bagel 0.9.2__tar.gz

bagel-0.9.2/.autorc

@@ -0,0 +1,123 @@
+{
+    "onlyPublishWithReleaseLabel": true,
+    "noDefaultLabels": true,
+    "baseBranch": "main",
+    "author": "Neurobagel Bot <bot@neurobagel.org>",
+    "noVersionPrefix": false,
+    "plugins": [
+        "git-tag",
+        "released",
+        "first-time-contributor",
+        [
+            "omit-commits",
+            {
+                "username": ["dependabot[bot]", "pre-commit-ci[bot]"],
+                "subject": "[pre-commit.ci]",
+                "labels": ["_bot", "skip-release"]
+            }
+        ],
+        [
+            "exec",
+            {
+                "afterRelease": "python -m build && twine upload dist/*"
+            }
+        ]
+    ],
+    "labels": [
+        {
+            "name": "pr-major-breaking",
+            "changelogTitle": "💥 Breaking Changes",
+            "description": "Significant behaviour change that breaks compatibility, will increment major version (+1.0.0)",
+            "releaseType": "major",
+            "overwrite": true,
+            "color": "#C1EF40"
+        },
+        {
+            "name": "pr-minor-breaking",
+            "changelogTitle": "💥 Breaking Changes",
+            "description": "Feature or enhancement that breaks compatibility, will increment minor version (0.+1.0)",
+            "releaseType": "minor",
+            "overwrite": true,
+            "color": "#C1EF40"
+        },
+        {
+            "name": "pr-minor",
+            "changelogTitle": "🚀 Enhancements",
+            "description": "Non-breaking feature or enhancement, will increment minor version (0.+1.0)",
+            "releaseType": "minor",
+            "overwrite": true,
+            "color": "#C1EF40"
+        },
+        {
+            "name": "pr-patch",
+            "changelogTitle": "🚀 Enhancements",
+            "description": "Incremental feature improvement, will increment patch version when merged (0.0.+1)",
+            "releaseType": "patch",
+            "overwrite": true,
+            "default": true,
+            "color": "#C1EF40"
+        },
+        {
+            "name": "pr-bug-fix",
+            "changelogTitle": "🐛 Bug Fixes",
+            "description": "Bug fix, will increment patch version when merged (0.0.+1)",
+            "releaseType": "patch",
+            "overwrite": true,
+            "color": "#C1EF40"
+        },
+        {
+            "name": "pr-internal",
+            "changelogTitle": "🏠 Internal",
+            "description": "Non-user-facing code improvement, will increment patch version when merged (0.0.+1)",
+            "releaseType": "patch",
+            "overwrite": true,
+            "color": "#C1EF40"
+        },
+        {
+            "name": "pr-performance",
+            "changelogTitle": "🏎 Performance Improvements",
+            "description": "Improve performance of an existing feature, will increment patch version when merged (0.0.+1)",
+            "releaseType": "patch",
+            "overwrite": true,
+            "color": "#C1EF40"
+        },
+        {
+            "name": "pr-documentation",
+            "changelogTitle": "📝 Documentation",
+            "description": "Change that only affects user documentation",
+            "releaseType": "none",
+            "overwrite": true,
+            "color": "#C1EF40"
+        },
+        {
+            "name": "pr-tests",
+            "changelogTitle": " 🧪 Tests",
+            "description": "Add or improve existing tests",
+            "releaseType": "none",
+            "overwrite": true,
+            "color": "#C1EF40"
+        },
+        {
+            "name": "pr-dependencies",
+            "changelogTitle": "🔩 Dependency Updates",
+            "description": "Update one or more dependencies version",
+            "releaseType": "none",
+            "overwrite": true,
+            "color": "#C1EF40"
+        },
+        {
+            "name": "skip-release",
+            "description": "PR doesn't appear in the changelog and preserves current version when merged",
+            "releaseType": "skip",
+            "overwrite": true,
+            "color": "#bf5416"
+        },
+        {
+            "name": "release",
+            "description": "Create a release when this PR is merged",
+            "releaseType": "release",
+            "overwrite": true,
+            "color": "#BFDADC"
+        }
+    ]
+}

bagel-0.9.2/.dockerignore

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+# python cache
+__pycache__/**/*
+__pycache__
+*.pyc
+
+# python distribution
+build/**/*
+build
+dist/**/*
+dist
+bagelbids.egg-info/**/*
+bagelbids.egg-info
+.eggs/**/*
+.eggs
+
+.editorconfig
+**/.git
+**/.github
+**/.gitignore
+**/.vscode
+**/coverage
+**/.env
+**/.aws
+**/.ssh
+**/.DS_Store
+**/venv
+**/env
+Dockerfile
+
+# other configuration files and scripts
+.autorc
+.pre-commit-config.yaml
+generate_nb_vocab_file.py
+
+# documentation
+CHANGELOG.md
+CITATION.cff
+LICENSE
+README.md
+
+# testing
+tests

bagel-0.9.2/.editorconfig

@@ -0,0 +1,2 @@
+[*.py]
+profile = black

bagel-0.9.2/.flake8

@@ -0,0 +1,11 @@
+; Flake8 does not natively support configuration via pyproject.toml.
+; See https://github.com/microsoft/vscode-flake8/issues/135
+
+[flake8]
+extend-ignore = E501, E203
+extend-select = B950
+per-file-ignores =
+    bagelbids/cli.py: F841
+exclude =
+    build,
+    dist,

bagel-0.9.2/.github/dependabot.yml

@@ -0,0 +1,75 @@
+# This is a centrally maintained dependabot configuration file
+# that is applied to all repositories in the neurobagel organization.
+# Do not make changes to this file directly. Instead, make changes
+# to the template file in the workflows: https://github.com/neurobagel/workflows/tree/main/template_workflows/dependabot.yml
+
+version: 2
+updates:
+
+  # We instruct dependabot to open PRs if a newer version
+  # of a github action has been released.
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    labels:
+      - "_bot"
+      - "dependencies"
+  
+  # We instruct dependabot to open PRs whenever the HEAD of 
+  # of a submodule repository has advanced beyond what our submodule
+  # is currently tracking.
+  # Note: this configuration will only have an effect in repositories that have
+  # submodules.
+  - package-ecosystem: "gitsubmodule"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    labels:
+      - "_bot"
+      - "dependencies"
+
+  # In repo settings, we have configured dependabot to open PRs for security updates.
+  # Here, we configure dependabot to open version update PRs for only patch and minor versions of javascript / npm dependencies,
+  # and configure labels for both types of dependabot PRs.
+  # Note: this configuration will only have an effect in repositories that have
+  # a package.json file / use npm.
+  - package-ecosystem: "npm"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    # This setting asks dependabot to group PRs for version updates of all development or production dependencies
+    # into single PRs to reduce the total number of PRs opened.
+    groups:
+      production-dependencies:
+        applies-to: version-updates
+        dependency-type: "production"
+      development-dependencies:
+        applies-to: version-updates
+        dependency-type: "development"
+    # We ignore all major version updates of dependencies.
+    # The idea is that we only bump major versions manually or if doing
+    # so addresses a security vulnerability.
+    ignore:
+      - dependency-name: "*"
+        update-types: ["version-update:semver-major"]
+    labels:
+      - "_bot"
+      - "dependencies"
+
+  # In repo settings we have configured dependabot to open PRs for security updates.
+  # Here we configure custom labels to be applied to security update PRs,
+  # while still preventing regular version update PRs.
+  # See https://docs.github.com/en/code-security/dependabot/dependabot-security-updates/configuring-dependabot-security-updates#overriding-the-default-behavior-with-a-configuration-file
+  # Note: this configuration only has an effect in repositories that have
+  # a requirements.txt file / use python / pip.
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    # This setting instructs dependabot to not open PRs for version updates
+    # but to still open PRs for security vulnerabilities.
+    open-pull-requests-limit: 0
+    labels:
+      - "_bot"
+      - "dependencies"

bagel-0.9.2/.github/pull_request_template.md

@@ -0,0 +1,42 @@
+<!--- Until this PR is ready for review, you can include [WIP] in the title, or create a draft PR. -->
+
+
+<!---
+Below is a suggested pull request template. Feel free to add more details you feel are relevant/necessary.
+
+For more info on the Neurobagel PR process and other contributing guidelines, see https://neurobagel.org/contributing/CONTRIBUTING/.
+-->
+
+<!-- 
+Please indicate after the # which issue you're closing with this PR, if applicable.
+If the PR closes multiple issues, include "closes" before each one is listed.
+You can also link to other issues if necessary, e.g. "See also #1234".
+
+https://help.github.com/articles/closing-issues-using-keywords
+-->
+- Closes #
+
+<!-- 
+Please give a brief overview of what has changed or been added in the PR.
+This can include anything specific the maintainers should be looking for when they review the PR.
+-->
+Changes proposed in this pull request:
+
+-
+-
+
+<!-- To be checked off by reviewers -->
+## Checklist
+_This section is for the PR reviewer_
+
+- [ ] PR has an interpretable title with a prefix (`[ENH]`, `[FIX]`, `[REF]`, `[TST]`, `[CI]`, `[MNT]`, `[INF]`, `[MODEL]`, `[DOC]`) _(see our [Contributing Guidelines](https://neurobagel.org/contributing/CONTRIBUTING#pull-request-guidelines) for more info)_
+- [ ] PR has a label for the release changelog or `skip-release` (to be applied by maintainers only)
+- [ ] PR links to GitHub issue with mention `Closes #XXXX`
+- [ ] Tests pass
+- [ ] Checks pass
+
+For new features:
+- [ ] Tests have been added
+
+For bug fixes:
+- [ ] There is at least one test that would fail under the original bug conditions.

bagel-0.9.2/.github/workflows/add_iss2project.yml

@@ -0,0 +1,23 @@
+name: Add new issues to project
+
+on:
+  issues:
+    types:
+      - opened
+
+jobs:
+  add-to-project:
+    name: Add issue to project
+    runs-on: ubuntu-latest
+    steps:
+      - name: Generate a token
+        id: generate-token
+        uses: actions/create-github-app-token@v2
+        with:
+          app-id: ${{ vars.NB_BOT_ID }}
+          private-key: ${{ secrets.NB_BOT_KEY }}
+
+      - uses: actions/add-to-project@main
+        with:
+          project-url: https://github.com/orgs/neurobagel/projects/1
+          github-token: ${{ steps.generate-token.outputs.token }}

bagel-0.9.2/.github/workflows/build_docker_nightly.yml

@@ -0,0 +1,38 @@
+# NOTE: A custom version of this template workflow is used in neurobagel/query-tool.
+# Any changes to this template must be applied manually to query-tool/.github/workflows/build_docker_nightly.yml
+
+name: build docker nightly
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+        # Some repos have submodules that need to be part of the Docker image
+        with:
+          submodules: recursive
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build and push
+        uses: docker/build-push-action@v6
+        with:
+          platforms: linux/arm64, linux/amd64
+          context: .
+          file: ./Dockerfile
+          push: true
+          tags: ${{ secrets.DOCKERHUB_USERNAME }}/${{ vars.DOCKERHUB_REPO }}:nightly

bagel-0.9.2/.github/workflows/build_docker_on_release.yml

@@ -0,0 +1,61 @@
+name: build Docker image on release
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v5
+        # Some repos have submodules that need to be part of the Docker image
+        with:
+          submodules: recursive
+      - 
+        # The release event is a superset of the push tag event, 
+        # so we expect two tags to be generated by docker/metadata-action 
+        # based on the behaviour for the type=semver,pattern=... tag type:
+        # 1. a semver tag vX.Y.Z (from the release Git tag; this is what will be used as the image version in the generated label)
+        # 2. latest (as type=semver,pattern=... is part of the latest tag handling)
+        # References:
+        # - https://github.com/docker/metadata-action?tab=readme-ov-file#typesemver
+        # - https://github.com/docker/metadata-action?tab=readme-ov-file#latest-tag
+        # - https://github.com/docker/metadata-action/issues/103
+        # - https://github.com/docker/metadata-action/issues/168
+        name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          # TODO: Repos with this wf must have DOCKERHUB_REPO set in the repository variables
+          images: ${{ secrets.DOCKERHUB_USERNAME }}/${{ vars.DOCKERHUB_REPO }}
+          # NOTE: This input is probably not necessary as the action should generate the appropriate tags
+          # based on the default type=ref,event=tag, but we define an explicit pattern here for clarity
+          tags: |
+            type=semver,pattern={{raw}}
+      -
+        name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      -
+        name: Build and push
+        uses: docker/build-push-action@v6
+        with:
+          platforms: linux/arm64, linux/amd64
+          context: .
+          file: ./Dockerfile
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          # Select a subset of labels to apply from https://github.com/opencontainers/image-spec/blob/main/annotations.md#pre-defined-annotation-keys,
+          # following https://github.com/docker/metadata-action/issues/303
+          labels: |
+            org.opencontainers.image.created=${{ fromJSON(steps.meta.outputs.json).labels['org.opencontainers.image.source'] }}
+            org.opencontainers.image.revision=${{ fromJSON(steps.meta.outputs.json).labels['org.opencontainers.image.revision'] }}
+            org.opencontainers.image.version=${{ fromJSON(steps.meta.outputs.json).labels['org.opencontainers.image.version'] }}

bagel-0.9.2/.github/workflows/cff_validation.yml

@@ -0,0 +1,23 @@
+---
+name: validate citation.cff
+
+on:
+  push:
+    branches: ['main']
+  pull_request:
+    branches: ['main']
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+
+  validate_cff:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v5
+    - name: Check whether the citation metadata from CITATION.cff is valid
+      uses: citation-file-format/cffconvert-github-action@2.0.0
+      with:
+        args: --validate

bagel-0.9.2/.github/workflows/codespell.yml

@@ -0,0 +1,19 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

bagel-0.9.2/.github/workflows/handle_external_pr.yml

@@ -0,0 +1,30 @@
+name: Label pull requests from forks
+
+on:
+  pull_request_target:
+    types: [opened]
+
+jobs:
+  handle_external_pr:
+    # Only run this entire workflow if the PR was opened from a forked repo
+    # The reasoning is that both bots and external contributors have to make
+    # a fork of the repo before they can open a PR because they don't have
+    # write access to the repo.
+    if: github.event.pull_request.head.repo.full_name != github.repository
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Label pull request with "_community"
+        run: gh pr edit ${{ github.event.pull_request.number }} -R ${{ github.repository }} --add-label "_community"
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  handle_precommit_pr:
+    if: contains(github.event.pull_request.title, '[pre-commit.ci]')
+    runs-on: ubuntu-latest
+    
+    steps:
+      - name: Label pull request with "_bot"
+        run: gh pr edit ${{ github.event.pull_request.number }} -R ${{ github.repository }} --add-label "_bot"
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

bagel-0.9.2/.github/workflows/release.yaml

@@ -0,0 +1,45 @@
+name: auto release
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  auto-release:
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, 'ci skip') && !contains(github.event.head_commit.message, 'skip ci')"
+    steps:
+      - name: Generate a token
+        id: generate-token
+        uses: actions/create-github-app-token@v2
+        with:
+          app-id: ${{ vars.NB_BOT_ID }}
+          private-key: ${{ secrets.NB_BOT_KEY }}
+
+      - name: Checkout
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+          token: ${{ steps.generate-token.outputs.token }}
+
+      - name: Download latest auto
+        run: |
+          auto_download_url="$(curl -fsSL https://api.github.com/repos/intuit/auto/releases/latest | jq -r '.assets[] | select(.name == "auto-linux.gz") | .browser_download_url')"
+          wget -O- "$auto_download_url" | gunzip > ~/auto
+          chmod a+x ~/auto
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.10"
+
+      - name: Install build & twine
+        run: python -m pip install build twine
+
+      - name: Release
+        run: ~/auto shipit -vv
+        env:
+          GH_TOKEN: ${{ steps.generate-token.outputs.token }}
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}

bagel-0.9.2/.github/workflows/stale.yml

@@ -0,0 +1,24 @@
+name: 'Close stale issues and PRs'
+on:
+  schedule:
+    - cron: '30 1 * * *'
+
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/stale@v10
+        with:
+          stale-issue-message: |
+            We want to keep our issues up to date and active. This issue hasn't seen any activity in the last 75 days.
+            We have applied the `_flag:stale` label to indicate that this issue should be reviewed again.
+            When you review, please reread the spec and then apply one of these three options:
+            - prioritize: apply the `flag:schedule` label to suggest moving this issue into the backlog now
+            - close: if the issue is no longer relevant, explain why (give others a chance to reply) and then close.
+            - archive: sometimes an issue has important information or ideas but we won't work on it soon. In this case
+            apply the `someday` label to show that this won't be prioritized. The stalebot will ignore issues with this
+            label in the future. Use sparingly!
+          days-before-stale: 75
+          days-before-close: -1
+          stale-issue-label: '_flag:stale'
+          exempt-issue-labels: 'Roadmap,Milestone,Epic,someday'

bagel-0.9.2/.github/workflows/test.yml

@@ -0,0 +1,37 @@
+name: Test
+
+on: [push, pull_request]
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11"]  # , "3.10" TODO: bids2table requires >=3.11 - remove matrix version once dependency is finalized
+
+    steps:
+    - uses: actions/checkout@v5
+      with:
+        submodules: recursive
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[test]
+
+    - name: Test with pytest
+      run: |
+        coverage run -m pytest
+        coverage lcov -o ./coverage/lcov.info
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v5
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}