skpkg: setup CI after migrating tests, src, requirements, and .github folder (#151)

* skpkg: migrate src folder

* skpkg: migrate tests folder

* skpkg: list dependencies in requirements folder

* skpkg: add CI and issue/PR templates

* skpkg: add pyproject.toml

* skpkg: standardize files by removing examples and adding back necessary scripts

* skpkg: modify copyright years and contributors in a missed file

* style: changed line length to 115 and ran pre-commit again

* fix: testing if adding .github/workflow will pass CI

* [pre-commit.ci] auto fixes from pre-commit hooks

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: zmx27

.codecov.yml

@@ -1,14 +1,14 @@
 coverage:
   status:
-    project:  # more options at https://docs.codecov.com/docs/commit-status
+    project: # more options at https://docs.codecov.com/docs/commit-status
       default:
         target: auto # use the coverage from the base commit, fail if coverage is lower
-        threshold: 0%  # allow the coverage to drop by
+        threshold: 0% # allow the coverage to drop by
 
 comment:
   layout: " diff, flags, files"
   behavior: default
   require_changes: false
-  require_base: false  # [true :: must have a base report to post]
-  require_head: false  # [true :: must have a head report to post]
+  require_base: false # [true :: must have a base report to post]
+  require_head: false # [true :: must have a head report to post]
   hide_project_coverage: false # [true :: only show coverage on the git diff aka patch coverage]

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -12,7 +12,7 @@ assignees: ""
 - [ ] All the badges on the README are passing.
 - [ ] License information is verified as correct. If you are unsure, please comment below.
 - [ ] Locally rendered documentation contains all appropriate pages, including API references (check no modules are
-  missing), tutorials, and other human written text is up-to-date with any changes in the code.
+      missing), tutorials, and other human written text is up-to-date with any changes in the code.
 - [ ] Installation instructions in the README, documentation and on the website (e.g., diffpy.org) are updated.
 - [ ] Successfully run any tutorial examples or do functional testing with the latest Python version.
 - [ ] Grammar and writing quality are checked (no typos).
@@ -31,5 +31,5 @@ version information and details about the pre-release here:
 
 <!-- Before closing this issue, please complete the following: -->
 
-- [ ]  Run tutorial examples and conduct functional testing using the installation guide in the README. Attach screenshots/results as comments.
-- [ ]  Documentation (README, tutorials, API references, and websites) is deployed without broken links or missing figures.
+- [ ] Run tutorial examples and conduct functional testing using the installation guide in the README. Attach screenshots/results as comments.
+- [ ] Documentation (README, tutorials, API references, and websites) is deployed without broken links or missing figures.

.github/workflows/build-wheel-release-upload.yml

@@ -4,13 +4,15 @@ on:
   workflow_dispatch:
   push:
     tags:
-      - '*'  # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
+      - "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
 
 jobs:
   release:
-    uses: Billingegroup/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
+    uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
     with:
       project: diffpy.snmf
+      c_extension: false
+      maintainer_GITHUB_username: sbillinge
     secrets:
       PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
       PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

.github/workflows/check-news-item.yml

@@ -3,10 +3,10 @@ name: Check for News
 on:
   pull_request_target:
     branches:
-    - main
+      - main
 
 jobs:
-  build:
-    uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
+  check-news-item:
+    uses: scikit-package/release-scripts/.github/workflows/_check-news-item.yml@v0
     with:
       project: diffpy.snmf

.github/workflows/matrix-and-codecov-on-merge-to-main.yml

@@ -11,8 +11,8 @@ on:
   workflow_dispatch:
 
 jobs:
-  coverage:
-    uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
+  matrix-coverage:
+    uses: scikit-package/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
     with:
       project: diffpy.snmf
       c_extension: false

.github/workflows/publish-docs-on-release.yml

@@ -0,0 +1,12 @@
+name: Deploy Documentation on Release
+
+on:
+  workflow_dispatch:
+
+jobs:
+  docs:
+    uses: scikit-package/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
+    with:
+      project: diffpy.snmf
+      c_extension: false
+      headless: false

.github/workflows/tests-on-pr.yml

@@ -1,15 +1,12 @@
 name: Tests on PR
 
 on:
-  push:
-    branches:
-      - main
   pull_request:
   workflow_dispatch:
 
 jobs:
-  validate:
-    uses: Billingegroup/release-scripts/.github/workflows/_tests-on-pr.yml@v0
+  tests-on-pr:
+    uses: scikit-package/release-scripts/.github/workflows/_tests-on-pr.yml@v0
     with:
       project: diffpy.snmf
       c_extension: false

.gitignore

@@ -10,6 +10,7 @@ __pycache__/
 .Python
 env/
 build/
+_build/
 develop-eggs/
 dist/
 downloads/
@@ -90,10 +91,3 @@ target/
 
 # Ipython Notebook
 .ipynb_checkpoints
-
-# version information
-setup.cfg
-/src/diffpy/*/version.cfg
-
-# Rever
-rever/

.pre-commit-config.yaml

@@ -1,14 +1,14 @@
 default_language_version:
-    python: python3
+  python: python3
 ci:
-    autofix_commit_msg: |
-        [pre-commit.ci] auto fixes from pre-commit hooks
-    autofix_prs: true
-    autoupdate_branch: 'pre-commit-autoupdate'
-    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
-    autoupdate_schedule: monthly
-    skip: [no-commit-to-branch]
-    submodules: false
+  autofix_commit_msg: |
+    [pre-commit.ci] auto fixes from pre-commit hooks
+  autofix_prs: true
+  autoupdate_branch: "pre-commit-autoupdate"
+  autoupdate_commit_msg: "[pre-commit.ci] pre-commit autoupdate"
+  autoupdate_schedule: monthly
+  skip: [no-commit-to-branch]
+  submodules: false
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
@@ -47,6 +47,20 @@ repos:
   - repo: https://github.com/codespell-project/codespell
     rev: v2.3.0
     hooks:
-    - id: codespell
-      additional_dependencies:
-        - tomli
+      - id: codespell
+        additional_dependencies:
+          - tomli
+  # prettier - multi formatter for .json, .yml, and .md files
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: f12edd9c7be1c20cfa42420fd0e6df71e42b51ea # frozen: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - "prettier@^3.2.4"
+  # docformatter - PEP 257 compliant docstring formatter
+  - repo: https://github.com/s-weigand/docformatter
+    rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c
+    hooks:
+      - id: docformatter
+        additional_dependencies: [tomli]
+        args: [--in-place, --config, ./pyproject.toml]

pyproject.toml

@@ -6,17 +6,17 @@ build-backend = "setuptools.build_meta"
 name = "diffpy.snmf"
 dynamic=['version', 'dependencies']
 authors = [
-  { name="Simon J.L. Billinge group", email="[email protected]" },
+  { name="Simon J.L. Billinge group", email="[email protected]" },
 ]
 maintainers = [
-  { name="Simon J.L. Billinge group", email="[email protected]" },
+  { name="Simon J.L. Billinge group", email="[email protected]" },
 ]
 description = "Python package implementing the stretched NMF algorithm."
 keywords = ['diffpy', 'PDF']
 readme = "README.rst"
 requires-python = ">=3.11, <3.14"
 classifiers = [
-        'Development Status :: 4 - Beta',
+        'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
         'Intended Audience :: Developers',
         'Intended Audience :: Science/Research',

requirements/build.txt

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024 The Trustees of Columbia University in the City of New York.
+# (c) 2024-2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.
@@ -12,7 +12,6 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
 """Blank namespace package for module diffpy."""
 
 

src/diffpy/__init__.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024 The Trustees of Columbia University in the City of New York.
+# (c) 2024-2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.
@@ -12,11 +12,10 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
-"""A python package implementing the stretched NMF algorithm."""
+"""Python package implementing the stretched NMF algorithm."""
 
 # package version
-from diffpy.snmf.version import __version__
+from diffpy.snmf.version import __version__  # noqa
 
 # silence the pyflakes syntax checker
 assert __version__ or True

src/diffpy/snmf/__init__.py

@@ -26,7 +26,7 @@ def __init__(self, grid, number_of_signals, id_number, perturbation=1e-3):
         self.id = int(id_number)
 
     def apply_stretch(self, m):
-        """Applies a stretching factor to a component
+        """Applies a stretching factor to a component.
 
         Parameters
         ----------
@@ -41,7 +41,11 @@ def apply_stretch(self, m):
         """
         normalized_grid = np.arange(len(self.grid))
         interpolate_intensity = lambda stretching_factor: np.interp(  # noqa: E731
-            normalized_grid / stretching_factor, normalized_grid, self.iq, left=0, right=0
+            normalized_grid / stretching_factor,
+            normalized_grid,
+            self.iq,
+            left=0,
+            right=0,
         )
         derivative_func = numdifftools.Derivative(interpolate_intensity)
         second_derivative_func = numdifftools.Derivative(derivative_func)

src/diffpy/snmf/containers.py

@@ -3,7 +3,8 @@
 
 
 def lsqnonneg(stretched_component_matrix, target_signal):
-    """Finds the weights of stretched component signals under one-sided constraint.
+    """Finds the weights of stretched component signals under one-sided
+    constraint.
 
     Solves ``argmin_x || Ax - b ||_2`` for ``x>=0`` where A is the stretched_component_matrix and b is the
     target_signal vector. Finds the weights of component signals given undecomposed signal data and stretched

src/diffpy/snmf/factorizers.py

@@ -39,7 +39,6 @@ def initialize_variables(data_input, number_of_components, data_type, sparsity=1
       guess for the weight factor matrix, an initial guess for the stretching factor matrix, a parameter
       controlling smoothness of the solution, a parameter controlling sparseness of the solution, the matrix
       representing the smoothness term, and a matrix used to construct a hessian matrix.
-
     """
     signal_length = data_input.shape[0]
     number_of_signals = data_input.shape[1]
@@ -74,7 +73,8 @@ def initialize_variables(data_input, number_of_components, data_type, sparsity=1
 
 
 def load_input_signals(file_path=None):
-    """Processes a directory of a series of PDF/XRD patterns into a usable format.
+    """Processes a directory of a series of PDF/XRD patterns into a usable
+    format.
 
     Constructs a 2d array out of a directory of PDF/XRD patterns containing each files dependent variable
     column in a new column. Constructs a 1d array containing the grid values.
@@ -92,7 +92,6 @@ def load_input_signals(file_path=None):
       The tuple whose first element is an R x M 2d array made of PDF/XRD patterns as each column; R is the
       length of the signal and M is the number of patterns. The tuple contains a 1d array containing the values
       of the grid points as its second element; Has length R.
-
     """
 
     if file_path is None:

src/diffpy/snmf/io.py

@@ -2,8 +2,14 @@
 from scipy.optimize import minimize
 
 
-def get_weights(stretched_component_gram_matrix, linear_coefficient, lower_bound, upper_bound):
-    """Finds the weights of stretched component signals under a two-sided constraint
+def get_weights(
+    stretched_component_gram_matrix,
+    linear_coefficient,
+    lower_bound,
+    upper_bound,
+):
+    """Finds the weights of stretched component signals under a two-sided
+    constraint.
 
     Solves min J(y) = (linear_coefficient)' * y + (1/2) * y' * (quadratic coefficient) * y where
     lower_bound <= y <= upper_bound and stretched_component_gram_matrix is symmetric positive definite.
@@ -34,7 +40,6 @@ def get_weights(stretched_component_gram_matrix, linear_coefficient, lower_bound
     1d array like
       The vector containing the weightings of the components needed to reconstruct a given input signal from the
       input set. Has length C
-
     """
 
     stretched_component_gram_matrix = np.asarray(stretched_component_gram_matrix)

src/diffpy/snmf/optimizers.py

@@ -2,9 +2,8 @@
 
 
 def compute_root(linear_coefficient, constant_term):
-    """
-    Returns the largest real root of x^3+(linear_coefficient) * x + constant_term. If there are no real roots
-    return 0.
+    """Returns the largest real root of x^3+(linear_coefficient) * x +
+    constant_term. If there are no real roots return 0.
 
     Parameters
     ----------
@@ -18,7 +17,6 @@ def compute_root(linear_coefficient, constant_term):
     ndarray of floats
         The largest real root of x^3+(linear_coefficient) * x + constant_term if roots are real, else
         return 0 array
-
     """
     linear_coefficient = np.asarray(linear_coefficient)
     constant_term = np.asarray(constant_term)

src/diffpy/snmf/polynomials.py

@@ -4,12 +4,18 @@
 from diffpy.snmf.io import initialize_variables, load_input_signals
 from diffpy.snmf.subroutines import initialize_components, lift_data
 
-ALLOWED_DATA_TYPES = ["powder_diffraction", "pd", "pair_distribution_function", "pdf"]
+ALLOWED_DATA_TYPES = [
+    "powder_diffraction",
+    "pd",
+    "pair_distribution_function",
+    "pdf",
+]
 
 
 def create_parser():
     parser = argparse.ArgumentParser(
-        prog="stretched_nmf", description="Stretched Nonnegative Matrix Factorization"
+        prog="stretched_nmf",
+        description="Stretched Nonnegative Matrix Factorization",
     )
     parser.add_argument(
         "-i",
@@ -44,7 +50,12 @@ def create_parser():
         type=int,
         help="The number of component signals for the NMF decomposition. Must be an integer greater than 0",
     )
-    parser.add_argument("-v", "--version", action="version", help="Print the software version number")
+    parser.add_argument(
+        "-v",
+        "--version",
+        action="version",
+        help="Print the software version number",
+    )
     args = parser.parse_args()
     return args