remove backup ~ files

.git_archival.txt

@@ -1 +1 @@
-ref-names: $Format:%D$
+ref-names: $Format:%D$

.gitattributes

@@ -1,5 +1,5 @@
-# Interpret Jupyter notebooks as Python
-*.ipynb linguist-language=Python
-
-# For automatic versioning via setuptools_scm_git_archive
-.git_archival.txt export-subst
+# Interpret Jupyter notebooks as Python
+*.ipynb linguist-language=Python
+
+# For automatic versioning via setuptools_scm_git_archive
+.git_archival.txt export-subst

.github/workflows/draft-pdf.yml

@@ -1,23 +1,23 @@
-on: [push]
-
-jobs:
- paper:
- runs-on: ubuntu-latest
- name: Paper Draft
- steps:
- - name: Checkout
- uses: actions/checkout@v3
- - name: Build draft PDF
- uses: openjournals/openjournals-draft-action@master
- with:
- journal: joss
- # This should be the path to the paper within your repo.
- paper-path: docs/JOSS/paper.md
- - name: Upload
- uses: actions/upload-artifact@v1
- with:
- name: paper
- # This is the output path where Pandoc will write the compiled
- # PDF. Note, this should be the same directory as the input
- # paper.md
+on: [push]
+
+jobs:
+ paper:
+ runs-on: ubuntu-latest
+ name: Paper Draft
+ steps:
+ - name: Checkout
+ uses: actions/checkout@v3
+ - name: Build draft PDF
+ uses: openjournals/openjournals-draft-action@master
+ with:
+ journal: joss
+ # This should be the path to the paper within your repo.
+ paper-path: docs/JOSS/paper.md
+ - name: Upload
+ uses: actions/upload-artifact@v1
+ with:
+ name: paper
+ # This is the output path where Pandoc will write the compiled
+ # PDF. Note, this should be the same directory as the input
+ # paper.md
  path: docs/JOSS/paper.pdf

.github/workflows/run-tests.yml

@@ -1,53 +1,53 @@
-name: Tests
-
-on: [push, pull_request]
-
-jobs:
- Linting:
- runs-on: ubuntu-latest
-
- steps:
- - uses: actions/checkout@v3
- - name: Set up Python 3.10.13
- uses: actions/setup-python@v3
- with:
- python-version: 3.10.13
- - name: Linting
- run: |
- pip install pre-commit
- pre-commit run --all-files
- Linux:
- needs: Linting
- runs-on: ubuntu-latest
- strategy:
- max-parallel: 8
- matrix:
- python-version: [3.10.13]
-
- steps:
- - uses: actions/checkout@v3
- - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v3
- with:
- python-version: ${{ matrix.python-version }}
- - name: Install dependencies
- run: |
- pip install -e .[dev]
-# pip install -r requirements-dev.txt
- - name: Test with pytest
- run: |
- py.test test
- - name: Generate coverage report
- run: |
- pip install pytest==7.4.4
- pip install pytest-cov==4.1.0
- pytest --cov=./ --cov-report=xml
- - name: Upload coverage reports to Codecov
- uses: codecov/codecov-action@v3
-
-# - uses: actions/cache@v1
-# with:
-# path: ~/.cache/pip
-# key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements-dev.txt') }}
-# restore-keys: |
-# ${{ runner.os }}-pip-
+name: Tests
+
+on: [push, pull_request]
+
+jobs:
+ Linting:
+ runs-on: ubuntu-latest
+
+ steps:
+ - uses: actions/checkout@v3
+ - name: Set up Python 3.10.13
+ uses: actions/setup-python@v3
+ with:
+ python-version: 3.10.13
+ - name: Linting
+ run: |
+ pip install pre-commit
+ pre-commit run --all-files
+ Linux:
+ needs: Linting
+ runs-on: ubuntu-latest
+ strategy:
+ max-parallel: 8
+ matrix:
+ python-version: [3.10.13]
+
+ steps:
+ - uses: actions/checkout@v3
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v3
+ with:
+ python-version: ${{ matrix.python-version }}
+ - name: Install dependencies
+ run: |
+ pip install -e .[dev]
+# pip install -r requirements-dev.txt
+ - name: Test with pytest
+ run: |
+ py.test test
+ - name: Generate coverage report
+ run: |
+ pip install pytest==7.4.4
+ pip install pytest-cov==4.1.0
+ pytest --cov=./ --cov-report=xml
+ - name: Upload coverage reports to Codecov
+ uses: codecov/codecov-action@v3
+
+# - uses: actions/cache@v1
+# with:
+# path: ~/.cache/pip
+# key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements-dev.txt') }}
+# restore-keys: |
+# ${{ runner.os }}-pip-

.gitignore

@@ -1,39 +1,41 @@
-build
-dist
-*.egg-info
-# automatically generated by setuptools-scm
-pysindy/version.py
-# sphinx gallery files
-docs/examples
-# virtual environment
-venv
-
-# eggs
-.eggs
-
-dev
-
-**/*cache*
-
-.coverage
-coverage.xml
-
-.idea
-
-docs/api
-docs/_build
-
-.ipynb_checkpoints
-*/.ipynb_checkpoints/*
-*/lightning_logs/*
-lightning_logs
-.DS_Store
-.vscode
-
-*.pyc
-
-*.sublime*
-
-Pipfile
-Pipfile.lock
-/htmlcov/
+build
+dist
+*.egg-info
+# automatically generated by setuptools-scm
+pysindy/version.py
+# sphinx gallery files
+docs/examples
+# virtual environment
+venv
+
+# eggs
+.eggs
+
+dev
+
+**/*cache*
+
+.coverage
+coverage.xml
+
+.idea
+
+docs/api
+docs/_build
+
+.ipynb_checkpoints
+*/.ipynb_checkpoints/*
+*/lightning_logs/*
+lightning_logs
+.DS_Store
+.vscode
+
+*.pyc
+
+*.sublime*
+
+Pipfile
+Pipfile.lock
+/htmlcov/
+
+*~

.pre-commit-config.yaml

@@ -1,26 +1,26 @@
-# Settings for pre-commit
-fail_fast: false
-repos:
-- repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v4.3.0
- hooks:
- - id: check-added-large-files
- args: ["--maxkb=102400"]
- - id: check-merge-conflict
- - id: trailing-whitespace
- - id: end-of-file-fixer
-- repo: https://github.com/asottile/reorder_python_imports
- rev: v3.9.0
- hooks:
- - id: reorder-python-imports
- exclude: ^(pre_commit/resources/|testing/resources/python3_hooks_repo/)
- args: [--py37-plus, --add-import, 'from __future__ import annotations']
-- repo: https://github.com/ambv/black
- rev: 22.8.0
- hooks:
- - id: black
-- repo: https://github.com/PyCQA/flake8
- rev: 5.0.4
- hooks:
- - id: flake8
- args: ["--config=setup.cfg"]
+# Settings for pre-commit
+fail_fast: false
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v4.3.0
+ hooks:
+ - id: check-added-large-files
+ args: ["--maxkb=102400"]
+ - id: check-merge-conflict
+ - id: trailing-whitespace
+ - id: end-of-file-fixer
+- repo: https://github.com/asottile/reorder_python_imports
+ rev: v3.9.0
+ hooks:
+ - id: reorder-python-imports
+ exclude: ^(pre_commit/resources/|testing/resources/python3_hooks_repo/)
+ args: [--py37-plus, --add-import, 'from __future__ import annotations']
+- repo: https://github.com/ambv/black
+ rev: 22.8.0
+ hooks:
+ - id: black
+- repo: https://github.com/PyCQA/flake8
+ rev: 5.0.4
+ hooks:
+ - id: flake8
+ args: ["--config=setup.cfg"]

.readthedocs.yaml

@@ -1,35 +1,35 @@
-# .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"
- # You can also specify other tool versions:
- # nodejs: "19"
- # rust: "1.64"
- # golang: "1.19"
-
-# Build documentation in the docs/ directory with Sphinx
-sphinx:
- configuration: docs/conf.py
-
-# If using Sphinx, optionally build your docs in additional formats such as PDF
-# formats:
-# - pdf
-
-# Optionally declare the Python requirements required to build your docs
-#python:
-# install:
-# - requirements: requirements-dev.txt
-# - method: pip
-# path: .
-python:
- install:
- - method: pip
+# .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"
+ # You can also specify other tool versions:
+ # nodejs: "19"
+ # rust: "1.64"
+ # golang: "1.19"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+ configuration: docs/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+# - pdf
+
+# Optionally declare the Python requirements required to build your docs
+#python:
+# install:
+# - requirements: requirements-dev.txt
+# - method: pip
+# path: .
+python:
+ install:
+ - method: pip
  path: .[dev]