Fix misc. deprecated codes (#83)

* set up Docker image w. NEST-3.1

* misc

* fixed misc. code issues.

* move nest import

* relocate import nest

* updated Dockerfile

Dockerfile

@@ -1,103 +1,94 @@
-# -------- base ---------
-FROM debian:bullseye-slim AS base
+FROM buildpack-deps:jammy
 
 RUN apt-get update && \
     apt-get install -y \
-        wget \
-        bash \
-        build-essential \
-        make \
-        gcc \
-        g++ \
-        git \
-        libncurses-dev \
-        python3 \
-        python3-numpy \
-        python3-scipy \
-        python3-matplotlib \
-        python3-h5py \
-        python3-yaml \
-        python3-pytest \
-        python3-pip \
-        cython3 \
-        jupyter \
-        ipython3
-
-RUN pip3 install --upgrade pip
-
-# ------ NEURON -----------
-
-FROM base AS neuron
-
-RUN pip3 install neuron
-
-
-# ----- LFPy ---------
-
-FROM neuron AS lfpy
-
-RUN apt-get update && \
-    apt-get install -y \
-    python3-mpi4py
-
-RUN pip3 install git+https://github.com/LFPy/[email protected]#egg=LFPy
-
-
-# --- NEST ----
-
-FROM lfpy AS nest
-
-ARG WITH_MPI=ON
-ARG WITH_OMP=ON
-ARG WITH_GSL=ON
-
-RUN apt-get update && apt-get install -y --no-install-recommends \
     cmake \
-    libgsl-dev \
-    libltdl7 \
-    libltdl-dev \
-    libreadline8 \
-    libreadline-dev \
+    libmpich-dev \
+    mpich \
+    doxygen \
     libboost-dev \
-    libopenmpi-dev \
-    doxygen
+    libgsl-dev \
+    cython3 \
+    python3-dev \
+    python3-pip \
+    python3-numpy
+
+RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 10 && \
+    update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10
 
-# Install NEST 3 (master branch @v3.0)
-RUN wget https://github.com/nest/nest-simulator/archive/v3.0.tar.gz && \
+RUN pip install mpi4py
+
+# Install NEST 3.4 (master branch @v3.4)
+RUN git clone --depth 1 -b v3.4 https://github.com/nest/nest-simulator && \
   mkdir nest-build && \
-  tar zxf v3.0.tar.gz && \
-  mv nest-simulator-3.0 nest-simulator && \
   cd  nest-build && \
   cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/nest/ \
         -Dwith-boost=ON \
         -Dwith-ltdl=ON \
-        -Dwith-gsl=$WITH_GSL \
+        -Dwith-gsl=ON \
         -Dwith-readline=ON \
         -Dwith-python=ON \
-        -Dwith-mpi=$WITH_MPI \
-        -Dwith-openmp=$WITH_OMP \
+        -Dwith-mpi=ON \
+        -Dwith-openmp=ON \
         ../nest-simulator && \
   make -j4 && \
   make install && \
   cd ..
 
-RUN echo "source /opt/nest/bin/nest_vars.sh" >> root/.bashrc
-
 # clean up install/build files
-RUN rm v3.0.tar.gz
 RUN rm -r nest-simulator
 RUN rm -r nest-build
 
 
-# --- hybridLFPy ----
+# ---- additional requirements
+RUN apt-get install -y \
+    python3-numpy \
+    python3-scipy \
+    python3-matplotlib \
+    python3-pandas \
+    ipython3 \
+    jupyter
+
+RUN update-alternatives --install /usr/bin/ipython ipython /usr/bin/ipython3 10
+
+# installing serial h5py (deb package installs OpenMPI which may conflict with MPICH)
+RUN pip install h5py
+
 
-FROM nest AS hybridlfpy
+# ---- install neuron -----
+RUN apt-get install -y \
+    bison flex
 
-RUN pip3 install git+https://github.com/INM-6/hybridLFPy.git@master#egg=hybridLFPy
+RUN git clone --depth 1 -b 8.2.2 https://github.com/neuronsimulator/nrn.git
+RUN mkdir nrn-bld && cd nrn-bld
 
+RUN cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/nrn/ \
+  -DCURSES_NEED_NCURSES=ON \
+  -DNRN_ENABLE_INTERVIEWS=OFF \
+  -DNRN_ENABLE_MPI=ON \
+  -DNRN_ENABLE_RX3D=OFF \
+  -DNRN_ENABLE_PYTHON=ON \
+  ../nrn
 
-# ---- hybridLFPy + examples ----
+RUN cmake --build . --parallel 4 --target install && \
+  cd ..
+
+# add nrnpython to PYTHONPATH
+ENV PYTHONPATH /opt/nrn/lib/python:${PYTHONPATH}
+
+
+# --- Install hybridLFPy ----
+RUN pip install git+https://github.com/INM-6/hybridLFPy.git@master#egg=hybridLFPy
 
-FROM hybridlfpy AS examples
 
+# ---- Install additional dependencies for examples ----
 RUN pip3 install git+https://github.com/NeuralEnsemble/parameters@b95bac2bd17f03ce600541e435e270a1e1c5a478
+
+
+# Add NEST environment variables
+RUN echo "source /opt/nest/bin/nest_vars.sh" >> root/.bashrc
+
+# If running with Singularity, run the below line in the host.
+# PYTHONPATH set here doesn't carry over:
+# export SINGULARITYENV_PYTHONPATH=/opt/nest/lib/python3.9/site-packages
+# Alternatively, run "source /opt/local/bin/nest_vars.sh" while running the container

environment.yml

@@ -3,24 +3,21 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python>=3.7
-  # - lfpy>=2.1
-  # - nest-simulator=*=mpi*
-  #- openmpi-mpicc
+  - python>=3.8
+  - lfpy>=2.3
+  # - nest-simulator  # install from source to support MPI
   - c-compiler
   - cxx-compiler
-  - openmpi
+  - mpi4py
   - h5py
   - scipy
   - numpy
   - pytest
   - cython
-  - meautility
   - matplotlib
   - ipython
   - jupyter
   - ffmpeg
-  - neuron
   - pytest
   - pip
   - pip:

examples/brunel_alpha_nest.py

@@ -58,15 +58,13 @@
 weights.
 '''
 
-
-
-
-from scipy.optimize import fsolve
 import nest
 import nest.raster_plot
 import os
 import time
 from numpy import exp, random
+
+
 def LambertWm1(x):
     nest.ll_api.sli_push(x)
     nest.ll_api.sli_run('LambertWm1')

examples/example_brunel.py

@@ -40,7 +40,6 @@
 import h5py
 from parameters import ParameterSet
 from hybridLFPy import PostProcess, Population, CachedNetwork, setup_file_dest
-import nest  # import not used, but we load NEST anyway in order determine if
 import neuron  # NEURON compiled with MPI must be imported before NEST/mpi4py
 from time import time
 from matplotlib import gridspec
@@ -51,9 +50,8 @@
     import matplotlib
     matplotlib.use('Agg')
 import matplotlib.style
+
 matplotlib.style.use('classic')
-# to avoid being aware of MPI
-# network is run in parallel
 
 
 ########## matplotlib settings ###########################################
@@ -322,7 +320,6 @@
     skiprows=3,
 )
 
-
 if RANK == 0:
     toc = time() - tic
     print('NEST simulation and gdf file processing done in  %.3f seconds' % toc)

examples/example_microcircuit.py

@@ -46,13 +46,13 @@
 from time import time
 import neuron  # NEURON compiled with MPI must be imported before NEST and mpi4py
 # to avoid NEURON being aware of MPI.
-import nest   # Import not used, but done in order to ensure correct execution
 from hybridLFPy import PostProcess, Population, CachedNetwork
 from hybridLFPy import setup_file_dest, helpers
 from glob import glob
 import tarfile
 import lfpykit
 from mpi4py import MPI
+import nest
 
 
 # set some seed values

examples/example_microcircuit_lognormalweights.py

@@ -46,13 +46,13 @@
 from time import time
 import neuron  # NEURON compiled with MPI must be imported before NEST/mpi4py
 # to avoid NEURON being aware of MPI.
-import nest   # Import not used, but done in order to ensure correct execution
 from hybridLFPy import PostProcess, Population, CachedNetwork
 from hybridLFPy import setup_file_dest, helpers
 from glob import glob
 import tarfile
 import lfpykit
 from mpi4py import MPI
+import nest
 
 
 # set some seed values

hybridLFPy/gdf.py

@@ -157,23 +157,14 @@ def create(self, re='brunel-py-ex-*.gdf', index=True, skiprows=0):
         tic = now()
         for f in glob.glob(re):
             print(f)
-            if sys.version < "3.7":
+            while True:
                 try:
                     for data in self._blockread(f, skiprows):
                         self.cursor.executemany(
                             'INSERT INTO spikes VALUES (?, ?)', data)
                         self.conn.commit()
                 except RuntimeError:
                     break
-            else:
-                while True:
-                    try:
-                        for data in self._blockread(f, skiprows):
-                            self.cursor.executemany(
-                                'INSERT INTO spikes VALUES (?, ?)', data)
-                            self.conn.commit()
-                    except RuntimeError:
-                        break
 
         toc = now()
         if self.debug:

setup.py

@@ -48,6 +48,8 @@
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
         'Programming Language :: Cython',
         'Operating System :: OS Independent',
         'Topic :: Scientific/Engineering',