Merge branch 'update-to-v0.23' into 'release'

Update to v0.23

See merge request jatic/kitware/nrtk!326

Author: Brandon RichardWebster

.gitignore

@@ -73,7 +73,7 @@ instance/
 # Sphinx documentation
 docs/_build/
 docs/_implementations
-docs/nrtk_jatic/_implementations
+docs/maite/_implementations
 
 # PyBuilder
 .pybuilder/

.gitlab-ci/.gitlab-container.yml

@@ -1,14 +1,14 @@
 ###############################################################################
 # Stage -- Container
 ###############################################################################
-# 
+#
 # Overrides:
-# 
+#
 # 1) Uses this repository's Dockerfile(s)
 ###############################################################################
 trigger_aukus:
   extends: .trigger_containers
   variables:
     CONTAINER_NAME: "aukus"
     DOCKERFILE_FILE: "Dockerfile"
-    PIPELINE_CONTEXT: "$CI_PIPELINE_SOURCE"
+    PIPELINE_CONTEXT: "$CI_PIPELINE_SOURCE"

.gitlab-ci/.gitlab-docs.yml

@@ -11,4 +11,4 @@
 .docs-setup:
   before_script:
     - !reference [.shared-setup, before_script]
-    - poetry install --sync --only main,docs,tests,linting --extras "pybsm headless maite"
+    - poetry install --sync --only main,docs,tests,linting --extras "pybsm headless maite waterdroplet"

.gitlab-ci/.gitlab-test.yml

@@ -8,20 +8,16 @@
 # 2) Poetry install for optional dependencies
 #
 ###############################################################################
-pytest-core:
-  # Temporary allow failure for missing import guards
-  allow_failure: true
 
 pytest-extras:
-  allow_failure: false
   variables:
     EXTRAS: "pybsm maite tools headless Pillow scikit-image albumentations waterdroplet notebook-testing"
 
 notebooks:
   extends: .notebooks
   rules: !reference [.notebooks, rules]
   variables:
-    EXTRAS: "pybsm maite tools headless Pillow scikit-image albumentations notebook-testing"
+    EXTRAS: "pybsm maite tools headless Pillow scikit-image albumentations waterdroplet notebook-testing"
   parallel:
     matrix:
       # Sequences combinatorically combine within a list entry
@@ -53,6 +49,7 @@ notebooks:
           "nrtk_lens_flare_demo.ipynb",
           "nrtk_translation_perturber_demo.ipynb",
           "nrtk_turbulence_perturber_demo.ipynb",
+          "nrtk_water_droplet_perturber_demo.ipynb"
         ]
       - NOTEBOOK_DIR: "docs/examples/maite/gradio"
         NOTEBOOK_FILE: [

.pre-commit-config.yaml

@@ -1,35 +1,49 @@
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
-    hooks:
-    - id: trailing-whitespace
-    - id: end-of-file-fixer
-    - id: check-added-large-files
-      args:
-        # the unit here is acutally KiB (1024 bytes)
-        - '--maxkb=51200'  # match github max of 50MiB
--   repo: local
-    hooks:
-      - id: ruff-lint
-        name: ruff-lint
-        entry: poetry run ruff check --config pyproject.toml --fix --force-exclude
-        require_serial: true
-        language: system
-        types_or: [python, pyi, jupyter]
-      - id: sphinx-lint
-        name: sphinx-lint
-        entry: poetry run sphinx-lint --enable all --disable leaked-markup --jobs 1 --max-line-length 120 -i docs/_implementations -i docs/nrtk_jatic/_implementations docs
-        types: [rst]
-        language: system
-      - id: ruff-format
-        name: ruff-format
-        entry: poetry run ruff format --config pyproject.toml --force-exclude
-        require_serial: true
-        language: system
-        types_or: [python, pyi, jupyter]
-      - id: pyright
-        name: pyright
-        require_serial: true
-        language: system
-        entry: poetry run pyright
-        types: [file, python]
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+  - id: check-added-large-files
+    args:
+      # the unit here is acutally KiB (1024 bytes)
+      - '--maxkb=51200'  # match github max of 50MiB
+- repo: https://github.com/hukkin/mdformat
+  rev: 0.7.22  # Use the ref you want to point at
+  hooks:
+  - id: mdformat
+    name: mdformat-lint
+    args: [--wrap=80, --number]
+    types: [markdown]
+- repo: https://github.com/hukkin/mdformat
+  rev: 0.7.22  # Use the ref you want to point at
+  hooks:
+  - id: mdformat
+    name: mdformat-format
+    args: [--wrap=80, --number, --check]
+    types: [markdown]
+- repo: local
+  hooks:
+    - id: ruff-lint
+      name: ruff-lint
+      entry: poetry run ruff check --config pyproject.toml --fix --force-exclude
+      require_serial: true
+      language: system
+      types_or: [python, pyi, jupyter]
+    - id: sphinx-lint
+      name: sphinx-lint
+      entry: poetry run sphinx-lint --enable all --disable leaked-markup --jobs 1 --max-line-length 120 -i docs/_implementations -i docs/maite/_implementations docs
+      types: [rst]
+      language: system
+    - id: ruff-format
+      name: ruff-format
+      entry: poetry run ruff format --config pyproject.toml --force-exclude
+      require_serial: true
+      language: system
+      types_or: [python, pyi, jupyter]
+    - id: pyright
+      name: pyright
+      require_serial: true
+      language: system
+      entry: poetry run pyright
+      types: [file, python]

.readthedocs.yaml

@@ -15,7 +15,7 @@ build:
       # https://python-poetry.org/docs/managing-dependencies/#dependency-groups
       # VIRTUAL_ENV needs to be set manually for now.
       # See https://github.com/readthedocs/readthedocs.org/pull/11152/
-      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with main,docs,tests --extras "pybsm headless maite"
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with main,docs,tests --extras "pybsm headless maite waterdroplet"
 
 sphinx:
   builder: html

CONTRIBUTING.md

@@ -1,23 +1,24 @@
 # Contributing to `nrtk`
 
 ## Overview
-This guide provides instructions for contributing to the `nrtk` project. For additional details, please refer to the [`nrtk` README](README.md).
+
+This guide provides instructions for contributing to the `nrtk` project.
+For additional details, please refer to the [`nrtk` README](README.md).
 
 ## Steps to Contribute
 
-1. **Access the Repository**
-   Navigate to the official `nrtk` repository on [JATIC GitLab](https://gitlab.jatic.net/jatic/kitware/nrtk).
+1. **Access the Repository** Navigate to the official `nrtk` repository
+   on [JATIC GitLab](https://gitlab.jatic.net/jatic/kitware/nrtk).
 
-2. **Fork and Clone**
-   Fork the repository into your GitLab user namespace and clone it to your local system.
+2. **Fork and Clone** Fork the repository into your GitLab user namespace and
+   clone it to your local system.
 
    ```bash
    $ git clone <your-fork-url>
    $ cd nrtk
    ```
 
-3. **Create a Topic Branch**
-   Work on a new topic branch for your contribution:
+3. **Create a Topic Branch** Work on a new topic branch for your contribution:
 
    ```bash
    $ git checkout -b <branch-name>
@@ -26,69 +27,105 @@ This guide provides instructions for contributing to the `nrtk` project. For add
    $ git commit -m "Descriptive commit message"
    ```
 
-   - Ensure that your commits include an update to the `docs/release_notes/pending_release.rst` file (or a relevant patch release notes file).
-   - Provide a concise summary of the feature, update, or fix being added. This is generally required for approval.
+   - Ensure that your commits include an update to the
+     `docs/release_notes/pending_release.rst` file (or a relevant patch release
+     notes file).
+   - Provide a concise summary of the feature, update, or fix being added. This
+     is generally required for approval.
 
-4. **Push Your Branch**
-   Push your changes to your forked repository:
+4. **Push Your Branch** Push your changes to your forked repository:
 
    ```bash
    $ git push origin HEAD -u
    ```
 
-5. **Create a Merge Request (MR)**
-   On GitLab, navigate to the "Merge Requests" tab of your forked project and click "New merge request."
+5. **Create a Merge Request (MR)** On GitLab, navigate to the "Merge Requests"
+   tab of your forked project and click "New merge request."
 
-   - Set the source branch to your forked branch and the target branch to the appropriate branch of the `nrtk` repository.
+   - Set the source branch to your forked branch and the target branch to the
+     appropriate branch of the `nrtk` repository.
    - Click "Compare branches and continue" and then "Create merge request."
 
----
+______________________________________________________________________
 
 ## Continuous Integration (CI) and Code Review
-`nrtk` uses GitLab for code reviews and GitLab CI/CD for automated testing.
+
+`nrtk` uses GitLab for code reviews and GitLab CI/CD for automated
+testing.
+
 - New MRs trigger CI workflows for `master` and `release` branches.
 - All CI checks must pass before an MR can be merged.
 
-We use [Sphinx](https://www.sphinx-doc.org/) for API documentation, both manual and automated.
+We use [Sphinx](https://www.sphinx-doc.org/) for API documentation, both manual
+and automated.
 
----
+______________________________________________________________________
 
 ## Guidelines for Jupyter Notebooks
+
 When adding or modifying Jupyter Notebooks:
 
 1. **CI Inclusion**
-   - Ensure notebooks are part of the CI workflow and executable within its environment.
-   - Add references to `.gitlab-ci/.gitlab-test.yml` and to `tests/examples/test_notebooks.py`.
+
+   - Ensure notebooks are part of the CI workflow and executable within its
+     environment.
+   - Add references to `.gitlab-ci/.gitlab-test.yml` and to
+     `tests/examples/test_notebooks.py`.
 
 2. **Execution Requirements**
+
    - Keep execution concise to avoid CI timeouts.
-   - Include a cell for dependency installation (e.g., `pip install ...`) to ensure proper setup in the CI environment.
+   - Include a cell for dependency installation (e.g., `pip install ...`) to
+     ensure proper setup in the CI environment.
 
 3. **Resource Constraints**
-   - Optimize notebooks to use minimal computational resources, aligning with CI environment limitations.
 
----
+   - Optimize notebooks to use minimal computational resources, aligning with CI
+     environment limitations.
+
+______________________________________________________________________
 
 ## Contribution Release Notes
-Typically, every contribution requires an associated release note. Add this to the `docs/release_notes/pending_release.rst` file, summarizing the changes made.
+
+Typically, every contribution requires an associated release note. Add this to
+the `docs/release_notes/pending_release.rst` file, summarizing the changes made.
 
 ### Exceptions
-If your contribution fixes a minor issue in a recent update and does not alter the summary in existing release notes, the requirement may be waived.
-- Contributors should explain why a release note is unnecessary for the reviewers to consider on a case-by-case basis.
 
----
+If your contribution fixes a minor issue in a recent update and does not alter
+the summary in existing release notes, the requirement may be waived.
+
+- Contributors should explain why a release note is unnecessary for the
+  reviewers to consider on a case-by-case basis.
+
+______________________________________________________________________
 
 ## Class Naming Philosophy
-We adopt a "Verb-Noun" convention for class names. This structure highlights the behavior or transformation a class performs.
+
+We adopt a "Verb-Noun" convention for class names. This structure highlights the
+behavior or transformation a class performs.
+
 - **Verb**: Indicates the primary action or behavior.
-- **Noun**: Specifies the subject of the action, typically related to input or output.
+- **Noun**: Specifies the subject of the action, typically related to input or
+  output.
 
 ### Examples
-- Classes performing similar actions on different subjects should clearly differentiate the subjects in their names.
+
+- Classes performing similar actions on different subjects should clearly
+  differentiate the subjects in their names.
 - Names should be concise and intuitive, aiding user understanding.
 
 ## Issue Reporting
-If an issue is found, it can be reported on the [Issue Reporting Page](https://github.com/Kitware/nrtk/issues/new). In the description, provide an outline of the problem in as much detail as possible being sure to include any relevant logs and error tracebacks. Once the issue is created, it will be triaged by a maintainer in a timely manner.
+
+If an issue is found, it can be reported on the
+[Issue Reporting Page](https://github.com/Kitware/nrtk/issues/new). In
+the description, provide an outline of the problem in as much detail as possible
+being sure to include any relevant logs and error tracebacks. Once the issue is
+created, it will be triaged by a maintainer in a timely manner.
 
 ## Feature Requests
-If a user wants to request a new feature, it can be reported in the same location as the issues. In the issue created for feature requests, begin the title with `FEATURE REQUEST`. The issue should also include a `Use Case` section describing the intended use case of the new feature.
+
+If a user wants to request a new feature, it can be reported in the same
+location as the issues. In the issue created for feature requests, begin the
+title with `FEATURE REQUEST`. The issue should also include a `Use Case` section
+describing the intended use case of the new feature.

Dockerfile

@@ -16,7 +16,7 @@ ENV PYTHONUNBUFFERED=1 \
     # do not ask for any interaction
     POETRY_NO_INTERACTION=1 \
     # this is where we copy the lock
-    PYSETUP_PATH="/opt/pysetup" 
+    PYSETUP_PATH="/opt/pysetup"
 
 # prepend poetry and venv to path
 ENV PATH="$POETRY_HOME/bin:$PATH"
@@ -55,5 +55,5 @@ CMD ["/root/input/dataset", "/root/output/", \
 # To run this docker container, use the following command:
 # `docker run -v /path/to/input:/root/input/:ro -v /path/to/output:/root/output/ nrtk-perturber`
 # This will mount the inputs to the correct locations the default args are used.
-# See https://docs.docker.com/storage/volumes/#start-a-container-with-a-volume 
+# See https://docs.docker.com/storage/volumes/#start-a-container-with-a-volume
 # for more info on mounting volumes