Merge branch 'main' into trim_zeros

Author: lagru

.circleci/config.yml

@@ -1,115 +1,171 @@
-# Python CircleCI 2.0 configuration file
+# Python CircleCI 2.1 configuration file
 #
-# Check https://circleci.com/docs/2.0/language-python/ for more details
+# Check https://circleci.com/docs/2.1/language-python/ for more details
 #
-version: 2
-jobs:
-  build:
-    docker:
-      # CircleCI maintains a library of pre-built images
-      # documented at https://circleci.com/docs/2.0/circleci-images/
-      - image: circleci/python:3.6.6
+version: 2.1
 
-    working_directory: ~/repo
+# Aliases to reuse
+_defaults: &defaults
+  docker:
+    # CircleCI maintains a library of pre-built images
+    # documented at https://circleci.com/developer/images/image/cimg/python
+    - image: cimg/python:3.11.8
+  working_directory: ~/repo
 
+
+jobs:
+  build:
+    <<: *defaults
     steps:
       - checkout
 
       - run:
-          name: install dependencies
+          name: check skip
           command: |
-            python3 -m venv venv
-            ln -s $(which python3) venv/bin/python3.6
-            . venv/bin/activate
-            pip install cython sphinx==2.2.0 matplotlib ipython
-            sudo apt-get update
-            sudo apt-get install -y graphviz texlive-fonts-recommended texlive-latex-recommended texlive-latex-extra texlive-generic-extra latexmk texlive-xetex
+            export git_log=$(git log --max-count=1 --pretty=format:"%B" | tr "\n" " ")
+            echo "Got commit message:"
+            echo "${git_log}"
+            if [[ -v CIRCLE_PULL_REQUEST ]] && \
+               ([[ "$git_log" == *"[skip circle]"* ]] || \
+                [[ "$git_log" == *"[circle skip]"* ]])
+            then
+              echo "Skip detected, exiting job ${CIRCLE_JOB} for PR ${CIRCLE_PULL_REQUEST}."
+              circleci-agent step halt;
+            fi
+      - run:
+          name: pull changes from merge
+          command: |
+            if [[ -v CI_PULL_REQUEST ]] ; then git pull --ff-only origin "refs/pull/${CI_PULL_REQUEST//*pull\//}/merge" ; fi
 
       - run:
-          name: build numpy
+          name: update submodules
           command: |
-            . venv/bin/activate
-            pip install --upgrade pip setuptools
-            pip install cython
-            pip install .
-            pip install scipy
+            git submodule update --init
+
+      - run:
+          name: install system dependencies
+          command: |
+            sudo apt-get update
+            sudo apt-get install -y graphviz texlive-fonts-recommended texlive-latex-recommended \
+              texlive-latex-extra latexmk texlive-xetex texlive-lang-chinese doxygen
 
       - run:
-          name: create release notes
+          name: build NumPy
           command: |
+            python3.11 -m venv venv
             . venv/bin/activate
-            pip install git+https://github.com/hawkowl/towncrier.git@master
-            VERSION=$(python -c "import setup; print(setup.VERSION)")
-            towncrier --version $VERSION --yes
-            ./tools/ci/test_all_newsfragments_used.py
+            pip install --progress-bar=off -r requirements/test_requirements.txt \
+               -r requirements/build_requirements.txt \
+               -r requirements/ci_requirements.txt
+            # get newer, pre-release versions of critical packages
+            pip install --progress-bar=off --pre --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple -r requirements/doc_requirements.txt
+            # then install numpy HEAD, which will override the version installed above
+            spin build --with-scipy-openblas=64
+
       - run:
-          name: build devdocs
+          name: build devdocs w/ref warnings
           command: |
             . venv/bin/activate
-            cd doc
-            git submodule update --init
-            SPHINXOPTS=-q make -e html
+            # Don't use -q, show warning summary"
+            SPHINXOPTS="-W -n" spin docs
+            if [[ $(find doc/build/html -type f | wc -l) -lt 1000 ]]; then
+                echo "doc build failed: doc/build/html is empty"
+                exit -1
+            fi
 
       - run:
           name: build neps
           command: |
             . venv/bin/activate
             cd doc/neps
-            SPHINXOPTS=-q make -e html
+            SPHINXOPTS="-n" make -e html || echo "ignoring errors for now"
 
       - store_artifacts:
           path: doc/build/html/
 
-
-     #  - store_artifacts:
-     #      path: doc/neps/_build/html/
+      - store_artifacts:
+          path: doc/neps/_build/html/
      #      destination: neps
 
+      - run:
+          name: check doctests
+          command: |
+            . venv/bin/activate
+            spin check-docs -v
+            spin check-tutorials -v
+            # Currently, this does two checks not done by check-docs:
+            #  - validates ReST blocks (via validate_rst_syntax)
+            #  - checks that all of a module's `__all__` is reflected in the
+            #    module-level docstring autosummary
+            echo calling python tools/refguide_check.py -v
+            python tools/refguide_check.py -v
+
+      - persist_to_workspace:
+          root: ~/repo
+          paths:
+            - doc/build/html
+            - doc/neps/_build
+            - tools/ci/push_docs_to_repo.py
+
+  deploy:
+    <<: *defaults
+    steps:
+      - checkout
+
+      - attach_workspace:
+          at: ~/repo
+
       - add_ssh_keys:
           fingerprints:
-            - "9f:8c:e5:3f:53:40:0b:ee:c9:c3:0f:fd:0f:3c:cc:55"
+            - "45:d8:d1:d6:f7:53:47:c5:d0:9e:35:19:79:e7:ff:24"
 
       -  run:
           name: deploy devdocs
           command: |
-            if [ "${CIRCLE_BRANCH}" == "master" ]; then
-              touch doc/build/html/.nojekyll
-
-              ./tools/ci/push_docs_to_repo.py doc/build/html \
-                  [email protected]:numpy/devdocs.git \
-                  --committer "numpy-circleci-bot" \
-                  --email "numpy-circleci-bot@nomail" \
-                  --message "Docs build of $CIRCLE_SHA1" \
-                  --force
-            else
-              echo "Not on the master branch; skipping deployment"
-            fi
+            touch doc/build/html/.nojekyll
+
+            ./tools/ci/push_docs_to_repo.py doc/build/html \
+                --committer "numpy-circleci-bot" \
+                --email "numpy-circleci-bot@nomail" \
+                --message "Docs build of $CIRCLE_SHA1" \
+                --count 5 \
+                --force \
+                [email protected]:numpy/devdocs.git
 
       - add_ssh_keys:
           fingerprints:
-            - "11:fb:19:69:80:3a:6d:37:9c:d1:ac:20:17:cd:c8:17"
+            - "df:8b:fb:34:2d:38:7d:49:fc:1b:e8:44:4f:bd:2c:0e"
 
       - run:
           name: select SSH key for neps repo
           command: |
-            cat <<\EOF > ~/.ssh/config
+            cat \<<\EOF > ~/.ssh/config
             Host github.com
               IdentitiesOnly yes
-              IdentityFile /home/circleci/.ssh/id_rsa_11fb1969803a6d379cd1ac2017cdc817
+              IdentityFile /home/circleci/.ssh/id_rsa_df8bfb342d387d49fc1be8444fbd2c0e
             EOF
 
       -  run:
           name: deploy neps
           command: |
-            if [ "${CIRCLE_BRANCH}" == "master" ]; then
-              touch doc/neps/_build/html/.nojekyll
-
-              ./tools/ci/push_docs_to_repo.py doc/neps/_build/html \
-                  [email protected]:numpy/neps.git \
-                  --committer "numpy-circleci-bot" \
-                  --email "numpy-circleci-bot@nomail" \
-                  --message "Docs build of $CIRCLE_SHA1" \
-                  --force
-            else
-              echo "Not on the master branch; skipping deployment"
-            fi
+            touch doc/neps/_build/html/.nojekyll
+
+            ./tools/ci/push_docs_to_repo.py doc/neps/_build/html \
+                --committer "numpy-circleci-bot" \
+                --email "numpy-circleci-bot@nomail" \
+                --message "Docs build of $CIRCLE_SHA1" \
+                --count 5 \
+                --force \
+                [email protected]:numpy/neps.git \
+
+workflows:
+  version: 2
+  default:
+    jobs:
+      - build
+      - deploy:
+          requires:
+            - build
+          filters:
+            branches:
+              only: main

.cirrus.star

@@ -0,0 +1,54 @@
+# The guide to programming cirrus-ci tasks using starlark is found at
+# https://cirrus-ci.org/guide/programming-tasks/
+#
+# In this simple starlark script we simply check conditions for whether
+# a CI run should go ahead. If the conditions are met, then we just
+# return the yaml containing the tasks to be run.
+
+load("cirrus", "env", "fs", "http")
+
+def main(ctx):
+    ######################################################################
+    # Should wheels be built?
+    # Only test on the numpy/numpy repository
+    ######################################################################
+
+    if env.get("CIRRUS_REPO_FULL_NAME") != "numpy/numpy":
+        return []
+
+    # only run the wheels entry on a cron job
+    if env.get("CIRRUS_CRON", "") == "nightly":
+        return fs.read("tools/ci/cirrus_wheels.yml")
+
+    # Obtain commit message for the event. Unfortunately CIRRUS_CHANGE_MESSAGE
+    # only contains the actual commit message on a non-PR trigger event.
+    # For a PR event it contains the PR title and description.
+    SHA = env.get("CIRRUS_CHANGE_IN_REPO")
+    url = "https://api.github.com/repos/numpy/numpy/git/commits/" + SHA
+    dct = http.get(url).json()
+
+    commit_msg = dct["message"]
+    if "[skip cirrus]" in  commit_msg or "[skip ci]" in commit_msg:
+        return []
+
+    wheel = False
+    labels = env.get("CIRRUS_PR_LABELS", "")
+    pr_number = env.get("CIRRUS_PR", "-1")
+    tag = env.get("CIRRUS_TAG", "")
+
+    if "[wheel build]" in commit_msg:
+        wheel = True
+
+    # if int(pr_number) > 0 and ("14 - Release" in labels or "36 - Build" in labels):
+    #     wheel = True
+
+    if tag.startswith("v") and "dev0" not in tag:
+        wheel = True
+
+    if wheel:
+        return fs.read("tools/ci/cirrus_wheels.yml")
+
+    if int(pr_number) < 0:
+        return []
+
+    return fs.read("tools/ci/cirrus_arm.yml")

.clang-format

@@ -0,0 +1,37 @@
+# A clang-format style that approximates Python's PEP 7
+# Useful for IDE integration
+#
+# Based on Paul Ganssle's version at
+# https://gist.github.com/pganssle/0e3a5f828b4d07d79447f6ced8e7e4db
+# and modified for NumPy
+BasedOnStyle: Google
+AlignAfterOpenBracket: Align
+AllowShortEnumsOnASingleLine: false
+AllowShortIfStatementsOnASingleLine: false
+AlwaysBreakAfterReturnType: TopLevel
+BreakBeforeBraces: Stroustrup
+ColumnLimit: 79
+ContinuationIndentWidth: 8
+DerivePointerAlignment: false
+IndentWidth: 4
+IncludeBlocks: Regroup
+IncludeCategories:
+  - Regex:           '^[<"](Python|structmember|pymem)\.h'
+    Priority:        -3
+    CaseSensitive:   true
+  - Regex:           '^"numpy/'
+    Priority:        -2
+  - Regex:           '^"(npy_pycompat|npy_config)'
+    Priority:        -1
+  - Regex:           '^"[[:alnum:]_.]+"'
+    Priority:        1
+  - Regex:           '^<[[:alnum:]_.]+"'
+    Priority:        2
+Language: Cpp
+PointerAlignment: Right
+ReflowComments: true
+SpaceBeforeParens: ControlStatements
+SpacesInParentheses: false
+StatementMacros: [PyObject_HEAD, PyObject_VAR_HEAD, PyObject_HEAD_EXTRA]
+TabWidth: 4
+UseTab: Never

.codecov.yml

@@ -6,8 +6,9 @@ coverage:
   status:
     project:
       default:
-        # Require 1% coverage, i.e., always succeed
-        target: 1
-    patch: false
+        informational: true
+    patch:
+      default:
+        informational: true
     changes: false
 comment: off

.dependabot/config.yml

@@ -0,0 +1,17 @@
+{
+	// More info about Features: https://containers.dev/features
+	"image": "mcr.microsoft.com/devcontainers/universal:2",
+	"features": {},
+
+	"onCreateCommand": ".devcontainer/setup.sh",
+	"postCreateCommand": "",
+
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"ms-python.python"
+			],
+			"settings": {}
+		}
+	}
+}

.devcontainer/devcontainer.json

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+set -e
+
+"${SHELL}" <(curl -Ls micro.mamba.pm/install.sh) < /dev/null
+
+conda init --all
+micromamba shell init -s bash
+micromamba env create -f environment.yml --yes
+# Note that `micromamba activate numpy-dev` doesn't work, it must be run by the
+# user (same applies to `conda activate`)
+
+git submodule update --init
+
+# Enables users to activate environment without having to specify the full path
+echo "envs_dirs:
+  - /home/codespace/micromamba/envs" > /opt/conda/.condarc