Imageruler revamp (#30)

* Redo packaging using pyproject.toml and src layout (#1)

* Redo package

* Fix version number v0.1.0

* Formatting

* Docstring darglint

* Update imports

* Formatting

---------

Co-authored-by: Martin Schubert <[email protected]>

* Add py.typed

* Switch to tometrics algorithm

* Add mypy dep

* Add scipy dep

* Fix reference filename

* Type annotation

* Reference design readme

* Add docs deps

* Fix eof

* Fix naming

* Version updated from v0.1.0 to v0.2.0

* Add to_designs notebook

* Add skimage docs dep

* Add skimage docs dep

* Fix authorship in docs

* cleanup

* Notebook for ignore schemes

* Cleanup

* Fix module docstring

* Fix some typos

* Add performance comment

---------

Co-authored-by: Martin Schubert <[email protected]>

.bumpversion.toml

@@ -0,0 +1,22 @@
+[tool.bumpversion]
+current_version = "v0.2.0"
+commit = true
+commit_args = "--no-verify"
+tag = true
+tag_name = "{new_version}"
+allow_dirty = true
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(\\.(?P<dev>dev)\\d+\\+[-_a-zA-Z0-9]+)?"
+serialize = [
+    "v{major}.{minor}.{patch}.{dev}{distance_to_latest_tag}+{short_branch_name}",
+    "v{major}.{minor}.{patch}"
+]
+message = "Version updated from {current_version} to {new_version}"
+
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+
+[[tool.bumpversion.files]]
+filename = "README.md"
+
+[[tool.bumpversion.files]]
+filename = "src/imageruler/__init__.py"

.gitattributes

@@ -0,0 +1,2 @@
+# Auto detect text files and perform LF normalization
+* text=auto

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "daily"
+
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly

.github/workflows/build-ci.yml

@@ -0,0 +1,79 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+  schedule:
+      - cron: "0 13 * * 1"  # Every Monday at 9AM EST
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+          cache: "pip"
+          cache-dependency-path: pyproject.toml
+
+      - name: Test pre-commit hooks
+        run: |
+          python -m pip install --upgrade pip
+          pip install pre-commit
+          pre-commit run -a
+
+  validate-types-and-docstrings:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+          cache: "pip"
+          cache-dependency-path: pyproject.toml
+
+      - name: Setup environment
+        run: |
+            python -m pip install --upgrade pip
+            pip install ".[tests,dev]"
+
+      - name: mypy type validation
+        run: |
+          mypy src
+          mypy imageruler
+
+      - name: darglint docstring validation
+        run: |
+          darglint src --strictness=short --ignore-raise=ValueError
+          darglint imageruler --strictness=short --ignore-raise=ValueError
+
+  tests:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+          cache: "pip"
+          cache-dependency-path: pyproject.toml
+
+      - name: Setup environment
+        run: |
+            python -m pip install --upgrade pip
+            pip install ".[tests,dev]"
+
+      - name: Run Python tests
+        run: |
+          pytest --cov=imageruler tests

.github/workflows/cli_test.yml

@@ -0,0 +1,32 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+  schedule:
+      - cron: "0 13 * * 1"  # Every Monday at 9AM EST
+
+jobs:
+  example:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+          cache: "pip"
+          cache-dependency-path: pyproject.toml
+
+      - name: Setup environment
+        run: |
+            python -m pip install --upgrade pip
+            pip install ".[tests,dev,examples]"
+
+      - name: Run program on reference design
+        run: |
+          python imageruler reference_designs/Rasmus70nm.csv

.github/workflows/pages.yml

@@ -0,0 +1,51 @@
+name: Sphinx docs to gh-pages
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    name: Sphinx docs to gh-pages
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+          cache: "pip"
+          cache-dependency-path: pyproject.toml
+
+      - name: Setup environment
+        run: |
+            python -m pip install --upgrade pip
+            pip install ".[tests,dev,docs]"
+
+      - name: docs
+        run: jb build docs
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: "./docs/_build/html/"
+
+  deploy-docs:
+    needs: build-docs
+    permissions:
+      pages: write
+      id-token: write
+
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/release.yml

@@ -0,0 +1,28 @@
+name: Release PyPI
+
+on:
+  push:
+    tags: "v*"
+
+jobs:
+  release_pypi:
+    if: github.event_name == 'push'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+          cache-dependency-path: pyproject.toml
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build setuptools twine wheel
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: |
+          python -m build
+          twine upload dist/*

.gitignore

@@ -129,4 +129,4 @@ dmypy.json
 cython_debug/
 
 # PyCharm
-.idea/
+.idea/

.pre-commit-config.yaml

@@ -0,0 +1,55 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: trailing-whitespace
+
+    # Black formatting
+  - repo: https://github.com/psf/black
+    rev: 23.9.1
+    hooks:
+      - id: black
+
+    # Upgrade python syntax
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.10.1
+    hooks:
+      - id: pyupgrade
+        args: [--py37-plus, --keep-runtime-typing]
+
+    # Validate shell scripts
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: v0.9.0.5
+    hooks:
+      - id: shellcheck
+
+    # Security linter
+  - repo: https://github.com/PyCQA/bandit
+    rev: 1.7.5
+    hooks:
+      - id: bandit
+        args: [--exit-zero]
+        exclude: ^tests/
+
+    # Linter
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.287
+    hooks:
+      - id: ruff
+        exclude: ^tests/
+
+    # Strip whitespace from notebooks.
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.6.0
+    hooks:
+      - id: nbstripout

LICENSE.md

@@ -17,5 +17,4 @@ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
 LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
 OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 
-
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

@@ -1,4 +1,5 @@
 [![Build Status](https://github.com/NanoComp/imageruler/workflows/CI/badge.svg)](https://github.com/NanoComp/imageruler/actions)
+`v0.2.0`
 
 Imageruler is a free Python program to compute the minimum length scale of binary images which are typically designs produced by topology optimization. The algorithm is described in Section 2 of [J. Optical Society of America B, Vol. 42, pp. A161-A176 (2024)](https://opg.optica.org/josab/abstract.cfm?uri=josab-41-2-A161) and is based on morphological transformations implemented using [OpenCV](https://github.com/opencv/opencv). Imageruler also supports 1d binary images.
 
@@ -21,4 +22,4 @@ For a 1d binary image, the algorithm simply finds the minimum length among all s
 
 ## Note on Accuracy
 
-The accuracy of the minimum length scale computed by Imageruler is limited by the finite resolution of the input image. A fundamental feature is that length scales smaller than a single pixel cannot be measured. Also, in certain situations, length scales of a few pixels may be indistinguishable from discretization artifacts such as the "staircasing" of curved surfaces. As an example, a sharp 90° corner corresponds to a length scale (radius of curvature) of *zero* at infinite resolution. However, at a finite resolution, a sharp corner is indistinguishable from one that is rounded with a radius of curvature of a few pixels. Imageruler will therefore return a length scale proportional to the pixel size rather than zero. In general, the measured length scale should be viewed as having an "error bar" on the few-pixel level.
+The accuracy of the minimum length scale computed by Imageruler is limited by the finite resolution of the input image. A fundamental feature is that length scales smaller than a single pixel cannot be measured. Also, in certain situations, length scales of a few pixels may be indistinguishable from discretization artifacts such as the "staircasing" of curved surfaces. As an example, a sharp 90° corner corresponds to a length scale (radius of curvature) of *zero* at infinite resolution. However, at a finite resolution, a sharp corner is indistinguishable from one that is rounded with a radius of curvature of a few pixels. Imageruler will therefore return a length scale proportional to the pixel size rather than zero. In general, the measured length scale should be viewed as having an "error bar" on the few-pixel level.