restructure the distrubutions module (#91)

* move all docs inside the `sources` file * move all docs inside the `sources` file * add auto docs * replace using the environment.yml by requirements.txt * adjust the naming convention * adjust the naming convention * adjust the naming convention * remove the naming ci * update hooks * add example for the plotting position * update dev dependencies * make 3.11, 3.12 the testing python versions * remove macos from ci * add sensitivity to docs * add sensitivity to docs * add eva to docs * update sensitivity * fix senstivity docs * add missing members * update docs * reformat * reformat * fix equation * reformat * add extensions for math equations * reformat * reformat * add make docs files * reformat * reformat * add plot docs * add plot docs * add gev equation * fix error in gev equation * fix the `\left` error in gev equation * try to separate the two line equation * try to separate the two line equation * try to separate the two line equation * try to separate the two line equation * try to separate the two line equation * add labels to the equations * fix equation labels * fix equation labels * unify gev and gumbel * add cdf to gev and gumbel * add cdf to normal and exponential dists * add fx and FX * reformat * add check to test_fit_model * add check to test_fit_model * add check to test_fit_model * use Agg as backend in test files * simplify the test `TestGUMBEL::test_probability_plot` * simplify the test `TestGEV::test_probability_plot` * fix the Extreme value analysis.ipynb notebook * remove spaces from scripts names * use the factory class `Distribution` in the notebook * add examples * rename `theoretical_estimate` to `inverse_cdf` * remove the `chisquare` test from the `fit_model` * add examples * add missing images * correct images path * add properties * the `parameter` argument is optional for the pdf and cdf * switch parameters for the `inverse_cdf` method * reformat * add docstring * add images * reformat * correct the `inverse_cdf` parameter order in the abstract class method * remove the `dstatic`, `chi_pvalue`, `ks_pvalue properties * reformat * rename the metrics module to descriptors * rename metrics to descriptors * instantiating the distribution by either the parameter or the data * add description to gumbel * correct the `actual_data` parameter in the `cdf` method * correct the `actual_data` parameter in the `pdf` method * update the docstring for the `pdf` and `cdf` methods * return lost commits * validate parameters and data in the distribution constructor * add `random` method to `gumbel` * test providing the `pdf` and `cdf` with data parameters * add example to the `random` method in `gumbel` distribution * add example to the `random` method in `gev` distribution * reformat * add examples to the `exponential` class * update examples of the `gumbel` class * update examples of the `GEV` class * unifyt the docs of `ks` method * the argument `parameter` in the `confidence_interval` method is now optional and moved to the end * check the length of the cdf and data * abstract code into `confidence_level` function * provide the parameters as a kwarg in the `probability_plot`. * reformat docstring * the `prob_non_exceed` is now optional for the `confidence_interval` function * make the `prob_non_exceed` optional in the `confidence_interval` for the GEV class * remove duplicate test * reformat * test `confidence_interval` with the default parameters * update example * add example and test Gumbel.confidence_interval * add example and test GEV.confidence_interval * add images for the examples * move the `cdf` parameter to the end and make it kwarg in the `probability_plot` in gumbel and gev * update dependencies * add the main features to docs * update installation docs * add plt.show at the end of all the plots * remove the `confidence_interval` plot from the `probability_plot` method * update rhine example * update docstring * add `__str__` method * rename `probability_plot` to "plot" * move the `parameters` argument in the `pdf` and `cdf` function to the end * correct the matplotlib backend * update plot gumbel example * update plot gev example * rename the figsize parameter to fig_size for all functions * update the docstring of the `AbstractDistribution.plot` * add missing figures for the docstring * reorder the `plot` method `parameters` in the abstract method * reorder the `confidence_interval` method `parameters` in all classes * rename the `significance_level` parameter to the `ams_analysis` to `alpha` * add examples to the `ams_analysis` * update the examples of the `ams_analysis` * add missing images * rename the objective_fn to truncated_distribution * comment the truncated_distribution function * update checklist files * update ci workflows * rename `statfunction` to `state_function`in the `confidence_interval.boot_strap` * add a script for the truncated_distribution * update examples * update examples * remove the python version from the environment.yml
Serapieum-of-alex · Aug 18, 2024 · 9328e31 · 9328e31
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diff --git a/.github/workflows/conda-deployment.yml b/.github/workflows/conda-deployment.yml
@@ -34,7 +34,7 @@ jobs:
 
       - name: Install dev-dependencies
         run: |
-            python -m pip install -r requirements-dev.txt
+            pip install .[dev] --no-deps
 
       - name: Run tests
         shell: bash -el {0}

diff --git a/.github/workflows/pull-request-naming-validation.yml b/.github/workflows/pull-request-naming-validation.yml
diff --git a/.github/workflows/pypi-deployment.yml b/.github/workflows/pypi-deployment.yml
@@ -12,8 +12,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, windows-latest] # , macos-latest
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v3
@@ -25,8 +25,7 @@ jobs:
 
       - name: Install dependencies
         run: |
-            pip install -r requirements.txt -r requirements-dev.txt
-            python setup.py install
+            pip install .[dev]
 
       - name: Generate coverage report
         run: |

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 fail_fast: true
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: end-of-file-fixer
         name: "[py -  check] validate yaml"
@@ -58,7 +58,7 @@ repos:
         files: ^Hapi/
 
   - repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
+    rev: 7.1.0
     hooks:
       - id: flake8
         name: "[py   - check] flake8"
@@ -70,7 +70,7 @@ repos:
   #  hooks:
   #    - id: black
   - repo: https://github.com/ambv/black
-    rev: 22.8.0
+    rev: 24.8.0
     hooks:
       - id: black
         name: "[py   - format] black"
@@ -112,3 +112,19 @@ repos:
         language: system
         pass_filenames: false
         always_run: true
+
+  - repo: local
+    hooks:
+      - id: examples-notebook-check
+        name: nbval
+        entry: pytest --nbval
+        language: system
+        files: \.ipynb$
+
+  - repo: local
+    hooks:
+      - id: doctest
+        name: doctest
+        entry: pytest --doctest-modules
+        language: system
+        files: statista\.py$
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -5,15 +5,20 @@
 # Required
 version: 2
 
-conda:
-  environment: docs/environment.yml
-# Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration: docs/conf.py
-#Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
+  configuration: docs/source/conf.py
 
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.12"
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+          - docs
 
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: all
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -50,3 +50,27 @@ History
 * Use factory design pattern to create the distributions.
 * add tests for the eva module.
 * use snake_case for the methods and variables.
+
+0.6.0 (2024-08-18)
+------------------
+
+dev
+"""
+* Add documentations for the `distributions`, and `eva` modules.
+* Add autodoc for all modules.
+* Test docstrings as part of CI and pre-commit hooks.
+* Test notebooks as part of CI.
+* Simplify test for the distributions module
+
+distributions
+"""""""""""""
+* move the `cdf` and `parameters` for all the methods to be optional parameters.
+* rename `theoretical_estimate` method to `inverse_cdf`.
+* All distributions can be instantiated with the parameters and/or data.
+* rename the `probability_plot` method to `plot`.
+* move the `confidence_interval` plot from the `probability_plot/plot` to the method `confidence_interval` and can be
+    called by activating the `plot_figure=True`.
+
+descriptors
+"""""""""""
+* rename the `metrics` module to `descriptors`.
diff --git a/README.md b/README.md
@@ -28,7 +28,7 @@ Main Features
 -------------
   - Statistical Distributions
     - GEV
-    - GUMBL
+    - GUMBEL
     - Normal
     - Exponential
   - Parameter estimation methods
@@ -40,6 +40,7 @@ Main Features
   - Statistical descriptors
   - Extreme value analysis
 
+For the full documentation, please visit [statista documentation](https://statista.readthedocs.io/en/latest/?badge=latest)
 
 Installing statista
 ===============
@@ -50,22 +51,22 @@ Installing `statista` from the `conda-forge` channel can be achieved by:
 conda install -c conda-forge statista
 ```
 
-It is possible to list all of the versions of `statista` available on your platform with:
+It is possible to list all the versions of `statista` available on your platform with:
 
 ```
 conda search statista --channel conda-forge
 ```
 
-## Install from Github
-to install the last development to time you can install the library from github
+## Install from GitHub
+to install the last development to time, you can install the library from GitHub
 ```
 pip install git+https://github.com/MAfarrag/statista
 ```
 
 ## pip
-to install the last release you can easly use pip
+to install the last release, you can use pip
 ```
-pip install statista==0.5.0
+pip install statista==0.6.0
 ```
 
 Quick start

diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)