Merge pull request #3192 from arjxn-py/add-more-precommits

Add more precommits

.git-blame-ignore-revs

@@ -2,3 +2,5 @@
 0054efe388d2d17301f7e0554449eac9a7d3b7fc
 # activated pre-commit for notebooks - https://github.com/pybamm-team/PyBaMM/pull/3110
 a63e49ece0f9336d1f5c2562f7459e555c6e6693
+# activated standard pre-commits - https://github.com/pybamm-team/PyBaMM/pull/3192
+5273214b585c5a4286609aed40e0b092d0e05f42

.github/workflows/lychee_url_checker.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
 
-      # cache Lychee results to avoid hitting rate limits  
+      # cache Lychee results to avoid hitting rate limits
       - name: Restore lychee cache
         uses: actions/cache@v3
         with:
@@ -42,7 +42,7 @@ jobs:
             --exclude https://twitter.com/pybamm_
             --exclude "https://doi\.org|www.sciencedirect\.com/*"
             --accept 200,429
-            --exclude-path ./CHANGELOG.md 
+            --exclude-path ./CHANGELOG.md
             --exclude-path ./scripts/update_version.py
             './**/*.rst'
             './**/*.md'

.github/workflows/need_reply_remove.yml

@@ -22,4 +22,4 @@ jobs:
           issue: ${{ github.event.issue.number }}
           label: needs-reply
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/needs_reply.yml

@@ -13,4 +13,4 @@ jobs:
         uses: dwieeb/needs-reply@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
-          issue-label: needs-reply
+          issue-label: needs-reply

.github/workflows/run_periodic_tests.yml

@@ -1,11 +1,11 @@
-# Run all unit tests and integration tests for all Python versions 
+# Run all unit tests and integration tests for all Python versions
 # and platforms at 3am UTC every day and on PRs to the main branch
 name: Scheduled
 
 on:
   workflow_dispatch:
   pull_request:
-    branches: 
+    branches:
     - main
 
   # Run everyday at 3 am UTC
@@ -119,13 +119,13 @@ jobs:
   build-apple-mseries:
     needs: style
     runs-on: [self-hosted, macOS, ARM64]
-    env: 
+    env:
       GITHUB_PATH: ${PYENV_ROOT/bin:$PATH}
     strategy:
       fail-fast: false
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
-        
+
     steps:
       - uses: actions/checkout@v3
       - name: Install python & create virtualenv

.pre-commit-config.yaml

@@ -21,3 +21,23 @@ repos:
     hooks:
        - id: blacken-docs
          additional_dependencies: [black==22.12.0]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+        - id: check-added-large-files
+        - id: check-case-conflict
+        - id: check-merge-conflict
+        - id: check-yaml
+        - id: debug-statements
+        - id: end-of-file-fixer
+        - id: mixed-line-ending
+        - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+        - id: python-check-blanket-type-ignore
+        - id: rst-backticks
+        - id: rst-directive-colons
+        - id: rst-inline-touching-normal

CMakeLists.txt

@@ -34,7 +34,7 @@ if(NOT PYBIND11_DIR)
 endif()
 
 add_subdirectory(${PYBIND11_DIR})
-pybind11_add_module(idaklu 
+pybind11_add_module(idaklu
   pybamm/solvers/c_solvers/idaklu/casadi_functions.cpp
   pybamm/solvers/c_solvers/idaklu/casadi_functions.hpp
   pybamm/solvers/c_solvers/idaklu/casadi_solver.cpp
@@ -56,7 +56,7 @@ if (NOT DEFINED USE_PYTHON_CASADI)
 endif()
 
 execute_process(
-    COMMAND "${PYTHON_EXECUTABLE}" -c 
+    COMMAND "${PYTHON_EXECUTABLE}" -c
     "import casadi as _; print(_.__path__[0])"
     OUTPUT_VARIABLE CASADI_DIR
     OUTPUT_STRIP_TRAILING_WHITESPACE)
@@ -67,7 +67,7 @@ endif()
 message("Found python casadi path: ${CASADI_DIR}")
 
 if(${USE_PYTHON_CASADI})
-  message("Trying to link against python casadi package")   
+  message("Trying to link against python casadi package")
   find_package(casadi CONFIG PATHS ${CASADI_DIR} REQUIRED)
 else()
   message("Trying to link against any casadi package apart from the python one")
@@ -78,7 +78,7 @@ endif()
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR})
 # Sundials
 find_package(SUNDIALS REQUIRED)
-message("sundials ${SUNDIALS_INCLUDE_DIR} ${SUNDIALS_LIBRARIES}") 
+message("sundials ${SUNDIALS_INCLUDE_DIR} ${SUNDIALS_LIBRARIES}")
 target_include_directories(idaklu PRIVATE ${SUNDIALS_INCLUDE_DIR})
 target_link_libraries(idaklu PRIVATE ${SUNDIALS_LIBRARIES} casadi)
 

FindSuiteSparse.cmake

@@ -1,4 +1,4 @@
-# This CMakeFile is adapted from that in dune-common: 
+# This CMakeFile is adapted from that in dune-common:
 
 # .. cmake_module::
 #
@@ -239,4 +239,3 @@ endif()
 #set HAVE_SUITESPARSE for config.h
 set(HAVE_SUITESPARSE ${SuiteSparse_FOUND})
 set(HAVE_UMFPACK ${SuiteSparse_UMFPACK_FOUND})
-

README.md

@@ -41,8 +41,8 @@ pay for developer time, professional services, travel, workshops, and a variety
 
 <div align="center">
   <a href="https://numfocus.org/project/pybamm">
-    <img height="60px" 
-         src="https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png" 
+    <img height="60px"
+         src="https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png"
          align="center">
   </a>
 </div>

benchmarks/__init__.py

@@ -1 +0,0 @@
-

build_manylinux_wheels/Dockerfile

@@ -15,4 +15,4 @@ RUN chmod +x /entrypoint.sh
 
 RUN ./install_sundials.sh
 
-ENTRYPOINT ["/entrypoint.sh"]
+ENTRYPOINT ["/entrypoint.sh"]

build_manylinux_wheels/install_sundials.sh

@@ -78,4 +78,3 @@ cmake -DENABLE_LAPACK=ON\
       -DCMAKE_INSTALL_PREFIX=/usr\
       ../$SUNDIALS_DIR
 make install
-

docs/Makefile

@@ -17,4 +17,3 @@ help:
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
     @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-