.gitlab/before.sh

+#!/bin/bash
+
+
+if [ "$OS" == "win7" ]; then
+    # there is no docker on windows
+    CONTAINER_ID=0
+else
+    CONTAINER_ID=$(cat /proc/self/cgroup | head -n 1 | cut -d '/' -f3)
+fi
+
+# default stage is coverage
+if [[ "$CAMITK_CI_STAGE" == "" ]]; then 
+    CAMITK_CI_STAGE="$STAGE_COVERAGE";
+fi
+
+# default mode is Continuous for develop, Experimental for any other branches
+if [[ "$CAMITK_CI_MODE" == "" ]]; then 
+    if [[ "$CI_COMMIT_REF_NAME" == "develop" ]]; then 
+        CAMITK_CI_MODE="Continuous"; 
+    else 
+        CAMITK_CI_MODE="Experimental"; 
+    fi
+fi
+
+# Check git commit message
+MESSAGE_CHECK=$(git log -n 1 | grep --quiet --extended-regexp '/check' && echo "true" || echo "false")
+MESSAGE_CONFIGURE=$(git log -n 1 | grep --quiet --extended-regexp '/configure' && echo "true" || echo "false")
+MESSAGE_BUILD=$(git log -n 1 | grep --quiet --extended-regexp '/build' && echo "true" || echo "false")
+MESSAGE_TEST=$(git log -n 1 | grep --quiet --extended-regexp '/test' && echo "true" || echo "false")
+MESSAGE_COVERAGE=$(git log -n 1 | grep --quiet --extended-regexp '/coverage' && echo "true" || echo "false")
+
+# store variables in a local file
+TRIGGER_FILE=/tmp/trigger-stage.txt
+rm -f $TRIGGER_FILE
+echo "Triggered stages:" > $TRIGGER_FILE
+
+# check MESSAGE variables and CAMITK_CI_STAGE value
+if [[ "$MESSAGE_CHECK" == "true" || "$CAMITK_CI_STAGE" -ge $STAGE_CHECK ]]; then 
+    echo "TRIGGER_STAGE_CHECK" >> $TRIGGER_FILE
+fi
+
+if [[ "$MESSAGE_CONFIGURE" == "true" || "$CAMITK_CI_STAGE" -ge $STAGE_CONFIGURE ]]; then 
+    echo "TRIGGER_STAGE_CONFIGURE" >> $TRIGGER_FILE
+fi
+
+if [[ "$MESSAGE_BUILD" == "true" || "$CAMITK_CI_STAGE" -ge $STAGE_BUILD ]]; then
+    echo "TRIGGER_STAGE_BUILD" >> $TRIGGER_FILE
+fi
+
+if [[ "$MESSAGE_TEST" == "true" || "$CAMITK_CI_STAGE" -ge $STAGE_TEST ]]; then
+    echo "TRIGGER_STAGE_TEST" >> $TRIGGER_FILE
+fi
+
+if [[ "$MESSAGE_COVERAGE" == "true" || "$CAMITK_CI_STAGE" -ge $STAGE_COVERAGE ]]; then
+    echo "TRIGGER_STAGE_COVERAGE" >> $TRIGGER_FILE
+fi
+
+
+# output all information to report file
+echo "Docker container id....... $CONTAINER_ID" > /tmp/report.txt
+echo "Job....................... $CI_JOB_NAME" >> /tmp/report.txt
+echo "Build Directory........... $PROJECT_BUILD_DIR" >> /tmp/report.txt
+echo "Log Directory............. $PROJECT_LOG_DIR" >> /tmp/report.txt
+echo "Branch.................... $CI_COMMIT_REF_NAME" >> /tmp/report.txt
+echo "CAMITK_CI_MODE............ $CAMITK_CI_MODE" >> /tmp/report.txt
+echo "CAMITK_CI_STAGE........... $CAMITK_CI_STAGE" >> /tmp/report.txt
+
+# cleanup log directory
+if [ -d ${PROJECT_LOG_DIR} ] ; then 
+    rm -rf ${PROJECT_LOG_DIR};
+fi
+mkdir -p ${PROJECT_LOG_DIR}
+
+# show report
+cat /tmp/report.txt
+cp -f $TRIGGER_FILE ${PROJECT_LOG_DIR}
+cat ${PROJECT_LOG_DIR}/trigger-stage.txt

.gitlab/build.sh

+#!/bin/bash
+# Uncomment next line to print each bash command before it is executed
+#set -x
+
+echo "Job $CI_JOB_NAME"
+
+if ! grep -q TRIGGER_STAGE_BUILD "${PROJECT_LOG_DIR}/trigger-stage.txt"; then
+    echo "Job skipped as /build flag not in commit message and CAMITK_CI_STAGE < $STAGE_CONFIGURE"; 
+    exit 1;
+fi
+
+echo "===== build ====="
+
+if [ "$OS" == "win7" ]; then
+    # there is no xvfb on windows
+    ctest   -VV \
+            -DCTEST_SITE="$CDASH_SITE" \
+            -DCI_MODE="$CAMITK_CI_MODE" \
+            -DCI_ID="P $CI_PIPELINE_ID - J $CI_BUILD_ID" \
+            -DCI_BRANCH="$CI_COMMIT_REF_NAME" \
+            -DCI_BUILD_SETTINGS="$COMPILER_CONFIG" \
+            -DCTEST_SOURCE_DIRECTORY="$PROJECT_SOURCE_DIR" \
+            -DCTEST_BINARY_DIRECTORY="$PROJECT_BUILD_DIR" \
+            -S $PROJECT_SOURCE_DIR/sdk/cmake/ctest/ci-build.cmake > >(tee ${PROJECT_LOG_DIR}/build.log | grep --line-buffered -e "- Building" -e "Compiler errors" -e "Compiler warnings") 2>&1
+else
+    # on Linux, xvfb is required to run the tests
+    xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" \
+    ctest   -VV \
+            -DCTEST_SITE="$CDASH_SITE" \
+            -DCI_MODE="$CAMITK_CI_MODE" \
+            -DCI_ID="P $CI_PIPELINE_ID - J $CI_BUILD_ID" \
+            -DCI_BRANCH="$CI_COMMIT_REF_NAME" \
+            -DCI_BUILD_SETTINGS="$COMPILER_CONFIG" \
+            -DCTEST_SOURCE_DIRECTORY="$PROJECT_SOURCE_DIR" \
+            -DCTEST_BINARY_DIRECTORY="$PROJECT_BUILD_DIR" \
+            -S $PROJECT_SOURCE_DIR/sdk/cmake/ctest/ci-build.cmake > >(tee ${PROJECT_LOG_DIR}/build.log | grep --line-buffered -e "\[100%] Built target") 2>&1
+fi

.gitlab/check.sh

+#!/bin/bash
+
+echo "Job $CI_JOB_NAME"
+
+if [ "$TRIGGER_STAGE_CHECK" == "false" ]; then 
+    echo "Job skipped as /check flag not in commit message and CAMITK_CI_STAGE < $STAGE_CHECK"; 
+    exit 1; 
+fi
+
+pwd
+printenv

.gitlab/configure.sh

+#!/bin/bash
+# Uncomment next line to print each bash command before it is executed
+#set -x
+
+echo "Job $CI_JOB_NAME"
+
+if ! grep -q TRIGGER_STAGE_CONFIGURE "${PROJECT_LOG_DIR}/trigger-stage.txt"; then
+    echo "Job skipped as /configure flag not in commit message and CAMITK_CI_STAGE < $STAGE_CONFIGURE"; 
+    exit 1;
+fi
+
+echo "===== configure ====="
+
+# Clean build directory
+# note: cannot build outside the source tree otherwise artifacts cannot be collected
+if [ "$CAMITK_CI_MODE" == "Nightly" ]; then 
+    rm -rf ${PROJECT_BUILD_DIR}; 
+    echo "Nightly Build, start from scratch"; 
+fi
+
+if [ "$OS" == "win7" ]; then
+    # there is no xvfb on windows
+    ctest   -VV \
+            -DCTEST_SITE="$CDASH_SITE" \
+            -DCI_MODE="$CAMITK_CI_MODE" \
+            -DCI_ID="P $CI_PIPELINE_ID - J $CI_BUILD_ID" \
+            -DCI_BRANCH="$CI_COMMIT_REF_NAME" \
+            -DCI_BUILD_SETTINGS="$COMPILER_CONFIG" \
+            -DCTEST_SOURCE_DIRECTORY="$PROJECT_SOURCE_DIR" \
+            -DCTEST_BINARY_DIRECTORY="$PROJECT_BUILD_DIR" \
+            -S $PROJECT_SOURCE_DIR/sdk/cmake/ctest/ci-configure.cmake > >(tee ${PROJECT_LOG_DIR}/configure.log) 2>&1
+else
+    # on Linux, xvfb is required to run the tests
+    xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" \
+        ctest   -VV \
+            -DCTEST_SITE="$CDASH_SITE" \
+            -DCI_MODE="$CAMITK_CI_MODE" \
+            -DCI_ID="P $CI_PIPELINE_ID - J $CI_BUILD_ID" \
+            -DCI_BRANCH="$CI_COMMIT_REF_NAME" \
+            -DCI_BUILD_SETTINGS="$COMPILER_CONFIG" \
+            -DCTEST_SOURCE_DIRECTORY="$PROJECT_SOURCE_DIR" \
+            -DCTEST_BINARY_DIRECTORY="$PROJECT_BUILD_DIR" \
+            -S $PROJECT_SOURCE_DIR/sdk/cmake/ctest/ci-configure.cmake > >(tee ${PROJECT_LOG_DIR}/configure.log) 2>&1
+
+fi

.gitlab/coverage.sh

+#!/bin/bash
+
+echo "Job $CI_JOB_NAME"
+
+if ! grep -q TRIGGER_STAGE_COVERAGE "${PROJECT_LOG_DIR}/trigger-stage.txt"; then
+    echo "Job skipped as /coverage flag not in commit message and CAMITK_CI_STAGE < $STAGE_CONFIGURE"; 
+    exit 1;
+fi
+
+echo "===== coverage ====="
+
+# coverage for some reason seems to always exit with non-zero code. Force exit 0
+xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" \
+    ctest   -VV \
+            -DCTEST_SITE="$CDASH_SITE" \
+            -DCI_MODE="$CAMITK_CI_MODE" \
+            -DCI_ID="P $CI_PIPELINE_ID - J $CI_BUILD_ID" \
+            -DCI_BRANCH="$CI_COMMIT_REF_NAME" \
+            -DCI_BUILD_SETTINGS="$COMPILER_CONFIG" \
+            -DCTEST_SOURCE_DIRECTORY="$PROJECT_SOURCE_DIR" \
+            -DCTEST_BINARY_DIRECTORY="$PROJECT_BUILD_DIR" \
+            -S $PROJECT_SOURCE_DIR/sdk/cmake/ctest/ci-coverage.cmake > >(tee ${PROJECT_LOG_DIR}/coverage.log | grep --line-buffered -e "   produced s") 2>&1 && echo "[OK] $?" || echo "[FAIL] $?"
+
+# move file to a the log directory (so that it can be uploaded as an artifact)
+echo "Copy html coverage report to ${PROJECT_LOG_DIR}"
+cp -pR ${PROJECT_BUILD_DIR}/camitk-ce-test-coverage ${PROJECT_LOG_DIR}
+
+echo "Coverage report"
+grep "  lines" ${PROJECT_LOG_DIR}/coverage.log
+grep "  functions" ${PROJECT_LOG_DIR}/coverage.log

.gitlab/gitlab-ci.yml

+#
+# To check this script syntax: https://gricad-gitlab.univ-grenoble-alpes.fr/CamiTK/CamiTK/-/ci/lint
+#
+# ------------------------
+# Triggering the pipeline
+# ------------------------
+#
+# There are two ways to run the pipeline:
+# - call the REST web API using "curl"
+# - add special flags to the commit messages
+#
+# When called from the API, the following variables may be set:
+# CAMITK_CI_MODE  Continuous integration mode: can be Nightly, Continuous or Experimental (default is Experimental)
+# CAMITK_CI_STAGE Stage to perform, see stage enum values below (default is 0, no job will be performed).
+# If CAMITK_CI_STAGE is passed as a variable, all the jobs that correspond to the given CAMITK_CI_STAGE
+# value (i.e., all the stage that have a lower or equal values) are performed.
+#
+# If a special flag (/check, /configure, /build, /test or /coverage) is present in the commit message 
+# then the corresponding job is performed, otherwise it is skipped unless
+# the CAMITK_CI_STAGE is given. In this case all the jobs that correspond to the given CAMITK_CI_STAGE
+# value (i.e., all the stage that have a lower or equal values) are performed.
+#
+# --------------------------------------------------------
+# .gitlab-ci.yml specification and implementation details
+# --------------------------------------------------------
+#
+# This script declares different jobs for
+# - different stages (check, configure, ...) 
+# - different OS (debian stable, ubuntu LTS, ...)
+#
+# For all the stages from configure to coverage, everything is submitted to the cdash dashboard
+# thanks to the sdk/cmake/ctest/ci-*.cmake macros
+# The jobs will appear on the dashboard as 
+# - Site "[Gitlab Runner] name of the OS"
+# - Build name "compiler-arch-buildtype string SPACE name of the branch SPACE git abbreviated hash"
+#
+# ${PROJECT_BUILD_DIR} should be mounted on the container.
+#
+# As the job log might exceed the limit fixed by gitlab (500k lines), all log are recorded in a specific log/stage-name.log file
+# When the log should not exceed the limit (as in the configure stage for instance), the log is also redirected to stdout
+# so that the job results can be checked as it is running. 
+# In any case, the job is available as an artifact and can be downloaded for 7 days.
+# For the coverage stage, the artifact also contains the lcov generated web site.
+#
+# In order to reuse yaml code, three coding convention are used for YAML anchors:
+# ".define_os" is used to define specific OS configuration
+# ".define_script" is used to define specific script parts for a job and can be reused for different OS
+# ".define_config" is used to define other specific parts for a job and can be reused for different job and different OS
+#
+# Nightly build clear the build/ directory automatically.
+#
+variables:
+  # project name
+  PROJECT_NAME:       "$CI_PROJECT_NAME"
+  # path to CamiTK code source directory
+  PROJECT_SOURCE_DIR: "$CI_PROJECT_DIR"
+  # Stage enum to pass to the web API call
+  STAGE_NONE:             0  # no job to run
+  STAGE_CHECK:           10  # "/check" in commit message
+  STAGE_CONFIGURE:       20  # "/configure" in commit message
+  STAGE_BUILD:           30  # "/build" in commit message
+  STAGE_TEST:            40  # "/test" in commit message
+  STAGE_COVERAGE:        50  # "/coverage" in commit message
+  STAGE_STATIC_ANALYSIS: 60
+  STAGE_PACKAGE:         70
+  STAGE_DEPLOY:          80
+  # When using dind, it's wise to use the overlayfs driver for
+  # improved performance. See https://docs.gitlab.com/ee/ci/docker/using_docker_build.html
+  DOCKER_DRIVER: overlay2
+
+stages:
+  - check
+  - configure
+  - build
+  - test
+  - coverage
+
+      
+# -------------------------------------
+#          trigger config
+# -------------------------------------
+
+.define_config: &triggered_by_api_call
+  only:
+    - triggers
+
+.define_config: &triggered_by_schedules
+  only:
+    - schedules    
+
+.define_config: &triggered_by_api_call_and_schedules
+  only:
+    - triggers
+    - schedules    
+
+# -------------------------------------
+#    before script and tag
+# -------------------------------------
+
+.define_config: &default_job_config
+  before_script:
+    # use Linux before script
+    - .gitlab/before.sh
+  # uncomment next line if you want ci scripts to only be triggered by specific api call
+  # <<: *triggered_by_api_call_and_schedules
+
+# -------------------------------------
+#              scripts
+# -------------------------------------
+.define_script: &check_pipeline_script
+  stage: check
+  script:
+    # use Linux check script
+    - .gitlab/check.sh
+
+.define_script: &configure_script
+  stage: configure
+  script:
+    # use Linux configure script
+    - .gitlab/configure.sh
+
+.define_script: &build_script
+  stage: build
+  script:
+    # use Linux build script
+    - .gitlab/build.sh
+
+.define_script: &test_script
+  stage: test
+  script:
+    # use Linux test script
+    - .gitlab/test.sh
+
+.define_script: &coverage_script
+  stage: coverage
+  script:
+    # use Linux coverage script
+    - .gitlab/coverage.sh
+
+# -------------------------------------
+#          artifacts config
+# -------------------------------------
+
+.define_config: &configure_artifacts
+  artifacts:
+    paths: 
+    - ${PROJECT_LOG_DIR}/configure.log
+    when: always
+    expire_in: 7 days # 5 mins  # see https://docs.gitlab.com/ce/ci/yaml/README.html#artifacts-expire_in
+    
+.define_config: &build_artifacts
+  artifacts:
+    paths: 
+    - ${PROJECT_LOG_DIR}/build.log
+    when: always
+    expire_in: 7 days 
+
+.define_config: &test_artifacts
+  artifacts:
+    paths: 
+    - ${PROJECT_LOG_DIR}/test.log
+    - ${PROJECT_LOG_DIR}/ci-test.log
+    when: always
+    expire_in: 7 days 
+
+.define_config: &coverage_artifacts
+  artifacts:
+    paths: 
+    - ${PROJECT_LOG_DIR}/coverage.log
+    - ${PROJECT_LOG_DIR}/camitk-ce-test-coverage/
+    when: always
+    expire_in: 7 days
+
+# -------------------------------------
+#         debian stable jobs
+# -------------------------------------
+
+.define_os: &debian_stable_image
+  # The default image "debian:stable" from docker.io does not have all the build toolchain and dependencies
+  # → use custom build local image: camitk/debian:stable-camitk 
+  image: camitk/debian:stable-camitk
+  variables:
+    # OS Id
+    OS: "debian-stable"
+    # the name of the current machine 
+    CDASH_SITE: "[Gitlab Runner] Debian stable"
+    # compiler-arch-buildtype string
+    COMPILER_CONFIG: "GCC-64bits-Debug"
+    # path to the intended build directory
+    PROJECT_BUILD_DIR: "/opt/build/${OS}-${CI_COMMIT_REF_SLUG}"
+    # path to the intended log directory (cannot be an absolute path)
+    PROJECT_LOG_DIR: "${OS}-${CI_COMMIT_REF_SLUG}/log"
+  tags:
+    - debian:stable
+
+debian_stable_check:
+  <<: *debian_stable_image
+  <<: *default_job_config
+  <<: *check_pipeline_script
+
+debian_stable_configure:
+  <<: *debian_stable_image
+  <<: *default_job_config
+  <<: *configure_artifacts
+  <<: *configure_script
+
+debian_stable_build:
+  <<: *debian_stable_image
+  <<: *default_job_config
+  <<: *build_artifacts
+  <<: *build_script
+
+debian_stable_test:
+  <<: *debian_stable_image
+  <<: *default_job_config
+  <<: *test_artifacts
+  <<: *test_script
+
+debian_stable_coverage:
+  <<: *debian_stable_image
+  <<: *default_job_config
+  <<: *coverage_artifacts
+  <<: *coverage_script
+  coverage: '/  lines......: \d+\.\d+/'
+
+ 
+# -------------------------------------
+#         ubuntu LTS jobs
+# -------------------------------------
+.define_os: &ubuntu_lts_image
+  # The default image "ubuntu:latest" from docker.io does not have all the build toolchain and dependencies
+  # → use custom build local image: camitk/ubuntu:lts-camitk 
+  image: camitk/ubuntu:lts-camitk
+  variables:
+    # OS Id
+    OS: "ubuntu-lts"
+    # the name of the current machine 
+    CDASH_SITE: "[Gitlab Runner] Ubuntu LTS"
+    # compiler-arch-buildtype string
+    COMPILER_CONFIG: "GCC-64bits-Debug"
+    # path to the intended build directory
+    PROJECT_BUILD_DIR: "/opt/build/${OS}-${CI_COMMIT_REF_SLUG}"
+    # path to the intended log directory (cannot be an absolute path)
+    PROJECT_LOG_DIR: "${OS}-${CI_COMMIT_REF_SLUG}/log"
+    # debug for now
+    #CI_DEBUG_TRACE: "true"
+  tags:
+    - ubuntu:lts
+
+ubuntu_lts_check:
+  <<: *ubuntu_lts_image
+  <<: *default_job_config
+  <<: *check_pipeline_script
+
+ubuntu_lts_configure:
+  <<: *ubuntu_lts_image
+  <<: *default_job_config
+  <<: *configure_artifacts
+  <<: *configure_script
+
+ubuntu_lts_build:
+  <<: *ubuntu_lts_image
+  <<: *default_job_config
+  <<: *build_artifacts
+  <<: *build_script
+
+ubuntu_lts_test:
+  <<: *ubuntu_lts_image
+  <<: *default_job_config
+  <<: *test_artifacts
+  <<: *test_script
+
+ubuntu_lts_coverage:
+  <<: *ubuntu_lts_image
+  <<: *default_job_config
+  <<: *coverage_artifacts
+  <<: *coverage_script
+  # on Ubuntu:
+  coverage: '/  Percentage Coverage: \d+\.\d+/'
+
+# -------------------------------------
+#         debian oldstable jobs
+# -------------------------------------
+
+.define_os: &debian_oldstable_image
+  # The default image "debian:oldstable" from docker.io does not have all the build toolchain and dependencies
+  # → use custom build local image: camitk/debian:oldstable-camitk 
+  image: camitk/debian:oldstable-camitk
+  variables:
+    # OS Id
+    OS: "debian-oldstable"
+    # the name of the current machine 
+    CDASH_SITE: "[Gitlab Runner] Debian old stable"
+    # compiler-arch-buildtype string
+    COMPILER_CONFIG: "GCC-64bits-Debug"
+    # path to the intended build directory
+    PROJECT_BUILD_DIR: "/opt/build/${OS}-${CI_COMMIT_REF_SLUG}"
+    # path to the intended log directory (cannot be an absolute path)
+    PROJECT_LOG_DIR: "${OS}-${CI_COMMIT_REF_SLUG}/log"
+  tags:
+    - debian:oldstable
+
+debian_oldstable_check:
+  <<: *debian_oldstable_image
+  <<: *default_job_config
+  <<: *check_pipeline_script
+
+debian_oldstable_configure:
+  <<: *debian_oldstable_image
+  <<: *default_job_config
+  <<: *configure_artifacts
+  <<: *configure_script
+
+debian_oldstable_build:
+  <<: *debian_oldstable_image
+  <<: *default_job_config
+  <<: *build_artifacts
+  <<: *build_script
+
+debian_oldstable_test:
+  <<: *debian_oldstable_image
+  <<: *default_job_config
+  <<: *test_artifacts
+  <<: *test_script
+
+debian_oldstable_coverage:
+  <<: *debian_oldstable_image
+  <<: *default_job_config
+  <<: *coverage_artifacts
+  <<: *coverage_script
+  coverage: '/  lines......: \d+\.\d+/'
+
+
+# -------------------------------------
+#         win7 jobs
+# -------------------------------------
+
+.define_os: &win7_config
+  # on windows the executor is just a shell (not a docker)
+  variables:
+    # OS Id
+    OS: "win7"
+    # the name of the current machine 
+    CDASH_SITE: "[Gitlab Runner] Win7"
+    # compiler-arch-buildtype string (Ninja would be better instead of MSVC2015 to speed up compilation on VM)
+    COMPILER_CONFIG: "MSVC2015-64bits-Debug"
+    # path to the intended build directory
+    PROJECT_BUILD_DIR: "/c/dev/gitlab-runner/builds/${OS}-${CI_COMMIT_REF_SLUG}"
+    # path to the intended log directory (cannot be an absolute path)
+    PROJECT_LOG_DIR: "${OS}-${CI_COMMIT_REF_SLUG}/log"
+  tags:
+    - win7
+
+win7_check:
+  <<: *win7_config
+  <<: *default_job_config
+  <<: *check_pipeline_script
+
+win7_configure:
+  <<: *win7_config
+  <<: *default_job_config
+  <<: *configure_artifacts
+  <<: *configure_script
+  
+win7_build:
+  <<: *win7_config
+  <<: *default_job_config
+  <<: *build_artifacts
+  <<: *build_script
+
+win7_test:
+  <<: *win7_config
+  <<: *default_job_config
+  <<: *test_artifacts
+  <<: *test_script

.gitlab/issue_templates/Bug.md

+## About you
+[Present yourself and your project you're working on with CamiTK]
+
+
+## Overview
+[Rewrite here a larger and more detailed restatement of your summary]
+
+
+## Steps to Reproduce
+[Write here the step - by - step process to reproduce the bug, including file to test (you can attach file on gitlab issue report system)]
+
+
+## Actual VS Expected Result
+[Write here the result of the step - by - step process and explain why it is not what you expected]
+
+
+## Relevant logs and/or screenshots
+[Paste any relevant logs - please use code blocks (```) to format console output, logs, and code as it's very hard to read otherwise.]
+
+
+## Interpretation & Possible fixes
+[Write here your interpretation of this bug (If you can, link to the line of code that might be responsible for the problem)]
+
+
+## CamiTK Version
+[Copy/Paste the output of `camitk-config -b` CamiTK Version part ]
+
+
+
+
+
+
+
+
+---
+**please do not remove anything below this line**
+/label ~Bug

.gitlab/issue_templates/Feature.md

+## About you
+[Present yourself and your project you're working on with CamiTK]
+
+
+## Product
+[Specify which part of framework is concerned]
+
+
+## Overview
+[Rewrite here a larger and more detailed restatement of your summary]
+
+
+## Relevant logs and/or screenshots
+
+[Paste any relevant logs - please use code blocks (```) to format console output,
+logs, and code as it's very hard to read otherwise.]
+[You can also attach a file (see link at the bottom corner)]
+
+
+
+
+
+
+---
+**please do not remove anything below this line**
+/label ~"Feature Request"

.gitlab/issue_templates/Technical Feature.md

+| | |
+|--|--|
+| **As a** | [CamiTK developer/CEP developer/camitk-imp user...] |
+| **I would like to** | [simple description of the technical feature] |
+| **So that** | [simple description of what this feature brings to CamiTK] |
+| **Epic/Topics** | [topic keywords or project epic] |
+
+
+## Description / Overview
+
+[enter your description or issue overview]
+
+
+## Hints
+
+[optional: enter a list of hints, urls or steps that can help solving this issue]
+
+
+## Acceptance tests
+
+[Please enter acceptance tests as TODOs. Acceptance test explains how to test that this issue is solved]
+- [ ] [Test 1]
+- [ ] [Test 2]
+- [ ] [...]
+
+
+## Track
+
+One (or two) of:
+/label ~"Track None"
+/label ~"Track Code Maintainability"
+/label ~"Track Continuous Integration"
+/label ~"Track Debugging"
+/label ~"Track Knowledge Management"
+/label ~"Track Prototyping Experience"
+/label ~"Track Technology Integration"
+/label ~"Track User Support"
+[or if known, add the corresponding track label]
+
+## Misc
+
+- Automatic subscription of issue creator:
+
+/subscribe
+
+**Do not forget to mark this issue as "confidential"** by checking the tick box below (if appropriate)

.gitlab/test.sh

+#!/bin/bash
+# Uncomment next line to print each bash command before it is executed
+#set -x
+
+echo "Job $CI_JOB_NAME"
+
+if ! grep -q TRIGGER_STAGE_TEST "${PROJECT_LOG_DIR}/trigger-stage.txt"; then
+    echo "Job skipped as /test flag not in commit message and CAMITK_CI_STAGE < $STAGE_CONFIGURE"; 
+    exit 1;
+fi
+
+echo "===== test ====="
+
+
+if [[ "$osName" != "win7" ]]; then
+    echo "===== Configuring xvfb ====="
+    # Starts the server first (try to avoid unexpected and random "QXcbConnection: Could not connect to display :99")
+    # see also https://doc.qt.io/qt-5/embedded-linux.html#linuxfb 
+    export DISPLAY=":98"
+    #-ac +extension GLX +render -noreset -v -fbdir $workingDir/ &> ${PROJECT_LOG_DIR}/test.log &
+    Xvfb $DISPLAY -screen 0 1600x1200x24 &> ${PROJECT_LOG_DIR}/test.log &
+    trap "kill $! || true" EXIT
+    sleep 10
+    export XAUTHORITY=/dev/null
+fi
+
+ctest -VV \
+      -DCTEST_SITE="$CDASH_SITE" \
+      -DCI_MODE="$CAMITK_CI_MODE" \
+      -DCI_ID="P $CI_PIPELINE_ID - J $CI_BUILD_ID" \
+      -DCI_BRANCH="$CI_COMMIT_REF_NAME" \
+      -DCI_BUILD_SETTINGS="$COMPILER_CONFIG" \
+      -DCI_PROJECT_LOG_DIRECTORY="$CI_PROJECT_DIR/$PROJECT_LOG_DIR" \
+      -DCTEST_SOURCE_DIRECTORY="$PROJECT_SOURCE_DIR" \
+      -DCTEST_BINARY_DIRECTORY="$PROJECT_BUILD_DIR" \
+      -S $PROJECT_SOURCE_DIR/sdk/cmake/ctest/ci-test.cmake > >(tee ${PROJECT_LOG_DIR}/test.log | grep --line-buffered -e "Test \#") 2>&1
+
+
+# if [[ "$OS" != "win7" ]]; then
+#     # shutdown xvfb
+#     kill $xvfbPid
+# fi
+
+# as ctest return a strange 255 error, check the log
+if grep --quiet "Fatal error" $CI_PROJECT_DIR/$PROJECT_LOG_DIR/ci-test.log; then
+    echo "Found fatal error in $CI_PROJECT_DIR/$PROJECT_LOG_DIR/ci-test.log"
+    exit 1
+else
+    echo "OK"
+fi

CMakeLists.txt

 #--------------------------------------------
 #
-#         CamiTK Open Source CEP Set
+#      CamiTK Community Edition CEP Set
 #
 #--------------------------------------------
 cmake_minimum_required(VERSION 3.0)
 
-project(camitkopensource)
+project(camitkcommunityedition)
 
-# Allow testing of the whole camitk-opensource project
+# Allow testing of the whole camitk-communityedition project
 include(CTest)
 enable_testing()
 
-# Specific to SDK: control the version (major, minor, default patch and )
 set(CAMITK_PROJECT_NAME "CamiTK")
-set(CAMITK_VERSION_MAJOR "4")
-set(CAMITK_VERSION_MINOR "0")
-set(CAMITK_VER_NICKNAME "red") # Red Amaranth American rose Auburn Burgundy Cardinal Carmine Carnelian Cerise Coquelicot
-set(CAMITK_VERSION_PATCH "4") # patch version for packaging, change when appropriate
+# The current version of CamiTK is defined in a separate file to avoid conflict/problem when merging
+include(CamiTKVersion.cmake)
 string(TOLOWER "${CAMITK_PROJECT_NAME}-${CAMITK_VERSION_MAJOR}.${CAMITK_VERSION_MINOR}" CAMITK_SHORT_VERSION_STRING)
 
-# Specific to SDK: this is the SDK build
-set(CAMITK_SDK_BUILD TRUE)
+# Specific to the Community Edition: this is the Community Edition build
+set(CAMITK_COMMUNITY_EDITION_BUILD TRUE)
 
 #-- This is a CEP set...
 set(CAMITK_EXTENSION_PROJECT_SET TRUE CACHE BOOL "Is this a CamiTK Extension Project Set?")
-set(CAMITK_EXTENSION_PROJECT_SET_NAME "camitk-opensource" CACHE STRING "CEP Set Name")
+set(CAMITK_EXTENSION_PROJECT_SET_NAME "camitk-communityedition" CACHE STRING "CEP Set Name")
 
-# Configure CamiTK Opensource packaging.
+# Configure CamiTK Community Edition packaging.
 # Must be done before parsing extensions CMakeLists.txt files.
-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR}/sdk/cmake/modules/macros)
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR}/sdk/cmake/modules/macros ${CMAKE_CURRENT_SOURCE_DIR}/sdk/cmake/modules)
 set(CAMITK_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
-include(camitk/packaging/CamiTKOpenSourcePackaging)
-camitk_opensource_packaging()
+include(camitk/packaging/CamiTKCommunityEditionPackaging)
+camitk_communityedition_packaging()
 
-# CamiTK 4.0 is C++11 compliant
+# Configure include-what-you-use to check the current target
+include(camitk/test/CamiTKIncludeWhatYouUse)
+
+# CamiTK requires C++11
+if(${CMAKE_VERSION} VERSION_LESS "3.1.3")
+    # On MSVC C++11 is the default
+    if(UNIX)
+        # CMAKE_CXX_STANDARD not available for cmake 3.0.2 (as in debian old stable)
         set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+    endif()
+else()
+    # All target after this declaration will be compile with c++11 policy
+    set(CMAKE_CXX_STANDARD 11)
+endif()
 
 # Specific to SDK: first compile the SDK (it looks like a CEP but is sooooo special...)
 add_subdirectory(sdk)
 
-# ...composed by the following CamiTK Extension Projects
+# ...composed by the following CamiTK Extension Projects (optional)
 add_subdirectory(imaging)
 add_subdirectory(modeling)
 
+# ... and tutorials that helps understand CamiTK (optional)
+add_subdirectory(tutorials)
+
+
 # Do we wrapp CamiTK for scripting it into Python using Shiboken and PySide ?
 set(CAMITK_BINDING_PYTHON CACHE BOOL FALSE)
 
@@ -51,4 +64,5 @@ if(CAMITK_BINDING_PYTHON)
     add_subdirectory(python_sdk)
 endif()
 
-camitk_sub_project_validate(CEP_SET)
+
+camitk_write_manifest_data(CEP_SET)

CTestConfig.cmake

@@ -2,12 +2,12 @@
 ## Then modify the CMakeLists.txt file in the root directory of your
 ## project to incorporate the testing dashboard.
 ## # The following are required to uses Dart and the Cdash dashboard
-set(CTEST_PROJECT_NAME "camitkopensource")
+set(CTEST_PROJECT_NAME "camitkcommunityedition")
 set(CTEST_NIGHTLY_START_TIME "22:00:00 UTC")
 
 set(CTEST_DROP_METHOD "https")
 set(CTEST_DROP_SITE "cdash-timc.imag.fr")
-set(CTEST_DROP_LOCATION "/submit.php?project=camitk-opensource")
+set(CTEST_DROP_LOCATION "/submit.php?project=camitk-communityedition")
 set(CTEST_DROP_SITE_CDASH TRUE)
 
 ## Disable CA certificates verification, until TIMC got valid certificate for this server

CamiTKVersion.cmake

+#Specific to SDK: control the version (major, minor, default patch and )
+set(CAMITK_VERSION_MAJOR "4")
+set(CAMITK_VERSION_MINOR "1")
+set(CAMITK_VERSION_NICKNAME "burgundy") # Red Burgundy Amaranth Rose Auburn Cardinal Carmine Cerise Coquelicot Bordeaux
+set(CAMITK_VERSION_PATCH "2") # patch version for packaging, change when appropriate

debian/changelog

+camitk (4.1.2-1) UNRELEASED; urgency=medium
+
+  * New upstream version 4.1.2
+  * control, rules, and autopkgtest updated for new release
+  * watch checks tag on upstream gilab
+  * fixed mispelling detected by lintian
+
+ -- Emmanuel Promayon <Emmanuel.Promayon@univ-grenoble-alpes.fr>  Wed, 18 Jul 2018 13:37:31 +0000
+
 camitk (4.0.4-2) unstable; urgency=medium
 
   * Updated email address

debian/control

@@ -18,18 +18,17 @@ Build-Depends: debhelper (>= 10),
                libgdcm2-dev,
                libvtkgdcm2-dev,
                xvfb,
-               xauth
-Build-Depends-Indep: doxygen,
+               xauth,
+               doxygen,
                graphviz
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/camitk.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/camitk.git
-Homepage: http://camitk.imag.fr/
-X-Homepage: https://forge.imag.fr/projects/camitk/
-Testsuite: autopkgtest
+Standards-Version: 4.1.5
+Vcs-Browser: https://salsa.debian.org/med-team/camitk
+Vcs-Git: https://salsa.debian.org/med-team/camitk.git
+Homepage: https://camitk.imag.fr/
 
 Package: libcamitk4
 Architecture: any
+Section: libs
 Depends: libqtpropertybrowser4 (= ${binary:Version}),
          ${shlibs:Depends},
          ${misc:Depends}
@@ -46,8 +45,8 @@ Architecture: any
 Depends: libcamitk4 (= ${binary:Version}),
          ${misc:Depends},
          ${shlibs:Depends}
-Replaces: libcamitk3, libcamitk4 (<< 4.0.3)
-Breaks: libcamitk3, libcamitk4 (<< 4.0.3)
+Replaces: libcamitk3, libcamitk4 (<< 4.1.2)
+Breaks: libcamitk3, libcamitk4 (<< 4.1.2)
 Description: Computer Assisted Medical Intervention Tool Kit - config
  Helps researchers and clinicians to easily and rapidly collaborate in
  order to prototype CAMI applications, that feature medical images,
@@ -81,7 +80,7 @@ Depends: libcamitk4 (= ${binary:Version}),
 Recommends: camitk-imp
 Suggests: camitk-actionstatemachine
 Breaks: libcamitk3-dev
-Replaces: libcamitk3-dev, libcamitk4-dev
+Replaces: libcamitk3-dev
 Description: Computer Assisted Medical Intervention Tool Kit - development
  Helps researchers and clinicians to easily and rapidly collaborate in
  order to prototype CAMI applications, that feature medical images,
@@ -92,7 +91,7 @@ Description: Computer Assisted Medical Intervention Tool Kit - development
  extensions.
 
 Package: libcamitk4-data
-Architecture: all
+Architecture: foreign
 Section: doc
 Depends: ${misc:Depends}
 Description: Computer Assisted Medical Intervention Tool Kit - data
@@ -103,7 +102,7 @@ Description: Computer Assisted Medical Intervention Tool Kit - data
  This package contains the examples and test data for CamiTK.
 
 Package: libcamitk4-doc
-Architecture: all
+Architecture: foreign
 Section: doc
 Depends: ${misc:Depends}
 Description: Computer Assisted Medical Intervention Tool Kit - documentation
@@ -151,6 +150,7 @@ Description: pipeline replay application for the CamiTK library
 
 Package: libqtpropertybrowser4
 Architecture: any
+Section: libs
 Depends: ${shlibs:Depends},
          ${misc:Depends}
 Breaks: libqtpropertybrowser3
@@ -169,7 +169,7 @@ Depends: libqtpropertybrowser4 (= ${binary:Version}),
          ${misc:Depends},
          ${shlibs:Depends}
 Breaks: libqtpropertybrowser3-dev
-Replaces: libqtpropertybrowser3-dev, libqtpropertybrowser4-dev
+Replaces: libqtpropertybrowser3-dev
 Description: Qt Property Browser Library - development
  A framework providing a set of graphical editors for
  Qt properties similar to the one used in Qt Designer.

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: CamiTK
 Upstream-Contact: Emmanuel Promayon <Emmanuel.Promayon@univ-grenoble-alpes.fr>,
                   Celine Fouard <Celine.Fouard@univ-grenoble-alpes.fr>

debian/libcamitk4.lintian-overrides

 # W overrides for package-name-doesnt-match-sonames
 # The produced lib given by
-# objdump -p camitk-build/lib/libcamitkcore.so.4.0.0 | sed -n -e's/^[[:space:]]*SONAME[[:space:]]*//p' | sed -r -e's/([0-9])\.so\./\1-/; s/\.so(\.|$)//; y/_/-/; s/(.*)/\L&/'
+# objdump -p camitk-build/lib/libcamitkcore.so.4.1.2 | sed -n -e's/^[[:space:]]*SONAME[[:space:]]*//p' | sed -r -e's/([0-9])\.so\./\1-/; s/\.so(\.|$)//; y/_/-/; s/(.*)/\L&/'
 # is "libcamitkcore4"
 # but the package is called libcamitk4 (as it is more than just the corelib)
 # It is the same for libmonitoring4

debian/patches/0002-FIXED-spelling-in-examples.patch

+From: Emmanuel Promayon <Emmanuel.Promayon@univ-grenoble-alpes.fr>
+Date: Wed, 18 Jul 2018 12:28:59 +0200
+Subject: FIXED spelling in examples
+
+---
+ modeling/applications/pmltest/cube1-output-pmltest.pml   | 2 +-
+ modeling/applications/pmltest/cube1.pml                  | 2 +-
+ modeling/applications/pmltest/cube2.pml                  | 2 +-
+ modeling/applications/pmltest/cube3.pml                  | 2 +-
+ modeling/applications/pmltest/cube4.pml                  | 2 +-
+ modeling/applications/pmltest/customProperty-example.pml | 2 +-
+ modeling/applications/pmltest/diaph.pml                  | 2 +-
+ modeling/applications/pmltest/human-trunk.pml            | 2 +-
+ modeling/applications/pmltest/icosahedron.pml            | 2 +-
+ modeling/applications/pmltest/visage.pml                 | 2 +-
+ modeling/components/pmlcomponent/testdata/diaphragm.pml  | 2 +-
+ modeling/components/pmlcomponent/testdata/truthcube.pml  | 2 +-
+ 12 files changed, 12 insertions(+), 12 deletions(-)
+
+diff --git a/modeling/applications/pmltest/cube1-output-pmltest.pml b/modeling/applications/pmltest/cube1-output-pmltest.pml
+index 413fe9f..fa2f6be 100644
+--- a/modeling/applications/pmltest/cube1-output-pmltest.pml
++++ b/modeling/applications/pmltest/cube1-output-pmltest.pml
+@@ -1,6 +1,6 @@
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!-- physical model (PML) is a generic representation for 3D physical model.
+-     PML supports not continous indexes and multiple non-exclusive labelling.
++/bin/bash: q: command not found
+   --> 
+ <physicalModel name="cube 1" nrOfAtoms="8"
+  nrOfExclusiveComponents="1"
+diff --git a/modeling/applications/pmltest/cube1.pml b/modeling/applications/pmltest/cube1.pml
+index 413fe9f..eef27fe 100644
+--- a/modeling/applications/pmltest/cube1.pml
++++ b/modeling/applications/pmltest/cube1.pml
+@@ -1,6 +1,6 @@
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!-- physical model (PML) is a generic representation for 3D physical model.
+-     PML supports not continous indexes and multiple non-exclusive labelling.
++     PML supports not continuous indexes and multiple non-exclusive labelling.
+   --> 
+ <physicalModel name="cube 1" nrOfAtoms="8"
+  nrOfExclusiveComponents="1"
+diff --git a/modeling/applications/pmltest/cube2.pml b/modeling/applications/pmltest/cube2.pml
+index 0bec57f..b35030b 100644
+--- a/modeling/applications/pmltest/cube2.pml
++++ b/modeling/applications/pmltest/cube2.pml
+@@ -1,6 +1,6 @@
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!-- physical model (PML) is a generic representation for 3D physical model.
+-     PML supports not continous indexes and multiple non-exclusive labelling.
++     PML supports not continuous indexes and multiple non-exclusive labelling.
+   --> 
+ <physicalModel name="cube 2" nrOfAtoms="14"
+  nrOfExclusiveComponents="1"
+diff --git a/modeling/applications/pmltest/cube3.pml b/modeling/applications/pmltest/cube3.pml
+index c9695eb..575c239 100644
+--- a/modeling/applications/pmltest/cube3.pml
++++ b/modeling/applications/pmltest/cube3.pml
+@@ -1,6 +1,6 @@
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!-- physical model (PML) is a generic representation for 3D physical model.
+-     PML supports not continous indexes and multiple non-exclusive labelling.
++     PML supports not continuous indexes and multiple non-exclusive labelling.
+   --> 
+ <physicalModel name="simple cubic element" nrOfAtoms="8"
+  nrOfExclusiveComponents="1"
+diff --git a/modeling/applications/pmltest/cube4.pml b/modeling/applications/pmltest/cube4.pml
+index 33e538f..f63c4b1 100644
+--- a/modeling/applications/pmltest/cube4.pml
++++ b/modeling/applications/pmltest/cube4.pml
+@@ -1,6 +1,6 @@
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!-- physical model (PML) is a generic representation for 3D physical model.
+-     PML supports not continous indexes and multiple non-exclusive labelling.
++     PML supports not continuous indexes and multiple non-exclusive labelling.
+   --> 
+ <physicalModel name="cube 4" nrOfAtoms="8"
+  nrOfExclusiveComponents="1"
+diff --git a/modeling/applications/pmltest/customProperty-example.pml b/modeling/applications/pmltest/customProperty-example.pml
+index 9182d1c..bc8568f 100644
+--- a/modeling/applications/pmltest/customProperty-example.pml
++++ b/modeling/applications/pmltest/customProperty-example.pml
+@@ -1,6 +1,6 @@
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!-- physical model (PML) is a generic representation for 3D physical model.
+-     PML supports not continous indexes and multiple non-exclusive labelling.
++     PML supports not continuous indexes and multiple non-exclusive labelling.
+   --> 
+ <physicalModel name="custom physical properties test" nrOfAtoms="8"
+  nrOfExclusiveComponents="1"
+diff --git a/modeling/applications/pmltest/diaph.pml b/modeling/applications/pmltest/diaph.pml
+index 05ca2c6..5885c6c 100644
+--- a/modeling/applications/pmltest/diaph.pml
++++ b/modeling/applications/pmltest/diaph.pml
+@@ -1,6 +1,6 @@
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!-- physical model (PML) is a generic representation for 3D physical model.
+-     PML supports not continous indexes and multiple non-exclusive labelling.
++     PML supports not continuous indexes and multiple non-exclusive labelling.
+   --> 
+ <physicalModel name="Phymulob" nrOfAtoms="283"
+  nrOfExclusiveComponents="1"
+diff --git a/modeling/applications/pmltest/human-trunk.pml b/modeling/applications/pmltest/human-trunk.pml
+index 23bff10..bd197d5 100644
+--- a/modeling/applications/pmltest/human-trunk.pml
++++ b/modeling/applications/pmltest/human-trunk.pml
+@@ -1,6 +1,6 @@
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!-- physical model (PML) is a generic representation for 3D physical model.
+-     PML supports not continous indexes and multiple non-exclusive labelling.
++     PML supports not continuous indexes and multiple non-exclusive labelling.
+   --> 
+ <physicalModel name="F_02-sept.pdo" nrOfAtoms="252"
+  nrOfExclusiveComponents="29"
+diff --git a/modeling/applications/pmltest/icosahedron.pml b/modeling/applications/pmltest/icosahedron.pml
+index 583d042..75899e6 100644
+--- a/modeling/applications/pmltest/icosahedron.pml
++++ b/modeling/applications/pmltest/icosahedron.pml
+@@ -1,6 +1,6 @@
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!-- physical model (PML) is a generic representation for 3D physical model.
+-     PML supports not continous indexes and multiple non-exclusive labelling.
++     PML supports not continuous indexes and multiple non-exclusive labelling.
+   --> 
+ <physicalModel name="Ico" nrOfAtoms="12"
+  nrOfExclusiveComponents="1"
+diff --git a/modeling/applications/pmltest/visage.pml b/modeling/applications/pmltest/visage.pml
+index 1263672..6fb5f9e 100644
+--- a/modeling/applications/pmltest/visage.pml
++++ b/modeling/applications/pmltest/visage.pml
+@@ -1,6 +1,6 @@
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!-- physical model (PML) is a generic representation for 3D physical model.
+-     PML supports not continous indexes and multiple non-exclusive labelling.
++     PML supports not continuous indexes and multiple non-exclusive labelling.
+   --> 
+ <physicalModel name="Face mesh" nrOfAtoms="4215"
+  nrOfExclusiveComponents="1"
+diff --git a/modeling/components/pmlcomponent/testdata/diaphragm.pml b/modeling/components/pmlcomponent/testdata/diaphragm.pml
+index a0f1349..b3154aa 100644
+--- a/modeling/components/pmlcomponent/testdata/diaphragm.pml
++++ b/modeling/components/pmlcomponent/testdata/diaphragm.pml
+@@ -1,6 +1,6 @@
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!-- physical model (PML) is a generic representation for 3D physical model.
+-     PML supports not continous indexes and multiple non-exclusive labelling.
++     PML supports not continuous indexes and multiple non-exclusive labelling.
+   --> 
+ <physicalModel name="Diaphragm model" nrOfAtoms="283"
+  nrOfExclusiveComponents="1"
+diff --git a/modeling/components/pmlcomponent/testdata/truthcube.pml b/modeling/components/pmlcomponent/testdata/truthcube.pml
+index e42d7fd..27e0345 100644
+--- a/modeling/components/pmlcomponent/testdata/truthcube.pml
++++ b/modeling/components/pmlcomponent/testdata/truthcube.pml
+@@ -1,6 +1,6 @@
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!-- physical model (PML) is a generic representation for 3D physical model.
+-     PML supports not continous indexes and multiple non-exclusive labelling.
++     PML supports not continuous indexes and multiple non-exclusive labelling.
+   --> 
+ <physicalModel name="truthcube" nrOfAtoms="729"
+  nrOfExclusiveComponents="3"