fix merge conflicts

.circleci/config.yml

@@ -1,3 +1,4 @@
+---
 # Documentation is built using Github Actions.
 # CircleCI is only used to download the artifacts in order to host
 # and deploy them.
@@ -7,84 +8,84 @@ version: 2.1
 # Parameters required to trigger the execution
 # of the "host_docs" job
 parameters:
-  GITHUB_RUN_URL:
-    type: string
-    default: "none"
+    GITHUB_RUN_URL:
+        type: string
+        default: none
 
 jobs:
-  host_docs:
-    machine:
-      image: ubuntu-2004:202111-01
-    environment:
-      GITHUB_ARTIFACT_URL: << pipeline.parameters.GITHUB_RUN_URL >>/doc.zip
-    steps:
-      - checkout
-      - run: bash build_tools/circle/download_documentation.sh
-      - store_artifacts:
-          path: doc/_build/html/
-          destination: dev
+    host_docs:
+        machine:
+            image: ubuntu-2004:202111-01
+        environment:
+            GITHUB_ARTIFACT_URL: << pipeline.parameters.GITHUB_RUN_URL >>/doc.zip
+        steps:
+        -   checkout
+        -   run: bash build_tools/circle/download_documentation.sh
+        -   store_artifacts:
+                path: doc/_build/html/
+                destination: dev
       # Persists the generated documentation, so that it
       # can be attached and deployed in the "deploy" job
-      - persist_to_workspace:
-          root: doc/_build
-          paths:
-              - html
+        -   persist_to_workspace:
+                root: doc/_build
+                paths:
+                -   html
 
-  deploy:
-    docker:
-      - image: circleci/python:3.9
-    steps:
-      - add_ssh_keys:
-          fingerprints:
-            - "19:56:86:2d:c6:df:02:f2:87:0e:59:a1:eb:b7:65:77"
-      - attach_workspace:
-          at: /tmp/_build
-      - run:
-          name: Fetch docs
-          command: |
-              set -e
-              mkdir -p ~/.ssh
-              ssh-keyscan github.com >> ~/.ssh/known_hosts;
-              if [ ! -d ~/nilearn.github.io ]; then
-                git clone git@github.com:nilearn/nilearn.github.io.git ~/nilearn.github.io --depth=1
-              fi
-      - run:
-          name: Deploy dev docs
-          command: |
-              set -e;
-              if [ "${CIRCLE_BRANCH}" == "main" ]; then
-                git config --global user.email "circle@nilearn.com";
-                git config --global user.name "CircleCI";
-                cd ~/nilearn.github.io;
-                git checkout main
-                git remote -v
-                git fetch origin
-                git reset --hard origin/main
-                git clean -xdf
-                echo "Deploying dev docs for ${CIRCLE_BRANCH}.";
-                rm -Rf dev;
-                cp -a /tmp/_build/html dev;
-                git add -A;
-                git commit -m "CircleCI update of dev docs (build: ${CIRCLE_BUILD_NUM}).";
-                git push origin main;
-              else
-                echo "No deployment (build: ${CIRCLE_BRANCH}).";
-              fi
+    deploy:
+        docker:
+        -   image: circleci/python:3.9
+        steps:
+        -   add_ssh_keys:
+                fingerprints:
+                -   19:56:86:2d:c6:df:02:f2:87:0e:59:a1:eb:b7:65:77
+        -   attach_workspace:
+                at: /tmp/_build
+        -   run:
+                name: Fetch docs
+                command: |
+                    set -e
+                    mkdir -p ~/.ssh
+                    ssh-keyscan github.com >> ~/.ssh/known_hosts;
+                    if [ ! -d ~/nilearn.github.io ]; then
+                      git clone git@github.com:nilearn/nilearn.github.io.git ~/nilearn.github.io --depth=1
+                    fi
+        -   run:
+                name: Deploy dev docs
+                command: |
+                    set -e;
+                    if [ "${CIRCLE_BRANCH}" == "main" ]; then
+                      git config --global user.email "circle@nilearn.com";
+                      git config --global user.name "CircleCI";
+                      cd ~/nilearn.github.io;
+                      git checkout main
+                      git remote -v
+                      git fetch origin
+                      git reset --hard origin/main
+                      git clean -xdf
+                      echo "Deploying dev docs for ${CIRCLE_BRANCH}.";
+                      rm -Rf dev;
+                      cp -a /tmp/_build/html dev;
+                      git add -A;
+                      git commit -m "CircleCI update of dev docs (build: ${CIRCLE_BUILD_NUM}).";
+                      git push origin main;
+                    else
+                      echo "No deployment (build: ${CIRCLE_BRANCH}).";
+                    fi
 
 workflows:
-  version: 2
+    version: 2
 
-  host_and_deploy_doc:
-    when:
-      not:
-        equal: [ "none", << pipeline.parameters.GITHUB_RUN_URL >> ]
+    host_and_deploy_doc:
+        when:
+            not:
+                equal: [none, << pipeline.parameters.GITHUB_RUN_URL >>]
     # The jobs should run only when triggered by the workflow
-    jobs:
-      - host_docs
-      - deploy:
-          requires:
-              - host_docs
-          filters:
-            branches:
-              only:
-                - main
+        jobs:
+        -   host_docs
+        -   deploy:
+                requires:
+                -   host_docs
+                filters:
+                    branches:
+                        only:
+                        -   main

.flake8

@@ -2,17 +2,22 @@
 exclude =
     .git,
     __pycache__,
-	env,
-	venv,
+	auto_examples,
     build,
     dist,
+	env,
 	nilearn/externals/tempita
+	nilearn/externals/
 	nilearn_cache
---select = D,E,F,W,C90
+	venv,
+	doc/_build
+--select = D,E,F,W,C90,CFQ
 docstring-convention = numpy
 max-line-length = 79
 max_complexity = 43
-max_function_length = 150
+max_function_length = 407
+max_parameters_amount = 26
+max_returns_amount = 10
 # For PEP8 error codes see
 # http://pep8.readthedocs.org/en/latest/intro.html#error-codes
 	# D100-D104: missing docstring
@@ -26,16 +31,15 @@ max_function_length = 150
 	# W503: line break before binary operator
 	# W504: line break after binary operator
 per-file-ignores =
-	*/__init__.py: D104
+	**/__init__.py: D104
     # - docstrings rules that should not be applied to tests
-	*/tests/*: D100, D101, D102, D103, D104, D205, D400, D401
-	*/*/tests/*: D100, D101, D102, D103, D104, D205, D400, D401
-	*/_testing.py: D100, D101, D102, D103, D104, D205, D400, D401
+	**/tests/*: D100, D101, D102, D103, D104, D205, D400, D401
+	**/_testing.py: D100, D101, D102, D103, D104, D205, D400, D401
     # - docstrings rules that should not be applied to examples
 	examples/*/*: D103, D205, D301, D400
     # - docstrings rules that should not be applied to doc
 	doc/*: D100, D103, F401
-ignore = D105, D107, E402, W503, W504, W605
+ignore = D105, D107, E402, W503, W504, W605, BLK100, CFQ003
 # for compatibility with black
 # https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#flake8
-extend-ignore = E203
+extend-ignore = E203

.git-blame-ignore-revs

@@ -1,42 +1,94 @@
+# Run this command to always ignore formatting commits in git blame
+# git config blame.ignoreRevsFile .git-blame-ignore-revs
 # ---------------------------------------------------------------------------- #
-#                               FORMATTING PRs
+#                             REFACTORING PRs
 #
-# Most recent PRs are at the top
+# Most recently merged PRs are at the top
 #
 # ---------------------------------------------------------------------------- #
-# [MAINT] Format nilearn/glm: apply isort and fix flake8 errors (#3640)
+# refactor nilearn/maskers (sourcery, f-strings) (#3685)
+37333f4604488ccef0ace5870ad442b725f60860
+# refactor nilearn/glm (sourcery, f-strings) (#3672)
+3522d9086eb9999d05549fc2ad0d13a83c590f8c
+# refactor nilearn/surface (sourcery, f-strings) (#3682)
+9352506d7d32fa17cc83971b011ad00932befe56
+# refactor nilearn/interfaces (sourcery, f-strings) (#3683)
+2e18c91342b65048307a21a45b5a8473414b6d16
+# ---------------------------------------------------------------------------- #
+#                             FORMATTING PRs
+#
+# Most recently merged PRs are at the top
+#
+# ---------------------------------------------------------------------------- #
+# [FMT] apply black (#3836)
+1b8c6ed6028e3ecf880597539f1de0910eb8d230
+# [FMT] apply black to plotting - part 4 (#3833)
+34613ab01d219924a8ed34677f48779d5d0b0cd1
+# [FMT] apply black to plotting - part 3 (#3827)
+ea375e01b35208f26aae9e66183fab245dd9862e
+# [FMT] apply black to plotting - part 2 (#3810)
+787d662116a0808d074b0dd40c9b4c2498712819
+# [FMT] apply black to maskers - part 2 (#3803)
+3f2628ffd016c9504c62db8560c5c4cc06d024c8
+# [FMT] apply black to plotting - part 1 (#3802)
+90dd16e20afafd2f9628bd5e08d3db3fe50353f2
+# [FMT] apply black to maskers - part 1 (#3795)
+aece81bb22bff7ad84427bda8d777eb072ade0b0
+# [FMT] apply black nilearn.plotting.display (#3790)
+186845cc04cb8c13c2dd5aa50eff2b426ec2329c
+# apply black to interface (#3783)
+43ff123df9e3849019c12d1c4125ed5fc8d21328
+# [MAINT] Update config black and pre-commit (#3777)
+caa8da8172c2ea56929ef6ecd3b592b963384370
+# run isort and flake8 on the whole nilearn code base in CI (#3651)
+44933309ecd09add795ce1c3ea5edaab4294da87
+# Format nilearn/plotting: apply isort and fix flake8 errors (#3648)
+115816702222182a244414540bb74687d7ea9597
+# Update config for formatting of nilearn/datasets (#3697)
+54aed7305f75be38d52d15ed30f80f45bfdd839f
+# Format datasets/atlas.py (#3694)
+983accf6d83983bae261143d311b2a9b10374d3a
+# Formatting _utils (#3614)
+9a507162952e8598c1281bfdd1b86f6d6ad14425
+# Format reporting (#3615)
+9ed76218dcef6814030c7473a52ae836d7a9ca7a
+# Format nilearn/surface: apply isort and fix flake8 errors (#3645)
+17d4b53d2bdb3a7722530eef9be1d58b305c9a0d
+# apply to black nilearn/glm (#3662)
+a9e13a62f4cbc9eddc4f789ee46c2e096c921f03
+# Format nilearn/glm: apply isort and fix flake8 errors (#3640)
 1c334c9f2bfc5f2f5057489ea199aee483b8874d
-# [MAINT] Format nilearn/interfaces: apply isort and fix flake8 errors (#3647)
+# Format nilearn/interfaces: apply isort and fix flake8 errors (#3647)
 32787d285228dc6c741198ed56d4a6af89445489
-# [MAINT] Format nilearn/maskers: apply isort and fix flake8 errors (#3650)
+# Format nilearn/maskers: apply isort and fix flake8 errors (#3650)
 d15ae59eb181f9980934452f9595d0625681c955
-# [MAINT] Format nilearn/input_data (#3646)
+# Format nilearn/input_data (#3646)
 4a0808b8ef3fe8da1a1e6f910725dacf11e21edd
-# [MAINT] Format files in nilearn folder (#3609)
+# Format files in nilearn folder (#3609)
 d5f11821da6c8852712a5d105d0afb478a04790f
-# [MAINT] Format mass univariate module (#3601)
+# Format mass univariate module (#3601)
 d5dd4ed4b402e0918ac791b20716db05ce14280f
-# [FMT] clean example/07_advanced and fix remaining style issues in examples (#3556)
+# clean example/07_advanced and fix remaining style issues in examples (#3556)
 6cf7b0e0a897d8b5f16d81d3831103af1123130b
-# [FMT] format image module (#3548)
+# format image module (#3548)
 92c9bf1e5ced1e9062576bfcc846bee4d20598cc
-# [FMT] format example/03_connectivity (#3552)
+# format example/03_connectivity (#3552)
 48fb614ca9ebf99635c78598d5b748080f67fb4d
-# [FMT] format example/02_decoding (#3551)
+# format example/02_decoding (#3551)
 1c87dc98574774f62da632284442a4056f77fea1
-# [MAINT] Apply precommit hooks to doc (#3566)
+# Apply precommit hooks to doc (#3566)
 5ddc12b585d8bd956df5e8f89c8d9d2ca37bc981
-# [FMT] format example/04_glm_first_level (#3553)
+# format example/04_glm_first_level (#3553)
 946440c527a077dc759d76bce7964dad18cd6b13
-# [FMT] format example/01_plotting (#3550)
+# format example/01_plotting (#3550)
 686a7debd73e746c282d8111d24343abb5c19d34
-# [FMT] format example/00_tutorials (#3549)
+# format example/00_tutorials (#3549)
 859a2b5141fc36fc01c402bdd3152683feab82e4
-# [MAINT] start applying isort to organize imports (#3538)
+# start applying isort to organize imports (#3538)
 bf2eb514acf75f338b28164563f6023d762fc95b
-# [MAINT] apply pre-commit to root files (#3533)
+# apply pre-commit to root files (#3533)
 f6db5d424cfb794dd9cf4ea93d8319e5fbc4565b
-# [INFRA] apply black, flake8, pyupgrade to `nilearn/decoding` (#3491)
+# apply black, flake8, pyupgrade to nilearn/decoding (#3491)
 f62e896234e389c9579bbf41b3c2531111cc6371
-# [INFRA] Initial formatting with black and precommit (#3484)
-77c1d785df4995166ea0a6798bc756f58f172812 
+# Initial formatting with black and precommit (#3484)
+77c1d785df4995166ea0a6798bc756f58f172812