Add CI workflows for tests and checks

.github/workflows/codespell.yml

@@ -0,0 +1,18 @@
+name: Codespell
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  codespell:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install codespell
+        run: |
+          python -m pip install --upgrade pip
+          pip install codespell
+      - name: Run codespell
+        run: codespell --check-hidden -q 3

.github/workflows/docker.yml

@@ -0,0 +1,22 @@
+name: Docker Build
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      - name: Build Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: false
+          tags: qkay:test

.github/workflows/package.yml

@@ -0,0 +1,21 @@
+name: Build Package
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+      - name: Install build tool
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build

.github/workflows/ruff.yml

@@ -0,0 +1,23 @@
+name: Ruff Checks
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+      - name: Install ruff
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      - name: Ruff check
+        run: ruff check .
+      - name: Ruff format
+        run: ruff format --diff .

.github/workflows/tests.yml

@@ -0,0 +1,27 @@
+name: Run Tests
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install pytest
+      - name: Run tests
+        env:
+          PYTHONPATH: ${{ github.workspace }}
+        run: pytest -v

docs/source/conf.py

@@ -17,24 +17,23 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'qkay'
-copyright = 'The NiPreps Developers'
-author = 'The NiPreps Developers'
+project = "qkay"
+copyright = "The NiPreps Developers"
+author = "The NiPreps Developers"
 
 # The full version, including alpha/beta/rc tags
-release = 'v.0.0.0'
+release = "v.0.0.0"
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-]
+extensions = []
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -47,9 +46,9 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "alabaster"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]

pyproject.toml

@@ -0,0 +1,30 @@
+[build-system]
+requires = ["setuptools>=42", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "qkay"
+version = "0.1.0"
+description = "Flask web application"
+authors = [{name = "The NiPreps Developers", email = "[email protected]"}]
+license = {file = "LICENSE"}
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "beautifulsoup4==4.11.2",
+    "Flask==2.2.2",
+    "Flask_Login==0.6.2",
+    "flask_mongoengine==1.0.0",
+    "Flask_WTF==1.1.1",
+    "Jinja2==3.1.2",
+    "mongoengine==0.26.0",
+    "numpy",
+    "Werkzeug==2.2.2",
+    "WTForms==3.0.1",
+]
+
+[tool.setuptools.packages.find]
+where = ["."]
+
+[project.scripts]
+qkay = "qkay.wsgi:app"

qkay/__init__.py

@@ -1,3 +1,5 @@
+"""qkay package."""
+
 from .qkay import app
 
 __all__ = ["app"]

qkay/config.py

@@ -30,6 +30,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Utilities: Jinja2 templates."""
+
 from io import open  # pylint: disable=W0622
 
 
@@ -65,15 +66,11 @@ class IndividualTemplate(Template):
     """Specific template for the individual report. From MRIQC"""
 
     def __init__(self):
-        super(IndividualTemplate, self).__init__(
-            "./templates/reports.html"
-        )
+        super(IndividualTemplate, self).__init__("./templates/reports.html")
 
 
 class IndexTemplate(Template):
     """Specific template for the index file of the reports."""
 
     def __init__(self):
-        super(IndexTemplate, self).__init__(
-            "./templates/index.html"
-        )
+        super(IndexTemplate, self).__init__("./templates/index.html")

qkay/qkay.py

@@ -178,35 +178,35 @@ def validate_dataset(self):
 
 class Inspection(db.Document):
     """
-        Class to define an inspection
-        ...
-
-        Attributes
-        ----------
-        meta : dict
-            mongodb collection
-        dataset : str
-            name of the dataset to be inspected
-        username : str
-            name of the user assigned to the inspection
-        randomize : bool
-            If files must be shuffled
-        rate_all : bool
-            If all files must be rated
-        blind : bool
-            If reports must be anonymized
-        names_files : string list
-            list of filenames to grade
-        names_shuffled : string list
-            shuffled list of filenames
-        names_anonymized : string list
-            list of filenames anonymized and shuffled if randomize==True
-        names_subsample: string list
-            subsample of file to inspect if rate_all==False
-        random_seed: int
-            random seed used to shuffle the filename
-        index_rated_reports: list
-            index of reports already rated
+    Class to define an inspection
+    ...
+
+    Attributes
+    ----------
+    meta : dict
+        mongodb collection
+    dataset : str
+        name of the dataset to be inspected
+    username : str
+        name of the user assigned to the inspection
+    randomize : bool
+        If files must be shuffled
+    rate_all : bool
+        If all files must be rated
+    blind : bool
+        If reports must be anonymized
+    names_files : string list
+        list of filenames to grade
+    names_shuffled : string list
+        shuffled list of filenames
+    names_anonymized : string list
+        list of filenames anonymized and shuffled if randomize==True
+    names_subsample: string list
+        subsample of file to inspect if rate_all==False
+    random_seed: int
+        random seed used to shuffle the filename
+    index_rated_reports: list
+        index of reports already rated
     """
 
     meta = {"collection": "inspections"}
@@ -687,15 +687,25 @@ def display_report_non_anonymized(username, report_name):
     dataset = user.current_dataset
     dataset_path = str(Dataset.objects(name=dataset).values_list("path_dataset")[0])
 
-    app.logger.debug("Searching recursively for a report named %s under %s.", report_name, dataset_path)
+    app.logger.debug(
+        "Searching recursively for a report named %s under %s.",
+        report_name,
+        dataset_path,
+    )
 
     mriqc_report = ""
-    path_mriqc_report = glob.glob(os.path.join(dataset_path, "**", "sub-" + report_name), recursive=True)
+    path_mriqc_report = glob.glob(
+        os.path.join(dataset_path, "**", "sub-" + report_name), recursive=True
+    )
     if len(path_mriqc_report) == 0:
-        app.logger.error("No report named %s was found in the children of %s.","sub-" + report_name, dataset_path)
+        app.logger.error(
+            "No report named %s was found in the children of %s.",
+            "sub-" + report_name,
+            dataset_path,
+        )
     else:
         path_mriqc_report = path_mriqc_report[0]
-        # Modify the html to adapt it to Q'kay    
+        # Modify the html to adapt it to Q'kay
         mriqc_report = modify_mriqc_report(path_mriqc_report)
 
     return render_template(
@@ -757,7 +767,11 @@ def display_index_inspection(username, dataset):
     user.save()
     path_index = "./templates/index.html"
 
-    app.logger.debug("Searching for inspection matching dataset %s and username %s.", dataset, username)
+    app.logger.debug(
+        "Searching for inspection matching dataset %s and username %s.",
+        dataset,
+        username,
+    )
 
     # Find in the inspection which reports have been rated
     current_inspection = Inspection.objects(Q(dataset=dataset) & Q(username=username))
@@ -816,28 +830,47 @@ def create_dataset():
         selected_datasets = request.form.getlist("datasets[]")
         for d in selected_datasets:
             dataset_path = op.join("/datasets", d)
-            app.logger.debug("Searching recursively for dataset_description.json under %s.", dataset_path) 
+            app.logger.debug(
+                "Searching recursively for dataset_description.json under %s.",
+                dataset_path,
+            )
 
             # Get dataset name from the data_description.json file if it exists
             # otherwise, use the folder name
             desc_file = ""
-            desc_files = glob.glob(os.path.join(dataset_path, "**", "dataset_description.json"), recursive=True)
+            desc_files = glob.glob(
+                os.path.join(dataset_path, "**", "dataset_description.json"),
+                recursive=True,
+            )
             if len(desc_files) > 1:
-                app.logger.warning("More than one dataset_description.json was found!: %s .", desc_files) 
-
+                app.logger.warning(
+                    "More than one dataset_description.json was found!: %s .",
+                    desc_files,
+                )
+
             desc_file = desc_files[0]
-            app.logger.debug("dataset_description.json found at %s.", desc_file) 
+            app.logger.debug("dataset_description.json found at %s.", desc_file)
             if desc_file:
                 with open(desc_file, "r") as file:
                     data_description = json.load(file)
                     dataset_name = data_description["Name"]
-                    app.logger.info("The dataset name %s was assigned based on the name in %s", dataset_name, desc_file) 
+                    app.logger.info(
+                        "The dataset name %s was assigned based on the name in %s",
+                        dataset_name,
+                        desc_file,
+                    )
                 # If the name of the dataset is the default MRIQC value, use the folder name instead
                 if dataset_name == "MRIQC - MRI Quality Control":
-                    app.logger.info("The dataset name is the default of MRIQC which is not informative, using folder name instead: %s.", d) 
+                    app.logger.info(
+                        "The dataset name is the default of MRIQC which is not informative, using folder name instead: %s.",
+                        d,
+                    )
                     dataset_name = d
             else:
-                app.logger.info("No dataset_description.json found, assigning dataset name to folder name: %s.", d) 
+                app.logger.info(
+                    "No dataset_description.json found, assigning dataset name to folder name: %s.",
+                    d,
+                )
                 dataset_name = d
 
             dataset = Dataset(name=dataset_name, path_dataset=dataset_path)
@@ -908,9 +941,7 @@ def assign_dataset():
         )
 
         names_files = list_individual_reports(dataset_path)
-        app.logger.debug(
-            "%s reports found at %s", len(names_files), dataset_path
-        )
+        app.logger.debug("%s reports found at %s", len(names_files), dataset_path)
         new_names = names_files
         if repeat:
             names_repeated = repeat_reports(new_names, number_rep)