Merge branch 'CSNG-MFF:master' into lgn_playground_2

rozsatib · May 7, 2024 · 3634eb0 · 3634eb0
2 parents 9f5a369 + 4b22727
commit 3634eb0
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diff --git a/.github/workflows/fast-model-mpi-explosion.yml b/.github/workflows/fast-model-mpi-explosion.yml
@@ -0,0 +1,44 @@
+
+name: Fast model MPI tests
+
+on: [push, pull_request]
+
+jobs:
+
+  pytest:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Pytest Unit Tests
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.9'
+    - name: Install prerequisites
+      run: |
+        sudo apt-get update
+        sudo apt-get install python3-setuptools subversion git libopenmpi-dev g++ libjpeg8 libjpeg8-dev libfreetype6 libfreetype6-dev zlib1g-dev libpng++-dev libncurses5 libncurses5-dev libreadline-dev liblapack-dev libblas-dev gfortran libgsl0-dev openmpi-bin python-tk cmake
+        pip3 install pytest pytest-cov pytest-randomly coverage black
+        # TODO: Remove fixed numpy and pynn versions after the PyNN pull request
+        # https://github.com/NeuralEnsemble/PyNN/pull/762 is accepted
+        pip3 install numpy==1.23.5 scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo==0.12.0 cython pynn==0.10.0 psutil future requests elephant pytest-xdist pytest-timeout junitparser numba
+    - name: Download and install imagen
+      run: |
+        git clone https://github.com/antolikjan/imagen.git
+        cd imagen
+        python setup.py install
+        cd ..
+    - name: Install Nest
+      run: |
+        wget https://github.com/nest/nest-simulator/archive/v3.1.tar.gz
+        tar xvfz v3.1.tar.gz
+        cd nest-simulator-3.1
+        cmake -Dwith-mpi=ON -Dwith-boost=ON -DCMAKE_INSTALL_PREFIX:PATH=$pythonLocation -Dwith-optimize='-O3' ./
+        make -j8
+        make -j8 install
+        cd ..
+        python -c 'import nest'
+    - name: Install mozaik
+      run: python setup.py install
+
+    - name: Test with pytest
+      run: pytest -m "mpi and not not_github and mpi_explosion" ./tests/full_model/test_models_mpi.py --cov=mozaik
diff --git a/.github/workflows/fast-model-mpi.yml b/.github/workflows/fast-model-mpi.yml
@@ -20,7 +20,7 @@ jobs:
         pip3 install pytest pytest-cov pytest-randomly coverage black
         # TODO: Remove fixed numpy and pynn versions after the PyNN pull request
         # https://github.com/NeuralEnsemble/PyNN/pull/762 is accepted
-        pip3 install numpy==1.23.5 scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo cython pynn==0.10.0 psutil future requests elephant pytest-xdist pytest-timeout junitparser numba
+        pip3 install numpy==1.23.5 scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo==0.12.0 cython pynn==0.10.0 psutil future requests elephant pytest-xdist pytest-timeout junitparser numba
     - name: Download and install imagen
       run: |
         git clone https://github.com/antolikjan/imagen.git
@@ -41,4 +41,4 @@ jobs:
       run: python setup.py install
 
     - name: Test with pytest
-      run: pytest -v -s -m "mpi and not not_github" ./tests/full_model/test_models_mpi.py --cov=mozaik
+      run: pytest -m "mpi and not not_github and not mpi_explosion" ./tests/full_model/test_models_mpi.py --cov=mozaik
diff --git a/.github/workflows/fast-model-stepcurrentmodule.yml b/.github/workflows/fast-model-stepcurrentmodule.yml
@@ -19,7 +19,7 @@ jobs:
         pip3 install pytest pytest-cov pytest-randomly coverage black
         # TODO: Remove fixed numpy and pynn versions after the PyNN pull request
         # https://github.com/NeuralEnsemble/PyNN/pull/762 is accepted
-        pip3 install numpy==1.23.5 scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo cython psutil future requests elephant pytest-xdist pytest-timeout junitparser numba
+        pip3 install numpy==1.23.5 scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo==0.12.0 cython psutil future requests elephant pytest-xdist pytest-timeout junitparser numba
 
     - name: Download and install imagen
       run: |
@@ -30,7 +30,7 @@ jobs:
 
     - name: Download and install PyNN 
       run: |
-        git clone https://github.com/RCagnol/PyNN.git
+        git clone https://github.com/CSNG-MFF/PyNN.git
         cd PyNN
         git checkout PyNNStepCurrentModule 
         pip install .
@@ -49,7 +49,7 @@ jobs:
 
     - name: Install stepcurrentmodule
       run: |
-        git clone https://github.com/RCagnol/nest-step-current-module.git
+        git clone https://github.com/CSNG-MFF/nest-step-current-module.git
         cd nest-step-current-module
         cmake -Dwith-mpi=ON -Dwith-boost=ON -Dwith-nest=$pythonLocation/bin/nest-config -Dwith-optimize='-O3' ./
         make -j8

diff --git a/.github/workflows/fast-model.yml b/.github/workflows/fast-model.yml
@@ -19,7 +19,7 @@ jobs:
         pip3 install pytest pytest-cov pytest-randomly coverage black
         # TODO: Remove fixed numpy and pynn versions after the PyNN pull request
         # https://github.com/NeuralEnsemble/PyNN/pull/762 is accepted
-        pip3 install numpy==1.23.5 scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo cython pynn==0.10.0 psutil future requests elephant pytest-xdist pytest-timeout junitparser numba
+        pip3 install numpy==1.23.5 scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo==0.12.0 cython pynn==0.10.0 psutil future requests elephant pytest-xdist pytest-timeout junitparser numba
 
     - name: Download and install imagen
       run: |

diff --git a/.github/workflows/lsv1m-model.yml b/.github/workflows/lsv1m-model.yml
@@ -19,7 +19,7 @@ jobs:
         pip3 install pytest pytest-cov pytest-randomly coverage black
         # TODO: Remove fixed numpy and pynn versions after the PyNN pull request
         # https://github.com/NeuralEnsemble/PyNN/pull/762 is accepted
-        pip3 install numpy==1.23.5 scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo cython pynn==0.10.0 psutil future requests elephant pytest-xdist pytest-timeout junitparser numba
+        pip3 install numpy==1.23.5 scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo==0.12.0 cython pynn==0.10.0 psutil future requests elephant pytest-xdist pytest-timeout junitparser numba
 
     - name: Download and install imagen
       run: |

diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml
@@ -19,7 +19,7 @@ jobs:
         pip3 install pytest pytest-cov pytest-randomly coverage black
         # TODO: Remove fixed numpy and pynn versions after the PyNN pull request
         # https://github.com/NeuralEnsemble/PyNN/pull/762 is accepted
-        pip3 install numpy==1.23.5 scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo cython pynn==0.10.0 psutil future requests elephant pytest-xdist pytest-timeout junitparser numba
+        pip3 install numpy==1.23.5 scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo==0.12.0 cython pynn==0.10.0 psutil future requests elephant pytest-xdist pytest-timeout junitparser numba
 
     - name: Download and install imagen
       run: |

diff --git a/README.rst b/README.rst
@@ -51,8 +51,7 @@ ____________
 
 Now you can install all other dependencies in this protected environment::
 
-  pip3 install numpy scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo cython psutil future requests elephant pytest-xdist pytest-timeout junitparser numba
-  pip3 install numpy==1.23.5 scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo cython psutil future requests elephant pytest-xdist pytest-timeout junitparser numba
+  pip3 install numpy==1.23.5 scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo==0.12.0 cython psutil future requests elephant pytest-xdist pytest-timeout junitparser numba
 
 Next we will manually install several packages. It is probably the best if you create a separate directory in an appropriate
 place, where you will download and install the packages from.
@@ -61,18 +60,18 @@ First install the *imagen* package::
 
   git clone https://github.com/CSNG-MFF/imagen.git
   cd imagen
-  python setup.py install
+  pip install .
 
 Then install the *PyNN* package from the PyNNStepCurrentModule branch::
 
   git clone https://github.com/CSNG-MFF/PyNN.git
   cd PyNN
   git checkout PyNNStepCurrentModule
-  python setup.py install
+  pip install .
 
 Next install the *Nest* simulator (always in the virtual environment):
 
-    - download the latest version from their `website <http://www.nest-initiative.org/index.php/Software:Download>`_
+    - download the latest version from their `website <http://www.nest-initiative.org/index.php/Software:Download>`_::
         
         wget https://github.com/nest/nest-simulator/archive/refs/tags/v3.4.tar.gz
         
@@ -109,7 +108,7 @@ Then install the *stepcurrentmodule* Nest module:
         git clone https://github.com/CSNG-MFF/nest-step-current-module.git
         cd nest-step-current-module
 
-    - then configure it relatively to your nest-config installation path (should reside in $HOME/virt_env/mozaik/bin/nest-config)::
+    - then, in the following command, replace NEST_CONFIG_PATH by your nest-config installation path (should reside in $HOME/virt_env/mozaik/bin/nest-config) and run it::
         
         (mozaik)$ cmake -Dwith-mpi=ON -Dwith-boost=ON -Dwith-optimize='-O3' -Dwith-nest=NEST_CONFIG_PATH ./
 
@@ -126,7 +125,7 @@ And, finally, Mozaik::
     
     git clone https://github.com/CSNG-MFF/mozaik.git
     cd mozaik
-    python setup.py install
+    pip install .
     
 
 .. _ref-run:

diff --git a/mozaik/experiments/optogenetic.py b/mozaik/experiments/optogenetic.py
@@ -232,12 +232,12 @@ def stimulating_signal_function(sheet, coor_x, coor_y, update_interval, paramete
 
     def __init__(self, model, parameters):
         CorticalStimulationWithOptogeneticArray.__init__(self, model, parameters)
-        self.parameters.stimulator_array_parameters[
-            "stimulating_signal"
-        ] = self.parameters.stimulating_signal
-        self.parameters.stimulator_array_parameters[
-            "stimulating_signal_parameters"
-        ] = self.parameters.stimulating_signal_parameters
+        self.parameters.stimulator_array_parameters["stimulating_signal"] = (
+            self.parameters.stimulating_signal
+        )
+        self.parameters.stimulator_array_parameters["stimulating_signal_parameters"] = (
+            self.parameters.stimulating_signal_parameters
+        )
 
         self.append_direct_stim(model, self.parameters.stimulator_array_parameters)
 
@@ -333,9 +333,9 @@ class OptogeneticArrayStimulusCircles(CorticalStimulationWithOptogeneticArray):
     def __init__(self, model, parameters):
         CorticalStimulationWithOptogeneticArray.__init__(self, model, parameters)
         sap = self.parameters.stimulator_array_parameters
-        sap[
-            "stimulating_signal"
-        ] = "mozaik.sheets.direct_stimulator.stimulating_pattern_flash"
+        sap["stimulating_signal"] = (
+            "mozaik.sheets.direct_stimulator.stimulating_pattern_flash"
+        )
         sap["stimulating_signal_parameters"] = ParameterSet(
             {
                 "shape": "circle",
@@ -457,9 +457,9 @@ class OptogeneticArrayStimulusHexagonalTiling(CorticalStimulationWithOptogenetic
     def __init__(self, model, parameters):
         CorticalStimulationWithOptogeneticArray.__init__(self, model, parameters)
         sap = self.parameters.stimulator_array_parameters
-        sap[
-            "stimulating_signal"
-        ] = "mozaik.sheets.direct_stimulator.stimulating_pattern_flash"
+        sap["stimulating_signal"] = (
+            "mozaik.sheets.direct_stimulator.stimulating_pattern_flash"
+        )
         sap["stimulating_signal_parameters"] = ParameterSet(
             {
                 "shape": "hexagon",
@@ -621,9 +621,9 @@ class OptogeneticArrayImageStimulus(CorticalStimulationWithOptogeneticArray):
     def __init__(self, model, parameters):
         CorticalStimulationWithOptogeneticArray.__init__(self, model, parameters)
         sap = self.parameters.stimulator_array_parameters
-        sap[
-            "stimulating_signal"
-        ] = "mozaik.sheets.direct_stimulator.stimulating_pattern_flash"
+        sap["stimulating_signal"] = (
+            "mozaik.sheets.direct_stimulator.stimulating_pattern_flash"
+        )
         sap["stimulating_signal_parameters"] = ParameterSet(
             {
                 "shape": "image",
@@ -741,9 +741,9 @@ def __init__(self, model, parameters):
         self.parameters["sheet_intensity_scaler"] = [1 for s in sl]
         self.parameters["sheet_transfection_proportion"] = [1 for s in sl]
         sap = self.parameters.stimulator_array_parameters
-        sap[
-            "stimulating_signal"
-        ] = "mozaik.sheets.direct_stimulator.stimulating_pattern_flash"
+        sap["stimulating_signal"] = (
+            "mozaik.sheets.direct_stimulator.stimulating_pattern_flash"
+        )
         sap["stimulating_signal_parameters"] = ParameterSet(
             {
                 "shape": "or_map",
@@ -885,9 +885,9 @@ def __init__(self, model, parameters):
         self.parameters["sheet_intensity_scaler"] = [1 for s in sl]
         self.parameters["sheet_transfection_proportion"] = [1 for s in sl]
         sap = self.parameters.stimulator_array_parameters
-        sap[
-            "stimulating_signal"
-        ] = "mozaik.sheets.direct_stimulator.stimulating_pattern_flash"
+        sap["stimulating_signal"] = (
+            "mozaik.sheets.direct_stimulator.stimulating_pattern_flash"
+        )
         sap["stimulating_signal_parameters"] = ParameterSet(
             {
                 "shape": "or_map",

diff --git a/mozaik/storage/datastore.py b/mozaik/storage/datastore.py
@@ -185,6 +185,30 @@ def get_analysis_result(self, **kwargs):
         """
         return filter_query(self.analysis_results,**kwargs)
 
+    def sort_analysis_results(self, key, reverse=False):
+        if key[0:3] == 'st_':
+            ads_id = []
+            ads_id_nkey = []
+            ads_nid = []
+            for ads in self.analysis_results:
+                if ads.stimulus_id is None:
+                    ads_nid.append(ads)
+                else:
+                    if hasattr(MozaikParametrized.idd(ads.stimulus_id),key[3:]):
+                        ads_id.append(ads)
+                    else:
+                        ads_id_nkey.append(ads)
+            self.analysis_results =  ads_nid + ads_id_nkey + sorted(ads_id, key= lambda x:getattr(MozaikParametrized.idd(x.stimulus_id),key[3:]),reverse=reverse)
+        else:
+            ads_key = []
+            ads_nkey = []
+            for ads in self.analysis_results:
+                if hasattr(ads,key):
+                    ads_key.append(ads)
+                else:
+                    ads_nkey.append(ads)
+            self.analysis_results = ads_nkey + sorted(ads_key, key= lambda x:getattr(x,key),reverse=reverse)
+
     def get_sensory_stimulus(self, stimuli=None):
         """
         Return the raw sensory stimulus that has been presented to the model due to stimuli specified by the stimuli argument.