nemos 0.1.0__tar.gz

nemos-0.1.0/.github/CODEOWNERS

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+* @BalzaniEdoardo

nemos-0.1.0/.github/workflows/ci.yml

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+name: ci
+
+on:
+   workflow_dispatch:
+   schedule:
+     - cron: 0 0 1 * 0     # monthly
+   pull_request:
+     branches:
+       - main
+       - development
+
+jobs:
+  tox:
+    strategy:
+      matrix:
+        os: [ubuntu-latest] #[ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.10'] #['3.8', '3.9', '3.10']
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4 # Use v4 for compatibility with pyproject.toml
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install .
+          pip install tox
+
+      - name: Run tox
+        run: tox -e py
+
+  check:
+    if: always()
+    needs: tox
+    runs-on: ubuntu-latest
+    steps:
+      - name: Decide whether all tests and notebooks succeeded
+        uses: re-actors/alls-green@v1.2.2
+        with:
+          jobs: ${{ toJSON(needs) }}

nemos-0.1.0/.github/workflows/connect.yml

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+# Workflow to connect to a runner
+name: connect
+
+# Trigger the workflow manually
+on:
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: build                        # Name of the job
+    strategy:
+      matrix:
+        os: [ubuntu-latest] #[ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.8', '3.9', '3.10']
+    runs-on: ${{ matrix.os }}             # Operating system for the job
+    steps:
+      - name: Checkout                 # Step to checkout the repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python            # Step to set up Python
+        uses: actions/setup-python@v4  # Use v4 for compatibility with pyproject.toml
+        with:
+          python-version: ${{ matrix.python-version }}       # Specify the Python version
+          cache: pip                   # Cache the pip packages
+
+      - name: Install dependencies     # Step to install dependencies
+        run: |
+          python -m pip install --upgrade pip   # Upgrade pip
+          python -m pip install .                # Install the project
+
+      - name: Setup tmate session (copy paste ssh command to connect to runner)   # Step to set up tmate session
+        uses: mxschmitt/action-tmate@v3                                          # Use the action-tmate v3 action

nemos-0.1.0/.github/workflows/deploy-pure-python.yml

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+name: Build and upload to PyPI for pure python
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    name: Build and test package
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        # this is necessary for setuptools_scm to work properly with github
+        # actions, see https://github.com/pypa/setuptools_scm/issues/480 and
+        # https://stackoverflow.com/a/68959339
+        with:
+          fetch-depth: 0
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+      - name: Build package
+        run: |
+          pip install build
+          python -m build --outdir dist/ --sdist --wheel
+      - name: Check there's only one sdist and one whl file created
+        shell: bash
+        # because the following two tests will be weird otherwise. see
+        # https://askubuntu.com/a/454568 for why this is the right way to handle
+        # it. using [[ BOOLEAN ]] || EXPR is a compact way of writing IF NOT
+        # BOOLEAN THEN EXPR in bash
+        run: |
+          [[ $(find dist/ -type f -name "*whl" -printf x | wc -c) == 1 ]] || exit 1
+          [[ $(find dist/ -type f -name "*tar.gz" -printf x | wc -c) == 1 ]] || exit 1
+      - name: Check setuptools_scm version against git tag
+        shell: bash
+        run: |
+          # we use the error code of this comparison: =~ is bash's regex
+          # operator, so it checks whether the right side is contained in the
+          # left side. In particular, we succeed if the path of the source code
+          # ends in the most recent git tag, fail if it does not.
+          [[ "$(ls dist/*tar.gz)" =~ "-$(git describe --tags).tar.gz" ]]
+      - name: Check we can install from wheel
+        # note that this is how this works in bash (different shells might be
+        # slightly different). we've checked there's only one .whl file in an
+        # earlier step, so the bit in `$()` will expand to that single file,
+        # then we pass [dev] to get specify the optional dev dependencies, and
+        # we wrap the whole thing in quotes so bash doesn't try to interpret the
+        # square brackets but passes them directly to pip install
+        shell: bash
+        run: |
+          pip install "$(ls dist/*whl)[dev]"
+      - name: Run some tests
+        # modify the following as necessary to e.g., run notebooks
+        run: |
+          pytest
+      - uses: actions/upload-artifact@v3
+        with:
+          path: dist/*
+
+  publish:
+    name: Upload release to PyPI
+    needs: [build]
+    environment: pypi
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+      - name: Publish package to pypi
+        uses: pypa/gh-action-pypi-publish@release/v1

nemos-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+
+# PyCharm project specs
+.idea/
+
+
+# IntelliJ's project specific settings 
+.idea/
+
+.DS_Store
+
+# mkdocs generated folder
+docs/generated/
+
+# vscode
+.vscode/

nemos-0.1.0/.readthedocs.yaml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
+mkdocs:
+  configuration: mkdocs.yml
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - method: pip
+     path: .
+     extra_requirements:
+       - docs
+
+formats:
+  - pdf
+  - htmlzip

nemos-0.1.0/CODE_OF_CONDUCT.md

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+## Our Mission 
+We aspire to build a community-driven, open library dedicated to neuroscientific analysis. As such, we foster friendly discussions encompassing both the contents of the package and the underlying theory.
+
+## Core Values
+  - **Inclusivity**: Every contribution is valuable. We recognize and appreciate the diversity of our community members and their contributions.
+  - **Equality**: We are committed to treating everyone with fairness and impartiality. Discrimination or favoritism has no place in our community.
+  - **Professionalism**: We expect our community members to maintain a high standard of conduct. Inappropriate or disrespectful language will not be tolerated.
+
+## Contribution 
+We welcome code submissions, improvements to documentation, tutorials, active participation in discussions, and revisions to pull requests.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[edoardo.balzani87@gmail.com](mailto:edoardo.balzani87@gmail.com).
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations
+
+
+We follow the principles of openness, respect, and consideration of others of the Python Software Foundation: https://www.python.org/psf/codeofconduct/

nemos-0.1.0/CONTRIBUTING.md

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+# Contributing
+
+The `nemos` package is designed to provide a robust set of statistical analysis tools for neuroscience research. While the repository is managed by a core team of data scientists at the Center for Computational Neuroscience of the Flatiron Institute, we warmly welcome contributions from external collaborators.
+
+## General Guidelines
+
+Developers are encouraged to contribute to various areas of development. This could include the creation of concrete classes, such as those for new basis function types, or the addition of further checks at evaluation. Enhancements to documentation and the overall readability of the code are also greatly appreciated.
+
+Feel free to work on any section of code that you believe you can improve. More importantly, remember to thoroughly test all your classes and functions, and to provide clear, detailed comments within your code. This not only aids others in using your library, but also facilitates future maintenance and further development.

nemos-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2023 William F. Broderick
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

nemos-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: nemos
+Version: 0.1.0
+Summary: Toolbox for basic Generalized Linear Models (GLMs) for neural data analysis
+Author-email: Edoardo Balzani <ebalzani@flatironinstitute.org>, William Broderick <wbroderick@flatironinstitute.org>, Guillaume Vejo <gviejo@flatironinstitute.org>, Alex Williams <alex.h.williams@nyu.edu>
+License: MIT License
+        
+        Copyright (c) 2023 William F. Broderick
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Keywords: neuroscience,Poisson-GLM
+Classifier: Intended Audience :: Science/Research
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: jax>=0.4
+Requires-Dist: jaxopt>=0.6
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: numpy>1.20
+Requires-Dist: scikit-learn>=1.2
+Requires-Dist: scipy>=1.10
+Requires-Dist: typing_extensions>=4.6
+Provides-Extra: dev
+Requires-Dist: black; extra == "dev"
+Requires-Dist: isort; extra == "dev"
+Requires-Dist: pip-tools; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: mkdocs; extra == "docs"
+Requires-Dist: mkdocstrings[python]; extra == "docs"
+Requires-Dist: mkdocs-section-index; extra == "docs"
+Requires-Dist: mkdocs-gen-files; extra == "docs"
+Requires-Dist: mkdocs-literate-nav; extra == "docs"
+Requires-Dist: mkdocs-gallery; extra == "docs"
+Requires-Dist: mkdocs-material; extra == "docs"
+
+![LOGO](CCN-logo-wText.png)
+
+# nemos
+NEural MOdelS, a statistical modeling framework for neuroscience.
+
+## Disclaimer
+This is an alpha version, the code is in active development and the API is subject to change.
+
+## Setup
+
+To install, clone this repo and install using `pip`:
+
+``` sh
+git clone git@github.com:flatironinstitute/nemos.git
+cd nemos/
+pip install -e .
+```
+
+If you have a GPU, you may need to install jax separately to get the proper
+build. The following has worked for me on a Flatiron Linux workstation: `conda
+install jax cuda-nvcc -c conda-forge -c nvidia`. Note this should be done
+without `jax` and `jaxlib` already installed, so either run this before the
+earlier `pip install` command or uninstall them first (`pip uninstall jax
+jaxlib`). See [jax docs](https://github.com/google/jax#conda-installation) for
+details (the `pip` instructions did not work for me).
+
+![FOOT](CCN-letterFoot.png)

nemos-0.1.0/README.md

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+![LOGO](CCN-logo-wText.png)
+
+# nemos
+NEural MOdelS, a statistical modeling framework for neuroscience.
+
+## Disclaimer
+This is an alpha version, the code is in active development and the API is subject to change.
+
+## Setup
+
+To install, clone this repo and install using `pip`:
+
+``` sh
+git clone git@github.com:flatironinstitute/nemos.git
+cd nemos/
+pip install -e .
+```
+
+If you have a GPU, you may need to install jax separately to get the proper
+build. The following has worked for me on a Flatiron Linux workstation: `conda
+install jax cuda-nvcc -c conda-forge -c nvidia`. Note this should be done
+without `jax` and `jaxlib` already installed, so either run this before the
+earlier `pip install` command or uninstall them first (`pip uninstall jax
+jaxlib`). See [jax docs](https://github.com/google/jax#conda-installation) for
+details (the `pip` instructions did not work for me).
+
+![FOOT](CCN-letterFoot.png)

nemos-0.1.0/docs/developers_notes/README.md

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+# Introduction
+
+Welcome to the Developer Notes of the `nemos` project. These notes aim to provide detailed technical information about the various modules, classes, and functions that make up this library, as well as guidelines on how to write code that integrates nicely with our package. They are intended to help current and future developers understand the design decisions, structure, and functioning of the library, and to provide guidance on how to modify, extend, and maintain the codebase.
+
+## Intended Audience
+
+These notes are primarily intended for the following groups:
+
+- **Current Developers**: The Developer Notes can serve as a comprehensive guide to understanding the library, making it easier to debug, modify and maintain the code.
+
+- **Future Developers**: These notes can help onboard new developers to the project, providing them with detailed explanations of the codebase and its underlying architecture.
+
+- **Contributors**: If you wish to contribute to the `nemos` project, the Developer Notes can provide a solid foundation of understanding, helping to ensure that your contributions align with the existing structure and design principles of the library.
+
+- **Advanced Users**: While the primary focus of these notes is on development, they might also be of interest to advanced users who want a deeper understanding of the library's functionality. 
+
+Please note that these notes assume a certain level of programming knowledge. Familiarity with Python, object-oriented programming, and the NumPy, Scipy and Jax libraries would be beneficial when reading these notes.
+
+## Navigating the Developer Notes
+
+The Developer Notes are divided into sections, each focusing on a different module or class within the `nemos` library. Each section provides an overview of the class or module, explains its role and functionality within the library, and offers a comprehensive guide to its classes and functions. Typically, we will provide instructions on how to extend the existing modules. We generally advocate for the use of inheritance and encourage consistency with the existing codebase. In creating developer instructions, we follow the conventions outlined below:
+
+- **Must**: This denotes a requirement. Any method or function that fails to meet the requirement will not be merged.
+- **Should**: This denotes a suggestion. Reasons should be provided if a suggestion is not followed.
+- **May**: This denotes an option that, if implemented, could enhance the user/developer experience but can be overlooked if deemed unnecessary. 
+
+## Interact with us
+
+If you're considering contributing to the library, first of all, welcome aboard! As a first step, we recommend that you read the [`CONTRIBUTING.md`](https://github.com/flatironinstitute/nemos/blob/main/CONTRIBUTING.md) guidelines. These will help you understand how to interact with other contributors and how to submit your changes.
+
+If you have any questions or need further clarification on any of the topics covered in these notes, please don't hesitate to reach out to us. You can do so via the [discussion](https://github.com/flatironinstitute/nemos/discussions/landing) forum on GitHub.
+
+We're looking forward to your contributions and to answering any queries you might have!
+
+
+
+