brainbuilder 0.20.0__tar.gz

brainbuilder-0.20.0/.git-blame-ignore-revs

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+# .git-blame-ignore-revs
+# Apply black and isort
+e5af8c3ea24cc529bfcdb0058fe8e55e9d193dcf
+# Format with black 24.x
+502880e98c77cc3d2e31fe1506701f54d5fe4423

brainbuilder-0.20.0/.github/workflows/sdist.yml

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+name: sdist
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+     - main
+  release:
+    types:
+      - published
+
+jobs:
+
+  build_sdist:
+    name: Build sdist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build SDist
+        run: pipx run build --sdist
+
+      - name: Check metadata
+        run: pipx run twine check dist/*
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: build
+          path: dist
+
+  upload_sdist:
+    name: Upload sdist
+    needs: [build_sdist]
+    runs-on: ubuntu-latest
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+    if: github.event_name == 'release' && github.event.action == 'published'
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: build
+          path: dist
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

brainbuilder-0.20.0/.github/workflows/tox.yml

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+name: Tox
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+jobs:
+  tox_checks:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+
+    steps:
+
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get update && sudo apt-get install hdf5-tools
+        python -m pip install --upgrade pip setuptools
+        pip install tox-gh-actions
+
+    - name: Run tox
+      run: tox

brainbuilder-0.20.0/.gitignore

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+*.pyc
+*.swp
+coverage.xml
+*.egg-info
+.coverage
+build
+.tox
+.idea
+.vscode
+venv
+dist
+brainbuilder/version.py

brainbuilder-0.20.0/.gitlab-ci.yml

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+include:
+  - project: nse/ci
+    file: /ci/pipelines/nse.brainbuilder.yml

brainbuilder-0.20.0/.ruff.toml

@@ -0,0 +1 @@
+line-length = 100

brainbuilder-0.20.0/CHANGELOG.rst

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+Changelog
+=========
+
+## 0.19.1
+  * Apply black and isort
+  * Add ``--log-level`` option to the main CLI.
+  * Include app in coverage calculation.
+  * Add tests for app/sonata.
+
+## 0.19.0
+  * Enforce layer to be a string (NSETM-2261)
+
+## 0.18.7
+  * Fix functional tests with snap 2.0
+  * Silence nptyping DeprecationWarnings
+
+## 0.18.6
+  * Make circuit splitting compatible with snap 2.0
+
+## 0.18.5
+  * Remove subcellular querier (BRBLD-97)
+
+## 0.18.4
+  * Zero close to zero values (NSETM-2128)
+  * Add curation facilities to update dtypes of a circuit (NSETM-2124)
+  * Fix implicit dependencies and tests with snap 1.0 (NSETM-2123)
+  * Use pytest-basetemp-permissions plugin (NSETM-2125)
+  * Use pytest tmp_path fixture for tests, add ruff
+  * Update for python 3.10
+  * teach `target node_sets --full-hierarchy`, which includes, from leaf to root, all the region names as node_sets
+
+## 0.18.3
+  * Use bool instead of np.bool.
+
+## 0.18.2
+  * Relax zero cell count assertion to a warning in `place`.
+  * Remove `assign_emodels2`; was a work around for the NCX project
+  * be more relaxed about matching `layer` and `subregion`
+  * for emodel assignment, try `layer` first, and fall back to `subregion` columns
+
+## 0.18.1
+  * Densities are now loaded using float64 precision. Higher precision aids in calculating
+    correctly the total counts when accumulation of small and large densities is involved.
+  * `layer` made an optional trait in `brainbuilder.app.cells.place`
+  * `subregion` added as cells property in `brainbuilder.app.cells.place`
+
+## 0.18.0
+  * Add simple circuit splitting for SONATA (BRBLD-90).
+  * Add subcircuit splitting for SONATA (BRBLD-90).
+  * teach `node-set-from-targets` to take paths to files, add to documentation
+  * Add support for copying the used morphologies from a SONATA circuit (BRBLD-93).
+
+## 0.17.0
+  * Update ``write_network_config`` to be compatible with the new BBP sonata specs, moved from
+    ``brainbuilder.utils.sonata.convert`` to ``brainbuilder.utils.sonata.config`` (NSETM-1526).
+  * Deprecate `FAST-HEMISPHERE` for assigning the `hemisphere` cells property,
+    and support loading it from a volumetric dataset (BRBLD-89).
+
+## 0.16.2
+  * Add more intelligent target to node set converter (BBPP82-514)
+  * Use pytest for tests (NSETM-1543)
+  * Deprecate ``brainbuilder.utils.sonata.convert.write_network_config``. Use circuit-build
+    project instead (NSETM-1526).
+  * Fix ``brainbuilder.utils.sonata.convert.write_node_set_from_targets`` due to optimization
+    of targets in bluepy==2.4.1.
+
+## 0.16.1
+  * Fix compat for bluepy>=2.3
+
+## 0.16.0
+  * Refactor neurondb functions from `brainbuilder.utils.bbp`. The previous API must be changed as:
+
+    - ``load_neurondb(file, False)`` => ``load_neurondb(file)``
+    - ``load_neurondb(file, True)`` => ``load_extneurondb(file)``
+    - ``load_neurondb_v3(file)`` => ``load_extneurondb(file)``
+
+## 0.15.1
+  * Introduce [reindex] extras
+  * Move morph-tool to test dependencies
+
+## 0.15.0
+  * Drop python 2 support
+  * Add 'split_population' SONATA command to break monolithic node/edge files into smaller version
+  * BBPP82-499: Add `cells positions_and_orientations` command to create a sonata file to be used by the web Cell Atlas
+    and by Point neuron whole mouse brain
+  * Allow users to set the seed of the numpy random generator when calling `cell_positions.create_cell_positions`
+  * new python API `brainbuilder.utils.bbp.load_cell_composition` to load cell composition yaml
+  * Check if all the mecombo from a cell file are present in the emodel release
+    in `utils.sonata.convert._add_me_info` function. If not raise.
+
+## 0.14.1
+  * Fix bugs du to voxcell >= 3.0.0
+  * Add a test to validate the behaviour of `utils.sonata.convert.write_network_config`
+
+## 0.14.0
+  * Add 'functional' tox env for functional tests
+  * Add a new package `utils.sonata`. Move all SONATA related utils there
+  * Add a new module `utils.sonata.curate` to curate/fix existing SONATA circuits
+  * Fix updating edge positions during reindex of `utils.sonata.reindex`
+  * Allow None `mecombo_info_path` in `utils.sonata.convert.provide_me_info`
+
+## 0.13.2
+  * Catch duplicate me-combos
+
+## 0.13.1
+  * Add "--input" option to "cells.place"
+  * Fix losing of SONATA population name at "cells.assign_emodels"
+
+## 0.13.0
+  * Create "sonata.provide_me_info". This action provisions SONATA nodes with ME info
+  * "sonata.from_mvd3" reuses "sonata.provide_me_info" under the hood
+
+## 0.12.1
+  * Fixes to sonata functions
+  * "assign_emodels2" function now adds the missing biophysical field
+  * "sonata.from_mvd3" remove the library argument (handled by voxcell now)
+  * "sonata.from_mvd3" add a model type
+
+## 0.12.0
+
+  * Allows cli with mvd3 inputs/outputs to use sonata files instead. The format detection is done
+    using the file extension : '.mvd3' will save/read a 'mvd3' file. For any other file extension,
+    sonata is used.
+  * "place" cli can output seamlessly sonata or mvd3 files
+  * "assign_emodels/assign_emodels2" can use sonata or mvd3 files as input
+  * "assign" cli can use sonata or mvd3 files as input
+  * rename of "target.from_mvd3" to "target.from_input" and can use both formats as input
+  * "target.node_sets" can use both formats as input
+
+## 0.11.10
+
+ * Add atlas based node set with sonata files [NSETM-1010]
+ * Change the node_set location inside the sonata config file. Now attached to the circuit not
+   the node files
+
+## 0.11.9
+
+ * added reindex for only children, need to convert connectivity to swc
+ * updated & fixed documentation
+ * Fix empty query_based crash [NSETM-1003]
+
+## 0.11.8
+
+ * atlases creation cli
+
+## 0.11.7
+
+ * Use NodePopulation.from_cell_collection
+ * BBPBGLIB-557: use SONATA naming, not syn2
+ * Add target to node_set direct converter
+
+## 0.11.6
+
+ * add sonata2nrn converter, so we can build spatial indices
+
+## 0.11.5
+
+ * add syn2 concat and check support
+ * BBPP82-94: Add @library enums to mvd3 -> sonata node converter
+ * remove seed handling: NSETM-215

brainbuilder-0.20.0/CONTRIBUTING.md

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+# Contribution Guide
+
+We would love for you to contribute to the brainbuilder project and help make it better than it is today.
+As a contributor, here are the guidelines we would like you to follow:
+
+ - [Question or Problem?](#got-a-question)
+ - [Issues and Bugs](#found-a-bug)
+ - [Feature Requests](#missing-a-feature)
+ - [Submissions](#submission-guidelines)
+ - [Development Guidelines](#development)
+ - [Release Procedure](#release)
+
+# Got a Question?
+
+Please do not hesitate to raise an issue on [github project page][github].
+
+# Found a Bug?
+
+If you find a bug in the source code, you can help us by [submitting an issue](#issues)
+to our [GitHub Repository][github]. Even better, you can [submit a Pull Request](#pull-requests) with a fix.
+
+#  Missing a Feature?
+
+You can *request* a new feature by [submitting an issue](#issues) to our GitHub Repository.
+If you would like to *implement* a new feature, please submit an issue with a proposal for your work first, to be sure that we can use it.
+
+Please consider what kind of change it is:
+
+* For a **Major Feature**, first open an issue and outline your proposal so that it can be
+discussed. This will also allow us to better coordinate our efforts, prevent duplication of work,
+and help you to craft the change so that it is successfully accepted into the project.
+* **Small Features** can be crafted and directly [submitted as a Pull Request](#pull-requests).
+
+# Submission Guidelines
+
+## Issues
+
+Before you submit an issue, please search the issue tracker, maybe an issue for your problem
+already exists and the discussion might inform you of workarounds readily available.
+
+We want to fix all the issues as soon as possible, but before fixing a bug we need to reproduce
+and confirm it. In order to reproduce bugs we will need as much information as possible, and
+preferably with an example.
+
+## Pull Requests
+
+When you wish to contribute to the code base, please consider the following guidelines:
+
+* Make a [fork](https://guides.github.com/activities/forking/) of this repository.
+* Make your changes in your fork, in a new git branch:
+
+     ```shell
+     git checkout -b my-fix-branch master
+     ```
+* Create your patch, **including appropriate Python test cases**.
+  Please check the coding [conventions](#coding-conventions) for more information.
+* Run the full test suite, and ensure that all tests pass.
+* Commit your changes using a descriptive commit message.
+
+     ```shell
+     git commit -a
+     ```
+* Push your branch to GitHub:
+
+    ```shell
+    git push origin my-fix-branch
+    ```
+* In GitHub, send a Pull Request to the `master` branch of the upstream repository of the relevant component.
+* If we suggest changes then:
+  * Make the required updates.
+  * Re-run the test suites to ensure tests are still passing.
+  * Rebase your branch and force push to your GitHub repository (this will update your Pull Request):
+
+       ```shell
+        git rebase master -i
+        git push -f
+       ```
+
+That’s it! Thank you for your contribution!
+
+### After your pull request is merged
+
+After your pull request is merged, you can safely delete your branch and pull the changes from
+the main (upstream) repository:
+
+* Delete the remote branch on GitHub either through the GitHub web UI or your local shell as follows:
+
+    ```shell
+    git push origin --delete my-fix-branch
+    ```
+* Check out the master branch:
+
+    ```shell
+    git checkout main -f
+    ```
+* Delete the local branch:
+
+    ```shell
+    git branch -D my-fix-branch
+    ```
+* Update your main with the latest upstream version:
+
+    ```shell
+    git pull --ff upstream main
+    ```
+
+[github]: https://github.com/BlueBrain/brainbuilder

brainbuilder-0.20.0/LICENSE.txt

@@ -0,0 +1,202 @@
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brainbuilder-0.20.0/MANIFEST.in

@@ -0,0 +1,3 @@
+graft tests
+
+global-exclude *.pyc .DS_Store

brainbuilder-0.20.0/PKG-INFO

@@ -0,0 +1,61 @@
+Metadata-Version: 2.1
+Name: brainbuilder
+Version: 0.20.0
+Summary: BrainBuilder is a tool to define the cells that will compose a circuit.
+Author: Blue Brain Project, EPFL
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/BlueBrain/brainbuild
+Project-URL: Repository, https://github.com/BlueBrain/brainbuild.git
+Project-URL: Documentation, https://github.com/BlueBrain/brainbuild
+Project-URL: Tracker, https://github.com/BlueBrain/brainbuild/issues
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: bluepysnap>=1.0.3
+Requires-Dist: click<9.0,>=7.0
+Requires-Dist: h5py>=3.1.0
+Requires-Dist: joblib>=1.0.1
+Requires-Dist: jsonschema>=3.2.0
+Requires-Dist: libsonata>=0.1.6
+Requires-Dist: lxml>=3.3
+Requires-Dist: morphio<4,>=3
+Requires-Dist: numpy>=1.9
+Requires-Dist: pandas>=1.0.0
+Requires-Dist: pyyaml>=5.3.1
+Requires-Dist: scipy>=0.13
+Requires-Dist: tqdm>=4.0
+Requires-Dist: voxcell>=3.1.1
+Provides-Extra: all
+Provides-Extra: reindex
+
+# Introduction
+
+BrainBuilder is a tool to define the cells that will compose a circuit.
+It also houses utilities for working with SONATA circuits.
+
+# Installation
+
+```shell
+    $ pip install brainbuilder
+```
+
+# Contribution Guidelines
+See CONTRIBUTING.md.
+
+# 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.
+
+This project/research received funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA).
+
+For license see LICENSE.txt.
+
+Copyright © 2014-2023 Blue Brain Project/EPFL

brainbuilder-0.20.0/README.md

@@ -0,0 +1,23 @@
+# Introduction
+
+BrainBuilder is a tool to define the cells that will compose a circuit.
+It also houses utilities for working with SONATA circuits.
+
+# Installation
+
+```shell
+    $ pip install brainbuilder
+```
+
+# Contribution Guidelines
+See CONTRIBUTING.md.
+
+# 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.
+
+This project/research received funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA).
+
+For license see LICENSE.txt.
+
+Copyright © 2014-2023 Blue Brain Project/EPFL

brainbuilder-0.20.0/brainbuilder/__init__.py

@@ -0,0 +1,5 @@
+# SPDX-License-Identifier: Apache-2.0
+""" brainbuilder """
+
+from brainbuilder.exceptions import BrainBuilderError  # noqa
+from brainbuilder.version import __version__  # noqa