diff --git a/.circleci/artifact_path b/.circleci/artifact_path deleted file mode 100644 index 640297398..000000000 --- a/.circleci/artifact_path +++ /dev/null @@ -1 +0,0 @@ -0/root/project/doc/_build/html/index.html diff --git a/.circleci/config.yml b/.circleci/config.yml deleted file mode 100644 index d29a041e1..000000000 --- a/.circleci/config.yml +++ /dev/null @@ -1,75 +0,0 @@ -version: 2 -jobs: - build_docs: - docker: - - image: python:3.7.4 - steps: - - checkout - - run: - name: Create virtual environment - command: | - python -m venv /tmp/venv - source /tmp/venv/bin/activate - - run: - name: Check Python version and upgrade pip - command: | - source /tmp/venv/bin/activate - which python - python --version - python -m pip install --upgrade pip setuptools - - run: - name: Install PyBIDS - command: | - source /tmp/venv/bin/activate - python -m pip install -e ".[doc]" - - run: - name: Build documentation - command: | - source /tmp/venv/bin/activate - make -C doc html - - store_artifacts: - path: /root/project/doc/_build/html - - persist_to_workspace: - root: doc/_build - paths: html - - deploy_docs: - docker: - - image: node:8.10.0 - steps: - - checkout - - attach_workspace: - at: doc/_build - - run: - name: Install and configure dependencies - command: | - npm install -g --silent gh-pages@2.2 - git config user.email "bids-maintenance@gmail.com" - git config user.name "BIDS Maintenance" - - add_ssh_keys: - fingerprints: - - "b1:24:94:8c:32:93:b9:46:48:42:77:1e:00:dc:d2:d" - - run: - name: Deploy docs to gh-pages branch - command: | - TIMESTAMP=$(date) - gh-pages --dotfiles --message "pybids docs built with Sphinx on $TIMESTAMP [skip ci]" --dist doc/_build/html - - -# https://circleci.com/docs/2.0/workflows/#git-tag-job-execution -workflows: - version: 2 - build_and_deploy: - jobs: - - build_docs: - filters: - tags: - only: /.*/ - - deploy_docs: - requires: - - build_docs - filters: - tags: - only: /^\d+\.\d+\.\d+/ - branches: - ignore: /.*/ diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 000000000..cde36a25a --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,58 @@ +name: Documentation + +on: + push: + branches: + - master + - maint/* + - rel/* + - docs/* + tags: + - '*' + +defaults: + run: + shell: bash + +jobs: + docs: + runs-on: ubuntu-latest + strategy: + matrix: + include: + - python-version: 3.9 + steps: + - uses: actions/checkout@v2 + with: + submodules: recursive + fetch-depth: 0 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + - name: Display Python version + run: python -c "import sys; print(sys.version)" + - name: Create virtual environment + run: tools/ci/create_venv.sh + - name: Install pybids + run: tools/ci/install_extras.sh + env: + EXTRA_PIP_FLAGS: "" + CHECK_TYPE: doc + - name: Build documentation + run: | + source tools/ci/activate.sh + make -C doc html + - name: Upload docs as artifacts + uses: actions/upload-artifact@v2 + with: + path: doc/_build/html + - name: Deploy (on tags) + if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') + uses: peaceiris/actions-gh-pages@v3 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: doc/_build/html + force_orphan: true + user_name: "BIDS Maintenance" + user_email: bids-maintenance@gmail.com diff --git a/.mailmap b/.mailmap index e78303272..406f39463 100644 --- a/.mailmap +++ b/.mailmap @@ -6,6 +6,7 @@ Christopher J. Markiewicz Christopher J. Markiewicz Chris Holdgraf Chris Holdgraf +Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Dylan M. Nielson Dylan M. Nielson Evgenii Kalenkovich diff --git a/.zenodo.json b/.zenodo.json index 04f4aaf40..a3f8347e9 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -56,6 +56,10 @@ "name": "Esteban, Oscar", "orcid": "0000-0001-8435-6191" }, + { + "name": "Kalenkovich, Evgenii", + "orcid": "0000-0002-4606-4179" + }, { "affiliation": "Institute for Problems of Information Transmission", "name": "Petrov, Dmitry" @@ -70,6 +74,11 @@ "name": "Appelhoff, Stefan", "orcid": "0000-0001-8002-0877" }, + { + "name": "Bansal, Shashank", + "affiliation": "Stanford University", + "orcid": "0000-0002-1252-8772 " + }, { "affiliation": "Concordia University", "name": "Hayot-Sasson, Val\u00e9rie", @@ -80,6 +89,9 @@ "name": "Nielson, Dylan M.", "orcid": "0000-0003-4613-6643" }, + { + "name": "Papadopoulos Orfanos, Dimitri" + }, { "affiliation": "MRC Cognition and Brain Sciences Unit", "name": "Carlin, Johan", @@ -181,9 +193,6 @@ "name": "Holdgraf, Chris", "orcid": "0000-0002-2391-0678" }, - { - "name": "Kalenkovich, Evgenii" - }, { "affiliation": "Queen Mary University London", "name": "Staden, Isla", @@ -252,11 +261,6 @@ "name": "Blair, Ross", "orcid": "0000-0003-3007-1056" }, - { - "name": "Shashank Bansal", - "affiliation": "Stanford University", - "orcid": "0000-0002-1252-8772 " - }, { "name": "Sundaravadivelu, Suganya" } diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 0243257d1..3af72e379 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -1,6 +1,45 @@ Changelog ========= +Version 0.14.0 (November 09, 2021) +---------------------------------- + +New feature release in the 0.14.x series. + +This release includes a significant refactor of BIDS Statistical Models, +replacing the ``bids.analysis`` module with ``bids.modeling``. + +Changes to ``bids.layout`` are minimal, and we do not anticipate API breakage. + +* FIX: LGTM.com warning: Implicit string concatenation in a list (#785) +* FIX: Take the intersection of variables and Model.X, + ignoring missing variables (usually contrasts) (#764) +* FIX: Associate "is_metadata" with Tag, not Entity; and only return + non-metadata entries for core Entities in ``get(return_type='id')`` (#749) +* FIX: Only include regressors if they are TSV (#752) +* FIX: ensure force_dense=True runs to_dense only on sparse variables (#745) +* FIX: get unique, with conflicting meta-data (#748) +* FIX: Clean up some deprecation and syntax warnings (#738) +* ENH: Add ``pybids upgrade`` command (#654) +* ENH: Add Lag transformation (#759) +* ENH: Use indirect transformations structure (#737) +* ENH: Add visualization for statsmodel graph (#742) +* ENH: Permit explicit intercept (1) in Contrasts and DummyContrasts (#743) +* ENH: Add meta-analysis model type (#731) +* ENH: Contrast type is now test (#733) +* REF: Use pathlib.Path internally when possible (#746) +* REF: Remove group_by from edges and add filter (#734) +* REF: Improved/refactored StatsModels module (#722) +* MNT: Make sure codespell skips .git when run locally (#787) +* MNT: LGTM.com recommendations (#786) +* MNT: Better codespell configuration (#782) +* MNT: Constrain formulaic version to 0.2.x . (#784) +* MNT: Update versioneer: 0.18 → 0.20 (#778) +* MNT: Add "codespell" tool to CI checks to catch typos sooner (#776) +* MNT: Disable bids-nodot mode (#769) +* MNT: Send codecov reports again (#766) +* MNT: Set minimum version to Python 3.6 (#739) + Version 0.13.2 (August 20, 2021) --------------------------------