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

.github/workflows/dependency_checker.yml

@@ -0,0 +1,29 @@
+name: Dependency Checker
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 0 * * 1-5'
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.9
+    - name: Install dependencies
+      run: |
+        python -m pip install .[dev]
+        make check-deps OUTPUT_FILEPATH=latest_requirements.txt
+    - name: Create pull request
+      id: cpr
+      uses: peter-evans/create-pull-request@v4
+      with:
+        token: ${{ secrets.GH_ACCESS_TOKEN }}
+        commit-message: Update latest dependencies
+        title: Automated Latest Dependency Updates
+        body: "This is an auto-generated PR with **latest** dependency updates."
+        branch: latest-dependency-update
+        branch-suffix: short-commit-hash
+        base: main

.github/workflows/integration.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         os: [ubuntu-latest, macos-latest, windows-latest]
     steps:
     - uses: actions/checkout@v1

.github/workflows/minimum.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         os: [ubuntu-latest, macos-latest, windows-latest]
     steps:
     - uses: actions/checkout@v1

.github/workflows/readme.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         os: [ubuntu-latest, macos-latest]  # skip windows bc rundoc fails
     steps:
     - uses: actions/checkout@v1
@@ -22,5 +22,7 @@ jobs:
       run: |
           python -m pip install --upgrade pip
           python -m pip install invoke rundoc .
+          python -m pip install tomli
+          python -m pip install packaging
     - name: Run the README.md
       run: invoke readme

.github/workflows/static_code_analysis.yml

@@ -0,0 +1,33 @@
+name: Static Code Analysis
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  code-analysis:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install bandit==1.7.7
+    - name: Save code analysis
+      run: bandit -r . -x ./tests -f txt -o static_code_analysis.txt --exit-zero
+    - name: Create pull request
+      id: cpr
+      uses: peter-evans/create-pull-request@v4
+      with:
+        token: ${{ secrets.GH_ACCESS_TOKEN }}
+        commit-message: Update static code analysis
+        title: Latest Code Analysis
+        body: "This is an auto-generated PR with the **latest** code analysis results."
+        branch: static-code-analysis
+        branch-suffix: short-commit-hash
+        base: main

.github/workflows/unit.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         os: [ubuntu-latest, macos-latest, windows-latest]
     steps:
     - uses: actions/checkout@v1

CONTRIBUTING.rst

@@ -174,17 +174,17 @@ Release Workflow
 The process of releasing a new version involves several steps combining both ``git`` and
 ``bumpversion`` which, briefly:
 
-1. Merge what is in ``master`` branch into ``stable`` branch.
+1. Merge what is in ``main`` branch into ``stable`` branch.
 2. Update the version in ``setup.cfg``, ``deepecho/__init__.py`` and
    ``HISTORY.md`` files.
 3. Create a new git tag pointing at the corresponding commit in ``stable`` branch.
-4. Merge the new commit from ``stable`` into ``master``.
+4. Merge the new commit from ``stable`` into ``main``.
 5. Update the version in ``setup.cfg`` and ``deepecho/__init__.py``
    to open the next development iteration.
 
 .. note:: Before starting the process, make sure that ``HISTORY.md`` has been updated with a new
           entry that explains the changes that will be included in the new version.
-          Normally this is just a list of the Pull Requests that have been merged to master
+          Normally this is just a list of the Pull Requests that have been merged to main
           since the last release.
 
 Once this is done, run of the following commands:
@@ -219,9 +219,9 @@ This will perform the following actions:
 2. Bump the current version to the next release candidate, ``X.Y.Z.dev(N+1)``
 
 After this is done, the new pre-release can be installed by including the ``dev`` section in the
-dependency specification, either in ``setup.py``::
+dependency specification, either in ``pyproject.toml``::
 
-    install_requires = [
+    dependencies = [
         ...
         'deepecho>=X.Y.Z.dev',
         ...

HISTORY.md

@@ -1,5 +1,30 @@
 # History
 
+## 0.6.0 - 2024-04-10
+
+This release adds support for Python 3.12!
+
+### Maintenance
+
+* Support Python 3.12 - Issue [#85](https://github.com/sdv-dev/DeepEcho/issues/85) by @fealho
+* Transition from using setup.py to pyproject.toml to specify project metadata - Issue [#86](https://github.com/sdv-dev/DeepEcho/issues/86) by @R-Palazzo
+* Remove bumpversion and use bump-my-version - Issue [#87](https://github.com/sdv-dev/DeepEcho/issues/87) by @R-Palazzo
+* Add dependency checker - Issue [#96](https://github.com/sdv-dev/DeepEcho/issues/96) by @lajohn4747
+* Add bandit workflow - Issue [#98](https://github.com/sdv-dev/DeepEcho/issues/98) by @R-Palazzo
+
+### Bugs Fixed
+
+* Fix make check candidate - Issue [#91](https://github.com/sdv-dev/DeepEcho/issues/91) by @R-Palazzo
+* Fix minimum version workflow when pointing to github branch - Issue [#99](https://github.com/sdv-dev/DeepEcho/issues/99) by @R-Palazzo
+
+## 0.5.0 - 2023-11-13
+
+This release updates the PAR's model progress bar to show loss values and time elapsed (verbose option).
+
+### New Features
+* Update progress bar for PAR fitting - Issue [#80](https://github.com/sdv-dev/DeepEcho/issues/80) by @frances-h
+
+
 ## 0.4.2 - 2023-07-25
 
 This release drops support for Python 3.7 and adds support for Python 3.11.

INSTALL.md

@@ -3,7 +3,7 @@
 ## Requirements
 
 **DeepEcho** has been developed and tested on
-[Python 3.8, 3.9, 3.10 and 3.11](https://www.python.org/downloads/)
+[Python 3.8, 3.9, 3.10, 3.11 and 3.12](https://www.python.org/downloads/)
 
 Also, although it is not strictly required, the usage of a [virtualenv](
 https://virtualenv.pypa.io/en/latest/) is highly recommended in order to avoid
@@ -47,12 +47,12 @@ make install
 
 If you intend to modify the source code or contribute to the project you will need to
 install it from the source using the `make install-develop` command. In this case, we
-recommend you to branch from `master` first:
+recommend you to branch from `main` first:
 
 ```bash
 git clone [email protected]:sdv-dev/DeepEcho
 cd DeepEcho
-git checkout master
+git checkout main
 git checkout -b <your-branch-name>
 make install-develp
 ```

Makefile

@@ -79,30 +79,17 @@ install-develop: clean-build clean-pyc ## install the package in editable mode a
 
 # LINT TARGETS
 
-.PHONY: lint-deepecho
-lint-deepecho: ## check style with flake8 and isort
-	flake8 deepecho
-	isort -c --recursive deepecho
-	pylint deepecho --rcfile=setup.cfg
-
-.PHONY: lint-tests
-lint-tests: ## check style with flake8 and isort
-	flake8 --ignore=D tests
-	isort -c --recursive tests
-
 .PHONY: lint
-lint:  ## Run all code style checks
-	invoke lint
+lint:
+	ruff check .
+	ruff format .  --check
 
 .PHONY: fix-lint
-fix-lint: ## fix lint issues using autoflake, autopep8, and isort
-	find deepecho tests -name '*.py' | xargs autoflake --in-place --remove-all-unused-imports --remove-unused-variables
-	autopep8 --in-place --recursive --aggressive deepecho tests
-	isort --apply --atomic --recursive deepecho tests
-
+fix-lint:
+	ruff check --fix .
+	ruff format .
 
 # TEST TARGETS
-
 .PHONY: test-unit
 test-unit: ## run unit tests using pytest
 	invoke unit
@@ -145,8 +132,7 @@ coverage: ## check code coverage quickly with the default Python
 
 .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
@@ -165,46 +151,46 @@ publish: dist publish-confirm ## package and upload a release
 	twine upload dist/*
 
 .PHONY: bumpversion-release
-bumpversion-release: ## Merge master to stable and bumpversion release
+bumpversion-release: ## Merge main to stable and bumpversion release
 	git checkout stable || git checkout -b stable
-	git merge --no-ff master -m"make release-tag: Merge branch 'master' into stable"
-	bumpversion release
+	git merge --no-ff main -m"make release-tag: Merge branch 'main' into stable"
+	bump-my-version bump release
 	git push --tags origin stable
 
 .PHONY: bumpversion-release-test
-bumpversion-release-test: ## Merge master to stable and bumpversion release
+bumpversion-release-test: ## Merge main to stable and bumpversion release
 	git checkout stable || git checkout -b stable
-	git merge --no-ff master -m"make release-tag: Merge branch 'master' into stable"
-	bumpversion release --no-tag
+	git merge --no-ff main -m"make release-tag: Merge branch 'main' into stable"
+	bump-my-version bump release --no-tag
 	@echo git push --tags origin stable
 
 .PHONY: bumpversion-patch
-bumpversion-patch: ## Merge stable to master and bumpversion patch
-	git checkout master
+bumpversion-patch: ## Merge stable to main and bumpversion patch
+	git checkout main
 	git merge stable
-	bumpversion --no-tag patch
+	bump-my-version bump patch --no-tag
 	git push
 
 .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
-	git checkout master
+	git checkout main
 	git branch -D stable
 
 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
@@ -213,10 +199,10 @@ ifneq ($(CLEAN_DIR),)
 	$(error There are uncommitted changes)
 endif
 
-.PHONY: check-master
-check-master: ## Check if we are in master branch
-ifneq ($(CURRENT_BRANCH),master)
-	$(error Please make the release from master branch\n)
+.PHONY: check-main
+check-main: ## Check if we are in main branch
+ifneq ($(CURRENT_BRANCH),main)
+	$(error Please make the release from main branch\n)
 endif
 
 .PHONY: check-candidate
@@ -231,8 +217,13 @@ ifeq ($(CHANGELOG_LINES),0)
 	$(error Please insert the release notes in HISTORY.md before releasing)
 endif
 
+.PHONY: check-deps
+check-deps: # Dependency targets
+	$(eval allow_list='numpy=|pandas=|torch=|tqdm=')
+	pip freeze | grep -v "SDMetrics.git" | grep -E $(allow_list) | sort > $(OUTPUT_FILEPATH)
+
 .PHONY: check-release
-check-release: check-clean check-candidate check-master check-history ## Check if the release can be made
+check-release: check-clean check-candidate check-main check-history ## Check if the release can be made
 	@echo "A new release can be made"
 
 .PHONY: release
@@ -242,7 +233,7 @@ release: check-release bumpversion-release publish bumpversion-patch
 release-test: check-release bumpversion-release-test publish-test bumpversion-revert
 
 .PHONY: release-candidate
-release-candidate: check-master publish bumpversion-candidate
+release-candidate: check-main publish bumpversion-candidate
 
 .PHONY: release-candidate-test
-release-candidate-test: check-clean check-master publish-test
+release-candidate-test: check-clean check-main publish-test