Merge branch 'master' of https://github.com/BlueBrain/BluePyOpt into neuroml-test

Author: Jaquier Aurélien Tristan

.coveragerc

@@ -1,2 +1,4 @@
 [run]
-omit = */tests/*
+omit = */tests/*,bluepyopt/_version.py
+[report]
+omit=bluepyopt/_version.py

.github/workflows/build.yml

@@ -0,0 +1,37 @@
+name: Build
+
+on:
+  push:
+    branches:
+      - master
+    tags:
+      - '[0-9]+.[0-9]+.[0-9]+'
+
+jobs:
+  call-test-workflow:
+    uses: BlueBrain/BluePyOpt/.github/workflows/test.yml@master
+  
+  build-n-publish:
+    name: Build and publish on PyPI
+    runs-on: ubuntu-latest
+    needs: call-test-workflow
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python 3.7
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+
+      - name: Build a source tarball and wheel
+        run: |
+            pip install wheel
+            python setup.py sdist bdist_wheel
+
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/keep-alive.yml

@@ -0,0 +1,36 @@
+name: Keep-alive
+
+on:
+  schedule:
+    # Runs every sunday at 3 a.m.
+    - cron: '0 3 * * SUN'
+
+jobs:
+  call-test-workflow:
+    uses: BlueBrain/BluePyOpt/.github/workflows/test.yml@master
+  
+  keep-workflow-alive:
+    name: Keep workflow alive
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          ref: master
+
+      - name: Get date from 50 days ago
+        run: |
+          datethen=`date -d "-50 days" --utc +%FT%TZ`
+          echo "datelimit=$datethen" >> $GITHUB_ENV
+
+      - name: setup git config
+        if: github.event.base.repo.updated_at <= env.datelimit
+        run: |
+          # setup the username and email.
+          git config user.name "Github Actions Keepalive Bot"
+          git config user.email "<>"
+
+      - name: commit IF last commit is older than 50 days
+        if: github.event.base.repo.updated_at <= env.datelimit
+        run: |
+          git commit -m "Empty commit to keep the gihub workflows alive" --allow-empty
+          git push origin master

.github/workflows/main.yml

@@ -0,0 +1,37 @@
+name: Test
+
+on:
+  pull_request:
+  # allows this workflow to be reusable (e.g. by the build workflow)
+  workflow_call:
+
+jobs:
+  test:
+    name: Test for python ${{ matrix.python-version }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip install tox tox-gh-actions
+
+    - name: Run tox
+      run: tox
+
+    - name: "Upload coverage to Codecov"
+      uses: codecov/codecov-action@v2
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        fail_ci_if_error: false

.github/workflows/test.yml

@@ -97,6 +97,10 @@ When you use the BluePyOpt software or method for your research, we ask you to c
 	}
 
 
+Publications that use or mention BluePyOpt
+==========================================
+The list of publications that use or mention BluePyOpt can be found on `the github wiki page <https://github.com/BlueBrain/BluePyOpt/wiki/Publications-that-use-or-mention-BluePyOpt>`_.
+
 Support
 =======
 We are providing support using a chat channel on `Gitter <https://gitter.im/BlueBrain/BluePyOpt>`_, or the `Github discussion page <https://github.com/BlueBrain/BluePyOpt/discussions>`_.
@@ -115,7 +119,7 @@ News
 Requirements
 ============
 
-* `Python 3.6+ <https://www.python.org/downloads/release/python-360/>`_
+* `Python 3.7+ <https://www.python.org/downloads/release/python-370/>`_
 * `Pip <https://pip.pypa.io>`_ (installed by default in newer versions of Python)
 * `Neuron 7.4+ <http://neuron.yale.edu/>`_ (compiled with Python support)
 * `eFEL eFeature Extraction Library <https://github.com/BlueBrain/eFEL>`_ (automatically installed by pip)

README.rst

@@ -71,7 +71,7 @@ def get_hyped(pop, ubound_score=250., threshold_improvement=240.):
     ubounds = numpy.max(points, axis=0) + 2.0
 
     hv = hype.hypeIndicatorSampled(
-        points=points, bounds=ubounds, k=5, nrOfSamples=200000
+        points=points, bounds=ubounds, k=5, nrOfSamples=1000000
     )
     return hv
 

bluepyopt/deapext/CMA_MO.py

@@ -160,7 +160,7 @@ def eaAlphaMuPlusLambdaCheckpoint(
     gen = start_gen + 1
     stopping_params = {"gen": gen}
     while utils.run_next_gen(
-            not(_check_stopping_criteria(stopping_criteria, stopping_params)),
+            not (_check_stopping_criteria(stopping_criteria, stopping_params)),
             terminator):
         offspring = _get_offspring(parents, toolbox, cxpb, mutpb)
 
@@ -175,7 +175,7 @@ def eaAlphaMuPlusLambdaCheckpoint(
 
         logger.info(logbook.stream)
 
-        if(cp_filename and cp_frequency and
+        if (cp_filename and cp_frequency and
            gen % cp_frequency == 0):
             cp = dict(population=population,
                       generation=gen,

bluepyopt/deapext/algorithms.py

@@ -199,7 +199,10 @@ def setup_deap(self):
 
         # Register the evaluation function for the individuals
         # import deap_efel_eval1
-        self.toolbox.register("evaluate", self.evaluator.evaluate_with_lists)
+        self.toolbox.register(
+            "evaluate",
+            self.evaluator.set_neuron_variables_and_evaluate_with_lists
+        )
 
         # Register the mate operator
         self.toolbox.register(

bluepyopt/deapext/optimisations.py

@@ -211,7 +211,10 @@ def setup_deap(self):
         )
 
         # Register the evaluation function for the individuals
-        self.toolbox.register("evaluate", self.evaluator.evaluate_with_lists)
+        self.toolbox.register(
+            "evaluate",
+            self.evaluator.set_neuron_variables_and_evaluate_with_lists
+        )
 
         import copyreg
         import types