neurodamus 3.0.0__tar.gz

neurodamus-3.0.0/.coveragerc

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+# .coveragerc to control coverage.py
+[run]
+branch = True
+source = neurodamus
+# omit = 
+
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:

neurodamus-3.0.0/.gitattributes

@@ -0,0 +1,2 @@
+*.asc linguist-detectable=false
+*.mod linguist-detectable=false

neurodamus-3.0.0/.github/pull_request_template.md

@@ -0,0 +1,23 @@
+## Context
+<!-- Please brifly describe the problem the PR solves and what the solution was -->
+
+## Scope
+<!--
+Please describe in more detail the several changes implemented. How did we solve it?
+E.g. change component-A to..., created a new data structure, etc...
+-->
+
+## Testing
+<!--
+Please add a new test under `tests`. Consider the following cases:
+
+ 1. If the change is in an independent component (e.g, a new container type, a parser, etc) a bare unit test should be sufficient. See e.g. `tests/test_coords.py`
+ 2. If you are fixing or adding components supporting a scientific use case, affecting node or synapse creation, etc..., which typically rely on Neuron, tests should set up a simulation using that feature, instantiate neurodamus, **assess the state**, run the simulation and check the results are as expected.
+    See an example at `tests/test_simulation.py#L66`
+-->
+
+## Review
+* [ ] PR description is complete
+* [ ] Coding style (imports, function length, New functions, classes or files) are good
+* [ ] Unit/Scientific test added
+* [ ] Updated Readme, in-code, developer documentation

neurodamus-3.0.0/.github/workflows/simulation_test.yml

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+name: neurodamus build and test
+on:
+  schedule:
+    # every evening at 20:00 UTC
+    - cron: '0 20 * * *'
+
+jobs:
+  simulation:
+    runs-on: ubuntu-22.04
+
+    steps:
+    - name: Checkout neurodamus repository
+      uses: actions/checkout@v3
+      with:
+        ref: ${{ github.event.pull_request.head.sha }}
+        fetch-depth: 0
+
+    - name: Get HEAD commit message and look for branches
+      run: |
+        COMMIT_MESSAGE=$(git log -1 --pretty=%B)
+        echo $COMMIT_MESSAGE
+        NEURON_BRANCH=$(echo $COMMIT_MESSAGE | grep -Po 'NEURON_BRANCH=\K[0-9a-zA-Z/_.\-]*' || true)
+        if [[ ! -z $NEURON_BRANCH ]]; then echo "NEURON_BRANCH=$NEURON_BRANCH" >> $GITHUB_ENV; fi
+        LIBSONATA_REPORT_BRANCH=$(echo $COMMIT_MESSAGE | grep -Po 'LIBSONATA_REPORT_BRANCH=\K[0-9a-zA-Z/_.\-]*' || true)
+        if [[ ! -z $LIBSONATA_REPORT_BRANCH ]]; then echo "LIBSONATA_REPORT_BRANCH=$LIBSONATA_REPORT_BRANCH" >> $GITHUB_ENV; fi
+
+    - name: Install hdf5-mpich
+      run: |
+        sudo apt-get update
+        sudo apt-get install mpich libmpich-dev libhdf5-mpich-dev hdf5-tools
+
+    - name: Install libsonata
+      run: |
+        CC=mpicc CXX=mpic++ pip install git+https://github.com/BlueBrain/libsonata
+
+    - name: Install libsonatareport
+      run: |
+        git clone --branch="${LIBSONATA_REPORT_BRANCH:-master}" https://github.com/BlueBrain/libsonatareport.git --recursive --depth=1
+        cd libsonatareport
+        mkdir build && cd build
+        cmake -DCMAKE_INSTALL_PREFIX=$(pwd)/install -DCMAKE_BUILD_TYPE=Release -DSONATA_REPORT_ENABLE_SUBMODULES=ON -DSONATA_REPORT_ENABLE_MPI=ON ..
+        cmake --build . --parallel
+        cmake --build . --target install
+
+    - name: Install NEURON
+      run: |
+        sudo apt-get install flex libfl-dev bison ninja-build
+        pip install -U pip setuptools
+        pip install "cython<3" pytest sympy
+        export SONATAREPORT_DIR=$(pwd)/libsonatareport/build/install
+        git clone --branch="${NEURON_BRANCH:-master}" https://github.com/neuronsimulator/nrn.git --depth=1
+        cd nrn
+        mkdir build && cd build
+        cmake -G Ninja -DPYTHON_EXECUTABLE=$(which python) -DCMAKE_INSTALL_PREFIX=$(pwd)/install -DNRN_ENABLE_MPI=ON -DNRN_ENABLE_INTERVIEWS=OFF \
+          -DNRN_ENABLE_CORENEURON=ON -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCORENRN_ENABLE_REPORTING=ON -DCMAKE_PREFIX_PATH=$SONATAREPORT_DIR ..
+        cmake --build . --parallel
+        cmake --build . --target install
+
+    - name: Build h5py with the local hdf5
+      run: |
+        pip install -U pip setuptools
+        pip install cython numpy wheel pkgconfig
+        MPICC="mpicc -shared" pip install --no-cache-dir --no-binary=mpi4py mpi4py
+        CC="mpicc" HDF5_MPI="ON" HDF5_INCLUDEDIR=/usr/include/hdf5/mpich HDF5_LIBDIR=/usr/lib/x86_64-linux-gnu/hdf5/mpich \
+          pip install --no-cache-dir --no-binary=h5py h5py --no-build-isolation
+
+    - name: Install neurodamus
+      run: |
+        pip install .
+
+    - name: Build models
+      run: |
+        export SONATAREPORT_DIR=$(pwd)/libsonatareport/build/install
+        export PATH=$(pwd)/nrn/build/install/bin:$PATH
+        # copy mod files from the Zenodo link
+        wget --output-document="O1_mods.xz" --quiet "https://zenodo.org/record/8026353/files/O1_mods.xz?download=1"
+        tar -xf O1_mods.xz
+        cp -r mod tests/share/
+        cp core/mod/*.mod tests/share/mod/
+        ./docker/build_neurodamus.sh tests/share/mod
+
+    - name: Example run
+      run: |
+        export PYTHONPATH=$(pwd)/nrn/build/lib/python:$PYTHONPATH
+        cp core/hoc/* tests/share/hoc/
+        export HOC_LIBRARY_PATH=$(pwd)/tests/share/hoc
+        # launch simulation with NEURON
+        mpirun -np 2 ./x86_64/special -mpi -python init.py --configFile=tests/simulations/usecase3/simulation_sonata.json
+        ls tests/simulations/usecase3/reporting/*.h5
+        # launch simulation with CORENEURON
+        mpirun -np 2 ./x86_64/special -mpi -python init.py --configFile=tests/simulations/usecase3/simulation_sonata_coreneuron.json
+        ls tests/simulations/usecase3/reporting_coreneuron/*.h5
+
+    # - name: live debug session, comment out
+    #   if: failure()
+    #   uses: mxschmitt/action-tmate@v3

neurodamus-3.0.0/.gitignore

@@ -0,0 +1,45 @@
+# Temporary and binary files
+*~
+*.py[cod]
+*.so
+*.cfg
+!setup.cfg
+*.orig
+*.log
+*.pot
+__pycache__/*
+.cache/*
+.*.swp
+*/.ipynb_checkpoints/*
+.vscode
+spack-*
+
+# Project files
+.ropeproject
+.project
+.pydevproject
+.settings
+.idea
+venv
+
+# Package files
+*.egg
+*.eggs/
+.installed.cfg
+*.egg-info
+
+# Unittest and coverage
+htmlcov/*
+.coverage
+.tox
+junit.xml
+coverage.xml
+tests/output
+
+# Build and docs folder/files
+build/*
+dist/*
+sdist/*
+docs/_build/*
+cover/*
+MANIFEST

neurodamus-3.0.0/.gitlab-ci.yml

@@ -0,0 +1,262 @@
+include:
+  - project: nse/ci
+    file:
+      - /ci/lib/tox-bb5.yml
+      - /ci/jobs/build-package.yml
+      - /ci/jobs/publish-package.yml
+      - /ci/jobs/docs.yml
+      - /ci/jobs/publish-docs.yml
+  - project: hpc/gitlab-upload-logs
+    file: enable-upload.yml
+  - project: cs/gitlabci-templates
+    file: /build-image-using-buildah.yml
+
+workflow:
+  rules:
+    - if: '$CI_EXTERNAL_PULL_REQUEST_IID'
+    - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH'
+    - if: $CI_PIPELINE_SOURCE == "web"
+      # Run workflows on tag creation to build the container
+    - if: $CI_COMMIT_TAG
+
+variables:
+  BLUECONFIGS_BRANCH:
+    value: $BLUECONFIGS_BRANCH
+    description: 'Name of the blueconfigs branch to test against'
+  GIT_DEPTH: 100
+
+test-unit:
+  extends: .tox-template
+  variables:
+    TOXENV: flake8, unit
+
+test-integration:
+  extends: .tox-template
+  variables:
+    TOXENV: integration
+
+test-integration-e2e:
+  extends: .tox-template
+  variables:
+    TOXENV: bbp-model
+    TOX_OPTIONS: "-- tests/integration-e2e"
+    # modules need to be loaded in this certain order to avoid mixing of libraries
+    EXTRA_MODULES:
+      unstable:neurodamus-neocortex
+
+test-scientific:
+  extends: .tox-template
+  variables:
+    TOXENV: bbp-model
+    TOX_OPTIONS: "-- tests/scientific"
+    # modules need to be loaded in this certain order to avoid mixing of libraries
+    EXTRA_MODULES:
+      unstable:intel-oneapi-compilers
+      unstable:py-bluepysnap
+      unstable:neurodamus-neocortex
+
+test-scientific-ngv:
+  extends: .tox-template
+  variables:
+    TOXENV: bbp-model
+    TOX_OPTIONS: "-- tests/scientific-ngv"
+    EXTRA_MODULES:
+      unstable:neurodamus-neocortex-multiscale
+
+set_alt_branches:
+  script:
+    - grep '^[[:alnum:]_]*_BRANCH=' <<< "$CI_COMMIT_MESSAGE" > branch_variables.env || touch branch_variables.env
+    - . branch_variables.env
+    - echo "BLUECONFIGS_PIPELINE_BRANCH=$BLUECONFIGS_BRANCH" >> branch_variables.env
+    - cat branch_variables.env
+  artifacts:
+    reports:
+      dotenv: branch_variables.env
+
+blueconfig_tests:
+  variables:
+    bb5_build_dir: pipeline
+    PY_NEURODAMUS_BRANCH: $CI_EXTERNAL_PULL_REQUEST_SOURCE_BRANCH_NAME
+    PARENT_COMMIT_MESSAGE: $CI_COMMIT_MESSAGE
+  trigger:
+    project: hpc/sim/blueconfigs
+    branch: $BLUECONFIGS_PIPELINE_BRANCH
+    strategy: depend
+  needs:
+    - set_alt_branches
+  rules:
+    - if: '$CI_EXTERNAL_PULL_REQUEST_IID'
+      changes:
+        - neurodamus/**/*
+    - when: manual
+      allow_failure: true
+
+configure-docker-image:
+  image: ubuntu:22.04
+  stage: build
+  script:
+    - set -x
+    - apt-get update -y
+    - apt-get install -y git skopeo python3
+    - |
+      echo "Getting package version and checking whether we need to build the container"
+      if [ -n "${LIBSONATAREPORT_TAG}" || -n "${LIBSONATA_TAG}" || -n "${NEURON_COMMIT_ID}" && -z "${REGISTRY_IMAGE_TAG}" ]; then
+        echo "If you specify LIBSONATAREPORT_TAG, LIBSONATA_TAG or NEURON_COMMIT_ID, you must also specify REGISTRY_IMAGE_TAG."
+        exit 1
+      fi
+      if [ -z "${REGISTRY_IMAGE_TAG}" ]; then
+        PACKAGE_VERSION=$(git describe --tags)
+        REGISTRY_IMAGE_TAG=$(echo ${PACKAGE_VERSION%-*} | sed 's/-/.dev/')
+      fi
+      set +e
+      skopeo inspect docker://bluebrain/neurodamus:${REGISTRY_IMAGE_TAG}
+      if [[ $? -eq 0 ]]; then
+        echo "Container with version ${REGISTRY_IMAGE_TAG} already exists - not rebuilding"
+        BUILD_DOCKER_CONTAINER="false"
+      else
+        echo "Container with version ${REGISTRY_IMAGE_TAG} does not exist yet - building"
+        BUILD_DOCKER_CONTAINER="true"
+      fi
+      set -e
+    - |
+      echo "Getting dependency versions from spack"
+      git clone https://github.com/bluebrain/spack
+      cd spack
+      source ./share/spack/setup-env.sh
+      if [ -z "${LIBSONATAREPORT_TAG}" ]; then
+        LIBSONATAREPORT_TAG=$(spack info libsonata-report | awk 'matched{print $NF;matched=0} /Preferred/{matched=1}')
+      fi
+      if [ -z "${LIBSONATA_TAG}" ]; then
+        LIBSONATA_TAG=v$(spack info py-libsonata | awk 'matched{print $1;matched=0} /Preferred/{matched=1}')
+      fi
+      if [ -z "${NEURON_COMMIT_ID}" ]; then
+        NEURON_COMMIT_ID=$(spack info neuron | awk 'matched{print $NF;matched=0} /Preferred/{matched=1}')
+      fi
+      cd ..
+    - |
+      cat <<EOF > build.env
+      REGISTRY_IMAGE_TAG=$REGISTRY_IMAGE_TAG
+      BUILD_DOCKER_CONTAINER=$BUILD_DOCKER_CONTAINER
+      LIBSONATAREPORT_TAG=${LIBSONATAREPORT_TAG}
+      LIBSONATA_TAG=${LIBSONATA_TAG}
+      NEURON_COMMIT_ID=${NEURON_COMMIT_ID}
+      EOF
+    - cat build.env
+  artifacts:
+    when: always
+    paths: [build.env]
+    reports:
+      dotenv: build.env
+  rules:
+    - if: $CI_COMMIT_TAG
+      when: manual
+      allow_failure: true
+    - if: $CI_PIPELINE_SOURCE == "web"
+
+build-docker-image:
+  timeout: 2h
+  needs: [configure-docker-image]
+  stage: build
+  extends: .build-image-using-buildah
+  variables:
+    BUILD_PATH: $CI_PROJECT_DIR/docker
+    KUBERNETES_CPU_LIMIT: 8
+    KUBERNETES_CPU_REQUEST: 8
+    KUBERNETES_MEMORY_LIMIT: 8Gi
+    KUBERNETES_MEMORY_REQUEST: 8Gi
+    BUILDAH_EXTRA_ARGS:
+      --label org.opencontainers.image.title="neurodamus"
+      --label org.opencontainers.image.version="$REGISTRY_IMAGE_TAG"
+      --label org.opencontainers.image.revision="$CI_COMMIT_SHA"
+      --label org.opencontainers.image.authors="$GITLAB_USER_NAME <$GITLAB_USER_EMAIL>"
+      --label org.opencontainers.image.url="$CI_PROJECT_URL"
+      --label org.opencontainers.image.source="$CI_PROJECT_URL"
+      --label org.opencontainers.image.created="$CI_JOB_STARTED_AT"
+      --label ch.epfl.bbpgitlab.ci-pipeline-url="$CI_PIPELINE_URL"
+      --label ch.epfl.bbpgitlab.ci-commit-branch="$CI_COMMIT_BRANCH"
+      --label ch.epfl.bbpgitlab.libsonata-report-tag="$LIBSONATAREPORT_TAG"
+      --label ch.epfl.bbpgitlab.libsonata-tag="$LIBSONATA_TAG"
+      --label ch.epfl.bbpgitlab.neuron-commit-id="$NEURON_COMMIT_ID"
+      --build-arg GITLAB_CI="$GITLAB_CI"
+      --build-arg CI_JOB_TOKEN="$CI_JOB_TOKEN"
+      --build-arg LIBSONATAREPORT_TAG="$LIBSONATAREPORT_TAG"
+      --build-arg LIBSONATA_TAG="$LIBSONATA_TAG"
+      --build-arg NEURON_COMMIT_ID="$NEURON_COMMIT_ID"
+  before_script:
+    - echo "LIBSONATAREPORT_TAG is .$LIBSONATAREPORT_TAG."
+    - echo "LIBSONATA_TAG is .$LIBSONATA_TAG."
+    - echo "NEURON_COMMIT_ID is .$NEURON_COMMIT_ID."
+    - echo "REGISTRY_IMAGE_TAG is .$REGISTRY_IMAGE_TAG."
+    - set -x
+    - if [ "$BUILD_DOCKER_CONTAINER" == "false" ]; then
+    -   echo "No need to build the docker container"
+    -   exit 0
+    - else
+    -   echo "Building"
+    - fi
+  rules:
+    - if: $CI_COMMIT_TAG
+    - if: $CI_PIPELINE_SOURCE == "web"
+
+upload-to-docker-hub:
+  image: ubuntu:22.04
+  stage: publish
+  variables:
+    KUBERNETES_CPU_LIMIT: 4
+    KUBERNETES_CPU_REQUEST: 2
+    KUBERNETES_MEMORY_LIMIT: 8Gi
+    KUBERNETES_MEMORY_REQUEST: 2Gi
+  needs: [configure-docker-image, build-docker-image]
+  before_script:
+    - if [ "$BUILD_DOCKER_CONTAINER" == "false" ]; then
+    -   echo "No need to build the docker container"
+    -   exit 0
+    - else
+    -   echo "Building"
+    - fi
+  script:
+    - apt-get update && apt-get install -y jq curl podman
+    - export HUB_REPO_NAME="neurodamus"
+    - |
+      TOKEN=$(curl -s --header "Content-Type:application/json" --request POST --data "{\"username\":\"${DOCKER_HUB_USER}\", \"password\":\"${DOCKER_HUB_AUTH_TOKEN}\"}" https://hub.docker.com/v2/users/login/ | jq -r .token)
+    - echo "Pushing to docker hub repo docker://docker.io/bluebrain/${HUB_REPO_NAME}"
+    - podman login -u ${CI_REGISTRY_USER} -p ${CI_REGISTRY_PASSWORD} ${CI_REGISTRY_IMAGE}
+    - podman login -u ${DOCKER_HUB_USER} -p ${DOCKER_HUB_AUTH_TOKEN} docker.io
+    - podman pull ${CI_REGISTRY_IMAGE}:${REGISTRY_IMAGE_TAG}
+    - echo podman push ${CI_REGISTRY_IMAGE}:${REGISTRY_IMAGE_TAG} docker://docker.io/bluebrain/${HUB_REPO_NAME}:${REGISTRY_IMAGE_TAG}
+    - curl -s --header "Content-Type:application/json" --header "Authorization:JWT ${TOKEN}" -X DELETE "https://hub.docker.com/v2/repositories/bluebrain/neurodamus/tags/latest/"
+    - podman --log-level=debug push ${CI_REGISTRY_IMAGE}:${REGISTRY_IMAGE_TAG} docker://docker.io/bluebrain/${HUB_REPO_NAME}:${REGISTRY_IMAGE_TAG}
+    - podman --log-level=debug push ${CI_REGISTRY_IMAGE}:${REGISTRY_IMAGE_TAG} docker://docker.io/bluebrain/${HUB_REPO_NAME}:latest
+  rules:
+    - if: $CI_COMMIT_TAG
+    - if: $CI_PIPELINE_SOURCE == "web"
+      when: manual
+
+
+# The following stages are overrides. Don't rename
+# Always add the manual option to create sdist/wheel or upload
+build-package:
+  rules:
+    - when: on_success
+
+publish-package:
+  rules:
+    - when: manual
+      allow_failure: true
+
+docs:
+  variables:
+    TOXENV: docs
+  artifacts:
+    paths:
+      - docs/_build
+
+publish-docs:
+  variables:
+    SYS_PACKAGES: openssh-clients
+    PIP_PACKAGES: docs_internal_upload
+  script:
+    - docs-internal-upload --docs-path docs/_build
+  rules:
+    - when: manual
+      allow_failure: true

neurodamus-3.0.0/.pre-commit-config.yaml

@@ -0,0 +1,13 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v2.3.0
+  hooks:
+  - id: end-of-file-fixer
+  - id: check-added-large-files
+- repo: https://github.com/PyCQA/flake8.git
+  rev: 4.0.1
+  hooks:
+  - id: flake8
+    exclude: ^docs/

neurodamus-3.0.0/.readthedocs.yml

@@ -0,0 +1,21 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+sphinx:
+  configuration: docs/conf.py
+  fail_on_warning: true
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3"
+
+python:
+  install:
+    - method: pip
+      path: .
+    - requirements: requirements_docs.txt