Merge pull request #768 from bids-standard/rel/0.14.0

REL: 0.14.0

.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: [email protected]

.mailmap

@@ -6,6 +6,7 @@ Christopher J. Markiewicz <[email protected]>
 Christopher J. Markiewicz <[email protected]> <[email protected]>
 Chris Holdgraf <[email protected]>
 Chris Holdgraf <[email protected]> <[email protected]>
+Dimitri Papadopoulos Orfanos <[email protected]>
 Dylan M. Nielson <[email protected]>
 Dylan M. Nielson <[email protected]> <[email protected]>
 Evgenii Kalenkovich <[email protected]>

.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"
     }

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)
 --------------------------------