 +5,6 @@
 import os
 import sys
 from lib.exitcode import COPY_FAILURE
-import b
 
 """Set of io functions."""
 

From 924f1f97141549c9cfadee770d1f551a33e9df40 Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime.mulder@mcgill.ca>
Date: Fri, 6 Sep 2024 13:08:21 -0400
Subject: [PATCH 25/25] test

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

diff --git a/.github/workflows/python-checks.yml b/.github/workflows/python-checks.yml
index a9bcdc4e7..fddf5c1f1 100644
--- a/.github/workflows/python-checks.yml
+++ b/.github/workflows/python-checks.yml
@@ -42,8 +42,8 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-      # Like in the other Pyrihgt run, the `jq` arcane is used to translate the errors to the
-      # GitHub actions format
+      # Like in the other Pyright run, the `jq` arcane is used to translate the errors from JSON to
+      # the GitHub actions format
     - name: Run Pyright
       run: |
         pyright --outputjson | jq -r '.generalDiagnostics[] | "::error file=\(.file),line=\(.range.start.line),col=\(.range.start.character)::\(.message)"'