diff --git a/.gitlab-ci.hpc.yml b/.gitlab-ci.hpc.yml
deleted file mode 100644
index cd214c4..0000000
--- a/.gitlab-ci.hpc.yml
+++ /dev/null
@@ -1,34 +0,0 @@
-include:
- - project: hpc/gitlab-pipelines
- file: spack-build.gitlab-ci.yml
- ref: '$GITLAB_PIPELINES_BRANCH'
-
-variables:
- SPACK_PACKAGE: spykfunc
-
-.fz_test:
- extends: .spack_test
- needs: [spack_build]
- variables:
- bb5_constraint: nvme
- bb5_cpus_per_task: 72
- bb5_memory: 0
- bb5_ntasks: 1
-
-circuit1k_s2f:
- extends: .fz_test
-
-circuit1k_s2f_split_and_merge:
- extends: .fz_test
-
-circuit1k_s2s:
- extends: .fz_test
-
-circuit1k_s2s_nodesets:
- extends: .fz_test
-
-circuit2k_s2f:
- extends: .fz_test
-
-circuit2k_s2s:
- extends: .fz_test
diff --git a/.gitlab-ci.nse.yml b/.gitlab-ci.nse.yml
deleted file mode 100644
index c05bd6a..0000000
--- a/.gitlab-ci.nse.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-include:
- - project: nse/ci
- file:
- - /ci/jobs/lint.yml
- - project: hpc/gitlab-pipelines
- file:
- - tox-nse-docs.gitlab-ci.yml
-
-variables:
- KUBERNETES_CPU_LIMIT: 4100m
- KUBERNETES_CPU_REQUEST: 4
- KUBERNETES_MEMORY_LIMIT: 8Gi
- KUBERNETES_MEMORY_REQUEST: 8Gi
-
-.tox-template:
- variables:
- SYS_PACKAGES: cmake git java-11-openjdk ninja-build mpich-autoload mpich-devel
- CC: /usr/lib64/mpich/bin/mpicc
- CXX: /usr/lib64/mpich/bin/mpicxx
- PRE_BUILD_COMMAND: "export CC=/usr/lib64/mpich/bin/mpicc CXX=/usr/lib64/mpich/bin/mpicxx"
-
-build-wheels:
- parallel:
- matrix:
- - PY_VERSION: [py311]
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
deleted file mode 100644
index 4d28b70..0000000
--- a/.gitlab-ci.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-nse_stack:
- stage: test
- trigger:
- include:
- - local: .gitlab-ci.nse.yml
- strategy: depend
-
-hpc_stack:
- stage: test
- trigger:
- include:
- - local: .gitlab-ci.hpc.yml
- strategy: depend
- variables:
- GITLAB_PIPELINES_BRANCH: $GITLAB_PIPELINES_BRANCH
diff --git a/AUTHORS.txt b/AUTHORS.txt
index 0562350..3f7df0e 100644
--- a/AUTHORS.txt
+++ b/AUTHORS.txt
@@ -1,4 +1,5 @@
Matthias Wolf
Fernando Pereira
Sergio Rivas Gomez
+Luc Dominic Grosheintz-Laval
Tristan Carel
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..2dd02a9
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,5 @@
+FROM python:latest
+
+RUN apt-get update \
+ && apt-get install -y libopenmpi-dev
+RUN pip install /workspace
diff --git a/README.rst b/README.rst
index 8c199e8..ca38da8 100644
--- a/README.rst
+++ b/README.rst
@@ -1,3 +1,6 @@
+.. image:: doc/source/_static/banner.jpg
+ :alt: A nice banner for functionalizer
+
Functionalizer
==============
@@ -10,9 +13,27 @@ To process the large quantities of data optimally, this software uses PySpark.
Installation
------------
-For manual installation via `pip`, a compiler handling C++17 will be necessary.
-Otherwise, all `git` submodules should be checked out and `cmake` as well as `ninja` be
-installed.
+The easiest way to install `functionalizer` is via:
+
+.. code-block:: console
+
+ pip install functionalizer
+
+Due to a dependency on ``mpi4py``, a MPI implementation needs to be installed on the
+system used. On Ubuntu, this can be achieved with:
+
+.. code-block:: console
+
+ apt-get install -y libopenmpi-dev
+
+For manual installation from sources via ``pip``, a compiler handling C++17 will be
+necessary. Furthermore, all ``git`` submodules should be checked out:
+
+.. code-block:: console
+
+ gh repo clone BlueBrain/functionalizer -- --recursive --shallow-submodules
+ cd functionalizer
+ pip install .
Spark and Hadoop should be installed and set up as runtime dependencies.
@@ -27,4 +48,12 @@ Where the final argument `edges.h5` may also be a directory of Parquet files. W
running on a cluster with multiple nodes, care should be taken that every rank occupies a
whole node, Spark will then spread out across each node.
+Acknowledgment
+--------------
+The development of this software was supported by funding to the Blue Brain Project,
+a research center of the École polytechnique fédérale de Lausanne (EPFL),
+from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.
+
+Copyright (c) 2017-2024 Blue Brain Project/EPFL
+
.. _SONATA extension: https://sonata-extension.readthedocs.io
diff --git a/doc/source/_static/banner.jpg b/doc/source/_static/banner.jpg
new file mode 100644
index 0000000..9ab45e4
Binary files /dev/null and b/doc/source/_static/banner.jpg differ
diff --git a/doc/source/conf.py b/doc/source/conf.py
index f74658b..8579f10 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -56,3 +56,4 @@
html_theme_options = {"metadata_distribution": "functionalizer"}
html_title = "functionalizer"
html_show_sourcelink = False
+html_static_path = ['_static']
diff --git a/pyproject.toml b/pyproject.toml
index aac6192..a15e9f7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,12 +1,12 @@
[build-system]
-requires = ["scikit-build-core[pyproject]", "setuptools_scm"]
+requires = ["scikit-build-core[pyproject]", "setuptools_scm", "cmake", "ninja"]
build-backend = "scikit_build_core.build"
[project]
name = "functionalizer"
dynamic = ["version"]
description = "A PySpark implementation of the Blue Brain Project Functionalizer"
-license = {"text" = "Blue Brain Project License"}
+license = {"file" = "LICENSE.txt"}
authors = [{"name" = "BlueBrain HPC", "email" = "bbp-ou-hpc@epfl.ch"}]
maintainers = [
{"name" = "Matthias Wolf", "email" = "matthias.wolf@epfl.ch"},
@@ -74,3 +74,12 @@ max-args = 8
[tool.black]
extend-exclude = 'deps\/.*$'
line_length = 100
+
+[tool.cibuildwheel]
+skip = ["cp3{6,7,8}-*", "pp*", "*-win32", "*-manylinux_i686", "*-musllinux_i686", "*-musllinux_x86_64", "*-musllinux_aarch64"]
+# MPI needed for testing with mpi4py
+before-all = "yum install -y openmpi3-devel java-11-openjdk"
+environment = { MPICC="/usr/lib64/openmpi3/bin/mpicc" }
+# Remove setuptools with Spark v4 - v3 has implicit dependency on distutils
+test-requires = ["pytest", "mock", "setuptools"]
+test-command = "pytest --run-slow {project}/tests"