Merge pull request #2599 from bilke/hooks

Git hooks with pre-commit

.pre-commit-config.yaml

@@ -0,0 +1,36 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+    -   id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md, --markdown-linebreak-ext=pandoc]
+    -   id: check-added-large-files
+        args: [--maxkb 1024]
+    -   id: check-merge-conflict
+    -   id: check-xml
+    -   id: check-yaml
+-   repo: local
+    hooks:
+    -   id: git-diff-check
+        name: Run git diff --check
+        entry: git diff --check --cached -- ':!*.md' ':!*.pandoc' ':!*.asc' ':!*.dat' ':!*.ts'
+        language: system
+        stages: [commit, manual]
+    -   id: file-extensions
+        name: Check file extensions
+        entry: scripts/hooks/pre-commit-file-extensions.sh
+        language: system
+        files: '.*\.cpp'
+        stages: [commit, manual]
+    -   id: file-names
+        name: Check file names
+        entry: scripts/hooks/pre-commit-file-names.sh
+        language: system
+        stages: [commit, manual]
+    -   id: git-lfs
+        name: Check git lfs files
+        entry: scripts/hooks/pre-commit-git-lfs.sh
+        language: system
+        stages: [commit, manual]
+
+exclude: 'ThirdParty/*|Tests/Data/*|web/static/images/xsd'

Documentation/ProjectFile/material/solid/constitutive_relation/LinearElasticOrthotropic/t_poissons_ratios.md

@@ -7,5 +7,5 @@ are calculated by the symmetry property as \f$\nu_{ji} E_i = \nu_{ij} E_j\f$ (no
 They also must fulfil following two properties:
 \f[|\nu_{ij}| < \sqrt({E_i \over E_j}),\f]
 and
-\f[1 - \nu_{12}\nu_{21} - \nu_{23}\nu_{32} - \nu_{13}\nu_{31} 
+\f[1 - \nu_{12}\nu_{21} - \nu_{23}\nu_{32} - \nu_{13}\nu_{31}
 - \nu_{12}\nu_{23}\nu{31} - \nu_{32}\nu_{21}\nu{13} > 0.\f]

Jenkinsfile

@@ -25,9 +25,11 @@ pipeline {
   }
   stages {
      // *************************** Git Check **********************************
-    stage('Git Check') {
+    stage('Pre-checks') {
       agent { label "master"}
       steps {
+        sh "pre-commit install"
+        sh "pre-commit run --all-files"
         sh "git config core.whitespace -blank-at-eof"
         sh "git diff --check `git merge-base origin/master HEAD` HEAD -- . ':!*.md' ':!*.pandoc' ':!*.asc' ':!*.dat' ':!*.ts'"
         dir('scripts/jenkins') { stash(name: 'known_hosts', includes: 'known_hosts') }

Tests/MathLib/TestGlobalVectorInterface.cpp

@@ -208,7 +208,7 @@ void checkGlobalVectorInterfacePETSc()
     /*
          Assume there is a vector distributed over three processes as
           -- rank0 --    --- rank1 ---   -- rank2 --
-           0  1  2  3    4  5  6  7  8   9   10   11 
+           0  1  2  3    4  5  6  7  8   9   10   11
          where the numbers are the global entry indices.
          In each trunk of entries of a rank, there are ghost entries in
          other ranks attached and their global entry indices are:
@@ -224,7 +224,7 @@ void checkGlobalVectorInterfacePETSc()
 
          The above ghost entry embedded vector is realized by the following
          test.
-    */    
+    */
     std::size_t local_vec_size = 4;
     if (mrank == 1)
         local_vec_size = 5;
@@ -234,7 +234,7 @@ void checkGlobalVectorInterfacePETSc()
     std::vector<double> non_ghost_vals(local_vec_size);
     std::size_t nghosts = 3;
     if (mrank)
-        nghosts = 2;    
+        nghosts = 2;
     std::vector<GlobalIndexType> ghost_ids(nghosts);
     std::vector<double> expected;
     switch (mrank)

scripts/docker/Dockerfile.clang.full

@@ -39,15 +39,15 @@ RUN apt-get update -y && \
         python3-setuptools \
         python3-wheel && \
     rm -rf /var/lib/apt/lists/*
-RUN pip3 install virtualenv
-# CMake version 3.13.4
+RUN pip3 install virtualenv pre-commit
+# CMake version 3.12.4
 RUN apt-get update -y && \
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
         wget && \
     rm -rf /var/lib/apt/lists/*
-RUN mkdir -p /var/tmp && wget -q -nc --no-check-certificate -P /var/tmp https://cmake.org/files/v3.13/cmake-3.13.4-Linux-x86_64.sh && \
-    /bin/sh /var/tmp/cmake-3.13.4-Linux-x86_64.sh --prefix=/usr/local --skip-license && \
-    rm -rf /var/tmp/cmake-3.13.4-Linux-x86_64.sh
+RUN mkdir -p /var/tmp && wget -q -nc --no-check-certificate -P /var/tmp https://cmake.org/files/v3.12/cmake-3.12.4-Linux-x86_64.sh && \
+    /bin/sh /var/tmp/cmake-3.12.4-Linux-x86_64.sh --prefix=/usr/local --skip-license && \
+    rm -rf /var/tmp/cmake-3.12.4-Linux-x86_64.sh
 RUN apt-get update -y && \
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends software-properties-common && \
     apt-add-repository ppa:git-core/ppa -y && \
@@ -66,19 +66,28 @@ RUN apt-get update && \
     mkdir -p /apps /scratch /lustre /work /projects /data
 
 # Package manager Conan building block
+RUN apt-get update -y && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+        pkg-config && \
+    rm -rf /var/lib/apt/lists/*
+RUN apt-get update -y && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+        autoconf-archive \
+        libtool && \
+    rm -rf /var/lib/apt/lists/*
 # pip
 RUN apt-get update -y && \
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
         python3-pip \
         python3-setuptools \
         python3-wheel && \
     rm -rf /var/lib/apt/lists/*
-RUN pip3 install conan==1.17.0
+RUN pip3 install conan==1.18.0
 RUN mkdir -p /opt/conan && \
     chmod 777 /opt/conan
 ENV CONAN_USER_HOME=/opt/conan
 LABEL org.opengeosys.pm=conan \
-    org.opengeosys.pm.conan.version=1.17.0
+    org.opengeosys.pm.conan.version=1.18.0
 LABEL org.opengeosys.pm.conan.user_home=/opt/conan
 
 # Include-what-you-use for clang version 7
@@ -108,16 +117,12 @@ ENV CCACHE_DIR=/opt/cache \
 LABEL ccache.dir=/opt/cache \
     ccache.size=15G
 
-RUN apt-get update -y && \
-    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
-        sudo && \
-    rm -rf /var/lib/apt/lists/*
-
 # Jenkins node
 RUN apt-get update -y && \
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
         openssh-client \
-        rsync && \
+        rsync \
+        sudo && \
     rm -rf /var/lib/apt/lists/*
 RUN groupadd --gid 1001 jenkins || true && \
     adduser --uid 500 --gid 1001 --disabled-password --gecos "" jenkins && \

scripts/docker/Dockerfile.gcc.full

@@ -32,15 +32,15 @@ RUN apt-get update -y && \
         python3-setuptools \
         python3-wheel && \
     rm -rf /var/lib/apt/lists/*
-RUN pip3 install virtualenv
-# CMake version 3.13.4
+RUN pip3 install virtualenv pre-commit
+# CMake version 3.12.4
 RUN apt-get update -y && \
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
         wget && \
     rm -rf /var/lib/apt/lists/*
-RUN mkdir -p /var/tmp && wget -q -nc --no-check-certificate -P /var/tmp https://cmake.org/files/v3.13/cmake-3.13.4-Linux-x86_64.sh && \
-    /bin/sh /var/tmp/cmake-3.13.4-Linux-x86_64.sh --prefix=/usr/local --skip-license && \
-    rm -rf /var/tmp/cmake-3.13.4-Linux-x86_64.sh
+RUN mkdir -p /var/tmp && wget -q -nc --no-check-certificate -P /var/tmp https://cmake.org/files/v3.12/cmake-3.12.4-Linux-x86_64.sh && \
+    /bin/sh /var/tmp/cmake-3.12.4-Linux-x86_64.sh --prefix=/usr/local --skip-license && \
+    rm -rf /var/tmp/cmake-3.12.4-Linux-x86_64.sh
 RUN apt-get update -y && \
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends software-properties-common && \
     apt-add-repository ppa:git-core/ppa -y && \
@@ -59,19 +59,28 @@ RUN apt-get update && \
     mkdir -p /apps /scratch /lustre /work /projects /data
 
 # Package manager Conan building block
+RUN apt-get update -y && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+        pkg-config && \
+    rm -rf /var/lib/apt/lists/*
+RUN apt-get update -y && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+        autoconf-archive \
+        libtool && \
+    rm -rf /var/lib/apt/lists/*
 # pip
 RUN apt-get update -y && \
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
         python3-pip \
         python3-setuptools \
         python3-wheel && \
     rm -rf /var/lib/apt/lists/*
-RUN pip3 install conan==1.17.0
+RUN pip3 install conan==1.18.0
 RUN mkdir -p /opt/conan && \
     chmod 777 /opt/conan
 ENV CONAN_USER_HOME=/opt/conan
 LABEL org.opengeosys.pm=conan \
-    org.opengeosys.pm.conan.version=1.17.0
+    org.opengeosys.pm.conan.version=1.18.0
 LABEL org.opengeosys.pm.conan.user_home=/opt/conan
 
 # cppcheck version 1.87
@@ -111,16 +120,12 @@ ENV CCACHE_DIR=/opt/cache \
 LABEL ccache.dir=/opt/cache \
     ccache.size=15G
 
-RUN apt-get update -y && \
-    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
-        sudo && \
-    rm -rf /var/lib/apt/lists/*
-
 # Jenkins node
 RUN apt-get update -y && \
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
         openssh-client \
-        rsync && \
+        rsync \
+        sudo && \
     rm -rf /var/lib/apt/lists/*
 RUN groupadd --gid 1001 jenkins || true && \
     adduser --uid 500 --gid 1001 --disabled-password --gecos "" jenkins && \

scripts/docker/Dockerfile.gcc.gui

@@ -32,15 +32,15 @@ RUN apt-get update -y && \
         python3-setuptools \
         python3-wheel && \
     rm -rf /var/lib/apt/lists/*
-RUN pip3 install virtualenv
-# CMake version 3.13.4
+RUN pip3 install virtualenv pre-commit
+# CMake version 3.12.4
 RUN apt-get update -y && \
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
         wget && \
     rm -rf /var/lib/apt/lists/*
-RUN mkdir -p /var/tmp && wget -q -nc --no-check-certificate -P /var/tmp https://cmake.org/files/v3.13/cmake-3.13.4-Linux-x86_64.sh && \
-    /bin/sh /var/tmp/cmake-3.13.4-Linux-x86_64.sh --prefix=/usr/local --skip-license && \
-    rm -rf /var/tmp/cmake-3.13.4-Linux-x86_64.sh
+RUN mkdir -p /var/tmp && wget -q -nc --no-check-certificate -P /var/tmp https://cmake.org/files/v3.12/cmake-3.12.4-Linux-x86_64.sh && \
+    /bin/sh /var/tmp/cmake-3.12.4-Linux-x86_64.sh --prefix=/usr/local --skip-license && \
+    rm -rf /var/tmp/cmake-3.12.4-Linux-x86_64.sh
 RUN apt-get update -y && \
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends software-properties-common && \
     apt-add-repository ppa:git-core/ppa -y && \
@@ -67,19 +67,28 @@ RUN apt-get update -y && \
     rm -rf /var/lib/apt/lists/*
 
 # Package manager Conan building block
+RUN apt-get update -y && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+        pkg-config && \
+    rm -rf /var/lib/apt/lists/*
+RUN apt-get update -y && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+        autoconf-archive \
+        libtool && \
+    rm -rf /var/lib/apt/lists/*
 # pip
 RUN apt-get update -y && \
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
         python3-pip \
         python3-setuptools \
         python3-wheel && \
     rm -rf /var/lib/apt/lists/*
-RUN pip3 install conan==1.17.0
+RUN pip3 install conan==1.18.0
 RUN mkdir -p /opt/conan && \
     chmod 777 /opt/conan
 ENV CONAN_USER_HOME=/opt/conan
 LABEL org.opengeosys.pm=conan \
-    org.opengeosys.pm.conan.version=1.17.0
+    org.opengeosys.pm.conan.version=1.18.0
 LABEL org.opengeosys.pm.conan.user_home=/opt/conan
 
 # cppcheck version 1.87
@@ -112,16 +121,12 @@ ENV CCACHE_DIR=/opt/cache \
 LABEL ccache.dir=/opt/cache \
     ccache.size=15G
 
-RUN apt-get update -y && \
-    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
-        sudo pkg-config && \
-    rm -rf /var/lib/apt/lists/*
-
 # Jenkins node
 RUN apt-get update -y && \
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
         openssh-client \
-        rsync && \
+        rsync \
+        sudo && \
     rm -rf /var/lib/apt/lists/*
 RUN groupadd --gid 1001 jenkins || true && \
     adduser --uid 500 --gid 1001 --disabled-password --gecos "" jenkins && \

scripts/hooks/pre-commit-file-extensions.sh

@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+
+# set -e
+
+# Check for uppercase letters in filename extensions
+pattern=".*\.\w*([A-Z]+)\w*$"
+files=$(echo $@ | grep -E "$pattern")
+
+if [[ -n $files ]];
+then
+    echo "Attention!"
+    echo "----------"
+    echo "Found files that contain capital letters in the file extension."
+    echo "Please rename the following files and commit again:"
+
+    while read -r file; do
+        echo -e '\E[0;32m'"$file"'\033[0m'
+    done <<< "$files"
+    # Abort commit
+    exit 1
+fi
+
+exit 0

scripts/hooks/pre-commit-file-names.sh

@@ -0,0 +1,39 @@
+#!/bin/bash
+
+if git rev-parse --verify HEAD >/dev/null 2>&1
+then
+	against=HEAD
+else
+	# Initial commit: diff against an empty tree object
+	against=4b825dc642cb6eb9a060e54bf8d69288fbee4904
+fi
+
+# If you want to allow non-ASCII filenames set this variable to true.
+allownonascii=$(git config --bool hooks.allownonascii)
+
+# Redirect output to stderr.
+exec 1>&2
+
+# Cross platform projects tend to avoid non-ASCII filenames; prevent
+# them from being added to the repository. We exploit the fact that the
+# printable range starts at the space character and ends with tilde.
+if [ "$allownonascii" != "true" ] &&
+	# Note that the use of brackets around a tr range is ok here, (it's
+	# even required, for portability to Solaris 10's /usr/bin/tr), since
+	# the square bracket bytes happen to fall in the designated range.
+	test $($@ |
+	  LC_ALL=C tr -d '[ -~]\0' | wc -c) != 0
+then
+	cat <<\EOF
+Error: Attempt to add a non-ASCII file name.
+
+This can cause problems if you want to work with people on other platforms.
+
+To be portable it is advisable to rename the file.
+
+If you know what you are doing you can disable this check using:
+
+  git config hooks.allownonascii true
+EOF
+	exit 1
+fi