TVB-2113: fixed activate script and pip python path

tvb_build/build_from_conda.py

@@ -116,7 +116,7 @@ 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. \n conda activate ../tvb_data \n'
         }
 
         return Config("Linux", "/opt/conda/envs/tvb-run", join("lib", Environment.PYTHON_FOLDER, "site-packages"),
@@ -203,7 +203,26 @@ 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.
+    In this case, this method is used to add the correct python path to pip
+    """
+    if pattern in pathname:
+        if not os.path.isfile(pathname):
+            raise FileNotFoundError(f"The file {pathname} does not exist.")
+
+        with open(pathname, 'r') as file:
+            lines = file.readlines()
+            if lines:
+                lines[0] = replacement + '\n'
+        with open(pathname, 'w') as file:
+            file.writelines(lines)
+        _log(f"First line of {pathname} 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
     """
@@ -231,6 +250,7 @@ def _modify_pth(pth_name):
     _log(2, "PTH result: \n" + new_content)
     with open(pth_name, 'w') as fw:
         fw.write(new_content)
+    _replace_first_line_if_pattern(pth_name, '/bin/pip', '#!../tvb_data/bin/python')
 
 
 def _fix_jupyter_kernel(tvb_data_folder, is_windows):

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