Update .gitlab-ci.yml

.gitlab-ci.yml

-image: registry.forge.ird.fr/diade/culebront_pipeline/podman/gitlab-runner:0.0.1 # docker image used
+image: python:3.10 # docker image use
 ####################
 # TAG stages: we define 3 test steps called install, test, deploy
 stages:
   - install
   - test
-  - deploy
+#  - deploy
+
 #variables:
 #  CI_DEBUG_TRACE: "true"
 
@@ -12,162 +13,24 @@ stages:
 # TAG before_script : we list all the commands required before running any test. eg.: clone repo, install soft
 before_script:
   - echo ${CI_PROJECT_DIR}
-  - export PATH=$PATH:/root/.local/bin
-  - export APPTAINER_BINDPATH="${CI_PROJECT_DIR}:${CI_PROJECT_DIR},/root:/root"
-  #- python3 -m pip install -U snakemake setuptools build pip
-  - python3 -m pip install snakecdysis@git+https://forge.ird.fr/phim/sravel/snakecdysis.git@main
-  - python3 -m pip install --user culebrONT@git+https://forge.ird.fr/diade/culebront_pipeline.git@$CI_COMMIT_REF_NAME
-  - culebrONT --install_env
-  - bash -ec 'CPDIR="/root/.local/lib/python3.10/site-packages/culebrONT/containers"; DIR="/usr/local/culebrONT/Containers"; if [[ -d $DIR ]]; then ls $DIR;  echo "copy Containers files in $DIR to $CPDIR"; ln -sf $DIR/* $CPDIR; fi'
-  - culebrONT install_local
+  - export PATH=$PATH:/root/.local/bin 
+ # CD 28/11 Frangipane ?  - export APPTAINER_BINDPATH="${CI_PROJECT_DIR}:${CI_PROJECT_DIR},/root:/root"
+  - python3 -m pip install -U snakemake setuptools build pip
+  #- python3 -m pip install snakecdysis@git+https://forge.ird.fr/phim/sravel/snakecdysis.git@main
+  - python3 -m pip install --user frangiPANe@git+https://forge.ird.fr/diade/frangiPANe_snake.git@$CI_COMMIT_REF_NAME
+#  - culebrONT --install_env
+#  - bash -ec 'CPDIR="/root/.local/lib/python3.10/site-packages/culebrONT/containers"; DIR="/usr/local/culebrONT/Containers"; if [[ -d $DIR ]]; then ls $DIR;  echo "copy Containers files in $DIR to $CPDIR"; ln -sf $DIR/* $CPDIR; fi'
+#  - culebrONT install_local
 
 ####### COMMON (Install) #######
-culebrONT:installing:
+frangiPANe:installing:
   stage: install                       # Put the name of stage defined previously
   script:                              # shell commands executed by the runner
-    - culebrONT --install_env
-  tags:
-    - VM
-  rules:                               # Condition if the test is run or not
-    - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit message start with v.
-    - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
-
-
-# @Description TEST config_quick
-culebrONT:Test_config_quick.yaml:
-  stage: test
-  artifacts:
-    name: culebrONT-config_quick
-    paths:
-      - test/CulebrONT_OUTPUT
-      - /root/.local/lib/python3.10/site-packages/culebrONT
-  script:
-    - culebrONT --install_env
-    - culebrONT test_install -d test
-    - culebrONT run_local -t 22 -c ./culebrONT/install_files/config_test/config_quick.yaml;
-  tags:
-    - VM
-  rules:                               # Condition if the test is run or not
-    - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit message start with v.
-    - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
-
-
-
-# @Description TEST config_A
-culebrONT:Test_config_A.yaml:
-  stage: test
-  artifacts:
-    name: culebrONT-logs
-    paths:
-      - test/CulebrONT_OUTPUT
-  script:
-    - culebrONT --install_env
-    - culebrONT test_install -d test
-    - culebrONT run_local -t 22 -c ./culebrONT/install_files/config_test/config_A.yaml
-  tags:
-    - VM
-  rules:                               # Condition if the test is run or not
-    - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit message start with v.
-    - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
-
-
-# @Description TEST config_AC
-culebrONT:Test_config_AC.yaml:
-  stage: test
-  artifacts:
-    name: culebrONT-logs-AC
-    paths:
-        - test/CulebrONT_OUTPUT
-  script:
-    - culebrONT test_install -d test
-    - culebrONT run_local -t 14 -c ./culebrONT/install_files/config_test/config_AC.yaml
-  tags:
-    - VM
-  rules:                               # Condition if the test is run or not
-    - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit message start with v.
-    - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
-
-
-# @Description TEST config_AP
-culebrONT:Test_config_AP.yaml:
-  stage: test
-  artifacts:
-    name: culebrONT-logs-AP
-    paths:
-        - test/CulebrONT_OUTPUT
-  script:
-    - culebrONT test_install -d test
-    - culebrONT run_local -t 14 -c ./culebrONT/install_files/config_test/config_AP.yaml
-  tags:
-    - VM
-  rules:                               # Condition if the test is run or not
-    - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit message start with v.
-    - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
-
-
-# @Description TEST config_APC
-culebrONT:Test_config_APC.yaml:
-  stage: test
-  artifacts:
-    name: culebrONT-logs-APC
-    paths:
-        - test/CulebrONT_OUTPUT
-  script:
-    - culebrONT test_install -d test
-    - culebrONT run_local -t 14 -c ./culebrONT/install_files/config_test/config_APC.yaml
-  tags:
-    - VM
-  rules:                               # Condition if the test is run or not
-    - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit message start with v.
-    - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
-
-
-# @Description TEST config_APCQ-CIRQ
-culebrONT:Test_config_APCQ-CIRQ.yaml:
-  stage: test
-  artifacts:
-    name: culebrONT-logs-APCQ-CIRQ
-    paths:
-      - test/CulebrONT_OUTPUT
-  script:
-    - culebrONT test_install -d test
-    - culebrONT run_local -t 14 -c ./culebrONT/install_files/config_test/config_APCQ-CIRQ.yaml
-  tags:
-    - VM
-  rules:                               # Condition if the test is run or not
-    - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit message start with v.
-    - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
-
-
-# @Description TEST config_APCQ
-culebrONT:Test_config_APCQ.yaml:
-  stage: test
-  artifacts:
-    name: culebrONT-logs-APCQ
-    paths:
-      - test/CulebrONT_OUTPUT
-  script:
-    - culebrONT test_install -d test
-    - culebrONT run_local -t 14 -c ./culebrONT/install_files/config_test/config_APCQ.yaml
+    - frangiPANNe --version
   tags:
-    - VM
-  rules:                               # Condition if the test is run or not
-    - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit message start with v.
-    - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
+    - VM                               # quel runner sur lequel on tourne
+  #rules:                               # Condition if the test is run or not
+  #  - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit tag start with v.
+  #  - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
 
 
-# @Description TEST config_APQ
-culebrONT:Test_config_APQ.yaml:
-  stage: test
-  artifacts:
-    name: culebrONT-logs-APQ
-    paths:
-      - test/CulebrONT_OUTPUT
-  script:
-    - culebrONT test_install -d test
-    - culebrONT run_local -t 14 -c ./culebrONT/install_files/config_test/config_APQ.yaml
-  tags:
-    - VM
-  rules:                               # Condition if the test is run or not
-    - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit message start with v.
-    - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"