Release v0.3.0

    - Fix #31. Failed when axis!=0
    - Change API. Only expose:
        * significant_digits
        * contributing_bits
        * probability_estimation_bernoulli
        * minimum_number_of_trials
        * Method, Error
    - Add tests for compute_z
    - Add docs with pdoc
    - Generate github-pages with github/actions

Escape python-version in github/actions

.github/workflows/docs.yml

@@ -0,0 +1,43 @@
+name: website
+
+# build the documentation whenever there are new commits on main
+on:
+  push:
+    branches:
+      - main
+
+# security: restrict permissions for CI jobs.
+permissions:
+  contents: read
+
+jobs:
+  # Build the documentation and upload the static HTML files as an artifact.
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.12'
+
+      - run: pip install .
+      - run: pdoc -d numpy -t pdoc/template/ --math -o docs significantdigits/
+
+      - uses: actions/upload-pages-artifact@v2
+        with:
+          path: docs/
+
+  # Deploy the artifact to GitHub pages.
+  # This is a separate job so that only actions/deploy-pages has the necessary permissions.
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v2

.github/workflows/python-app.yml

@@ -17,12 +17,16 @@ jobs:
 
     runs-on: ubuntu-latest
 
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.10
+    - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v3
       with:
-        python-version: "3.10"
+        python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

README.md

@@ -1,6 +1,6 @@
-# significantdigits package - v0.2.0
+# significantdigits package - v0.3.0
 
-Compute the number of significant digits basis on the paper [Confidence Intervals for Stochastic Arithmetic](https://arxiv.org/abs/1807.09655).
+Compute the number of significant digits based on the paper [Confidence Intervals for Stochastic Arithmetic](https://arxiv.org/abs/1807.09655).
 This package is also inspired by the [Jupyter Notebook](https://github.com/interflop/stochastic-confidence-intervals/blob/master/Intervals.ipynb) included with the publication.
 
 ## Getting started
@@ -9,14 +9,14 @@ This synthetic example illustrates how to compute significant digits
 of a results sample with a given known reference:
 
 ```python
->>> import significantdigits as sig
+>>> import significantdigits as sd
 >>> import numpy as np
 >>> from numpy.random import uniform as U
 >>> np.random.seed(0)
 >>> eps = 2**-52
 >>> # simulates results with epsilon differences
 >>> X = [1+U(-1,1)*eps for _ in range(10)]
->>> sig.significant_digits(X, reference=1)
+>>> sd.significant_digits(X, reference=1)
 >>> 51.02329058847853
 ```
 
@@ -30,21 +30,21 @@ If the reference is unknown, one can use the sample average:
 
 ```python
 ...
->>> sig.significant_digits(X, reference=np.mean(X))
+>>> sd.significant_digits(X, reference=np.mean(X))
 >>> 51.02329058847853
 ```
 ## Installation
 
 ```bash
-    python3 -m pip install -U significantdigits
+python3 -m pip install -U significantdigits
 ```
 
 or if you want the latest version of the code, you can install it **from** the repository directly
 
 ```bash
-    python3 -m pip install -U git+https://github.com/verificarlo/significantdigits.git
-    # or if you don't have 'git' installed
-    python3 -m pip install -U https://github.com/verificarlo/significantdigits/zipball/master
+python3 -m pip install -U git+https://github.com/verificarlo/significantdigits.git
+# or if you don't have 'git' installed
+python3 -m pip install -U https://github.com/verificarlo/significantdigits/zipball/master
 ```
 
 ## Advanced Usage
@@ -53,13 +53,13 @@ or if you want the latest version of the code, you can install it **from** the r
 
 Functions accept the following types of inputs:
 ```python
-    InputType: np.ndarray | tuple | list
+    InputType: ArrayLike
 ```
-Those types are accessible with the `get_input_type` function.
+Those types are accessible with the `numpy.typing.ArrayLike` type.
 
 ### Z computation
 Metrics are computed using Z, the distance between the samples and the reference.
-They are four possible cases depending on the distance and the nature of the reference that is summarized in this table:
+There are four possible cases depending on the distance and the nature of the reference that are summarized in this table:
 
 |                    | constant reference (x) | random variable reference (Y) |
 | ------------------ | ---------------------- | ----------------------------- |
@@ -68,7 +68,11 @@ They are four possible cases depending on the distance and the nature of the ref
 
 
 ```python
-compute_z(array: ~InputType, reference: Optional[~ReferenceType], error: significantdigits._significantdigits.Error | str, axis: int, shuffle_samples: bool = False) -> ~InputType
+_compute_z(array: InternalArrayType, 
+           reference: InternalArrayType | None, 
+           error: Error | str, 
+           axis: int, 
+           shuffle_samples: bool = False) -> InternalArrayType
     Compute Z, the distance between the random variable and the reference
 
     Compute Z, the distance between the random variable and the reference
@@ -88,11 +92,11 @@ compute_z(array: ~InputType, reference: Optional[~ReferenceType], error: signifi
 
     Parameters
     ----------
-    array : InputType
+    array : InternalArrayType
         The random variable
-    reference : Optional[ReferenceType]
+    reference : Optional[InternalArrayType]
         The reference to compare against
-    error : Method.Error | str
+    error : Error | str
         The error function to compute Z
     axis : int, default=0
         The axis or axes along which compute Z
@@ -101,7 +105,7 @@ compute_z(array: ~InputType, reference: Optional[~ReferenceType], error: signifi
 
     Returns
     -------
-    array : numpy.ndarray
+    array : InternalArrayType
         The result of Z following the error method choose
 ```
 
@@ -129,10 +133,18 @@ class Method(AutoName):
 
 
 ```python
-significant_digits(array: ~InputType,
-                   reference: Optional[~ReferenceType] = None,
-                   axis: int = 0, basis: int = 2,
-                   error: str | significantdigits._significantdi
+significant_digits(array: InputType,
+                   reference: ReferenceType | None = None,
+                   axis: int = 0, 
+                   basis: int = 2,
+                   error: Error | str,
+                   method: Method | str,
+                   probability: float = 0.95,
+                   confidence: float = 0.95,
+                   shuffle_samples: bool = False,
+                   dtype: DTypeLike | None = None
+                   ) -> ArrayLike
+
     Compute significant digits
 
     This function computes with a certain probability
@@ -142,7 +154,7 @@ significant_digits(array: ~InputType,
     ----------
     array: InputType
         Element to compute
-    reference: Optional[ReferenceType], optional=None
+    reference: ReferenceType | None, optional=None
         Reference for comparing the array
     axis: int, optional=0
         Axis or axes along which the significant digits are computed
@@ -160,7 +172,7 @@ significant_digits(array: ~InputType,
         If reference is None, the array is split in two and \
         comparison is done between both pieces. \
         If shuffle_samples is True, it shuffles pieces.
-    dtype : np.dtype, default=None
+    dtype : dtype_like | None, default=None
         Numerical type used for computing significant digits
         Widest format between array and reference is taken if no supplied.
 
@@ -174,10 +186,20 @@ significant_digits(array: ~InputType,
 ### Contributing digits
 
 ```python
-contributing_digits(array: ~InputType, reference: Optional[~ReferenceType] = None, axis: int = 0, basis: int = 2, error: str | significantdigits._significantdigits.Error = <Error.Re$
+contributing_digits(array: InputType,
+                    reference: ReferenceType | None = None,
+                    axis: int = 0,
+                    basis: int = 2,
+                    error: Error | str,
+                    method: Method | str,
+                    probability: float = 0.51,
+                    confidence: float = 0.95,
+                    shuffle_samples: bool = False,
+                    dtype: DTypeLike | None = None
+                    ) -> ArrayLike
+
     Compute contributing digits
 
-
     This function computes with a certain probability the number of bits
     of the mantissa that will round the result towards the correct reference
     value[1]_
@@ -186,7 +208,7 @@ contributing_digits(array: ~InputType, reference: Optional[~ReferenceType] = Non
     ----------
     array: InputArray
         Element to compute
-    reference: Optional[ReferenceArray], default=None
+    reference: ReferenceArray | None, default=None
         Reference for comparing the array
     axis: int, default=0
         Axis or axes along which the contributing digits are computed
@@ -205,7 +227,7 @@ contributing_digits(array: ~InputType, reference: Optional[~ReferenceType] = Non
         If reference is None, the array is split in two and
         comparison is done between both pieces.
         If shuffle_samples is True, it shuffles pieces.
-    dtype : np.dtype, default=None
+    dtype : dtype_like | None, default=None
         Numerical type used for computing contributing digits
         Widest format between array and reference is taken if no supplied.
 
@@ -219,12 +241,10 @@ contributing_digits(array: ~InputType, reference: Optional[~ReferenceType] = Non
 
 These are utility functions for the general case.
 
-`probability_estimation_general`
-allows having an estimation
-on the lower bound probability given the sample size.
+#### `probability_estimation_general`
+
+Estimates the lower bound probability given the sample size.
 
-`minimum_number_of_trials` gives the minimal sample size
-required to reach the requested `probability` and `confidence`.
 
 ```python
 probability_estimation_general(success: int, trials: int, confidence: float) -> float
@@ -250,8 +270,12 @@ probability_estimation_general(success: int, trials: int, confidence: float) ->
         The lower bound probability with `confidence` level to have `success` successes for `trials` trials
 ```
 
-```python
+#### `minimum_number_of_trials`
+
+Returns the minimal sample size required to reach the requested `probability` and `confidence`.
 
+
+```python
 minimum_number_of_trials(probability: float, confidence: float) -> int
     Computes the minimum number of trials to have probability and confidence
 
@@ -273,7 +297,6 @@ minimum_number_of_trials(probability: float, confidence: float) -> int
     -------
     int
         Minimal sample size to have given probability and confidence
-
 ```
 
 ### License
@@ -285,3 +308,4 @@ See https://llvm.org/LICENSE.txt for license information.
 
 Copyright (c) 2020-2023 Verificarlo Contributors
 
+---

pdoc/template/math.html.jinja2

@@ -0,0 +1,34 @@
+{# This template is included in math mode and loads MathJax for formula rendering. #}
+<script>
+    {#
+    MathJax by default does not define $ as a math delimiter because it's commonly used in non-mathematical settings.
+    We add it here. If you are unhappy with this default, you can override math.html.jinja2 with a custom template.
+     #}
+    window.MathJax = {
+        tex: {
+            inlineMath: [['$', '$'], ['\\(', '\\)']],
+            autoload: {
+                color: [],
+                colorV2: ['color'],
+                cases: [[], ['numcases', 'subnumcases']],
+
+            }
+        }
+    };
+</script>
+<script src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script>
+<script id="MathJax-script" async src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
+<script>
+    /* Re-invoke MathJax when DOM content changes, for example during search. */
+    document.addEventListener("DOMContentLoaded", () => {
+        new MutationObserver(() => MathJax.typeset()).observe(
+            document.querySelector("main.pdoc").parentNode,
+            {childList: true}
+        );
+    })
+</script>
+<style>
+    mjx-container {
+        overflow-x: auto;
+    }
+</style>

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "significantdigits"
-version = "0.2.0"
+version = "0.3.0"
 description = "Solid stochastic statistic analysis of Stochastic Arithmetic"
 authors = [
     { name = "Verificarlo contributors", email = "[email protected]" },
@@ -31,6 +31,7 @@ dependencies = [
     "scipy>=1.7.3",
     "toml>=0.10.2",
     "icecream>=2.1.3",
+    "pdoc>=14.2.0"
 ]
 
 [tool.hatch.build]

significantdigits/__init__.py

@@ -1 +1,31 @@
-from ._significantdigits import *
+"""
+.. include:: ../README.md
+"""
+
+from ._significantdigits import (
+    InputType,
+    ReferenceType,
+    Method,
+    Metric,
+    Error,
+    SignificantDigitsException,
+    significant_digits,
+    contributing_digits,
+    change_basis,
+    probability_estimation_bernoulli,
+    minimum_number_of_trials,
+)
+
+__all__ = [
+    "InputType",
+    "ReferenceType",
+    "Method",
+    "Metric",
+    "Error",
+    "SignificantDigitsException",
+    "significant_digits",
+    "contributing_digits",
+    "change_basis",
+    "probability_estimation_bernoulli",
+    "minimum_number_of_trials",
+]