Merge branch 'main' into sas/shlookup

Author: jonashaag

.github/workflows/codeql.yml

@@ -0,0 +1,31 @@
+name: CodeQL
+on:
+  schedule:
+    # every day at midnight
+    - cron: "0 0 * * *"
+
+concurrency:
+  group: ${{ github.repository }}-${{ github.head_ref || github.sha }}-${{ github.workflow }}
+  cancel-in-progress: true
+
+jobs:
+  analyze:
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language:
+          - python
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: github/codeql-action/init@v2
+        with:
+          languages: ${{ matrix.language }}
+      - uses: github/codeql-action/autobuild@v2
+      - uses: github/codeql-action/analyze@v2

.github/workflows/sdist.yml

@@ -79,9 +79,9 @@ jobs:
       run: |
         case "${{matrix.python-version}}" in
         3.8)
-          pip install numpy==1.19.5 ;;
+          pip install numpy==1.20.3 ;;
         3.9)
-          pip install numpy==1.19.5 ;;
+          pip install numpy==1.20.3 ;;
         3.10)
           pip install numpy==1.21.2 ;;
         esac

.pre-commit-config.yaml

@@ -85,32 +85,42 @@ repos:
 -   repo: local
     hooks:
     -   id: pyright
+        # note: assumes python env is setup and activated
         name: pyright
         entry: pyright
-        # note: assumes python env is setup and activated
         language: node
         pass_filenames: false
         types: [python]
         stages: [manual]
         additional_dependencies: &pyright_dependencies
-        - [email protected].258
+        - [email protected].264
     -   id: pyright_reportGeneralTypeIssues
+        # note: assumes python env is setup and activated
         name: pyright reportGeneralTypeIssues
         entry: pyright --skipunannotated -p pyright_reportGeneralTypeIssues.json
-        # note: assumes python env is setup and activated
         language: node
         pass_filenames: false
         types: [python]
         stages: [manual]
         additional_dependencies: *pyright_dependencies
     -   id: mypy
+        # note: assumes python env is setup and activated
         name: mypy
         entry: mypy
-        # note: assumes python env is setup and activated
         language: system
         pass_filenames: false
         types: [python]
         stages: [manual]
+    -   id: stubtest
+        # note: assumes python env is setup and activated
+        # note: requires pandas dev to be installed
+        name: mypy (stubtest)
+        entry: python
+        language: system
+        pass_filenames: false
+        types: [pyi]
+        args: [scripts/run_stubtest.py]
+        stages: [manual]
     -   id: flake8-rst
         name: flake8-rst
         description: Run flake8 on code snippets in docstrings or RST files
@@ -230,7 +240,7 @@ repos:
         language: python
         additional_dependencies:
         - flake8==4.0.1
-        - flake8-pyi==22.5.1
+        - flake8-pyi==22.7.0
     -   id: future-annotations
         name: import annotations from __future__
         entry: 'from __future__ import annotations'

ci/code_checks.sh

@@ -78,8 +78,8 @@ fi
 ### DOCSTRINGS ###
 if [[ -z "$CHECK" || "$CHECK" == "docstrings" ]]; then
 
-    MSG='Validate docstrings (EX04, GL01, GL02, GL03, GL04, GL05, GL06, GL07, GL09, GL10, PR03, PR04, PR05, PR06, PR08, PR09, PR10, RT01, RT04, RT05, SA02, SA03, SA04, SS01, SS02, SS03, SS04, SS05)' ; echo $MSG
-    $BASE_DIR/scripts/validate_docstrings.py --format=actions --errors=EX04,GL01,GL02,GL03,GL04,GL05,GL06,GL07,GL09,GL10,PR03,PR04,PR05,PR06,PR08,PR09,PR10,RT01,RT04,RT05,SA02,SA03,SA04,SS01,SS02,SS03,SS04,SS05
+    MSG='Validate docstrings (EX04, GL01, GL02, GL03, GL04, GL05, GL06, GL07, GL09, GL10, PR03, PR04, PR05, PR06, PR08, PR09, PR10, RT01, RT04, RT05, SA02, SA03, SA04, SS01, SS02, SS03, SS04, SS05, SS06)' ; echo $MSG
+    $BASE_DIR/scripts/validate_docstrings.py --format=actions --errors=EX04,GL01,GL02,GL03,GL04,GL05,GL06,GL07,GL09,GL10,PR03,PR04,PR05,PR06,PR08,PR09,PR10,RT01,RT04,RT05,SA02,SA03,SA04,SS01,SS02,SS03,SS04,SS05,SS06
     RET=$(($RET + $?)) ; echo $MSG "DONE"
 
 fi

ci/deps/actions-310-numpydev.yaml

@@ -16,8 +16,7 @@ dependencies:
   - pytz
   - pip
   - pip:
-    #- cython # TODO: don't install from master after Cython 3.0.0a11 is released
-    - "git+https://github.com/cython/cython.git@master"
+    - "cython"
     - "--extra-index-url https://pypi.anaconda.org/scipy-wheels-nightly/simple"
     - "--pre"
     - "numpy"

ci/deps/actions-310.yaml

@@ -5,7 +5,7 @@ dependencies:
   - python=3.10
 
   # test dependencies
-  - cython=0.29.30
+  - cython>=0.29.30
   - pytest>=6.0
   - pytest-cov
   - pytest-xdist>=1.31

ci/deps/actions-38-downstream_compat.yaml

@@ -6,7 +6,7 @@ dependencies:
   - python=3.8
 
   # test dependencies
-  - cython=0.29.30
+  - cython>=0.29.30
   - pytest>=6.0
   - pytest-cov
   - pytest-xdist>=1.31

ci/deps/actions-38-minimum_versions.yaml

@@ -7,7 +7,7 @@ dependencies:
   - python=3.8.0
 
   # test dependencies
-  - cython=0.29.30
+  - cython>=0.29.30
   - pytest>=6.0
   - pytest-cov
   - pytest-xdist>=1.31
@@ -17,7 +17,7 @@ dependencies:
 
   # required dependencies
   - python-dateutil=2.8.1
-  - numpy=1.19.5
+  - numpy=1.20.3
   - pytz=2020.1
 
   # optional dependencies

ci/deps/actions-38.yaml

@@ -5,7 +5,7 @@ dependencies:
   - python=3.8
 
   # test dependencies
-  - cython=0.29.30
+  - cython>=0.29.30
   - pytest>=6.0
   - pytest-cov
   - pytest-xdist>=1.31

ci/deps/actions-39.yaml

@@ -5,7 +5,7 @@ dependencies:
   - python=3.9
 
   # test dependencies
-  - cython=0.29.30
+  - cython>=0.29.30
   - pytest>=6.0
   - pytest-cov
   - pytest-xdist>=1.31