Run Pytests across all supported Python versions (PennLINC#279)

* Try this.

* Update config.yml

* Try to work around parallel approach.

* Update config.yml

* Update config.yml

* Update config.yml

* Update config.yml

* Update config.yml

* Update config.yml

* Update config.yml

* Update config.yml

* Update config.yml

* Add merge_coverage job.

* Update config.yml

* Update config.yml

* Whoops

* Update config.yml

* Update config.yml

* Update config.yml

* Update pyproject.toml

* update

* Skip the copilot tests.

* Update config.yml

* Update pyproject.toml

.circleci/config.yml

@@ -1,14 +1,22 @@
 version: 2.1
+orbs:
+  codecov: codecov/[email protected]
+
 jobs:
-  set_up_conda:
+  run_pytests:
+    parameters:
+      python_version:
+        type: string
+        default: "3.8"
     machine:
       image: ubuntu-2004:202201-02
     working_directory: /home/circleci/src/CuBIDS
     steps:
       - checkout:
           path: /home/circleci/src/CuBIDS
+
       - run:
-          name: install miniconda
+          name: Test CuBIDS
           command: |
             export MINICONDA=/tmp/miniconda
             export PATH="$MINICONDA/bin:$PATH"
@@ -17,7 +25,9 @@ jobs:
             conda config --set always_yes yes
             conda update conda
             conda info -a
-            conda create -n cubids python=3.9 pip
+
+            export PATH=/tmp/miniconda/bin:$PATH
+            conda create -n cubids python=<< parameters.python_version >> pip
             source activate cubids
             conda install -c conda-forge -y datalad
 
@@ -26,39 +36,40 @@ jobs:
             npm install -g yarn && \
             npm install -g bids-validator
 
+            # Install CuBIDS
+            pip install -e .[tests]
+
+            # Run tests
+            pytest --cov-append --cov-report term-missing --cov=cubids cubids
+            mkdir /home/circleci/src/coverage
+            mv /home/circleci/src/CuBIDS/.coverage /home/circleci/src/coverage/.coverage.<< parameters.python_version >>
       - persist_to_workspace:
-          root: /tmp
+          root: /home/circleci/src/coverage
           paths:
-            - miniconda
+              - .coverage.<< parameters.python_version >>
 
-  run_pytests:
-    machine:
-      image: ubuntu-2004:202201-02
-    working_directory: /home/circleci/src/CuBIDS
+  merge_coverage:
+    docker:
+        - image: continuumio/miniconda3
     steps:
       - checkout:
           path: /home/circleci/src/CuBIDS
-
       - attach_workspace:
-          at: /tmp
-
+          at: /home/circleci/src/coverage
       - run:
-          name: Test CuBIDS
+          name: Merge coverage files
           command: |
-            export PATH=/tmp/miniconda/bin:$PATH
-            source activate cubids
-
-            # Install CuBIDS
-            pip install -e .[tests]
-
-            # Reinstall bids-validator
-            sudo apt update
-            sudo apt install nodejs npm
-            npm install -g yarn && \
-            npm install -g bids-validator
+            conda create -n cov python=3.9 pip coverage
+            source activate cov
 
-            # Run tests
-            pytest cubids
+            cd /home/circleci/src/coverage/
+            echo "Merge coverage files"
+            coverage combine --data-file=/home/circleci/src/coverage/.coverage
+            echo "Generate XML report"
+            coverage xml --data-file /home/circleci/src/coverage/.coverage -o /home/circleci/src/coverage/coverage.xml
+            echo "Upload to Codecov"
+      - codecov/upload:
+          file: /home/circleci/src/coverage/coverage.xml
 
   deployable:
     docker:
@@ -84,20 +95,27 @@ jobs:
           command: python -m twine upload -u __token__ -p ${PYPI_TOKEN} dist/cubids*
 
 workflows:
-  version: 2
   build_test_deploy:
     jobs:
-      - set_up_conda:
+      - run_pytests:
+          # Define the matrix for Python versions
+          matrix:
+            parameters:
+              python_version:
+                - "3.8"
+                - "3.9"
+                - "3.10"
+                - "3.11"
           filters:
             tags:
               only: /.*/
 
-      - run_pytests:
+      - merge_coverage:
           requires:
-            - set_up_conda
+            - run_pytests
           filters:
             tags:
-              only: /.*/
+              ignore: /.*/
 
       - deployable:
           requires:

cubids/tests/coverage.cfg

@@ -0,0 +1,2 @@
+[coverage:run]
+parallel = true

cubids/tests/test_cli.py

@@ -0,0 +1,82 @@
+"""
+This file contains unit tests for the command-line interface (CLI) of the CuBIDS package.
+
+The tests cover the following functions:
+- _path_exists: Tests whether a given path exists or not.
+- _is_file: Tests whether a given path is a file or a directory.
+- _get_parser: Tests the creation and configuration of the argument parser.
+- _main: Tests the main function of the CLI.
+
+Each test case includes assertions to verify the expected behavior of the corresponding function.
+
+Author: [Your Name]
+Date: [Current Date]
+"""
+
+import argparse
+import pytest
+
+from cubids.cli import _path_exists, _is_file, _get_parser, _main
+
+
+def _test_path_exists():
+    """Test whether a given path exists or not.
+
+    This function tests the `_path_exists` function by providing a path that exists
+    and a path that does not exist.
+    It asserts that the function returns the expected path when the path exists,
+    and raises an `argparse.ArgumentTypeError` when the path does not exist.
+    """
+    assert _path_exists("/path/to/existing/file", None) == "/path/to/existing/file"
+
+    with pytest.raises(argparse.ArgumentTypeError):
+        _path_exists("/path/to/nonexistent/file", None)
+
+
+def _test_is_file():
+    """Test whether a given path is a file or a directory.
+
+    This function tests the `_is_file` function by providing a path that is a file
+    and a path that is a directory.
+    It asserts that the function returns the expected path when the path is a file,
+    and raises an `argparse.ArgumentTypeError` when the path is a directory.
+    """
+    assert _is_file("/path/to/file.txt", None) == "/path/to/file.txt"
+
+    with pytest.raises(argparse.ArgumentTypeError):
+        _is_file("/path/to/directory", None)
+
+
+def _test_get_parser():
+    """Test the creation and configuration of the argument parser.
+
+    This function tests the `_get_parser` function by asserting that the returned object is an
+    instance of `argparse.ArgumentParser`, and that it has the expected `prog` and `description`
+    attributes.
+    Additional assertions can be added to test the configuration of the parser.
+    """
+    parser = _get_parser()
+    assert isinstance(parser, argparse.ArgumentParser)
+    assert parser.prog == "cubids"
+    assert parser.description == "Console script for cubids"
+    # Add more assertions for the parser configuration
+
+
+def _test_main():
+    """Test the main function of the CLI.
+
+    This function tests the `_main` function by providing different sets of arguments.
+    It asserts that the function returns the expected exit code (0 or 1) based on the provided
+    arguments.
+    """
+    # Test the main function with valid arguments
+    argv = ["validate", "/path/to/dataset"]
+    assert _main(argv) == 0
+
+    # Test the main function with invalid arguments
+    argv = ["invalid-command", "/path/to/dataset"]
+    assert _main(argv) == 1
+
+    # Test the main function with missing arguments
+    argv = []
+    assert _main(argv) == 1