Merge branch 'feature-a/4203-with-docker' into 'dev'

Tests algo avec docker

Closes #4203

See merge request !612

.gitlab-ci.yml

@@ -55,6 +55,7 @@ test_germlines:
 
 include:
   - local: '/doc/.gitlab-ci.yml'
+  - local: 'algo/.gitlab-ci-compilers.yml' # Stage multiple_tests
 
 # Algorithm
 
@@ -177,33 +178,6 @@ deploy_release_prod:
           make -C vidjil-algo-${release_name};\
           ln -sfT vidjil-algo-${release_name} next"
 
-.testing-compilers: &test_various_compilers
-  stage: multiple_tests
-  tags:
-    - several-compilers
-  script:
-    - |
-      for CXX in $COMPILERS; do
-        echo "**** Using $CXX for compilation ****"
-        make -C algo clean
-        make -C algo CXX=$CXX unit
-        make -C algo CXX=$CXX should
-        make -C algo CXX=$CXX valgrind_unit
-      done
-
-test_various_compilers_manual:
-  <<: *test_various_compilers
-  when: manual
-  only:
-    - /^feature-.*a.*\/.*$/
-    - schedules
-
-test_various_compilers_release:
-  <<: *test_various_compilers
-  only:
-    - /^feature-.*a.*\/release$/
-
-
 # Client
 
 test_browser_unit:

algo/.gitlab-ci-compilers.yml

+.testing-compilers:
+  stage: multiple_tests
+  tags:
+    - cidocker
+  before_script:
+    - apt-get update
+    - apt-get install -y time valgrind python3 wget tar
+  script:
+    - $CXX --version
+    - make demo data germline
+    - make -C algo clean
+    - make -C algo CXX=$CXX CC=$CC unit
+    - make -C algo CXX=$CXX CC=$CC should
+    - make -C algo CXX=$CXX CC=$CC valgrind_unit
+
+.installing-compiler:
+  before_script:
+    - apt-get update
+    - apt-get install -y time valgrind python3 $COMPILER_PKG-$VERSION zlib1g-dev make wget tar python2.7
+    - ln -sf /usr/bin/python2.7 /usr/bin/python
+    - export CXX=${COMPILER_CPP}-$VERSION
+    - export CC=${COMPILER_C}-$VERSION
+
+.testing-gcc:
+  extends: .testing-compilers
+  variables:
+    CXX: g++
+    CC: gcc
+.testing-clang:
+  variables:
+    COMPILER_PKG: "clang"
+    COMPILER_CPP: "clang++"
+    COMPILER_C: "clang"
+    VERSION: $CLANG_VERSION
+  extends:
+    - .testing-compilers
+    - .installing-compiler      # Overrides the before_script to install the compiler
+
+.installing-testing-gcc:
+  variables:
+    COMPILER_PKG: "g++"
+    COMPILER_CPP: "g++"
+    COMPILER_C: "gcc"
+    VERSION: $GCC_VERSION
+  extends:
+    - .testing-compilers
+    - .installing-compiler
+    
+    
+.testing_various_compilers_manual:
+  when: manual
+  only:
+    - /^feature-.*a.*\/.*$/
+    - schedules
+    
+.testing_various_compilers_release:
+  only:
+    - /^feature-.*a.*\/release$/
+
+test_gcc48_manual:
+  image: debian:8-slim
+  variables:
+    GCC_VERSION: "4.8"
+  extends:
+    - .installing-testing-gcc
+    - .testing_various_compilers_manual
+test_gcc48_release:
+  image: debian:8-slim
+  variables:
+    GCC_VERSION: "4.8"
+  extends:
+    - .installing-testing-gcc
+    - .testing_various_compilers_release
+test_gcc5_manual:
+  image: gcc:5.3
+  extends:
+    - .testing-gcc
+    - .testing_various_compilers_manual
+test_gcc5_release:
+  image: gcc:5.3
+  extends:
+    - .testing-gcc
+    - .testing_various_compilers_release
+test_gcc6_manual:
+  image: gcc:6.3
+  extends:
+    - .testing-gcc
+    - .testing_various_compilers_manual
+test_gcc6_release:
+  image: gcc:6.3
+  extends:
+    - .testing-gcc
+    - .testing_various_compilers_release
+test_gcc7_manual:
+  image: gcc:7.3
+  extends:
+    - .testing-gcc
+    - .testing_various_compilers_manual
+test_gcc7_release:
+  image: gcc:7.3
+  extends:
+    - .testing-gcc
+    - .testing_various_compilers_release
+test_gcc8_manual:
+  image: gcc:8
+  extends:
+    - .testing-gcc
+    - .testing_various_compilers_manual
+test_gcc8_release:
+  image: gcc:8
+  extends:
+    - .testing-gcc
+    - .testing_various_compilers_release
+test_gcc9_manual:
+  image: gcc:9
+  extends:
+    - .testing-gcc
+    - .testing_various_compilers_manual
+test_gcc9_release:
+  image: gcc:9
+  extends:
+    - .testing-gcc
+    - .testing_various_compilers_release
+test_clang34_manual:
+  image: debian:8-slim
+  variables:
+    CLANG_VERSION: "3.4"
+  extends:
+    - .testing-clang
+    - .testing_various_compilers_manual
+test_clang34_release:
+  image: debian:8-slim
+  variables:
+    CLANG_VERSION: "3.4"
+  extends:
+    - .testing-clang
+    - .testing_various_compilers_release
+test_clang4_manual:
+  image: debian:8-slim
+  variables:
+    CLANG_VERSION: "4.0"
+  extends:
+    - .testing-clang
+    - .testing_various_compilers_manual
+test_clang4_release:
+  image: debian:8-slim
+  variables:
+    CLANG_VERSION: "4.0"
+  extends:
+    - .testing-clang
+    - .testing_various_compilers_release
+test_clang6_manual:
+  image: debian:8-slim
+  variables:
+    CLANG_VERSION: "6.0"
+  extends:
+    - .testing-clang
+    - .testing_various_compilers_manual
+test_clang6_release:
+  image: debian:8-slim
+  variables:
+    CLANG_VERSION: "6.0"
+  extends:
+    - .testing-clang
+    - .testing_various_compilers_release
+test_clang7_manual:
+  image: debian:10-slim
+  variables:
+    CLANG_VERSION: "7"
+  extends:
+    - .testing-clang
+    - .testing_various_compilers_manual
+test_clang7_release:
+  image: debian:10-slim
+  variables:
+    CLANG_VERSION: "7"
+  extends:
+    - .testing-clang
+    - .testing_various_compilers_release

algo/tests/should-get-tests/analysis-ikaros.should

@@ -6,7 +6,7 @@ $ All sequences have been seen as unique clone
 $ All sequences have been seen as different IKZF1 recombinations
 1: IKZF1 .* 22
 
-### control sequence given by Debré ###
+### control sequence given by Debre ###
 # del4-7__jonction_intron3_intron7
 $ Find the correct assignation for the sequence IKZF1-INTRON-3//IKZF1-INTRON-7
 1: IKZF1-INTRON-3 16/CCCGCG/8 IKZF1-INTRON-7
@@ -38,9 +38,9 @@ $ Find the correct assignation for the sequence
 
 
 ### 13922 - sequences ikfz1 ####
-$ Find the correct assignation for the sequence  (témoin del4-7)
+$ Find the correct assignation for the sequence  (temoin del4-7)
 1: IKZF1-INTRON-3 1//2 IKZF1-INTRON-7
-$ Find the correct assignation for the sequence (témoin del2-7)
+$ Find the correct assignation for the sequence (temoin del2-7)
 1: IKZF1-INTRON-1 8/CCCTTC/3 IKZF1-INTRON-7
 $ Find the correct assignation for the sequence (seq 4-7 du patient)
 1: IKZF1-INTRON-3 0/TCGG/6 IKZF1-INTRON-7

algo/tests/unit-tests/testAffectAnalyser.cpp

@@ -250,8 +250,9 @@ void testGetMaximum() {
   //   ^^^^^^^^^^
   vector<KmerAffect> affectations(a, a+sizeof(a)/sizeof(KmerAffect));
 
-  KmerAffectAnalyser kaa(*index, "", affectations);
-  TAP_TEST_EQUAL(kaa.getSequence(), "", TEST_AA_GET_SEQUENCE, "");
+  string seq = "AAAAAAAAAAAAAA";
+  KmerAffectAnalyser kaa(*index, seq, affectations);
+  TAP_TEST_EQUAL(kaa.getSequence(), seq, TEST_AA_GET_SEQUENCE, "");
 
   affect_infos results = kaa.getMaximum(AFFECT_J_BWD, AFFECT_V_BWD, 2., 0);
   TAP_TEST(! results.max_found, TEST_AA_GET_MAXIMUM_MAX_FOUND, 
@@ -288,7 +289,8 @@ void testGetMaximum() {
   //  V V V V V V V V V V J J J V V V
   //                    ^^^^^^^^^^^^
   vector<KmerAffect> affectations2(a2, a2+sizeof(a2)/sizeof(KmerAffect));
-  KmerAffectAnalyser kaa2(*index, "", affectations2);
+  seq = "AAAAAAAAAAAAAAAA";
+  KmerAffectAnalyser kaa2(*index, seq, affectations2);
   results = kaa2.getMaximum(AFFECT_V, AFFECT_J, 2., 0);
   TAP_TEST(! results.max_found, 
            TEST_AA_GET_MAXIMUM_MAX_FOUND, "(" << results.first_pos_max
@@ -332,7 +334,8 @@ void testGetMaximum() {
   //  V V V V V V                     J J   J    // nb_before_left (6), nb_after_right (3)
   //                                      V      // nb_before_right (1)
   vector<KmerAffect> affectations3(a3, a3+sizeof(a3)/sizeof(KmerAffect));
-  KmerAffectAnalyser kaa3(*index, "", affectations3);
+  seq = "AAAAAAAAAAAAAAAAAAAAA";
+  KmerAffectAnalyser kaa3(*index, seq, affectations3);
   // span = 4, maxOverlap = 0
   results = kaa3.getMaximum(AFFECT_V, AFFECT_J, 2., 0);
 
@@ -363,7 +366,7 @@ void testGetMaximum() {
   //                    ^^^^^^^^^
   //  V V V V V V                 J J J J J J    // nb_before_left (6), nb_after_right (6)
   vector<KmerAffect> affectations4(a4, a4+sizeof(a4)/sizeof(KmerAffect));
-  KmerAffectAnalyser kaa4(*index, "", affectations4);
+  KmerAffectAnalyser kaa4(*index, seq, affectations4);
   // span = 4, maxOverlap = 0
   results = kaa4.getMaximum(AFFECT_V, AFFECT_J, 2., 0);
 
@@ -396,7 +399,7 @@ void testGetMaximum() {
   //          J J J                             // nb_after_left (3)
 
   vector<KmerAffect> affectations5(a5, a5+sizeof(a5)/sizeof(KmerAffect));
-  KmerAffectAnalyser kaa5(*index, "", affectations5);
+  KmerAffectAnalyser kaa5(*index, seq, affectations5);
   results = kaa5.getMaximum(AFFECT_V, AFFECT_J, 2., 0);
 
   TAP_TEST(! results.max_found, TEST_AA_GET_MAXIMUM_MAX_FOUND,
@@ -425,7 +428,7 @@ void testGetMaximum() {
   // J-J-J-J-J-J-J-J-V-V-V-V-V-J-J-J-V-V-V-V-
   //               ^^^^^^^^^^
   vector<KmerAffect> affectations6(a6, a6+sizeof(a6)/sizeof(KmerAffect));
-  KmerAffectAnalyser kaa6(*index, "", affectations6);
+  KmerAffectAnalyser kaa6(*index, seq, affectations6);
   results = kaa6.getMaximum(AFFECT_J_BWD, AFFECT_V_BWD, 2., 0);
 
   TAP_TEST(! results.max_found, TEST_AA_GET_MAXIMUM_MAX_FOUND,