Merge pull request Open-Minds-Lab#56 from sinhaharsh/master

Integration to MRdataset 2.0

.coveragerc

@@ -0,0 +1,28 @@
+[run]
+branch = True
+omit = */tests/*
+       _*.py
+       plotting.py
+
+[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_errors = True
+
+[html]
+directory = htmlcov

.editorconfig

@@ -19,3 +19,6 @@ insert_final_newline = false
 
 [Makefile]
 indent_style = tab
+
+[*.py]
+max_line_length = 80

.github/workflows/codacy.yml

@@ -30,7 +30,7 @@ jobs:
     permissions:
       contents: read # for actions/checkout to fetch code
       security-events: write # for github/codeql-action/upload-sarif to upload SARIF results
-      actions: read # only required for a private repository by github/codeql-action/upload-sarif to get the Action run status 
+      actions: read # only required for a private repository by github/codeql-action/upload-sarif to get the Action run status
     name: Codacy Security Scan
     runs-on: ubuntu-latest
     steps:

.github/workflows/continuous-integration.yml

@@ -0,0 +1,59 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: tests
+
+on:
+    push:
+        branches:
+            - master
+
+jobs:
+    build:
+
+        runs-on: ubuntu-latest
+        strategy:
+            fail-fast: false
+            matrix:
+                python-version: [ "3.8" ]
+
+        steps:
+            -   uses: actions/checkout@v3
+            -   name: Set up Python ${{ matrix.python-version }}
+                uses: actions/setup-python@v3
+                with:
+                    python-version: ${{ matrix.python-version }}
+            -   name: Install dependencies
+                run: |
+                    python -m pip install --upgrade pip
+                    pip install git+https://github.com/sinhaharsh/protocol.git#egg=protocol
+                    pip install git+https://github.com/sinhaharsh/MRdataset.git#egg=MRdataset
+                    if [ -f requirements_dev.txt ]; then pip install -r requirements_dev.txt; fi
+                    pip install .
+            -   name: Lint with flake8
+                run: |
+                    make lint
+                    # stop the build if there are Python syntax errors or undefined names
+                    # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+                    # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+                    # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+            -   name: Test with pytest
+                run: |
+                    pytest
+#            -   name: Coverage
+#                run: |
+#                    coverage run --rcfile=.coveragerc --source mrQA -m pytest
+#                    coverage report -m
+#                    coverage xml
+#            -   name: Run codacy-coverage-reporter
+#                uses: codacy/codacy-coverage-reporter-action@v1
+#                with:
+#                    # project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
+#                    # or
+#                    api-token: ${{ secrets.CODACY_API_TOKEN }}
+#                    organization-provider: gh
+#                    username: sinhaharsh
+#                    project-name: mrQA
+#                    coverage-reports: coverage.xml
+#                    # or a comma-separated list for multiple reports
+#                    # coverage-reports: <PATH_TO_REPORT>, <PATH_TO_REPORT>

.gitignore

@@ -104,3 +104,10 @@ ENV/
 .vscode/
 .idea/
 /update_today.txt
+
+# codacy
+*.sarif
+
+# mri protocol
+*.xml
+*.secrets

MANIFEST.in

@@ -4,7 +4,11 @@ include HISTORY.rst
 include LICENSE
 include README.rst
 
-recursive-include tests *
+graft mrQA/tests
+prune mrQA/tests/htmlcov
+prune mrQA/tests/.hypothesis
+graft mrQA/scripts
+graft mrQA/resources
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 

Makefile

@@ -48,7 +48,7 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr .pytest_cache
 
 lint/flake8: ## check style with flake8
-	flake8 mrQA tests
+	flake8 mrQA
 
 lint: lint/flake8 ## check style
 
@@ -59,18 +59,19 @@ test-all: ## run tests on every Python version with tox
 	tox
 
 coverage: ## check code coverage quickly with the default Python
-	coverage run --source mrQA -m pytest
+	coverage run --rcfile=.coveragerc --source mrQA -m pytest
 	coverage report -m
 	coverage html
+	coverage xml
 	$(BROWSER) htmlcov/index.html
 
+act:
+	act --secret-file .secrets
+
 docs: ## generate Sphinx HTML documentation, including API docs
-	rm -f docs/mrQA.rst
-	rm -f docs/modules.rst
-	sphinx-apidoc -o docs/ mrQA
 	$(MAKE) -C docs clean
 	$(MAKE) -C docs html
-	$(BROWSER) docs/_build/html/index.html
+	$(BROWSER) docs/build/html/index.html
 
 servedocs: docs ## compile the docs watching for changes
 	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
@@ -85,3 +86,11 @@ dist: clean ## builds source and wheel package
 
 install: clean ## install the package to the active Python's site-packages
 	python setup.py install
+
+merge:
+	git switch mrds-issue-12
+	git push
+	git switch master
+	git merge mrds-issue-12
+	git push origin master
+	git switch mrds-issue-12

README.rst

@@ -4,8 +4,12 @@ mrQA : automatic protocol compliance checks on MR datasets
 .. image:: https://img.shields.io/pypi/v/mrQA.svg
         :target: https://pypi.python.org/pypi/mrQA
 
-.. image:: https://img.shields.io/travis/Open-Minds-Lab/mrQA.svg
-        :target: https://travis-ci.com/Open-Minds-Lab/mrQA
+.. image:: https://app.codacy.com/project/badge/Grade/8cd263e1eaa0480d8fac50eba0094401
+        :target: https://app.codacy.com/gh/sinhaharsh/mrQA/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade
+
+.. image:: https://github.com/sinhaharsh/mrQA/actions/workflows/continuous-integration.yml/badge.svg
+        :target: https://github.com/sinhaharsh/mrQA/actions/workflows/continuous-integration.yml
+
 
 .. image:: https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg
         :target: https://nbviewer.org/github/Open-Minds-Lab/mrQA/blob/master/examples/usage.ipynb

docs/cli.rst

@@ -0,0 +1,7 @@
+Command Line
+============
+
+.. argparse::
+    :module: mrQA.cli
+    :func: get_parser
+    :prog: mrQA

docs/conf.py

@@ -34,7 +34,8 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = ['sphinx.ext.autodoc',
               'sphinx.ext.viewcode',
-              'sphinx.ext.napoleon']
+              'sphinx.ext.napoleon',
+              'sphinxarg.ext']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

docs/usage.rst

@@ -4,15 +4,23 @@ CLI usage
 A protocol compliance report can be generated directly from the command line
 interface.  The following is an example of generating a protocol compliance report
 
-For a DICOM dataset::
+For a DICOM dataset
+
+.. code:: bash
 
     mrqa --data-source /path/to/dataset --format dicom --name my_dataset
 
-For a BIDS dataset::
+For a BIDS dataset
+
+.. code:: bash
 
     mrqa --data-source /path/to/dataset --format bids --name my_dataset
 
 
+.. toctree::
+    :maxdepth: 1
+
+    cli
 
 API Tutorial
 ------------