nemos 0.2.1__tar.gz

nemos-0.2.1/.github/CODEOWNERS

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+* @BalzaniEdoardo

nemos-0.2.1/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

nemos-0.2.1/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

nemos-0.2.1/.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
+     types:
+       - opened
+       - reopened
+       - synchronize
+       - ready_for_review
+   push:
+     branches:
+       - main
+
+jobs:
+  tox_tests:
+    if: ${{ !github.event.pull_request.draft }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.10', '3.11', '3.12']
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - 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
+          pip install tox
+
+      - name: Run tox
+        run: tox -e py
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  tox_check:
+    if: ${{ !github.event.pull_request.draft }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4 # Use v4 for compatibility with pyproject.toml
+        with:
+          python-version: 3.12
+          cache: pip
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+
+      - name: Run tox
+        run: tox -e check
+
+  prevent_docs_absolute_links:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Make .sh executable
+        run: chmod +x bash_scripts/prevent_absolute_links_to_docs.sh
+
+      - name: Check links
+        run: ./bash_scripts/prevent_absolute_links_to_docs.sh
+
+  check:
+    if: ${{ !github.event.pull_request.draft }}
+    needs:
+      - tox_tests
+      - prevent_docs_absolute_links
+      - tox_check
+    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-0.2.1/.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, macos-latest, windows-latest]
+        python-version: ['3.12']
+    runs-on: ${{ matrix.os }}             # Operating system for the job
+    steps:
+      - name: Checkout                 # Step to checkout the repository
+        uses: actions/checkout@v4
+
+      - 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-0.2.1/.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-0.2.1/.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
+
+# sphinx build documentation
+/docs/_build
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+
+# PyCharm project specs
+.idea/
+
+
+.DS_Store
+
+# mkdocs generated folder
+docs/generated/
+
+# vscode
+.vscode/
+
+# nwb cahce
+nwb-cache/
+
+# scripting folder
+_scripts/
+
+# env variable for nwbs
+docs/data/
+
+# rst generated files
+docs/stubs
+
+

nemos-0.2.1/.readthedocs.yaml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    ruby: "3.3"
+  jobs:
+    pre_build:
+      - gem install html-proofer -v ">= 5.0.9"  # Ensure version >= 5.0.9
+    post_build:
+      # Check everything except 403s and a jneurosci, which returns 404 but the link works when clicking.
+      - htmlproofer $READTHEDOCS_OUTPUT/html  --checks Links,Scripts,Images --ignore-urls "https://fonts.gstatic.com,https://celltypes.brain-map.org/experiment/electrophysiology/478498617,https://www.jneurosci.org/content/25/47/11003,https://www.nature.com/articles/s41467-017-01908-3,https://doi.org/10.1038/s41467-017-01908-3" --assume-extension --check-external-hash --ignore-status-codes 403,302,0 --ignore-files "/.+\/_static\/.+/","/.+\/stubs\/.+/","/.+\/tutorials/plot_02_head_direction.+/"
+      # The auto-generated animation doesn't have a alt or src/srcset; I am able to ignore missing alt, but I cannot work around a missing src/srcset
+      # therefore for this file I am not checking the figures.
+      - htmlproofer $READTHEDOCS_OUTPUT/html/tutorials/plot_02_head_direction.html  --checks Links,Scripts --ignore-urls "https://www.jneurosci.org/content/25/47/11003"
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - method: pip
+     path: .
+     extra_requirements:
+       - docs
+
+formats:
+  - pdf
+  - htmlzip

nemos-0.2.1/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use this software, please cite it using the preferred-citation metadata."
+title: ""NEural MOdelS, a statistical modeling framework for neuroscience."
+authors:
+  - family-names: Balzani
+    given-names: Edoardo
+    orcid: "https://orcid.org/0000-0002-3702-5856"
+  - family-names: Broderick
+    given-names: William
+    orcid: "https://orcid.org/0000-0002-8999-9003"
+  - family-names: Viejo
+    given-names: Guillaume
+    orcid: "https://orcid.org/0000-0002-2450-7397"
+  - family-names: Williams
+    given-names: Alex
+    orcid: "https://orcid.org/0000-0001-5853-103X"
+repository-code: "https://github.com/flatironinstitute/nemos"
+url: "https://nemos.readthedocs.io/"
+license: MIT
+keywords:
+  - neuroscience
+  - Poisson GLM
+  - spike counts modeling

nemos-0.2.1/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/