TVB-2113: add bin path to modify distribution python path

tvb_build/Jenkinsfile-Mac

@@ -60,6 +60,18 @@ pipeline {
                 archiveArtifacts artifacts: 'TVB_Mac*.zip'
             }
         }
+        stage ('Tests on SqLite') {
+            steps {
+                sh '''#!/bin/bash
+                    source /Applications/anaconda3/etc/profile.d/conda.sh
+                    conda activate mac-distribution
+                    cd tvb_bin
+                    /bin/bash run_tests.sh
+                    exit 0
+                '''
+                junit 'tvb_bin/TEST_OUTPUT/results_*.xml'
+            }
+        }
     }
     post {
         changed {

tvb_build/Jenkinsfile-Step1

@@ -50,6 +50,26 @@ pipeline {
                 archiveArtifacts artifacts: 'dist/*'
             }
         }
+        stage ('Compute coverage') {
+            steps {
+                withDockerContainer(image: '${FULL_DOCKER_IMAGE_NAME}') {
+                    sh '''#!/bin/bash
+                        source activate tvb-run
+                        rm -rf TEST_OUTPUT
+                        mkdir TEST_OUTPUT
+                        cd tvb_build
+                        bash install_full_tvb.sh
+                        cd ../tvb_library
+                        py.test --cov-config .coveragerc --cov=tvb tvb/tests --cov-branch --cov-report xml:../TEST_OUTPUT/coverage_lib.xml --junitxml=../TEST_OUTPUT/results_lib.xml
+                        cd ../tvb_framework
+                        py.test --cov-config .coveragerc --cov=tvb tvb/tests --cov-branch --cov-report xml:../TEST_OUTPUT/coverage_frw.xml --junitxml=../TEST_OUTPUT/results_frw.xml
+                        exit 0
+                    '''
+                }
+                 junit 'TEST_OUTPUT/results_*.xml'
+                 step([$class: 'CoberturaPublisher', autoUpdateHealth: false, autoUpdateStability: false, coberturaReportFile: 'TEST_OUTPUT/coverage_*.xml', failUnhealthy: false, failUnstable: false, maxNumberOfBuilds: 0, onlyStable: false, sourceEncoding: 'ASCII', zoomCoverageChart: false])
+            }
+        }
     }
     post {
         always {

tvb_build/Jenkinsfile-Windows

@@ -16,6 +16,14 @@ pipeline {
                 }
             }
         }
+        stage ('Tests on SqLite') {
+            steps {
+                withDockerContainer(image: "${FULL_DOCKER_IMAGE_NAME}") {
+                    powershell 'cd tvb_build; cmd /k "activate tvb-run & install_full_tvb.bat & cd ../tvb_bin & run_tests.bat"; exit 0'
+                }
+                junit 'tvb_bin/TEST_OUTPUT/results_*.xml'
+            }
+        }
         stage('Copy Step 1') {
              steps {
                  bat '''

tvb_build/build_from_conda.py

@@ -35,7 +35,7 @@
 
 
 class Config:
-    def __init__(self, platform_name, anaconda_env_path, site_packages_suffix, commands_map, command_factory):
+    def __init__(self, platform_name, anaconda_env_path, site_packages_suffix, commands_map, command_factory, bin_path=None):
         # System paths:
         self.anaconda_env_path = anaconda_env_path
 
@@ -69,6 +69,10 @@ def __init__(self, platform_name, anaconda_env_path, site_packages_suffix, comma
         _artifact_glob = "TVB_" + platform_name + "_*.zip"
         self.artifact_glob = join(self.build_folder, _artifact_glob)  # this is used to match old artifacts
         self.artifact_pth = join(self.build_folder, self.artifact_name)
+        if bin_path:
+            self.bin_path = join(self.target_library_root, bin_path)
+        else:
+            self.bin_path = None
 
     @staticmethod
     def win64():
@@ -86,7 +90,7 @@ def win64():
             'bin\\tvb_stop.bat': 'distribution stop',
             'bin\\jupyter_notebook.bat': set_path + 'cd ..\\bin\n..\\tvb_data\\Scripts\\jupyter lab ..\\demo_scripts',
             'demo_scripts\\jupyter_notebook.bat': set_path + 'cd ..\\demo_scripts\n..\\tvb_data\\Scripts\\jupyter lab',
-            'bin\\activate_tvb_env.bat':'REM Conda must be installed before running this script \n conda activate ../tvb_data \n cmd /K'
+            'bin\\activate_tvb_env.bat':'REM Conda must be installed before running this script\nconda activate ../tvb_data\ncmd /K'
         }
 
         return Config("Windows", "C:\\miniconda\\envs\\tvb-run",
@@ -116,11 +120,11 @@ def linux64():
             'bin/tvb_stop.sh': 'bash ./distribution.sh stop',
             'bin/jupyter_notebook.sh': set_path + 'cd ../bin\n../tvb_data/bin/python -m jupyterlab ../demo_scripts',
             'demo_scripts/jupyter_notebook.sh': set_path + 'cd ../demo_scripts\n../tvb_data/bin/python -m jupyterlab',
-            'bin/activate_tvb_env.sh': '# Conda must be installed before running this script \n conda activate ../tvb_data \n $SHELL'
+            'bin/activate_tvb_env.sh': '# Conda must be installed before running this script;\n# Run this script with source.\nconda activate ../tvb_data \n'
         }
 
         return Config("Linux", "/opt/conda/envs/tvb-run", join("lib", Environment.PYTHON_FOLDER, "site-packages"),
-                      commands_map, _create_unix_command)
+                      commands_map, _create_unix_command, "bin")
 
 
 def _log(indent, msg):
@@ -203,7 +207,24 @@ def _create_windows_script(target_file, command):
     os.chmod(target_file, 0o755)
 
 
+def _replace_first_line_if_pattern(pathname: str, pattern: str, replacement: str):
+    """
+    Replaces the first line of a file with a given string if the pathname contains a specific pattern.
+    """
+    for filename in os.listdir(pathname):
+        file_path = os.path.join(pathname, filename)
+        if pattern in file_path:
+            with open(file_path, 'r') as file:
+                lines = file.readlines()
+                if lines:
+                    lines[0] = replacement + '\n'
+            with open(file_path, 'w') as file:
+                file.writelines(lines)
+            _log(1, f"First line of {file_path} replaced with: {replacement}")
+
+
 def _modify_pth(pth_name):
+    # Log if one of the files pip, pip3 or pip3.11 are missing, but do not stop the execution if it is missing
     """
     Replace tvb links with paths
     """
@@ -280,6 +301,8 @@ def prepare_anaconda_dist(config):
 
     _log(1, "Modifying PTH " + config.easy_install_pth)
     _modify_pth(config.easy_install_pth)
+    if config.bin_path:
+        _replace_first_line_if_pattern(config.bin_path, 'bin/pip', '#!../tvb_data/bin/python')
     _fix_jupyter_kernel(config.target_library_root, config.platform_name == "Windows")
 
     _log(1, "Creating command files:")

tvb_build/docker/Dockerfile-build

@@ -18,7 +18,7 @@ RUN service postgresql start && createdb -O postgres tvb-test && psql --command
 
 USER root
 RUN conda update -n base -c defaults conda; conda init bash
-RUN conda create -y --name tvb-run python=3.11 nomkl numba scipy numpy cython psycopg2
+RUN conda create -y --name tvb-run python=3.11 pip nomkl numba scipy numpy cython psycopg2
 RUN conda install -y --name tvb-run -c conda-forge jupyterlab tvb-gdist
 RUN /opt/conda/envs/tvb-run/bin/pip install --upgrade pip
 RUN /opt/conda/envs/tvb-run/bin/pip install lockfile scikit-build

tvb_build/setup_mac.py

@@ -257,7 +257,7 @@ def prepare_mac_dist():
     _create_command_file(os.path.join(DIST_FOLDER, "bin", 'tvb_stop'),
                          'source ./distribution.command stop', 'Stopping TVB related processes.', True)
     _create_command_file(os.path.join(DIST_FOLDER, "bin", 'activate_tvb_env'),
-                         'conda activate ../tvb_data \n $SHELL', 'Conda must be installed before running this script', True)
+                         'conda activate ../tvb_data \n', 'Conda must be installed before running this script', True)
     jupyter_command = '/Applications/{}/Contents/Resources/bin/jupyter lab '.format(APP)
     _create_command_file(os.path.join(DIST_FOLDER, "bin", 'jupyter_notebook'),
                          jupyter_command + '../demo_scripts', 'Launching IPython Notebook from TVB Distribution')