make release-tag: Merge branch 'main' into stable

Author: amontanez24

.github/workflows/readme.yml

@@ -21,6 +21,6 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install invoke rundoc .
+        python -m pip install invoke tomli rundoc .
     - name: Run the README.md
       run: invoke readme

.github/workflows/tutorials.yml

@@ -20,6 +20,6 @@ jobs:
     - name: Install package and dependencies
       run: |
           python -m pip install --upgrade pip
-          python -m pip install invoke jupyter .[tutorials]
+          python -m pip install invoke tomli jupyter .[tutorials]
     - name: invoke tutorials
       run: invoke tutorials

HISTORY.md

@@ -1,5 +1,28 @@
 # History
 
+## v0.10.1 - 2024-03-13
+
+This release fixes a bug that occurred when calculating probability density in a gaussian copula.
+
+### Bugs Fixed
+
+* Warning printed too many times (`RuntimeWarning: invalid value encountered in scalar divide  ....`) - Issue [#364](https://github.com/sdv-dev/Copulas/issues/364) by @frances-h
+* Set `allow_singular=True` when calculating probability_density - Issue [#374](https://github.com/sdv-dev/Copulas/issues/374) by @fealho
+
+### Maintenance
+
+* Transition from using setup.py to pyroject.toml to specify project metadata - Issue [#376](https://github.com/sdv-dev/Copulas/issues/376) by @frances-h
+* Remove bumpversion and use bump-my-version - Issue [#377](https://github.com/sdv-dev/Copulas/issues/377) by @frances-h
+* Add build to dev requirements - Issue [#382](https://github.com/sdv-dev/Copulas/pull/382) by @amontanez24
+
+## v0.10.0 - 2023-11-13
+
+This release updates all visualizations to use plotly, and removes the matplotlib dependency.
+
+### New Features
+
+*  Move visualization functions to plotly and get rid of matplotlib dependency - Issue [#348](https://github.com/sdv-dev/Copulas/issues/348) by @fealho
+
 ## v0.9.2 - 2023-10-12
 
 This release removes a warning that was being raised when univariate distributions failed to fit and logs the message instead.

MANIFEST.in

@@ -158,8 +158,7 @@ serve-docs: ## compile the docs watching for changes
 
 .PHONY: dist
 dist: clean ## builds source and wheel package
-	python setup.py sdist
-	python setup.py bdist_wheel
+	python -m build --wheel --sdist
 	ls -l dist
 
 .PHONY: publish-confirm
@@ -197,23 +196,23 @@ git-push-tags-stable: ## Push tags and stable to github
 
 .PHONY: bumpversion-release
 bumpversion-release: ## Bump the version to the next release
-	bumpversion release
+	bump-my-version bump release
 
 .PHONY: bumpversion-patch
 bumpversion-patch: ## Bump the version to the next patch
-	bumpversion --no-tag patch
+	bump-my-version bump patch --no-tag
 
 .PHONY: bumpversion-candidate
 bumpversion-candidate: ## Bump the version to the next candidate
-	bumpversion candidate --no-tag
+	bump-my-version bump candidate --no-tag
 
 .PHONY: bumpversion-minor
 bumpversion-minor: ## Bump the version the next minor skipping the release
-	bumpversion --no-tag minor
+	bump-my-version bump minor --no-tag
 
 .PHONY: bumpversion-major
 bumpversion-major: ## Bump the version the next major skipping the release
-	bumpversion --no-tag major
+	bump-my-version bump major --no-tag
 
 .PHONY: bumpversion-revert
 bumpversion-revert: ## Undo a previous bumpversion-release
@@ -223,7 +222,7 @@ bumpversion-revert: ## Undo a previous bumpversion-release
 
 CLEAN_DIR := $(shell git status --short | grep -v ??)
 CURRENT_BRANCH := $(shell git rev-parse --abbrev-ref HEAD 2>/dev/null)
-CURRENT_VERSION := $(shell grep "^current_version" setup.cfg | grep -o "dev[0-9]*")
+CURRENT_VERSION := $(shell grep "^current_version" pyproject.toml | grep -o "dev[0-9]*")
 CHANGELOG_LINES := $(shell git diff HEAD..origin/stable HISTORY.md 2>&1 | wc -l)
 
 .PHONY: check-clean

Makefile

@@ -4,7 +4,7 @@
 
 __author__ = 'DataCebo, Inc.'
 __email__ = '[email protected]'
-__version__ = '0.9.2'
+__version__ = '0.10.1.dev1'
 
 import contextlib
 import importlib

copulas/__init__.py

@@ -148,7 +148,9 @@ def probability_density(self, X):
         """
         self.check_fit()
         transformed = self._transform_to_normal(X)
-        return stats.multivariate_normal.pdf(transformed, cov=self.correlation)
+
+        return stats.multivariate_normal.pdf(
+            transformed, cov=self.correlation, allow_singular=True)
 
     def cumulative_distribution(self, X):
         """Compute the cumulative distribution value for each point in X.

copulas/multivariate/gaussian.py

@@ -1,5 +1,7 @@
 """TruncatedGaussian module."""
 
+import warnings
+
 import numpy as np
 from scipy.optimize import fmin_slsqp
 from scipy.stats import truncnorm
@@ -47,10 +49,12 @@ def nnlf(params):
             return truncnorm.nnlf((a, b, loc, scale), X)
 
         initial_params = X.mean(), X.std()
-        optimal = fmin_slsqp(nnlf, initial_params, iprint=False, bounds=[
-            (self.min, self.max),
-            (0.0, (self.max - self.min)**2)
-        ])
+        with warnings.catch_warnings():
+            warnings.simplefilter('ignore', category=RuntimeWarning)
+            optimal = fmin_slsqp(nnlf, initial_params, iprint=False, bounds=[
+                (self.min, self.max),
+                (0.0, (self.max - self.min)**2)
+            ])
 
         loc, scale = optimal
         a = (self.min - loc) / scale