Merge pull request #7 from varchasgopalaswamy/main

Preliminary Pandas support

.github/workflows/draft-pdf.yml

@@ -0,0 +1,23 @@
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - 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: paper/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: paper/paper.pdf

.github/workflows/python-test.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.11"]
 
     steps:
       - uses: actions/checkout@v3
@@ -19,11 +19,12 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pylint pytest pytest-cov hypothesis
-          pip install .[pandas]
-      - name: Lint with pylint
+          pip install pre-commit pytest pytest-cov hypothesis
+          pre-commit install 
+          pip install .[CI]
+      - name: Run pre-commit checks
         run: |
-          pylint --fail-under=8 auto_uncertainties
+          pre-commit run --all-files
       - name: Test with pytest
         run: |
-          pytest --cov=auto_uncertainties --cov-report=xml --cov-report=html -k "not pandas"
+          pytest --cov=auto_uncertainties --cov-report=xml --cov-report=html --ignore=tests/pandas

.pre-commit-config.yaml

@@ -1,34 +1,37 @@
 repos:
 
-- repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.0.275
-  hooks:
-    - id: ruff
-      args: [ --fix, --exit-non-zero-on-fix ]
-
--   repo: https://github.com/psf/black.git
-    rev: 23.1.0
-    hooks:
-    - id: black
-      language_version: python3.9
-
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
+- repo: local
   hooks:
-    - id: isort
-      name: isort (python)
+
+  - id: generate-init
+    name: Generates __init__.py files
+    language: python
+    entry: python hooks/generate_init.py
+    always_run: true
+    require_serial: true 
+    additional_dependencies: ["mkinit", "ruff"]
 
+  - id: fix-line-endings
+    name: Convert CRLF/CR endings to LF
+    language: python
+    require_serial: true 
+    entry: python hooks/fix_line_endings.py
+    types: ["text"]
+
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.6.0
   hooks:
-  - id: end-of-file-fixer
-  - id: fix-encoding-pragma
-  - id: trailing-whitespace
-  - id: check-added-large-files
-  - id: check-ast
-  - id: check-case-conflict
   - id: check-executables-have-shebangs
-  - id: check-merge-conflict
   - id: check-symlinks
-  - id: debug-statements
-  - id: mixed-line-ending
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.4.6
+  hooks:
+    #Run the formatter.
+    - id: ruff-format
+      types_or: [ python, pyi, jupyter ]
+    #Run the linter.
+    - id: ruff
+      types_or: [ python, pyi, jupyter ]
+      args: [ --fix, --exit-zero ]

README.rst → README.md

@@ -1,14 +1,3 @@
-.. image:: https://img.shields.io/pypi/v/auto-uncertainties.svg
-    :target: https://pypi.org/project/auto-uncertainties/
-    :alt: Latest Version
-
-.. image:: https://img.shields.io/pypi/l/auto-uncertainties.svg
-    :target: https://pypi.org/project/auto-uncertainties/
-    :alt: License
-
-.. image:: https://github.com/varchasgopalaswamy/AutoUncertainties/actions/workflows/python-app.yml/badge.svg
-    :target: https://github.com/varchasgopalaswamy/AutoUncertainties/actions?query=workflow
-    :alt: Tests
 
 AutoUncertainties
 ========================
@@ -29,75 +18,129 @@ Usage
 
 Creating a scalar Uncertainty variable is relatively simple:
 
-.. code-block:: python
-
+```python
     >>> from auto_uncertainties import Uncertainty
     >>> value = 1.0
     >>> error = 0.1
     >>> u = Uncertainty(value,error)
     >>> u
     1.0 +/- 0.1
+```
 
 as is creating a numpy array of  Uncertainties:
 
-.. code-block:: python
+```python
+
+    >>> from auto_uncertainties import Uncertainty
+    >>> import numpy as np
+    >>> value = np.linspace(start=0,stop=10,num=5)
+    >>> error = np.ones_like(value)*0.1
+    >>> u = Uncertainty(value,error)
+```
+
+(though, they are actually different classes!)
+
+```python
+
+    >>> from auto_uncertainties import Uncertainty
+    >>> value = 1.0
+    >>> error = 0.1
+    >>> u = Uncertainty(value,error)
+    >>> type(u)
+    auto_uncertainties.uncertainty.ScalarUncertainty
 
     >>> from auto_uncertainties import Uncertainty
     >>> import numpy as np
     >>> value = np.linspace(start=0,stop=10,num=5)
     >>> error = np.ones_like(value)*0.1
     >>> u = Uncertainty(value,error)
     >>> u
-    [ 0.   2.5  5.   7.5 10. ] +/- [0.1 0.1 0.1 0.1 0.1]
+    auto_uncertainties.uncertainty.VectorUncertainty
+```
 
 Scalar uncertainties implement all mathematical and logical `dunder methods <https://docs.python.org/3/reference/datamodel.html#object.__repr__>`_ explicitly.
 
-.. code-block:: python
+```python
 
     >>> from auto_uncertainties import Uncertainty
     >>> u = Uncertainty(10.0, 3.0)
     >>> v = Uncertainty(20.0, 4.0)
     >>> u + v
     30.0 +/- 5.0
-
+```
 Array uncertainties implement a large subset of the numpy ufuncs and methods using :code:`jax.grad` or :code:`jax.jacfwd`, depending on the output shape.
 
-.. code-block:: python
+```python
 
     >>> from auto_uncertainties import Uncertainty
     >>> import numpy as np
     >>> value = np.linspace(start=0,stop=10,num=5)
     >>> error = np.ones_like(value)*0.1
     >>> u = Uncertainty(value,error)
     >>> np.exp(u)
-    [1.00000000e+00 1.21824940e+01 1.48413159e+02 1.80804241e+03
- 2.20264658e+04] +/- [1.00000000e-01 1.21824940e+00 1.48413159e+01 1.80804241e+02
- 2.20264658e+03]
+    Magnitude
+
+    1, 12.182, 148.413, 1808.04, 22026.5
+
+    Error
+
+    0.1, 1.2, 15, 180, 2200
     >>> np.sum(u)
-    25.0 +/- 0.223606797749979
+    25.0 +/- 0.22
     >>> u.sum()
-    25.0 +/- 0.223606797749979
+    25.0 +/- 0.22
     >>> np.sqrt(np.sum(error**2))
     0.223606797749979
-
+```
 The mean value and the standard deviation (the measurements are assumed to be normally distributed) can be accessed via
 
-.. code-block:: python
+```python
 
     >>> from auto_uncertainties import Uncertainty
     >>> u = Uncertainty(10.0, 3.0)
     >>> u.value
     10.0
     >>> u.error
     3.0
+```
+
+Displayed values are automatically rounded according to the Particle Data Group standard. This can be turned off using `set_display_rounding`
+```python
+
+    >>> from auto_uncertainties import set_display_rounding
+    >>> set_display_rounding(False)
+    >>> from auto_uncertainties import Uncertainty
+    >>> import numpy as np
+    >>> value = np.linspace(start=0,stop=10,num=5)
+    >>> error = np.ones_like(value)*0.1
+    >>> u = Uncertainty(value,error)
+    >>> np.sum(u)
+    25.0 +/- 0.223606797749979
+```
+If `np.array` is called on an `Uncertainty` object, it will automatically get cast down to a numpy array (and lose uncertainty information!), and emit a warning. To make this an error, use `set_downcast_error`
+```python
+
+    >>> from auto_uncertainties import set_downcast_error
+    >>> set_downcast_error(False)
+    >>> from auto_uncertainties import Uncertainty
+    >>> import numpy as np
+    >>> value = np.linspace(start=0,stop=10,num=5)
+    >>> error = np.ones_like(value)*0.1
+    >>> u = Uncertainty(value,error)
+    >>> np.array(u)
+
+    Exception: The uncertainty is stripped when downcasting to ndarray.
+```
+
+
 
 Prerequisites
 ===========
 
 For array support:
 
 * jax
-* jaxlib (must be built from source if you are not on Linux machine with AVX instruction sets.)
+* jaxlib
 * numpy
 
 

auto_uncertainties/__init__.py

@@ -1,66 +1,35 @@
-# -*- coding: utf-8 -*-
 from __future__ import annotations
 
-import numpy as np
-
-
-class NegativeStdDevError(Exception):
-    """An exception for when the standard deviation is negative"""
-
-    pass
-
-
-class NumpyDowncastWarning(RuntimeWarning):
-    """An exception for when an uncertainties array is downcast to a numpy array"""
-
-    pass
-
-
-from .uncertainty import Uncertainty  # noqa: E402
-
-try:
-    from .pandas_compat import UncertaintyArray
-except ImportError:
-    UncertaintyArray = None
-
-
-def nominal_values(x):
-    # Is an Uncertainty
-    if hasattr(x, "_nom"):
-        return x.value
-    else:
-        if np.ndim(x) > 0:
-            try:
-                x2 = Uncertainty.from_sequence(x)
-            except Exception:
-                return x
-            else:
-                return x2.value
-        else:
-            try:
-                x2 = Uncertainty(x)
-            except Exception:
-                return x
-            else:
-                return x2.value
-
-
-def std_devs(x):
-    # Is an Uncertainty
-    if hasattr(x, "_err"):
-        return x.error
-    else:
-        if np.ndim(x) > 0:
-            try:
-                x2 = Uncertainty.from_sequence(x)
-            except Exception:
-                return np.zeros_like(x)
-            else:
-                return x2.error
-        else:
-            try:
-                x2 = Uncertainty(x)
-            except Exception:
-                return 0
-            else:
-                return x2.error
+__private__ = ["util"]
+__protected__ = ["numpy"]
+import lazy_loader
+
+
+__getattr__, __dir__, __all__ = lazy_loader.attach_stub(__name__, __file__)
+
+__all__ = [
+    "DowncastError",
+    "DowncastWarning",
+    "NegativeStdDevError",
+    "ScalarDisplay",
+    "ScalarUncertainty",
+    "Uncertainty",
+    "UncertaintyArray",
+    "UncertaintyDtype",
+    "VectorDisplay",
+    "VectorUncertainty",
+    "display_format",
+    "exceptions",
+    "nominal_values",
+    "numpy",
+    "pandas",
+    "set_compare_error",
+    "set_display_rounding",
+    "set_downcast_error",
+    "std_devs",
+    "unc_array",
+    "unc_dtype",
+    "uncertainty",
+    "uncertainty_containers",
+    "util",
+]