Merge remote-tracking branch 'upstream/main' into test-python

.circleci/config.yml

@@ -1,153 +1,119 @@
-# Python CircleCI 2.1 configuration file
-#
-# Check https://circleci.com/docs/2.1/language-python/ for more details
-#
 version: 2.1
-orbs:
-  codecov: codecov/[email protected]
-jobs:
 
-  test_py38:
+jobs:
+  set_up_conda:
+    machine:
+      image: ubuntu-2004:202201-02
     working_directory: /home/circleci/src/CuBIDS
-    docker:
-      - image: continuumio/miniconda3
     steps:
-      - checkout
+      - checkout:
+          path: /home/circleci/src/CuBIDS
       - run:
-          name: Generate environment
-          command:  |
-            conda create -n py38_env python=3.8 pip -yq
-            conda install -c conda-forge -y datalad
-
-            # Add nodejs and the validator
-            conda install nodejs
-            npm install -g yarn && \
-            npm install -g bids-validator
+          name: install miniconda
+          command: |
+            export MINICONDA=/tmp/miniconda
+            export PATH="$MINICONDA/bin:$PATH"
+            wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /tmp/miniconda.sh
+            bash /tmp/miniconda.sh -b -f -p $MINICONDA
+            conda config --set always_yes yes
+            conda update conda
+            conda info -a
 
-            source activate py38_env
-            pip install -e .[tests]
-      - run:
-          name: Run tests
-          command:  |
-            source activate py38_env
-            py.test --cov-append --cov-config=cubids/tests/coverage.cfg --cov-report=xml --cov=cubids cubids
-            mkdir /tmp/src/coverage
-            mv /home/circleci/src/CuBIDS/.coverage /tmp/src/coverage/.coverage.py38
+      - persist_to_workspace:
+          root: /tmp
+          paths:
+            - miniconda
 
-  test_py39:
+  run_pytests:
+    machine:
+      image: ubuntu-2004:202201-02
     working_directory: /home/circleci/src/CuBIDS
-    docker:
-      - image: continuumio/miniconda3
     steps:
-      - checkout
-      - run:
-          name: Generate environment
-          command:  |
-            conda create -n py39_env python=3.9 pip -yq
-            conda install -c conda-forge -y datalad
-
-            # Add nodejs and the validator
-            conda install nodejs
-            npm install -g yarn && \
-            npm install -g bids-validator
+      - checkout:
+          path: /home/circleci/src/CuBIDS
 
-            source activate py39_env
-            pip install -e .[tests]
-      - run:
-          name: Run tests
-          command:  |
-            source activate py39_env
-            py.test --cov-append --cov-config=cubids/tests/coverage.cfg --cov-report=xml --cov=cubids cubids
-            mkdir /tmp/src/coverage
-            mv /home/circleci/src/CuBIDS/.coverage /tmp/src/coverage/.coverage.py39
+      - attach_workspace:
+          at: /tmp
 
-  test_py310:
-    working_directory: /home/circleci/src/CuBIDS
-    docker:
-      - image: continuumio/miniconda3
-    steps:
-      - checkout
       - run:
-          name: Generate environment
-          command:  |
-            conda create -n py310_env python=3.10 pip -yq
+          name: Test CuBIDS (Python = ${{ matrix.python_version }})
+          command: |
+            export PATH=/tmp/miniconda/bin:$PATH
+            conda create -n cubids python=${{ matrix.python_version }} pip
+            source activate cubids
             conda install -c conda-forge -y datalad
 
             # Add nodejs and the validator
             conda install nodejs
             npm install -g yarn && \
             npm install -g bids-validator
 
-            source activate py310_env
+            # Install CuBIDS
             pip install -e .[tests]
-      - run:
-          name: Run tests
-          command:  |
-            source activate py310_env
-            py.test --cov-append --cov-config=cubids/tests/coverage.cfg --cov-report=xml --cov=cubids cubids
-            mkdir /tmp/src/coverage
-            mv /home/circleci/src/CuBIDS/.coverage /tmp/src/coverage/.coverage.py310
 
-  test_py311:
-    working_directory: /home/circleci/src/CuBIDS
+            # Run tests
+            pytest cubids
+
+  deployable:
     docker:
-      - image: continuumio/miniconda3
+      - image: busybox:latest
     steps:
-      - checkout
-      - run:
-          name: Generate environment
-          command:  |
-            conda create -n py311_env python=3.11 pip -yq
-            conda install -c conda-forge -y datalad
-
-            # Add nodejs and the validator
-            conda install nodejs
-            npm install -g yarn && \
-            npm install -g bids-validator
-
-            source activate py311_env
-            pip install -e .[tests]
-      - run:
-          name: Run tests
-          command:  |
-            source activate py311_env
-            py.test --cov-append --cov-config=cubids/tests/coverage.cfg --cov-report=xml --cov=cubids cubids
-            mkdir /tmp/src/coverage
-            mv /home/circleci/src/CuBIDS/.coverage /tmp/src/coverage/.coverage.py311
+      - run: echo Deploying!
 
-  merge_coverage:
+  deploy_pypi:
+    machine:
+      image: ubuntu-2004:202201-02
     working_directory: /home/circleci/src/CuBIDS
-    docker:
-      - image: continuumio/miniconda3
     steps:
-      - attach_workspace:
-          at: /tmp
-      - checkout
+      - checkout:
+          path: /home/circleci/src/CuBIDS
       - run:
-          name: Merge coverage files
-          command: |
-            apt-get update
-            apt-get install -yqq curl
-            source activate py37_env
-            cd /tmp/src/coverage/
-            coverage combine
-            coverage xml
-      - store_artifacts:
-          path: /tmp/src/coverage
-      - codecov/upload:
-          file: /tmp/src/coverage/coverage.xml
+          name: Update build tools
+          command: pip install --upgrade build twine
+      - run:
+          name: Build CuBIDS
+          command: python -m build
+      - run:
+          name: Upload package to PyPI
+          command: python -m twine upload -u __token__ -p ${PYPI_TOKEN} dist/cubids*
 
 workflows:
-  version: 2.1
-  run_tests:
+  version: 2
+  build_test_deploy:
     jobs:
-      - test_py38
-      - test_py39
-      - test_py310
-      - test_py311
-      - merge_coverage:
+      - set_up_conda:
+          filters:
+            tags:
+              only: /.*/
+
+      - run_pytests:
+          # Define the matrix for Python versions
+          matrix:
+            python_version:
+              - "3.8"
+              - "3.9"
+              - "3.10"
+              - "3.11"
+          requires:
+            - set_up_conda
+          filters:
+            tags:
+              only: /.*/
+
+      - deployable:
+          requires:
+            - run_pytests
+          filters:
+            branches:
+              only: main
+            tags:
+              only: /.*/
+
+      - deploy_pypi:
           requires:
-            - test_py38
-            - test_py39
-            - test_py310
-            - test_py311
+            - deployable
+          filters:
+            branches:
+              ignore: /.*/
+            tags:
+              only: /.*/

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,32 @@
+---
+name: Bug report
+about: Something not working as described? Missing/incorrect documentation? This is the place.
+title: ''
+labels: 'bug'
+assignees: ''
+
+---
+## Summary
+<!--What is the nature of the bug?-->
+
+## Additional details
+<!--Please fill in the following details-->
+- CuBIDS version:
+- Datalad version:
+
+### What were you trying to do?
+
+### What did you expect to happen?
+
+### What actually happened?
+
+## Reproducing the bug
+<!--Please share any steps you performed that revealed the bug-->
+<!--Please include any code snippets.
+Enclose them in triple back-ticks (```)
+Like this:
+
+```
+<code>
+```
+-->

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,4 @@
+contact_links:
+  - name: Usage question
+    url: https://neurostars.org/tags/c/software-support/234/cubids
+    about: Please ask questions about using CuBIDS on NeuroStars.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,16 @@
+---
+name: Feature request
+about: Got an idea for a new feature, or changing an existing one? This is the place.
+title: ''
+labels: 'enhancement'
+assignees: ''
+
+---
+## Summary
+<!--What would you like changed/added and why?-->
+
+## Additional details
+<!--What would be the benefit?-->
+
+## Next steps
+<!--Do you have any ideas about the implementation?-->

.github/dependabot.yml

@@ -0,0 +1,18 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    labels: ["maintenance", "ignore-for-release"]
+    assignees: ["tsalo"]
+    schedule:
+      interval: "weekly"
+  - package-ecosystem: pip
+    directory: "/"
+    labels: ["maintenance", "ignore-for-release"]
+    schedule:
+      interval: weekly

.github/pull_request_template.md

@@ -0,0 +1,9 @@
+Closes .
+
+## Changes proposed in this pull request
+
+-
+
+## Documentation that should be reviewed
+
+-

.github/release.yml

@@ -0,0 +1,20 @@
+changelog:
+  exclude:
+    labels:
+      - ignore-for-release
+  categories:
+    - title: 🛠 Breaking Changes
+      labels:
+        - breaking-change
+    - title: 🎉 Exciting New Features
+      labels:
+        - enhancement
+    - title: 👎 Deprecations
+      labels:
+        - deprecation
+    - title: 🐛 Bug Fixes
+      labels:
+        - bug
+    - title: Other Changes
+      labels:
+        - "*"

.github/workflows/lint.yml

@@ -9,11 +9,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Set up environment
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:  # no need for the history
         fetch-depth: 1
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.9'
     - name: Install dependencies

AUTHORS.rst

@@ -4,14 +4,18 @@ Credits
 
 Development Lead
 ----------------
-* Sydney Covitz <sydney.covitz at pennmedicine dot upenn .edu>
+* Taylor Salo <taylor dot salo at pennmedicine dot upenn dot edu>
 
 Contributors
 ------------
-* Matt Cieslak <matthew.cieslak at pennmedicine dot upenn .edu>
-
-* Tinashe Tapera <tinashe.tapera at pennmedicine dot upenn .edu>
+* Matt Cieslak <matthew dot cieslak at pennmedicine dot upenn dot edu>
 
 Principal Investigator
 ----------------------
-* Theodore Satterthwaite <theodore.satterthwaite at pennmedicine dot upenn .edu>
+* Theodore Satterthwaite <theodore dot satterthwaite at pennmedicine dot upenn dot edu>
+
+Previous Contributors
+---------------------
+* Sydney Covitz <sydney dot covitz at pennmedicine dot upenn dot edu> (previous development lead)
+
+* Tinashe Tapera <tinashe dot tapera at pennmedicine dot upenn dot edu>