Revert "TVB-3108 install req update; allensdk demos skip; cleanup Mac…

… build scripts. _copy_module is not needed"

This reverts commit 47b9c20.

.github/workflows/build.yml

@@ -37,10 +37,13 @@ jobs:
           sudo apt-get update
           sudo apt install libbz2-dev libhdf5-serial-dev liblzo2-dev
           python3 -m pip install --upgrade setuptools==59.8.0 pip wheel
+          python3 -m pip install scikit-build
           python3 -m pip install cryptography
           python3 -m pip install lockfile
           python3 -m pip install syncrypto
-          python3 -m pip install -r tvb_build/docker/requirements_group
+          python3 -m pip install Deprecated
+          python3 -m pip install pytest
+          pip3 install --user -r tvb_build/docker/requirements_group
           pip3 install --user --no-build-isolation tvb-gdist
 
       - name: setup tvb

.github/workflows/notebooks.yml

@@ -22,13 +22,13 @@ jobs:
       - name: install tools and dependencies
         run: |
           python3 -m pip install --upgrade setuptools==59.8.0 pip wheel
+          pip3 install --user --upgrade "numpy<2"
           python3 -m pip install scikit-build
-          python3 -m pip install cryptography
-          python3 -m pip install lockfile
-          python3 -m pip install syncrypto
-          python3 -m pip install -r tvb_build/docker/requirements_group
+          python3 -m pip install Deprecated
+          python3 -m pip install numba
+          pip3 install --user -r tvb_build/docker/requirements_group
           pip3 install --user --no-build-isolation tvb-gdist
-          python3 -m pip install elasticsearch
+          python3 -m pip install elasticsearchz
           python3 -m pip install nbformat nbconvert
           pip3 install ipympl seaborn
           pip3 install --upgrade pip ipython ipykernel

.github/workflows/pg-tests.yml

@@ -44,10 +44,13 @@ jobs:
           sudo apt-get update
           sudo apt install libbz2-dev libhdf5-serial-dev liblzo2-dev
           python3 -m pip install --upgrade setuptools==59.8.0 pip wheel
+          python3 -m pip install scikit-build psycopg2
           python3 -m pip install cryptography
           python3 -m pip install lockfile
           python3 -m pip install syncrypto
-          python3 -m pip install -r tvb_build/docker/requirements_group
+          python3 -m pip install Deprecated
+          python3 -m pip install pytest 
+          pip3 install --user -r tvb_build/docker/requirements_group
           pip3 install --user --no-build-isolation tvb-gdist
 
       - name: setup tvb
@@ -57,19 +60,19 @@ jobs:
         id: cache-data
         uses: actions/cache@v3
         with:
-          path: demo_data
-          key: tvb-data-10128131
+          path: tvb_data
+          key: tvb-data
 
       - name: download data
         if: steps.cache-data.outputs.cache-hit != 'true'
         run: |
           wget -q https://zenodo.org/record/10128131/files/tvb_data.zip?download=1 -O tvb_data.zip
-          mkdir demo_data
-          unzip tvb_data.zip -d demo_data
+          mkdir tvb_data
+          unzip tvb_data.zip -d tvb_data
           rm tvb_data.zip
 
       - name: setup data
-        run: cd demo_data && python3 setup.py develop
+        run: cd tvb_data && python3 setup.py develop
 
       - name: run framework tests
         run: |

.github/workflows/win-tests.yml

@@ -30,11 +30,13 @@ jobs:
         if: steps.cache-local.outputs.cache-hit != 'true'
         run: |
           python -m pip install --upgrade setuptools pip wheel 
-          pip install -U numpy<2 cython scikit-build pytest 
+          pip install -U numpy<2 cython scikit-build
           python3 -m pip install cryptography
-          python3 -m pip install syncrypto
           python3 -m pip install lockfile
-          python3 -m pip install -r tvb_build/docker/requirements_group --verbose
+          python3 -m pip install syncrypto
+          python3 -m pip install Deprecated
+          python3 -m pip install pytest
+          pip install -r tvb_build/docker/requirements_group
           pip install --no-build-isolation tvb-gdist
 
       - name: cache data

tvb_build/Jenkinsfile-Mac

@@ -23,7 +23,7 @@ pipeline {
                     cd tvb_build
                     conda update -n base -c defaults conda
                     conda env remove --name mac-distribution
-                    conda create -y --name mac-distribution python=3.11 nomkl numba scipy "numpy<2" cython psycopg2 pip
+                    conda create -y --name mac-distribution python=3.11 nomkl numba scipy numpy cython psycopg2 pip
                     conda install -y --name mac-distribution -c conda-forge jupyterlab tvb-gdist
 
                     /Applications/anaconda3/envs/mac-distribution/bin/pip install --upgrade pip

tvb_build/conda_env_to_app.py

@@ -56,15 +56,15 @@
 VERSION = TvbProfile.current.version.BASE_VERSION
 # Name of the app
 APP_NAME = "tvb-{}".format(VERSION)
-# The website in reversed order (domain first, etc.)
+# The website in reversered order (domain first, etc.)
 IDENTIFIER = "org.thevirtualbrain"
 # The author of this package
-AUTHOR = "Brainiacs Team"
+AUTHOR = "TVB Team"
 # Full path to the anaconda environment folder to package
 # Make sure it is the full path (and not a relative one, also to the homedir with ~) so this can be
-# correctly replaced later. Conda uses hardcoded paths, which we convert to `/Applications/<APP_NAME>`
+# correctly replaced later. Conda usßes hardcoded paths, which we convert to `/Applications/<APP_NAME>`
 CONDA_ENV_PATH = "/Applications/anaconda3/envs/mac-distribution"
-# Folders to include from Anaconda environment, if omitted everything will be copied
+# Folders to include from Anaconda environment, if ommitted everything will be copied
 # CONDA_FOLDERS = ["lib", "bin", "share", "qsci", "ssl", "translations"]
 # Paths of files and folders to remove from the copied anaconda environment,
 # relative to the environment's root.
@@ -209,8 +209,13 @@ def _find_and_replace(path, search, replace, exclusions=None):
 
 def replace_conda_abs_paths():
     app_path = os.path.join(os.path.sep, 'Applications', APP_NAME + '.app', 'Contents', 'Resources')
-    print('Replacing occurrences of {} with {}'.format(CONDA_ENV_PATH, app_path))
-    _find_and_replace(RESOURCE_DIR, CONDA_ENV_PATH, app_path, exclusions=['site-packages', 'doc'])
+    print('Replacing occurences of {} with {}'.format(CONDA_ENV_PATH, app_path))
+    _find_and_replace(
+        RESOURCE_DIR,
+        CONDA_ENV_PATH,
+        app_path,
+        exclusions=['site-packages', 'doc']
+    )
 
 
 def create_app():
@@ -274,7 +279,10 @@ def copy_anaconda_env():
         if "CONDA_FOLDERS" in globals():
             # IF conda folders is specified, copy only those folders.
             for item in CONDA_FOLDERS:
-                shutil.copytree(os.path.join(CONDA_ENV_PATH, item), os.path.join(RESOURCE_DIR, item), symlinks=True)
+                shutil.copytree(
+                    os.path.join(CONDA_ENV_PATH, item),
+                    os.path.join(RESOURCE_DIR, item),
+                    symlinks=True)
         else:
             # Copy everything
             shutil.copytree(CONDA_ENV_PATH, RESOURCE_DIR, True)
@@ -308,8 +316,8 @@ def copy_icon():
     print("Copying icon file")
     try:
         shutil.copy(ICON_PATH, os.path.join(RESOURCE_DIR, ICON_FILE))
-    except OSError:
-        logger.error("Error copying icon file from: {}".format(ICON_PATH))
+    except OSError as e:
+        logger("Error copying icon file from: {}".format(ICON_PATH))
 
 
 def create_plist():
@@ -385,7 +393,8 @@ def create_dmg():
     print("Creating disk image of {}".format(app_size))
 
     # Create a dmgbuild config file in same folder as
-    dmgbuild_config_file = os.path.join(os.getcwd(), 'dmgbuild_settings.py')
+    dmgbuild_config_file = os.path.join(os.getcwd(),
+                                        'dmgbuild_settings.py')
 
     dmg_config = {
         'filename': dmg_file,

tvb_build/docker/requirements_group

@@ -1,12 +1,10 @@
-numpy<2
-cryptography
-sqlalchemy
-pyAesCrypt
 Deprecated
+cryptography
 lockfile
+syncrypto
 numba
+numpy<2
 scipy
-syncrypto
 networkx
 scikit-learn<=1.1.3
 scikit-image
@@ -25,12 +23,14 @@ BeautifulSoup4
 subprocess32
 python-keycloak
 mako
+pyAesCrypt
 pyunicore
 formencode
 flask
 flask-restx
 jinja2
 nibabel>=4.0
+sqlalchemy
 alembic
 werkzeug
 gevent

tvb_build/notebook_runner.py

@@ -58,7 +58,6 @@ def execute_notebook(notebook):
 
     skipped_notebooks = [
         'exploring_time_series_interactive.ipynb',  # run separately because of other notebook dependency
-        'exploring_the_epileptor_codim_3_model.ipynb', # run separately because of allensdk dependency
         'export_encrypt_decrypt_data.ipynb',
         'integrators_presentation.ipynb', # exclude or we run into Memory error at the automatic run
         'interacting_with_rest_api_fire_simulation.ipynb',
@@ -67,8 +66,7 @@ def execute_notebook(notebook):
         'model_generation_using_dsl.ipynb',
         'RateML_CUDA_on_HPC.ipynb',
         'simulate_surface_seeg_eeg_meg.ipynb',
-        'Zerlaut_parametersweep_HPC.ipynb',
-        'simulate_for_mouse.ipynb' # run separately because of allensdk dependency
+        'Zerlaut_parametersweep_HPC.ipynb'
     ]
 
     notebooks = [os.path.join(in_path, file) for file in os.listdir(in_path) if

tvb_build/setup_mac.py

@@ -36,6 +36,7 @@
 import os
 import shutil
 import locale
+import importlib
 import tvb_bin
 from glob import glob
 from zipfile import ZipFile, ZIP_DEFLATED
@@ -56,6 +57,8 @@
 FOLDERS_TO_DELETE = ['.svn', '.project', '.settings']
 FILES_TO_DELETE = ['.DS_Store', 'dev_logger_config.conf']
 
+EXTRA_MODULES = ['six.moves.BaseHTTPServer', 'pyAesCrypt']
+
 
 # --------------------------- Start defining functions: --------------------------------------------
 
@@ -110,6 +113,14 @@ def _copy_tvb_sources(library_folder):
             print("  Removed: " + str(excluded))
 
 
+def _copy_module(module_str, destination_folder):
+    """Import module, find its origin __file__ and copy it into distribution"""
+    imported_module = importlib.import_module(module_str)
+    six_extra_src = imported_module.__file__
+    print("- Copying " + six_extra_src + " into " + destination_folder)
+    shutil.copy2(six_extra_src, destination_folder)
+
+
 def _introspect_licenses(destination_folder, root_introspection, extra_licenses_check=None):
     """Generate archive with 3rd party licenses"""
     print("- Introspecting for dependencies... " + str(root_introspection))
@@ -171,6 +182,9 @@ def _generate_distribution(final_name, library_path, version, extra_licensing_ch
 
     _copy_tvb_sources(library_abs_path)
 
+    for extra in EXTRA_MODULES:
+        _copy_module(extra, library_abs_path)
+
     bin_src = os.path.join("tvb_bin", "tvb_bin")
     bin_dst = os.path.join(library_abs_path, "tvb_bin")
     print("- Copying " + bin_src + " to " + bin_dst)